Miracle-dz/UniFAR-FTUs huggingface dataset:
Compositional Mediation Analysis for Microbiome Studies

Motivated by recent advances in causal mediation analysis and problems in the analysis of microbiome data, we consider the setting where the effect of a treatment on an outcome is transmitted through perturbing the microbial communities or compositional mediators. Compositional and high-dimensional nature of such mediators makes the standard mediation analysis not directly applicable to our setting. We propose a sparse compositional mediation model that can be used to estimate the causal direct and indirect (or mediation) effects utilizing the algebra for compositional data in the simplex space. We also propose tests of total and component-wise mediation effects using bootstrap. We conduct extensive simulation studies to assess the performance of the proposed method and apply the method to a real metagenomic dataset to investigate the effect of fat intake on body mass index mediated through the gut microbiome composition.
Proteasomal Inhibition Attenuates Transcriptional Activity of Hypoxia-Inducible Factor 1 (HIF-1) via Specific Effect on the HIF-1α C-Terminal Activation Domain

ABSTRACT The ubiquitin-proteasome pathway (UPP) is involved in regulation of multiple cellular processes. Hypoxia-inducible factor 1α (HIF-1α) is a prototypic target of the UPP and, as such, is stabilized under conditions of proteasomal inhibition. Using carbonic anhydrase IX (CAIX) and vascular endothelial growth factor (VEGF) expression as paradigmatic markers of HIF-1 activity, we found that proteasomal inhibitors (PI) abrogated hypoxia-induced CAIX expression in all cell lines tested and VEGF expression in two out of three. Mapping of the inhibitory effect identified the C-terminal activation domain (CAD) of HIF-1α as the primary target of PI. PI specifically inhibited the HIF-1α CAD despite activating the HIF-1α coactivator p300 and another p300 cysteine/histidine-rich domain 1-dependent transcription factor, STAT-2. Coimmunoprecipitation and glutathione S-transferase pull downs indicated that PI does not disrupt interactions between HIF-1α and p300. Mutational analysis failed to confirm involvement of sites of known or putative posttranslational modifications in regulation of HIF-1α CAD function by PI. Our data provide evidence for the counterintuitive hypothesis that inhibition of HIF-1 function could be responsible for at least some of the antitumor effects of proteasomal inhibition. Further studies of the mechanism of the PI-induced attenuation of HIF-1α will provide important, potentially novel insight into regulation of HIF-1 activity and possibly identify new targets for HIF-directed therapy.
Risk and Preventive Factors for Type 2 Diabetes and Heart Disease Among Foreign-Born Older Vietnamese Americans

The 2009 California Health Interview Survey (CHIS) data was used to examine associations of bodyweight, lifestyles, and demographic variables with type 2 diabetes (T2DM) and heart disease among foreign-born older Vietnamese adults. CHIS consisted of 709 Vietnamese Americans aged 50 to 85. Thirteen percent reported T2DM and 11% had heart disease. Using logistic regression, body mass index ≥ 24, age ≥ 65, and female were significantly associated with T2DM. There was significant interaction effect of alcohol consumption and psychological distress with T2DM. The interaction of vegetable consumption, poverty, and length of living in the U.S. was significantly associated with heart disease.
A Fast Application-Based Supply Voltage Optimization Method for Dual Voltage FPGA

Dual supply voltage was a mature method to reduce the dynamic power of specific and programmable circuits, and the unsettled low voltage level (VL) was proved to have impact on its effect. In this paper, a circuit-level power model is developed to estimate the optimal VL fast for field-programmable gate array (FPGA). The model is mainly based on the path delay distribution of applications and the delay function of the integrated circuit technology. It can also count minor factors, such as path overlap, transition density, and capacitance. Experiment was conducted on a 90-nm FPGA model using MCNC benchmark. The results showed that the proposed method could generate near optimum VL for most benchmarks. The best power reduction ratio is only 5.6% less than the gate-level heuristic method, which is relatively precise, but our method is ~100-10000 times faster. It implies that the dual voltage design with variable VL is a possible and promising low power method for field-programmable devices.
Evaluation of breast self-examination program using Health Belief Model in female students

BACKGROUND: Breast cancer has been considered as a major health problem in females, because of its high incidence in recent years. Due to the role of breast self-examination (BSE) in early diagnosis and prevention of morbidity and mortality rate of breast cancer, promoting student knowledge, capabilities and attitude are required in this regard. This study was conducted to evaluation BSE education in female University students using Health Belief Model. METHODS: In this semi-experimental study, 243 female students were selected using multi-stage randomized sampling in 2008. The data were collected by validated and reliable questionnaire (43 questions) before intervention and one week after intervention. The intervention program was consisted of one educational session lasting 120 minutes by lecturing and showing a film based on HBM constructs. The obtained data were analyzed by SPSS (version11.5) using statistical paired t-test and ANOVA at the significant level of α = 0.05. RESULTS: 243 female students aged 20.6 ± 2.8 years old were studied. Implementing the educational program resulted in increased knowledge and HBM (perceived susceptibility, severity, benefit and barrier) scores in the students (p ≤ 0.01). Significant increases were also observed in knowledge and perceived benefit after the educational program (p ≤ 0.05). ANOVA statistical test showed significant difference in perceived benefit score in students of different universities (p = 0.05). CONCLUSIONS: Due to the positive effects of education on increasing knowledge and attitude of university students about BSE, the efficacy of the HBM in BSE education for female students was confirmed.
GENE CHARACTERISATION , ISOFORMS AND RECOMBINANT EXPRESSION IN VITRO OF CARCININ , AN ANTIBACTERIAL PROTEIN FROM THE SHORE CRAB , CARCINUS MAENAS

Carcinin is a whey acidic protein (WAP) domain-containing antimicrobial protein, produced by the circulating haemocytes of the shore crab, Carcinus maenas. Cloning of its full coding cDNA reveals that it shows some similarity to invertebrate defensins and has a valine-rich signal sequence followed by a defined cleavage site but no obvious acidic anionic ‘pro’ sequence. The C-terminus exhibits a unique cysteine array that is predicted to form 6 disulphide bonds in the tertiary structure. This 12 cysteine array arrangement is conserved in ESTs from related genera and seems to represent a novel tertiary structure amongst AMPs, unique to the Crustacea. There are at least 5 putative isoforms of the mature protein that may arise through the transcription of one or two alleles of a multi-exon gene. Several of the same transcripts have been found in different animals. These isoforms do not arise as a result of alternate splicing of the exons, but by the transcription of different alleles and /or single point mutation of the transcript at up to four loci in the gene. The most commonly expressed transcript of the protein was recombinantly expressed in bacterial fusion system to a yield of ca 2-3 μg ml of culture. In vitro expression with or without the leader sequence confirms the bioinformatic prediction that the stability of the mature protein is reduced when the leader sequence is removed. Carcinin is one of very few invertebrate AMPs characterised at the gene, transcript and protein level and to be recombinantly expressed in vitro in a bacterial system.
The modified base isopentenyladenosine and its derivatives in tRNA

ABSTRACT Base 37 in tRNA, 3′-adjacent to the anticodon, is occupied by a purine base that is thought to stabilize codon recognition by stacking interactions on the first Watson-Crick base pair. If the first codon position forms an A.U or U.A base pair, the purine is likely further modified in all domains of life. One of the first base modifications found in tRNA is N6-isopentenyl adenosine (i6A) present in a fraction of tRNAs in bacteria and eukaryotes, which can be further modified to 2-methyl-thio-N6-isopentenyladenosine (ms2i6A) in a subset of tRNAs. Homologous tRNA isopentenyl transferase enzymes have been identified in bacteria (MiaA), yeast (Mod5, Tit1), roundworm (GRO-1), and mammals (TRIT1). In eukaryotes, isopentenylation of cytoplasmic and mitochondrial tRNAs is mediated by products of the same gene. Accordingly, a patient with homozygous mutations in TRIT1 has mitochondrial disease. The role of i6A in a subset of tRNAs in gene expression has been linked with translational fidelity, speed of translation, skewed gene expression, and non-sense suppression. This review will not cover the action of i6A as a cytokinin in plants or the potential function of Mod5 as a prion in yeast.
Simultaneous Mutations in the CLCNKB and SLC12A3 Genes in Two Siblings with Phenotypic Heterogeneity in Classic Bartter Syndrome

Two siblings (brother and sister) with renal tubular hypokalemic alkalosis underwent clinical, biochemical and molecular investigations. Although the biochemical findings were similar (including hypokalemia, metabolic alkalosis, hyperreninemia, hyperaldosteronism and normal blood pressure), the clinical findings were different: the boy, who also presented syndromic signs, developed glomerular proteinuria and renal biopsy revealed focal segmental glomerular sclerosis; the girl showed the typical signs of classic Bartter syndrome. As described in a previous paper, a heterozygous mutation (frameshift 2534delT) was demonstrated in the gene encoding the thiazide-sensitive NaCl co-transporter (SLC12A3) of the distal convoluted tubule; the second molecular analysis revealed a compound heterozygous mutation (A61D/V149E) in the CLCNKB chloride channel gene in both subjects, inherited in trans from the parents. The children were finally diagnosed as having classic Bartter syndrome. These cases represent the first report of the simultaneous presence of heterozygous and compound heterozygous mutations in the SLC12A3 and CLCNKB genes, both of which are involved in renal salt losing tubulopathies, and confirm previous observations regarding classic Bartter syndrome phenotype variability in the same kindred.
Towards A Headline-based Deception Detection Approach for Data Veracity in Online Digital News

Since its existence in 1990's, online news has been the major source of news content for news readers. Unfortunately, based on a number of findings, readers tend to judge on certain event based on the news headlines rather than its contents. With the advancement of mobile and web technologies, it is easier to spread news to others and this unhealthy habits can cause negative impacts towards individuals, organizations or nations that are victimized by the news. This paper proposes a framework to detect deceptive online news based on the news headlines. By having an accurate detection upon deceptive news based on its content, it can assist readers to identify misleading news and to help them to find relevant news for their source of information.
Identification of Function Points in Software Specifications Using Natural Language Processing. (Identification des points de fonction dans les spécifications logicielles à l'aide du traitement automatique des langues)

The inevitable emergence of the necessity to estimate the size of a software thus estimating the probable cost and effort is a direct outcome of increasing need of complex and large software in almost every conceivable situation. Furthermore, due to the competitive nature of the software development industry, the increasing reliance on accurate size estimation at early stages of software development becoming a commonplace practice. Traditionally, estimation of software was performed a posteriori from the resultant source code and several metrics were in practice for the task. However, along with the understanding of the importance of code size estimation in the software engineering community, the realization of early stage software size estimation, became a mainstream concern. Once the code has been written, size and cost estimation primarily provides contrastive study and possibly productivity monitoring. On the other hand, if size estimation can be performed at an early development stage (the earlier the better), the benefits are virtually endless. The most important goals of the financial and management aspect of software development namely development cost and effort estimation can be performed even before the first line of code is being conceived. Furthermore, if size estimation can be performed periodically as the design and development progresses, it can provide valuable information to project managers in terms of progress, resource allocation and expectation management. This research focuses on functional size estimation metrics commonly known as Function Point Analysis (FPA) that estimates the size of a software in terms of the functionalities it is expected to deliver from a user’s point of view. One significant problem with FPA is the requirement of human counters, who need to follow a set of standard counting rules, making the process labour and cost intensive (the process is called Function Point Counting and the professional, either analysts or counters). Moreover, these rules, in many occasion, are open to interpretation, thus they often produce inconsistent counts. Furthermore, the process is entirely manual and requires Function Point (FP) counters to read large specification documents, making it a rather slow process. Some level of automation in the process can make a significant difference in the current counting practice. Automation of the process of identifying the FPs in a document accurately, will at least reduce the reading requirement of the counters, making the process faster and thus shall significantly reduce the cost. Moreover, consistent identification of FPs will allow the production of consistent raw function point counts. To the best of our knowledge, the works presented in this thesis is an unique attempt to analyse specification documents from early stages of the software development, using a generic approach adapted from well established Natural Language Processing (NLP) practices.
Imbalance compensation and automation balancing in magnetic bearing systems using the Q-parameterization theory

The problem caused by imbalance in rotating machinery can be solved using actively controlled magnetic bearing systems. There are two methods to solve this problem using feedback control: 1) compensate for the imbalance forces by generating opposing forces on the bearing surface; and 2) make the rotor rotate around its axis of inertia so no imbalance forces will be generated. The dynamics of the magnetic bearing are described in state-space form using airgap displacement, velocity, and airgap flux as state variables. The system which is unstable in nature is stabilized using the Q-parameterization theory. To compensate for the imbalance disturbance forces, the controller Q-parameter is chosen such that rejection of sinusoidal disturbances is achieved. To achieve automatic balancing, the imbalance is assumed as a sinusoidal noise in the measured signal, and the controller Q-parameter is chosen such that rejection of sinusoidal noise is achieved. Simulation results are presented and show the robustness of the proposed controllers and that the rejection of sinusoidal disturbances is achieved. The rotation of the rotor around its axis of inertia is also achieved. >
The Impact of Headquarter-Subsidiary Relations on Alliance Formation Behavior of MNC Subsidiaries

Previous literature has examined alliance formation at the firm-level, ignoring that MNCs actually consist of different but interrelated subsidiaries that are geographically dispersed. In this paper, we therefore shift focus to the subsidiary-level, identifying conditions that explain the alliance formation behavior of MNC subsidiaries. Based on transaction costs economics and recent MNC literature, we argue that, apart from inducements to form alliances and opportunities to find alliance partners, a third condition becomes apparent when studying alliance formation at the subsidiary-level – i.e. the relationship between the subsidiary and the headquarter. Based on a panel dataset of subsidiaries of seven large MNCs in the pharmaceutical industry, we find that the geographical distance, the level of ownership and the relative size of the subsidiary significantly influence the extent to which subsidiaries form strategic alliances. In this way, our study provides important insights into how MNCs access exter.
Local venous response to N‐desethylamiodarone in humans

Amiodarone, a class III antiarrhythmic agent, is a potent vasodilator in vivo. Its main metabolite, N‐desethylamiodarone, contributes to the antiarrhythmic action of amiodarone after long‐term treatment. It is unknown whether N‐desethylamiodarone has acute vascular effects. The aim of this study was to explore the mechanism of action of N‐desethylamiodarone in human hand veins. Methods: The dorsal hand vein compliance technique was applied in 36 healthy male volunteers. In hand veins preconstricted with the α1–adrenergic receptor agonist phenylephrine or prostaglandin F2α, N‐desethylamiodarone and an inhibitor of nitric oxide formation (NG‐monomethyl‐L‐arginine, L‐NMMA) were infused in the presence or absence of a cyclooxygenase inhibitor (acetylsalicylic acid), and the venodilator effect was measured. Furthermore, N‐desethylamiodarone was infused after oral treatment with hydrocortisone or coinfused with α‐tocopherol. Additional experiments were carried out in bovine aortic endothelial cells to explore the effects of N‐desethylamiodarone on the intracellular Ca2+ concentration ([Ca2+]i).
Multiple Imputation: Better than Single Imputation in Pain Studies?

Missing data is one of the genuine challenges we face during analysis of clinical trials. The main impact of missing data is that it can infuse bias in results which reduces the chance of getting the appropriate interpretation. Hence proper knowledge of techniques for handling missing data is crucial. A common method of handling this problem is by imputing missing values. There can be single or multiple imputations. While single imputation methods like LOCF or BOCF have been widely used, multiple imputation is of a comparatively recent origin but is gaining popularity. The main reason behind its popularity is it overcomes some of the drawbacks of single imputation. The current paper presents comparative effectiveness of each with the help of real life cases involving pain studies.
EXPLORING HOSTILE BUSINESS ENVIRONMENT AS A MODERATOR IN THE EFFECT OF INNOVATION ON FINANCIAL PERFORMANCE OF MANUFACTURING FIRMS IN KENYA

Using entrepreneurship orientationperformance relationship theory, we explore the effect of hostile business environment (HBE) in moderating the relationship between innovation and financial performance of manufacturing firms. Specifically, we explore the moderating effect of HBE on innovation and financial performance of manufacturing firms, and the effect of innovation on the financial performance of manufacturing firms in Kenya. To achieve this, a sample of 200 firms is used to provide data. Ex post facto design, which investigates possible cause and effect relationships between variables, is used. Hierarchical Multiple Regression analysis among the variables is conducted to statistically test the hypotheses. The findings of the HBE on the relationship between innovation and financial performance of manufacturing firms gave a strong positive coefficient as well as those of innovation on financial performance of manufacturing. The paper concludes that HBE moderates the effect of the relationship between innovation and financial performance of manufacturing firms in Kenya. On the basis of these findings the paper recommends that managers and entrepreneurs of manufacturing firms as well as academicians and policy makers should understand the roles of HBE and its effect on moderating the relationship between innovation and financial performance of manufacturing.
Modified CAMshift Algorithm Based on HSV Color Model for Tracking Objects

Tracking objects in real time and exact tracking have long been challenging area in the field of computer vision. This paper describes a modified Continuously Adaptive Mean Shift (CAMshift) algorithm based on the Hue Saturation Value (HSV) color model for tracking an object in real time. The existing CAMshift can detect precisely when an object has a simple color. However, it has some disadvantages. When a CAMshift algorithm tracks an object, it does not consider direction and velocity, and it is difficult to track an object that has various colors and when the background contains color(s) similar to those of an object. In such case, CAMshift is worse than Meanshift. To overcome these disadvantages, a Kalman filter is used with CAMshift, as a Kalman filter can obtain direction vectors and it can make CAMshift exact, even under the aforementioned conditions.
Antibody response and avidity of respiratory syncytial virus‐specific total IgG, IgG1, and IgG3 in young children

Respiratory syncytial virus (RSV) is a major cause of acute respiratory disease in infants and young children. Considering that several aspects of the humoral immune response to RSV infection remain unclear, this study aimed to investigate the occurrence, levels, and avidity of total IgG, IgG1, and IgG3 antibodies against RSV in serum samples from children ≤5 years old. In addition, a possible association between antibody avidity and severity of illness was examined. The occurrence and levels of RSV‐specific IgG depended on age, with infants <3 months old displaying high levels of antibodies, which were probably acquired from the mother. Children ≥24 months old also showed frequent occurrence and high levels of IgG, which was produced actively during infection. In addition, the avidity assay showed that the avidity of RSV‐specific total IgG and IgG1 was lower in infants <3 months old who had acute respiratory disease than in age‐matched controls. The avidity of RSV‐specific IgG detected in children ≥24 months old with lower respiratory infection was lower than that in children with upper respiratory infection. These results indicate that the presence of high avidity RSV‐specific IgG antibodies may lead to better protection against RSV infection in children <3 months old, who may have a lower probability of developing disease of increased severity. In addition, children ≥24 months old with RSV‐specific IgG antibodies of low avidity tended to develop more severe RSV illness. These findings may be helpful in establishing vaccination schedules when a vaccine becomes available. J. Med. Virol. 83:1826–1833, 2011. © 2011 Wiley‐Liss, Inc.
Performance Measurement and Evaluation Practices in Loss-Making Entities: Field and Survey Evidence

We provide evidence on how loss-making entities use earnings in performance evaluations. Relying on field observations from 12 loss-making entities and survey evidence from 141 profitable and loss-making entities, we find that entities expecting losses place a lower weight on earnings for evaluation purposes and rely more on subjective evaluations. Loss-making entities also often set earnings targets at or just above zero, which are consequently very difficult to achieve. Finally, we find some evidence that the emphasis on earnings is lower when: (i) profit urgency is low; (ii) uncontrollable factors adversely affect performance; (iii) performance targets are inaccurate, and (iv) entities are more concerned about retention of their executives.