Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing statistical power and generalizability in genomics microarray research

The high-throughput technologies developed in the last decade have revolutionized the speed of data accumulation in the life sciences. As a result we have very rich and complex data that holds great promise to solving many complex biological questions. One such technology that is very well established and widespread is DNA microarrays, which allows one to simultaneously measure the expression levels of tens of thousands of genes in a biological tissue. This thesis aims to contribute to the development of statistics that allow the end users to obtain robust and meaningful results from DNA microarrays for further investigation. The methodology, implementation and pragmatic issues of two important and related topics – sample size estimations for designing new studies and meta-analysis of existing studies – are presented here to achieve this aim. Real life case studies and guided steps are also given. Sample size estimation is important at the design stage to ensure a study has sufficient statistical power to address the stated objective given the financial constraints. The commonly used formula for estimating the number of biological samples, its short-comings and potential amelioration are discussed. The optimal number of biological samples and number of measurements per sample that minimizes the cost is also presented. Meta-analysis or the synthesis of information from existing studies is very attractive because it can increase the statistical power by making comprehensive and inexpensive use of available information. Furthermore, one can also easily test the generalizability of findings (i.e. the extent of results from a particular valid study can be applied to other circumstances). The key issues in conducting a meta-analysis for microarrays studies, a checklist and R codes are presented here. Finally, the poor availability of raw data in microarray studies is discussed here with recommendations for authors, journal editors and funding bodies. Good availability of data is important for meta-analysis in order to avoid biased results and for sample size estimation.
Library Operating System with Mainline Linux Network Stack

Library operating system (LibOS) is a userspace version of Linux kernel to provide an operating system personalization (or ad-hoc network stack) as well as yet-another virtualization primitive. Although the concept of library operating system is not new and was established in back to 90’s, the idea here is adding a hardware independent architecture (i.e., arch/lib) into Linux kernel tree and reusing the rest of networking code as a library for userspace programs in order to avoid ’reinventing the wheel’. Unlike conventional Linux kernel/userspace model, system calls are redirected to the library in the same process or the other userspace processes, but the framework tries to be transparent so that all of the existing userspace applications like nginx and iproute2 are able to be used as-is. The LibOS framework provides several interesting use cases such as 1) a fast-path for the new protocol deployment (no need to replace or insert new kernel code), 2) a feature-rich network stack for a high-speed packet I/O mechanism like Intel DPDK, 3) a continuous integration for testing networking code implemented in Linux kernel tree. Right now, most of in-kernel protocols like TCP, SCTP, DCCP, and MPTCP are tested to work on top of the LibOS. Newly implemented protocol may also work depending on the POSIX API coverage and kernel glue code. This paper covers the introduction of the LibOS framework and two sub projects, Network stack in userspace (NUSE) and Direct Code Execution (DCE), with the internal design of the indirections, and presents the ongoing work on the multiprocess support to share a single userspace network stack (e.g., share a userspace routing table between two processes) via inter-process communication implemented by rumpkernel IPC/RPC framework.
FORMULATION AND EVALUATION OF KETOROLAC TROMETHAMINE MICROPARTICLES FOR OCULAR DELIVERY

The objective of the present work was to formulate and evaluate microparticles of Ketorolac tromethamine and produced sustained drug delivery for ocular delivery. In this 9 batches(A1-C3) of Ketorolac tromethamine microparticle was prepared with chitosan, Sodium Tri-polyphosphate and other ingredients by Ionotropic gelation technique. The prepared microparticles were evaluated for different parameters i.e % Drug yield, % Drug entrapment, Surface morphology, Zeta potential and in-vitro drug release for 24hrs in phosphate buffer 7.4 and simulated tear fluid. The best batch was performed stability studies for 6 months. The research concluded that Ketorolac tromethamine microparticles could be alternative for conventional dosage form.
Performance Evaluation of Clustering Algorithms

— Data mining is the process of analysing data from different viewpoints and summarizing it into useful information. Data mining tool allows users to analyse data from different dimensions or angles, categorize it, and précis the relations recognized. Clustering is the important aspect of data mining. It is the process of grouping of data, where the grouping is recognized by finding similarities between data based on their features. Weka is a data mining tool. It provides the facility to classify and cluster the data through machine leaning algorithms. This paper compares various clustering algorithms
Mathematical Problem Solving for Everyone: A New Beginning

Mathematical problem solving has been at the core of the Singapore mathematics curriculum framework since the 1990s. We report here the features of the Mathematical Problem Solving for Everyone (M-ProSE) project which was carried out in a Singapore school to realise the learning of mathematical problem solving and as described by Polya and Schoenfeld. A mathematics problem solving package comprising "mathematics practical" lessons and assessment rubric was trialled in the school for Grade 8 in 2009. Responses from three students show mixed perceptions to the module, but an end-of-module assessment shows that the students were able to present their solutions along Polya's four stages. We also describe teacher preparation for teaching the module. After the trial period, the school adopted the module as part of the curriculum and it is now a compulsory course for all Grade 8 students in that school.
Serosurveillance and Molecular Characterization of H9N2 Avian Influenza Virus in Lebanon

Background: Since the first report concerning the existence of avian influenza subtype H9N2 (AI H9N2) in 2006 in Lebanon; a lot of pathological changes and mortalities were seen among chicken flocks suggesting the influence of the AI H9N2 virus. Objectives this study reports the circulation of H9N2 associated with mortalities in broiler sector and decrease egg production in layer hens and breeders in Lebanon. Methods: A total of 22 poultry flocks have been tested by real-time reverse transcription polymerase chain reaction (rt-RT-PCR) for the presence of H9N2 in different types of chickens including broilers, breeders, laying hens, backyard chickens and ducks. Tracheal swabs were collected from flocks raised in different governorates in Lebanon. Results: Testing of samples with rt-RT-PCR revealed that 6 flocks reared in 4 Lebanese governorates were positive (CT ranged from 20.42 to 33.86). A Positive sample with CT 20.42 was tested and partially sequenced and submitted to GenBank, acquired accessions number MH266696 and designated A/chicken/Lebanon/21-E03/2018 (H9N2). Phylogenetic analysis of the obtained sequence cluster the characterized strain along with (formerly) G1-like viruses subtype B like those circulating in the Middle East. Conclusion: the AI H9N2 avian influenza virus is circulating causing major problem among chickens. More studies need to be addressed to understand the real effect of the H9 virus on chickens and humans in Lebanon.
Construction of low density parity check codes: a combinatoric design approach

This paper presents a method for constructing low density parity check (LDPC) codes based on a special type of combinatoric designs, known as the balanced incomplete block designs (BIBDs). Several classes of BIBDs suitable for constructing LDPC codes are presented. Codes constructed based on these classes of BIBDs perform well with iterative decoding.
Reaching for a Radical Community-Based Research Model

This qualitative study contrasts two community-based research (CBR) projects. While the first project fell short of CBR goals, it influenced how the author carried out the second project, which did meet those goals. The two experiences enabled the author to create a conceptual model that can be used to structure and evaluate CBR projects for those who aspire to a more radical form of community-based research.
Antioxidant Activity of Ethanolic Extract and Various Fractions from Green Tea (Camellia sinensis L.) Leaves

Free radicals, known as reactive oxygen species (ROS), are the products of normal cellular metabolism. A free radical can be defined as an atom or molecule containing one or more unpaired electrons. The odd number of electron(s) of a free radical makes it unstable, short lived and highly reactive.1-3 Free radicals are compounds that trigger the aging process and degenerative diseases. Antioxidants are compounds that prevent the formation of free radicals. Antioxidants are divided into two types, natural and synthetic antioxidant. Natural antioxidant commonly found in plants such as fruits, grains, and vegetables. Some natural antioxidant compounds are derivatives of flavonoids, phenol, ascorbic acid, coumarin, hydroxycinnamic, dihydroflavone, tocopherol, and catechin. Synthetic antioxidants include butyl hydroxylanisol, butyl hidroxytoluen, propyl gallate, ethoxyquin.4 Synthetic antioxidants such as butylated hydroxy aniline (BHA) and butylated hydroxy toluene (BHT) have been known to have large side effects including causing liver damage.5 This encourages the development of natural product to be a source of antioxidants. Natural product that can be used as antioxidants is green tea leaves (Camellia sinensis L). The antioxidant activity of green tea is caused by polyphenolic compounds, especially flavonoid groups.6,7 Catechin is flavonoids compound that contained in green tea leaves. The types of catechins that contained in green tea are epigallocatechin (EGC), epigallocatechin gallate (EGCG), epicatechin gallate (ECG), and gallate epicatechin (GEC). 8-10
Peroral endoscopic myotomy (POEM): a comparative study between Chagasic and idiopathic achalasia

Abstract Background and study aims Achalasia can be classified as either primary (idiopathic) achalasia or secondary achalasia, which is a consequence of another systemic disease. Peroral endoscopic myotomy (POEM) is an effective and safe treatment for achalasia. We evaluated the efficacy and safety of POEM in patients with Chagasic achalasia compared to idiopathic achalasia. Patients and methods We evaluated POEM procedures performed at a single institution from November 2016 to January 2018. Demographic data, Eckardt score, lower esophageal sphincter (LES) pressure, body mass index, post-operative erosive esophagitis, adverse events, length of hospital stay, and procedure-related parameters were analyzed. Results Fifty-one patients underwent POEM as a treatment for achalasia in this period (20 patients with Chagasic and 31 with Idiopathic etiology). The overall clinical success rate was 92.1 %, with no statistical difference between groups (90 % in the Chagasic group vs. 93.5 % in the Idiopathic group, P = 0.640). Both groups had significant reduction in Eckardt score and in LES pressure, and increase in bodey mass index (BMI) at 1-year follow-up. There was no statistical difference between groups regarding Eckardt score (P = 0.439), LES pressure (p = 0.507), BMI (P = 0.254), post erosive esophagitis (35 % vs. 38.7 %, P = 0.789), adverse events (30 % vs. 12 %, P = 0.163,) length of hospital stay (3.75 days vs. 3.58 days, P = 0.622), and operative time (101.3 min vs. 99.1 min, P = 0.840). Conclusion POEM is an effective and safe treatment for patients with achalasia. There is no difference in POEM outcomes for those patients with Chagasic or Idiopathic achalasia.
Local Reconstruction Codes in Cloud

Cloud computing intendedfor providing software and hardware facilities are provided to users as a service over the internet through a web browser. Economic gains are the foremost driver for the Cloud. User need not worry about the internal details of the storage and physical infrastructure. But, privacy and security risks are high in this case. Hence correctness of data is a prime concern. This work proposesa novel approach for data correctness in cloud storage systems which is a reliable storage system based on Local Reconstruction Codes (LRC). While reconstructing data chunks LRC reduces the number of erasure coding chunk s that need to be read, but keeping the storage overhead low. The vital benefits of LRC are that it moderates the bandwidth and input output operations required for repair reads, while still agreeing a major reduction in storage overhead. With the support of Arbitrator this scheme guarantees data error correction along with integrity checking.
Transcranial focused ultrasound to rIFG improves response inhibition through modulation of the P300 onset latency

Response inhibition is important to avoid undesirable behavioral action consequences. Neuroimaging and lesion studies point to a locus of inhibitory control in right inferior frontal gyrus (rIFG). Electrophysiology studies have implicated a downstream event-related potential from rIFG, the fronto-central P300, as a putative neural marker of the success and timing of inhibition over behavioral responses. However, it remains to be established whether rIFG effectively drives inhibition as represented by the P300 activity, and whether rIFG contributions to inhibition are conveyed through either the P300 timing or amplitude. Here, we aimed to causally uncover the connection between rIFG and P300 for inhibition by using transcranial focused ultrasound (tfUS) to target rIFG of human subjects while they performed a Stop-Signal task. By applying tFUS simultaneous with different task events, we found behavioral inhibition was improved only when applied to rIFG simultaneous with a ‘stop’ signal. Applying tFUS simultaneous with the ‘go’ signal or control regions had no impact on behavior. The improvement in inhibition performance caused by tFUS to rIFG during stop conditions occurred through faster stopping times that were paired with significantly shorter P300 latencies, whereas amplitude was not affected. These results reveal a causal connection between rIFG in driving response inhibition in that it may regulate the speed of stopping directly, as indexed by the reduced P300 onset latency during tFUS. Our tFUS-EEG approach provides a causal connection, in healthy humans, between prefrontal rIFG regions and downstream P300 production in service of inhibitory control.
Qualidade do carvão vegetal comercializado no Sudeste Paraense para cocção de alimentos

In 2017, the residential and commercial sectors consumed around 677,000 tons of charcoal in Brazil. Due to the expressiveness of this consumption, some studies to attest the quality of this fuel were conducted in several states of Brazil; however, in Para, studies on this subject are still incipient. Therefore, this study aimed to characterize the charcoal for cooking food marketed in southeastern Para and to evaluate whether the quality observed meets the parameters indicated by the Selo Carvao Premium. The study was conducted in the city of Parauapebas, where three brands of charcoal (A, B, and C) were selected in three different points of sale, with packages of 5 kg being acquired in a three-month period, totaling 15 kg. The variables analyzed were apparent relative density, humidity, higher heating value, net heating value, energy density, volatile materials, ash, fixed carbon and elemental chemical composition (C, H, N, S, and O). The data were analyzed in a completely randomized design, being three treatments and eighteen replications, totaling fifty-four sample units. All brands had moisture content above 5%, apparent relative density greater than 420 kg m-3, and high percentages of ash (> 1.5%). The B and C brands had volatile material contents between 17 – 19% and fixed carbon between 78 – 80%, respectively. The average net heating value for the charcoals of the region was 6672 kcal kg-1. The charcoal for cooking foods analyzed have low quality; however, brands B and C were the closest to the minimum standard required by the Selo Carvao Premium of the state of Sao Paulo.
Pengaruh Puasa Ramadhan terhadap Kadar Gula Darah pada Pasien Diabetes Mellitus Tipe II

The purpose of this research is to know the influence of Ramadan Fasting towards blood sugar levels in diabetics in the health center in West Java of Purwakarta. The design of this research uses quasi experiment of pre and post test with the control group, the method uses Purposive sampling done by the sum of 36 samples of respondents. The results of this research are using Independent T-test fast differences in blood sugar levels after fasting Ramadaan in the control group and the intervention group obtained the value of p = 0.039 < α = 0.05. Conclusion the results of this study showed the presence of the influence of fasting of Ramadan towards blood sugar levels in type II diabetes mellitus patients in Healty Center of Purwakarta. It can be concluded that fasting during Ramadan can be used as an alternative diet method that has positive benefits if it is run by type II diabetes mellitus patients which can reduce blood sugar to be more stable. Keywords: Ramadhan Fasting, Blood Glukose Level, Diabetic Mellitus Type II
A Cluster based Data Collection Method for Wireless Sensor Networks

— The wireless Sensor Network (WSN) plays an important role in many applications. The performance of the WSN purely depends on the data collection schemes. One of the important factors to determine the performance of WSN is data collection. Topology management plays a vital role in reducing various constraints such as energy consumption, life time, node failure, long-range communication within a network etc. The data collection scheme such as flat, chain, tree, cluster and cluster tree are available for collecting data in WSNs. In this paper, a new data collection method is proposed. It is based on cluster topology. As compared to static sensor nodes, the mobile sensors have many advantages to gather and collect the data. The proposed data collection method has a Data Gathering Node (DGN). The DGN is made as a mobile node, which moves towards the cluster and collects the data and forwards to the sink. The DGN does not participate on sensing in this particular round, however, it simply gathers the data packet from the cluster and delivers it to the sink. The designed method minimizes the energy consumption, traffic and delay. The simulation results have demonstrated that proposed data collection method has better performance in terms of energy consumption, end-to-end delay, and throughput and network lifetime of WSNs.
Scenario Analysis in the Electric Power Industry under the Implementation of the Electricity Market Reform and a Carbon Policy in China

In China, electricity market reform was first implemented in 2015. At the same time, the national carbon market was built, along with the electricity industry, which was considered a breakthrough. Some key considerations for the future development of China’s electricity system include the implementation of demand-side measures in order to adjust the peak-to-valley difference and the economic dispatch of increasing intermittent renewable energy and traditional energy in the process of power marketization with the implementation of a carbon policy. This paper examines the impact of policies on electricity generation by modelling the evolution process of power marketization and the economic dispatch of generation technologies over a sixteen-year period beginning in 2020. We model four potential influencing factors of government policy: (1) the demand response mode; (2) power marketization process; (3) capacity adjustment of thermal power units; and (4) carbon taxes, which vary in terms of their timing and amount. This model assesses the impact of these influencing factors on the competition between electricity generators using a range of output variables, including generation portfolios, electricity prices, capacity factors, CO2 emissions, etc. The results show that the new round of electricity market reforms has had a positive impact on renewable energy generation. The influence of carbon policy is evident in the promotion, transformation and elimination of thermal units, and an indirect increase in renewable energy generation.
A CALIBRATION WORKFLOW FOR “PROSUMER” UAV CAMERAS

Abstract. High-end consumer quadcopter UAVs or so-called “prosumer devices”, have made inroads into the mapping industry over the past few years, arguably displacing more expensive purpose-built systems. In particular, the DJI Phantom series quadcopters, marketed primarily for videography, have shown considerable promise due to their relatively high-quality cameras. Camera pre-calibration has long been a part of the aerial photogrammetric workflow with calibration certificates being provided by operators for every project flown. Most UAV data, however, is processed today in Structure-from-Motion software where the calibration is generated “on-the-fly” from the same image-set being used for mapping. Often the scenes being mapped and their flight-plans are inappropriate for calibration as they do not have enough variation in altitude to produce a good focal-length solution, and do not have cross-strips to improve the estimation of the principal point. What we propose is a new type of flight-plan that can be run on highly textured scenes of varying height prior to mapping missions that will significantly improve the estimation of the interior orientation parameters and, as a consequence, improve the overall accuracy of projects undertaken with these sorts of UAV systems. We also note that embedded manufacturer camera profiles, which correct for distortion automatically, should be removed prior to all photogrammetric processing, something that is often overlooked as these profiles are not made visible to the end user in most image conversion software, particularly Adobe’s CameraRAW.
Local community detection based on network motifs

Local community detection aims to find a cluster of nodes by exploring a small region of the network. Local community detection methods are faster than traditional global community detection methods because their runtime does not depend on the size of the entire network. However, most existing methods do not take the higher-order connectivity patterns crucial to the network into consideration. In this paper, we develop a new Local Community Detection method based on network Motif (LCD-Motif) which incorporates the higher-order network information. LCD-Motif adopts the local expansion of a seed set to identify the local community with minimal motif conductance, representing a generalization of the conductance metric for network motifs. In contrast to PageRank-like diffusion methods, LCD-Motif finds the community by seeking a sparse vector in the span of the local spectra, such that the seeds are in its support vector. We evaluate our approach using real-world datasets across various domains and synthetic networks. The experimental results show that LCD-Motif can achieve a higher performance than state-of-the-art methods.