Miracle-dz/UniFAR-FTUs huggingface dataset:
Endogenous hormone 2‐methoxyestradiol suppresses venous hypertension‐induced angiogenesis through up‐ and down‐regulating p53 and id‐1

Brain arteriovenous malformations (AVMs) which associate with angiogenesis due to local hypertension, chronic cerebral ischaemia and tissue hypoxia usually lead to haemorrhage, however, the therapeutic medicine for the disease is still lacking. 2‐methoxyestradiol (2‐ME) has been shown effective in the anti‐angiogenic treatment. This study was conducted to examine whether and how 2‐ME could improve the vascular malformations. Intracranial venous hypertension (VH) model produced in adult male Sprague‐Dawley rats and culture of human umbilical vein endothelial cells (HUVECs) at the anoxia condition were used to induce in vivo and in vitro angiogenesis, respectively. Lentiviral vectors of ID‐1 and p53 genes and of their siRNA were intracranially injected into rats and transfected into HUVECs to overexpress and down‐regulate these molecules. 2‐ME treatment not only reduced the in vivo progression of brain tissue angiogenesis in the intracranial VH rats and the in vitro increases in microvasculature formation, cellular migration and HIF‐1α expression induced by anoxia in HUVECs but also reversed the up‐regulation of ID‐1 and down‐regulation of p53 in both the in vivo and in vitro angiogenesis models. All of the anti‐angiogenesis effects of 2‐ME observed in VH rats and anoxic HUVECs were abrogated by ID‐1 overexpression and p53 knockdown. Our data collectively suggest that 2‐ME treatment inhibits hypoxia/anoxia‐induced angiogenesis dependently on ID‐1 down‐regulation and p53 up‐regulation, providing a potential alternative medical treatment for un‐ruptured AVM patients.
On part of speech tagger for Indonesian language

In this paper we present an evaluation of six popular methods for Part-of-Speech (POS) tagging tasks of Indonesian language. They are Unigram, Hidden Markov Model, TnT, Brills, Naive Bayes, and Maximum Entropy taggers. Indonesian language, while is one of most spoken language in the world has very limited data for POS tagging tasks. Therefore, it is interesting to investigate and evaluate some popular approaches in POS tagging when dealing for such conditions. The results of our experiments show that Maximum Entropy provides the highest accuracy of all methods. It is consistently better even when the size of the training data is varied.
Molecular Analysis of a Hospital Cafeteria-Associated Salmonellosis Outbreak Using Modified Repetitive Element PCR Fingerprinting

ABSTRACT A hospital cafeteria-associated outbreak of gastroenteritis due toSalmonella enterica serotype Infantis was retrospectively evaluated using modified repetitive element PCR (rep-PCR) fingerprinting with the ERIC2 and BOXA1R primers and computer-assisted gel analysis and dendrogram construction. Rep-PCR yielded objective between-cycler, same-strain similarity values of from 92% (composite fingerprints) to 96% (ERIC2 fingerprints). The 70Salmonella isolates (which included 19 serotype Infantis isolates from the hospital outbreak, 10 other serotype Infantis isolates, and 41 isolates representing 14 other serotypes) were resolved well to the serotype level with each of the three fingerprint types (ERIC2, BOXA1R, and composite). Rep-PCR typing uncovered several historical serotyping errors and provided presumptive serotype assignments for other isolates with incomplete or undetermined serotypes. Analysis of replicate fingerprints for each isolate, as generated on two different thermal cyclers, indicated that most of the seeming subserotype discrimination noted in single-cycler dendrograms actually represented assay variability, since it was not reproducible in combined-cycler dendrograms. Rep-PCR typing, which would have been able to identify the presence of the hospital-associated serotype Infantis outbreak after the second outbreak isolate, could be used as a simple surrogate for serotyping by clinical microbiology laboratories that are equipped for diagnostic PCR.
Introducing multiple sites of acetylation to histone H3 via nonsense suppression

A common post-translational modification (PTM) of proteins is lysine acetylation. This is an especially ubiquitous PTM in the histones of chromatin, and is important for helping to regulate both structural and mechanistic aspects of chromatin. The fundamental unit of chromatin is called the nucleosome and is made up of DNA that wraps around a histone protein octamer. Protruding from the nucleosome are 10 unstructured “tails” which protrude into the aqueous environment. A number of strategies exist for generating acetylated nucleosomes for the in-vitro study of chromatin including: Purification from eukaryotic organisms, chemical acetylation, amino acid analog incorporation, enzyme mediated acetylation, native chemical ligation of peptides, and enzyme mediated ligation of peptdes. An especially attractive approach is to genetically encode acetyl-lysine residues using nonsense suppression. This strategy has been successfully applied to single sites of histone acetylation. However, because histone acetylation can often occur at multiple sites simultaneously, it is worth while to determine whether this approach could be extended. The results in this thesis show that recombinantly expressed histone H3 proteins that incorporate up to four sites of lysine acetylation on the histone tail can be produced in good yields. Because the amount of expressed multi-acetylated histone is reduced relative to the wild type, a purification strategy involving affinity purification and ion exchange chromatography was optimized. This expression and purification strategy ultimately generates H3 histone uniformly acetylated at the desired position at levels and purity sufficient to assemble histone octamers. Histone octamers containing four sites of lysine acetylation were
Genetic and Methylation-Induced Loss of miR-181a2/181b2 within chr9q33.3 Facilitates Tumor Growth of Cervical Cancer through the PIK3R3/Akt/FoxO Signaling Pathway

Purpose: Loss of Chr9q31–33 is one of the most common chromosome imbalances of cervical cancer, but the underlying mechanism has not been well documented. Experimental Design: The loss of heterozygosity (LOH) status of Chr9q31–33 was investigated utilizing 26 microsatellite markers. We detected the expression of miR-181a2/181b2 by qRT-PCR analysis of cervical cancer cell lines and 100 paired tumor samples and corresponding adjacent non-tumor tissues. Kaplan–Meier and Cox proportional hazard regression analyses were performed to identify the prognostic value of miR-181a2/181b2. Regulation of expression was analyzed by methylation-specific PCR. The tumor-suppressing effects of miR-181a2/181b2 were determined in vitro and in vivo. The target gene and signaling pathway that mediated the function of miR-181a2/181b2 were also identified. Results: Chr9q33.3 was identified as one of the most deleted regions in cervical cancer. Underexpression of miR-181a2/181b2 was detected in 46% of cervical cancer and was induced by the LOH of chr9q33.3 and promoter hypermethylation. Attenuated miR-181a2/181b2 expression predicted a poor prognostic phenotype and advanced clinical stage of cervical cancer. miR-181a2/181b2 prominently dampened cell-cycle progression, suppressed cell growth, and promoted apoptosis of tumor cells in vitro. They also effectively impeded tumor formation and growth in vivo. miR-181a2/181b2 exert the tumor suppressor ability by depressing the direct target PIK3R3 (p55γ) and consequently modulating the PIK3R3/Akt/FoxO signaling pathway. Conclusions: We demonstrated a cause-and-effect event beginning from loss of chr9q33.3, a frequent event in cervical cancer, to the underexpression of miR-181a2/181b2, leading to the elevated activation of the PI3K pathway. Clin Cancer Res; 23(2); 575–86. ©2016 AACR.
Statistical analysis of the reduction process of graphene oxide probed by Raman spectroscopy mapping

We propose a method for monitoring the large-scale homogeneity of the reduction process of graphene oxide. For this purpose, a Raman mapping technique is employed to probe the evolution of the phonon properties of two different graphene oxide (GO) thin films upon controllable thermal reduction. The reduction of GO is reflected by the upshift of the statistical distribution of the relative intensity ratio of the G and D peaks (ID/IG) of the Raman spectra and is consistent with the ratio obtained for chemically reduced GO. In addition, the shifts of the position distributions of the main Raman modes (ωD, ωG) and their cross-correlation with the ID/IG ratio provides evidence of a change of the doping level, demonstrating the influence of reduction processes on GO films.
Measuring Relative Coupling Strength in Circadian Systems

Modern imaging techniques allow the monitoring of circadian rhythms of single cells. Coupling between these single cellular circadian oscillators can generate coherent periodic signals on the tissue level that subsequently orchestrate physiological outputs. The strength of coupling in such systems of oscillators is often unclear. In particular, effects on coupling strength by varying cell densities, by knockouts, and by inhibitor applications are debated. In this study, we suggest to quantify the relative coupling strength via analyzing period, phase, and amplitude distributions in ensembles of individual circadian oscillators. Simulations of different oscillator networks show that period and phase distributions become narrower with increasing coupling strength. Moreover, amplitudes can increase due to resonance effects. Variances of periods and phases decay monotonically with coupling strength, and can serve therefore as measures of relative coupling strength. Our theoretical predictions are confirmed by studying recently published experimental data from PERIOD2 expression in slices of the suprachiasmatic nucleus during and after the application of tetrodotoxin (TTX). On analyzing the corresponding period, phase, and amplitude distributions, we can show that treatment with TTX can be associated with a reduced coupling strength in the system of coupled oscillators. Analysis of an oscillator network derived directly from the data confirms our conclusions. We suggest that our approach is also applicable to quantify coupling in fibroblast cultures and hepatocyte networks, and for social synchronization of circadian rhythmicity in rodents, flies, and bees.
Interpretation of Nominal Compounds Using Structured Knowledgebases

This thesis investigates different approaches proposed in literature to identify the semantic relations in nominal compounds. Nominal compounds have received a great deal of attention in the last decade, owing to two main reasons the increasing frequency with which nominal compounds occur in language, and the challenges they pose in most natural language processing applications like information extraction and retrieval, document summarization, machine translation and the like. Interpreting the semantics of nominal compounds in particular has been a popular research topic in recent times for reasons beyond just the impactful presence of compounds, like the challenges in explicating the semantic relation between constituents of the compound which is not-so-obvious to a machine as it is to a native speaker of the language. Most of the approaches proposed prior to this work are predominantly statistical techniques or treat compound interpretation as a classification task using a standard set of semantic relations as the prediction labels. The drawbacks of purely statistical and computational approaches is that they often a require large training dataset or corpus with a good distribution across all types of semantic relations, and often have no underlying lexical knowledgebases to support any data sparsity issues that may arise. Some of these approaches even involve preprocessing of large and unstructured databases like dictionaries and corpora which is inefficient and time-consuming. I motivate the need for exploring a new school of thought, quite opposite to the approaches that use computations backed up by knowledgebases . I explore in this thesis, the creation of hybrid systems that mine information from lexical and semantic knowledge resources like ConceptNet and WordNet, and are sufficiently backed by computational measures as necessary, to handle compounds outside the scope of these resources. Such systems overcome the obvious drawbacks of purely statistical and supervised learning tasks. I discuss two popular generic-domain ontologies called WordNet and ConceptNet in terms of the representational schema adopted in these ontologies to capture nominal compounds, and from the perspective of using these ontologies for labeling compounds with semantic relations. Most frequent issues encountered with these ontologies were identified as the lack of sufficient semantic information for certain nominal compounds, and the incompleteness of these ontologies in terms of capturing all the different categories of nominal compounds using a generic representational schema. I propose a new representation schema that identifies uniqueness of compounds and build a well structured purpose-centric ontology called PurposeNet centered around this representational schema. The ontology-search approach proposed in this thesis uses simple lookup techniques on indexed and
Changes in Urinary Excretion of Type-I Collagen Cross-Linked C-Telopeptide and N-Telopeptide in Perimenopausal Women

In order to assess the dynamics of bone turnover during menopausal transition, we measured the urinary excretion of C-telopeptide (CTX) and N-telopeptide (NTX) of type-I collagen, new markers of bone resorption, using two ELISAs which recognize the corresponding cross-linked peptide of type-I collagen. CTX and NTX levels in postmenopausal women were significantly higher than those in premenopausal women, confirming the enhancement of bone resorption after menopause. The measurement of CTX and NTX, which is convenient and specific for bone resorption compared with conventional bone resorption markers, pyridinoline and deoxypyridinoline, might be useful in the management of postmenopausal women.
Binary vector reconstruction via discreteness-aware approximate message passing

In this paper, we propose an algorithm to reconstruct a binary vector from its possibly underdetermined linear measurements. Taking advantage of the idea of the approximate message passing (AMP) algorithm for compressed sensing, we firstly formulate a probability distribution associated with the sum-of-absolute-value (SOAV) optimization. Then, by approximating the sum-product algorithm for the marginalization of the distribution, we obtain a low-complexity iterative algorithm, called discreteness-aware AMP (DAMP). We evaluate the performance of DAMP analytically via state evolution and derive a condition for the exact reconstruction with DAMP. Moreover, we also provide Bayes optimal DAMP for the binary vector reconstruction, which gives the minimum mean-square-error at each iteration in the large system limit. Simulation results show that DAMP can reconstruct the binary vector from underdetermined linear measurements and its performance can be well predicted by our theoretical results.
A survey on the Internet of Things-based service orientated architecture

Usage of technological devices is increasing and also increases the facility and the compatibility of the hardware. The internet can be accessed through many devices and the devices can be connected with other devices. Internet of Things (IoT) has increased highly in various types of device and complexity of the connection with the different type of devices also increases. This increases the demand for the Service Oriented Architecture (SOA) for the user. IoT-based SOA technique provides the effective information by obtaining the information about the user's devices and their locations. This technique requires the device to be connected to the several devices, which also increases problem in security. Several research has been carried on the IoT-based SOA method and provides better solutions for some problems. In this paper, research has been done on the IoT-based SOA technique research to analysis the major issues with this technique and their better solution provided for the system. The major problem with the technique is lightweight process is required for the embedded system.
Nucleolin phosphorylation regulates PARN deadenylase activity during cellular stress response

ABSTRACT Nucleolin (NCL) is an abundant stress-responsive, RNA-binding phosphoprotein that controls gene expression by regulating either mRNA stability and/or translation. NCL binds to the AU-rich element (ARE) in the 3′UTR of target mRNAs, mediates miRNA functions in the nearby target sequences, and regulates mRNA deadenylation. However, the mechanism by which NCL phosphorylation affects these functions and the identity of the deadenylase involved, remain largely unexplored. Earlier we demonstrated that NCL phosphorylation is vital for cell cycle progression and proliferation, whereas phosphorylation-deficient NCL at six consensus CK2 sites confers dominant-negative effect on proliferation by increasing p53 expression, possibly mimicking cellular DNA damage conditions. In this study, we show that NCL phosphorylation at those CK2 consensus sites in the N-terminus is necessary to induce deadenylation upon oncogenic stimuli and UV stress. NCL-WT, but not hypophosphorylated NCL-6/S*A, activates poly (A)-specific ribonuclease (PARN) deadenylase activity. We further demonstrate that NCL interacts directly with PARN, and under non-stress conditions also forms (a) complex (es) with factors that regulate deadenylation, such as p53 and the ARE-binding protein HuR. Upon UV stress, the interaction of hypophosphorylated NCL-6/S*A with these proteins is favored. As an RNA-binding protein, NCL interacts with PARN deadenylase substrates such as TP53 and BCL2 mRNAs, playing a role in their downregulation under non-stress conditions. For the first time, we show that NCL phosphorylation offers specificity to its protein-protein, protein-RNA interactions, resulting in the PARN deadenylase regulation, and hence gene expression, during cellular stress responses.
A Statewide Intervention to Increase Safety Belt Use: Adding to the Impact of a Belt Use Law

Motor vehicle crashes are the leading cause of accidental death among Americans and are responsible for millions of disabling injuries every year. ~ In addition to overwhelming human suffering, the costs of vehicle injuries are enormous and include property damage, lost wages, medical costs, and insurance expenses,z Evans reported "traffic deaths from 1977 through 1988 exceeded all U.S. battle deaths in all wars from the Revolutionary War through the Vietnam War. "3 The use of a safety belt in a vehicle crash reduces the chance of death or serious injury by at least 40%. 3 Geller, Berry, Ludwig, Gilmore, and Clarke 4 proposed that intervention effectiveness varies directly with the number of intervention agents per individual in the target population; however, there has been no empirical investigation of this hypothesis. The present research studied the impact of community safety belt promotion programs as a function of the number of intervention agents (i.e., police officers) and the amount of intervention activity (i.e., promotional gimmicks and citations) per population size (residents of the community). More specifically, we studied effectiveness of large-scale intervention as a function of officer-to-resident ratio, citation-to-resident ratio, and promotional gimmick-toresident ratio in each of eight communities. We hypothesized a direct relationship between percentage increases in vehicle safety belt use and number of officers or activities per community population.
Evaluation of GenoType NTM-DR Assay for Identification of Mycobacterium chimaera

ABSTRACT Identification of species within the Mycobacterium avium complex (MAC) is difficult, and most current diagnostic laboratory tests cannot distinguish between species included in the complex. Differentiation of species within the MAC is important, as Mycobacterium chimaera has recently emerged as a major cause of invasive cardiovascular infections following open heart surgery. A new commercial diagnostic assay, GenoType NTM-DR ver. 1.0, is intended to differentiate between three species within the MAC, namely, Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium chimaera. In this study, we investigated an archival collection of 173 MAC isolates using 16S rRNA and 16S-23S internal transcribed spacer (ITS) gene sequencing, and GenoType NTM-DR was evaluated for identifying M. chimaera and other species belonging to the MAC. Species identification of 157/173 (91%) isolates with the GenoType NTM-DR assay was in agreement with 16S rRNA and 16S-23S ITS gene sequencing results. Misidentification occurred with 16 isolates which belonged to four species included in the MAC that are rarely encountered in clinical specimens. Despite some limitations of this assay, GenoType NTM-DR had 100% specificity for identifying M. chimaera. This novel assay will enable diagnostic laboratories to differentiate species belonging to the Mycobacterium avium complex and to accurately identify M. chimaera. It can produce rapid results and is also more cost efficient than gene sequencing methods.
Improved Precursor Characterization for Data-Dependent Mass Spectrometry.

Modern ion trap mass spectrometers are capable of collecting up to 60 tandem MS (MS/MS) scans per second, in theory providing acquisition speeds that can sample every eluting peptide precursor presented to the MS system. In practice, however, the precursor sampling capacity enabled by these ultrafast acquisition rates is often underutilized due to a host of reasons (e.g., long injection times and wide analyzer mass ranges). One often overlooked reason for this underutilization is that the instrument exhausts all the peptide features it identifies as suitable for MS/MS fragmentation. Highly abundant features can prevent annotation of lower abundance precursor ions that occupy similar mass-to-charge (m/z) space, which ultimately inhibits the acquisition of an MS/MS event. Here, we present an advanced peak determination (APD) algorithm that uses an iterative approach to annotate densely populated m/z regions to increase the number of peptides sampled during data-dependent LC-MS/MS analyses. The APD algorithm enables nearly full utilization of the sampling capacity of a quadrupole-Orbitrap-linear ion trap MS system, which yields up to a 40% increase in unique peptide identifications from whole cell HeLa lysates (approximately 53 000 in a 90 min LC-MS/MS analysis). The APD algorithm maintains improved peptide and protein identifications across several modes of proteomic data acquisition, including varying gradient lengths, different degrees of prefractionation, peptides derived from multiple proteases, and phosphoproteomic analyses. Additionally, the use of APD increases the number of peptides characterized per protein, providing improved protein quantification. In all, the APD algorithm increases the number of detectable peptide features, which maximizes utilization of the high MS/MS capacities and significantly improves sampling depth and identifications in proteomic experiments.
Application of differential evolution algorithm for solving discounted {0–1} knapsack problem

Knapsack problem is a classical problem in combinatorial optimization. This paper first introduces the basic concepts of discount {0–1} knapsack problem and differential evolution algorithm, the improved differential evolution discount {0–1} knapsack problem algorithm for solving large scale data, and combined with the dynamic programming algorithm to verify its correctness. Simulation results show that this method can obtain the best solution with the highest fitness.