Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny-based classification of microbial communities

MOTIVATION Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiology called comparative metagenomics. Comparative metagenomic analysis studies compositional patterns within and between different environments providing a deep insight into the structure and function of complex microbial communities. It is a fast growing field that requires the development of novel supervised learning techniques for addressing challenges associated with metagenomic data, e.g. sensitivity to the choice of sequence similarity cutoff used to define operational taxonomic units (OTUs), high dimensionality and sparsity of the data and so forth. On the other hand, the natural properties of microbial community data may provide useful information about the structure of the data. For example, similarity between species encoded by a phylogenetic tree captures the relationship between OTUs and may be useful for the analysis of complex microbial datasets where the diversity patterns comprise features at multiple taxonomic levels. Even though some of the challenges have been addressed by learning algorithms in the literature, none of the available methods take advantage of the inherent properties of metagenomic data. RESULTS We proposed a novel supervised classification method for microbial community samples, where each sample is represented as a set of OTU frequencies, which takes advantage of the natural structure in microbial community data encoded by a phylogenetic tree. This model allows us to take advantage of environment-specific compositional patterns that may contain features at multiple granularity levels. Our method is based on the multinomial logistic regression model with a tree-guided penalty function. Additionally, we proposed a new simulation framework for generating 16S ribosomal RNA gene read counts that may be useful in comparative metagenomics research. Our experimental results on simulated and real data show that the phylogenetic information used in our method improves the classification accuracy. AVAILABILITY AND IMPLEMENTATION http://www.cs. ucr.edu/~tanaseio/metaphyl.htm.
Capital Structure and the Market for Corporate Control: The Defensive Role of Debt Financing

A capital structure theory based on corporate control considerations is presented. The optimal debt level balances a decrease in the probability of acquisition against a higher share of the synergy for the target's shareholders. This leads to the following implications: (1) the probability of firms becoming acquisition targets decreases with their leverage; (2) acquirers' share of the total equity gain increases with targets' leverage; (3) when acquisitions are initiated, targets' stock price, targets' debt value, and acquirers' firm value increase; and (4) during the acquisition, target firms' stock price changes further; the expected change is zero and the variance decreases with targets' debt level. Copyright 1991 by American Finance Association.
Impact of Dividend Policy on Stock Price Risk: Empirical Evidence from Equity Market of Pakistan

This study is conducted with the objective to find out impact of dividend policy on stock price risk in Pakistan. The data of the study is taken from the published resources of State Bank of Pakistan and Karachi Stock Exchange regarding to five important sectors for the period 2005-2009. Descriptive statistics, correlation and regression models are used to perform the data analysis. The results of the study reveals that the correlation of price volatility and dividend yield is quite significant as compare to other variables. Moreover price volatility has negative correlation to the growth in assets. It is also inferred from the study that all the Variables are linked to the price Volatility; however, second model justifies the relational impact of some variables on the price volatility.
Preparation of Armored RNA as a Control for Multiplex Real-Time Reverse Transcription-PCR Detection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus

ABSTRACT The common respiratory viruses, including influenza A, influenza B, and newly emerging severe acute respiratory syndrome (SARS) viruses, may cause similar clinical symptoms. Therefore, differential diagnosis of these virus pathogens is frequently required for single clinical samples. In addition, there is an urgent need for noninfectious and stable RNA standards and controls for multivirus detection. In this study, reverse transcription-PCR (RT-PCR) targeting of the RNAs of influenza A and influenza B viruses and SARS coronavirus was performed, and the resulting products were spliced into a fragment which was packaged into armored RNA for use as a noninfectious, quantifiable synthetic substitute. Furthermore, in the present study we developed a multiplex real-time RT-PCR assay in which the armored RNA was used as an external positive control and the three RNA viruses could be detected simultaneously in a single reaction mix. The detection limit of the multiplex real-time PCR was 10 copies/μl of armored RNA.
A balanced sub-millimeter wave power amplifier

In this paper, a new balanced sub-millimeter wave power amplifiers is presented. The amplifier uses CPW-grounded MIM capacitors to form low-loss, lumped element matching networks and uses a branchline coupler to achieve requisite quadrature phase shifts. The balanced amplifier achieves 12-dB small signal gain and 6.1-mW output power (not saturated) at a center frequency of 270-GHz. The high gain allows the amplifier to reach a moderate Power Added Efficiency (PAE) of 5.25% at the highest drive power. The results in this paper are the highest reported output powers achieved from a solid state amplifier at these frequencies, and were achieved with a high fMAX InP HEMT process.
Trade liberalization and productivity growth: new evidence from the Turkish rubber industry

This paper empirically examines the effects of a change in foreign trade regime on productivity growth. Based on a Generalized Leontief factor demand function system, total factor productivity growth (TFPG) rates are calculated for the Turkish rubber industry during a substantial trade liberalization in the 1980s: TFPG was significantly higher following trade liberalization. Technological change was the major contributor to this growth. When a panel data estimation technique is used to explain technological change, the effects of trade liberalization become clearer: a one percentage point increase in the protection level led to more than a one percentage point (1.27) decline in the technological change rate.
A Hybrid Dynamic Optimization Approach for Stability Constrained Optimal Power Flow

Stability-constrained optimal power flow (SOPF) is an effective and economic tool to enhance stability performance by adjusting initial steady-state operating conditions, with the consideration of rotor angle and short-term voltage performance criteria. SOPF belongs to the category of dynamic optimization problems which are computationally expensive. In order to reduce its computational complexity, a hybrid dynamic optimization approach is proposed for efficient and robust solving SOPF problems. Based on the direct multiple shooting method, this approach combines the algorithmic advantages from existing direct sequential and simultaneous approaches. Coarse-grained parallelism among multiple shooting intervals is explored. A modular-based implementation architecture is designed to take advantage of the loose coupling between time-domain simulation and optimization. Case studies on various test systems indicate that the proposed approach is able to reduce computation time compared with other direct approaches for dynamic optimization. Also, the investigated parallelizations are effective to achieve acceleration on a symmetric multiprocessing platform.
In vivo roles for myosin phosphatase targeting subunit‐1 phosphorylation sites T694 and T852 in bladder smooth muscle contraction

Force production and maintenance in smooth muscle is largely controlled by myosin regulatory light chain (RLC) phosphorylation, which relies on a balance between Ca2+/calmodulin‐dependent myosin light chain kinase (MLCK) and myosin light chain phosphatase (MLCP) activities. MYPT1 is the regulatory subunit of MLCP that biochemically inhibits MLCP activity via T694 or T852 phosphorylation in vitro. Here we separately investigated the contribution of these two phosphorylation sites in bladder smooth muscles by establishing two single point mutation mouse lines, T694A and T852A, and found that phosphorylation of MYPT1 T694, but not T852, mediates force maintenance via inhibition of MLCP activity and enhancement of RLC phosphorylation in vivo. Our findings reveal the role of MYPT1 T694/T852 phosphorylation in vivo in regulation of smooth muscle contraction.
An Empirical Analysis of the Relationship Between Brand Loyalty and Consumer Price Elasticity

This empirical paper explores the relationship between consumer brand preference or loyalty and price elasticity in purchase behavior. This behavior is conceptualized as resulting from two distinct but related decisions, namely a brand choice decision and a purchase quantity decision. We argue that loyal consumers will be price sensitive in the choice decision than nonloyal consumers. However, this direction is expected to be reversed in the quantity decision with loyal consumers expected to be price sensitive than nonloyal consumers. We model the choice and quantity decisions jointly using the limited dependent variable framework described in Krishnamurthi and Raj. The data used are diary panel data on a frequently purchased product class from BURKE and caffeinated ground coffee scanner data from IRI. We show that loyals are less price sensitive than nonloyals in the choice decision but more price sensitive in the quantity decision. Managerial implications of the differing elasticities are discussed.
PROJECT 720: A CASE STUDY OF HIGH SCHOOL REFORM

The purpose of this qualitative case study was to examine a major Pennsylvania high school reform initiative: Project 720. Through document review and interviews, the author found that Pennsylvania allocated $40 million to 143 school districts in an attempt to transform Pennsylvania high schools into child-centered, small learning communities focused on 21st Century learning skills. This study examined the design, implementation, and sustainability of Project 720. This study posed three research questions: (1) What events led to the development of Project 720? (2) How was Project 720 implemented? (3) What is the status of Project 702? The focus for Pennsylvania's high school reform began during the 2005 National Governors' Association conference. The agenda for the conference was a need for high school reform. Along with the nation's governors, the nation's business leaders represented by the National Business Roundtable and the Bill & Melinda Gates Foundation identified a need for high school reform. As a result of this conference Pennsylvania developed Project 720. Project 720 focused on several factors, those being; (1) poor performance on standardized tests, (2) lack of rigor in the high school curriculum, (3) lack of career preparation, and (4) concern regarding the rate of students not completing high school in four years.Implementation of Project 720 was difficult to determine. Lacking available documents, there continues to be an ambiguity regarding how Project 720 funds were allocated. This confusing allocation of funds coupled with a lack of information regarding an auditing procedure of grantee funds left the investigator to speculate how allocated funds were used for Project 720. This study concluded that there are very few formal reports regarding the sustained efforts of Project 720. Pennsylvania's 2011 proposed budget contains no funding for Project 720, or any other identified high school reform effort. Therefore, it is crucial that Project 720 funded school districts build capacity to sustain high school reform. The value of $40 million of Pennsylvania State grants depends on how well Project 720 districts implemented activities that improved education and how well districts ensured funding to sustain those implemented activities.
A Tagging Approach to Ontology Mapping

The invention relates to new cationic surfactants based on quaternary ammonium compounds corresponding to the general formula R1-CHOH-CHR2-N+R3R4R5 R6CO2-(1) wherein R1 is a linear or branched alkyl residue having from 1 to 22 carbon atoms; R2 is hydrogen or a linear or branched alkyl residue having from 1 to 21 carbon atoms, the total number of carbon atoms of the substituents R1 and R2 being in the range of from 8 to 22; R3 and R4 each represent methyl, ethyl, 2-hydroxyethyl or 2-hydroxypropyl; R5 represents an alkyl residue having from 4 to 6 carbon atoms or a phenalkyl residue having from 1 to 3 carbon atoms in the alkyl residue; and R6 represents a linear or branched alkyl residue having from 4 to 15 carbon atoms. The cationic surfactants have particular utility in cleaning agents.
Insider Trading Activities Before the Simultaneous Announcements of Earnings and Dividends

We employ a sample of 3,177 events from Hong Kong industrial firms during the 1993–1999 period to examine insider trading activities around earnings and dividends announcements. By controlling for earnings management, special dividends, and other firm level financial indicators, we find that the presence of insider trading, its trading direction, and its trading intensity are related to the signals of these simultaneous earnings and dividends announcements. Various tests show that our findings are robust regardless of the proxies used for measuring insider trading activities, earnings, and dividend changes.
Mathematical model for pancreatic cancer progression using non-constant gene mutation rate

Cancer of the pancreas is a highly lethal disease and has an extremely poor prognosis. Mathematical modelling and computer simulations have been proposed as important tool to predictor initiation and progression of cancer diseases, which are very important in cancer study. Among these studies, it is widely assumed that the gene mutation rate is unchanged, which is not realistic based on recently biological and medical studies. In this work, we present a new approach using non-constant mutation rate and hence reveal several important biological parameters of cancer progression. Under more realistic assumptions regarding gene mutation and a more reasonable mutation rate, our proposed model and calculated results may provide insights into dynamics of cancer metastasis and have clinic implications.
Living Rationally Under the Volcano? Heavy Drinking and Smoking Among the Elderly

Most rational addiction models focus on how drinking and smoking are made when young. Yet, the costs of drinking and smoking generally come later in life. We focus on the decisions of the elderly where individuals know their propensity for addiction but are uncertain about their future earnings and helath status. Using data from the Health and Retirement Survey, we estimate a dynamic stochastic model of heavy drinking and smoking of the elderly. Individuals make decisions not only based upon the current effects of heavy drinking and smoking, but also the future effects of drinking and smoking on earnings, health, and mortality. We are especially interested in the identification of the discount factor. We show how the likelihood function varies with the discount factor and also how behavior decisions vary from not estimating a dyanmic model. In particular, we find that the dynamic model forecasts more drinking and smoking as well as individuals living longer. This is because individuals know when, and when not to, engage in heavy drinking and smoking behavior.
Most cases of primary salivary mucosa‐associated lymphoid tissue lymphoma are associated either with Sjoegren syndrome or hepatitis C virus infection

Salivary gland mucosa‐associated lymphoid tissue (MALT) lymphomas (SGML) are rare, as are data concerning their behaviour. We analysed clinical features at presentation, particularly the association with Sjoegren syndrome (SS) and hepatitis C virus (HCV) infection, and outcome in 33 cases of SGML diagnosed between March 1985 and April 2003. There were five males and 28 females, with a median age of 61 years. At presentation, 12/33 (36%) had multiple salivary glands or mucosal involvement and four had bone marrow infiltration. Ann Arbor stage was IE in 15 (46%), IIE in four (12%) and IV in 14 patients (42%). Fifteen patients had a history of SS (46%), two of other autoimmune diseases, seven of HCV infection. No case had both SS and HCV. Of the 29 treated patients, 17 received surgery or local radiotherapy; 69% achieved complete remission. Histological transformation occurred in four (12%). Five patients died (three of lymphoma, two of unrelated causes). The 5 year‐overall survival (OS), cause‐specific survival and progression‐free survival was 85 ± 8%, 94 ± 6% and 65 ± 10% respectively. Overall, the disease course was indolent, despite the advanced stage at diagnosis, and local therapy often appeared to be adequate. The only prognostic factors influencing OS were histological transformation and age. The close association of SGML with either autoimmune diseases or HCV infection in our series (73%) confirms their possible role in the pathogenesis of these lymphomas.
Vestibular Nerve Section Versus Intratympanic Gentamicin for Meniere's Disease

Objectives/Hypothesis: Vestibular nerve section and transtympanic gentamicin administration are procedures with proven efficacy in the treatment of vertigo associated with Meniere's disease refractory to medical management. Hearing loss is a known complication of each of these procedures; however, there has not been a report of hearing results of both treatments from a single institution.
Estimation of the upper bound horizon for input constrained MPC based on reachable sets

Based on the reachable sets, two new effective and less conservative algorithms for computing the upper bound of the control horizon for the input constrained model predictive control problem are presented. Reachable sets of the current state are used to predict the evolution and the minimal cost of each step from the current state. The K-step null-controllable set is used to determine which set the initial state belongs to. Then the state can reach the origin after K steps at least. The minimal cost within the reachable set is applied to compute the upper bound for an initial state. The state within the polytope can be expressed as a convex combination of the vertices of the polytope, which is used to deduce a global upper bound by solving a linear programming problem quickly. The proposed algorithms are compared with the others by an example.
Living with non-state policing in South Africa: the issues and dilemmas

Though policing is widely regarded as an inherently public good, in reality non-state policing is widespread in South Africa, doing everything that the public police force does. The paper examines the extent, nature and attitudes towards non-state policing in South Africa in its different forms, that is, autonomous citizen responses, ‘responsible’ citizen responses and commercial private security. The paper concludes by assessing the social and political implications of non-state policing.
Asset building and livelihood rebuilding in post-disaster Sichuan, China

In May 2008, a severe earthquake struck Sichuan Province, devastating many rural communities. Mudslides followed in 2010, undermining some attempts to rebuild. Despite rapid reconstruction efforts by the Chinese central government, many survivors faced uncertainty and substantial challenges. To support rural survivors' efforts to regain livelihoods and hope, social workers launched several asset-building initiatives in the area. The use of asset building as a strategy to address poverty emerged in the United States in the 1990s and spread to Chinese communities in Taiwan and Hong Kong, but there have been only a few efforts to apply the strategy in rural China. This article discusses the conceptual framework of asset building and details asset-building efforts in disaster-stricken rural communities. The article also documents an evolution in the concept of assets and proposes that the concept should be broadened further to include two additional types of assets: social and cultural.
The distribution of UK personal income tax compliance costs

Governments are committed to reducing the regulatory burden on business and individuals, while at the same time transferring many tasks from bureaucrats. One such example is tax compliance where self-assessment (SA) has raised concerns that such transfers may place a particularly heavy burden on lower income and elderly taxpayers. This is the first study since its introduction into the UK in 1996 of the regulatory burden, which SA imposes on individuals. We identify both the total compliance burden and its components for individuals who might be expected to incur high compliance costs because they pay tax on nonbusiness employment income. We use a specially designed questionnaire and find that within this group the burden seems to have increased by less than 25%. Compliance costs are regressive, but do not impinge disproportionately on the elderly. The compliance burden is determined by income, occupation, education (but not specifically in accounting subjects) and difficulty in attending to tax affairs, indicating some possibilities for reducing these compliance costs.
Antegrade enemas for the treatment of severe idiopathic constipation

The technique of appendicocaecostomy produces a continent catheterizable channel through which colonic washouts are given. This procedure was performed on six women of mean age 33·5 years with severe idiopathic constipation (mean stool frequency less than 1 per week) resistant to medical therapy. All patients had prolonged colonic transit times, three had evidence of obstructed defaecation and all had reduced or absent voluntary anal squeeze pressure. Patients found the appendicocaecostomy and catheterization acceptable, and symptoms of abdominal distension and pain resolved. All patients were able to initiate defaecation and evacuate the colon within 1h of irrigation, and no patient had appreciable incontinence. Irrigation was necessary every 48–72h. Adults with intractable constipation and pelvic floor weakness would be at risk of faecal incontinence after ileorectal anastomosis; it is in these patients that appendicocaecostomy has potential for the greatest benefit.
Predictable Uncertainty in Economic Forecasting

This paper provides an introduction to predictable forecast uncertainty in empirical economic modelling. The sources of both predictable and unpredictable forecast uncertainty are categorized. Key features of predictable forecast uncertainty are illustrated by several analytical models, including static and dynamic models, and single-equation and multiple-equation models. Empirical models of the U.S. trade account, U.K. inflation, and U.K. real national income help clarify the issues involved.
Effects of Exchange Rate Volatility on the Volume and Volatility of Bilateral Exports

We present an empirical investigation of a recently suggested but untested proposition that exchange rate volatility can have an impact on both the volume and variability of trade flows, considering a broad set of countries' bilateral real trade flows over the period 1980-1998. We generate proxies for the volatility of real trade flows and real exchange rates after carefully scrutinizing these variables' time series properties. Similar to the findings of earlier theoretical and empirical research, our first set of results show that the impact of exchange rate uncertainty on trade flows is indeterminate. Our second set of results provide new and novel findings that exchange rate volatility has a consistent positive and significant effect on the volatility of bilateral trade flows.