Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence requirements for transcriptional arrest in exon 1 of the murine adenosine deaminase gene

We have previously shown that a transcription arrest site near the 5' end of the murine adenosine deaminase (ADA) gene is significantly involved in the regulation of ADA gene expression. To facilitate the analysis of this transcription arrest site, we have analyzed the transcription products from cloned ADA gene fragments injected into Xenopus laevis oocytes. When genomic fragments spanning the 5' end of the ADA gene were injected into oocytes, a 96-nucleotide (nt) ADA RNA was the major transcription product. The 5' end of this RNA mapped to the transcription initiation site for the ADA gene, and its 3' terminus mapped 7 nt downstream of the translation initiation codon within exon 1. A 300-base-pair fragment of genomic DNA spanning the 5' end of the ADA gene was sufficient to generate the 96-nt transcript which accounted for approximately one-half of the transcription products from injected templates. Deletion of a segment of approximately 65 base pairs, located immediately downstream of the 3' terminus of the 96-nt transcript, resulted in a substantial reduction in the synthesis of the 96-nt transcript and a corresponding increase in the production of larger transcripts. These studies show that the transcriptional apparatus of X. laevis oocytes responds to the transcription arrest site associated with exon 1 of the murine ADA gene and that oocyte injections provide a convenient functional assay for additional mechanistic studies.
Retinal MMP-12, MMP-13, TIMP-1, and TIMP-2 expression in murine experimental retinal detachment.

PURPOSE Matrix metalloproteinases (MMPs) and their inhibitors play a role in the pathobiology of retinal detachment (RD) and proliferative vitreoretinopathy (PVR). Proliferative vitreoretinopathy is facilitated by chronic retinal detachment and involves excessive deposition of extracellular matrix (ECM) proteins. Matrix metalloproteinase-2 and -13 are important modulators of the ECM which have not been evaluated in RD. The purpose of this study was to investigate the retinal expression of select MMPs, including MMP-12, MMP-13, and associated inhibitors in a murine model of retinal detachment. METHODS Transient or chronic retinal detachments (RDs) were induced by subretinal injection of either saline (SA) or hyaluronic acid (HA) in C57BL/6 mice. To confirm that the HA-RD model has features consistent with PVR-like changes, glial activation and subretinal fibrosis were evaluated with immunofluorescence, dilated fundus examination, and spectral-domain optical coherence tomography (SD-OCT). Gene expression was quantified by qRT-PCR. Proteins were assayed by immunoblot and immunohistochemistry. RESULTS Hyaluronic acid RD eyes developed gliosis and subretinal fibrosis on dilated exam, SD-OCT, and immunofluorescence analysis. Gene expression of Mmp-12 and Mmp-13, and Timp-1 was strongly upregulated at all time points in RD compared with controls. Timp-2, Mmp-2, and Mmp-9 expression was modest. Hyaluronic acid RDs exhibited more MMP and TIMP expression than SA-RDs. MMP-12, -13, and TIMP-1 proteins were elevated in RDs compared with controls. Immunohistochemistry revealed moderate to strong MMP-13 levels in subretinal space macrophages. CONCLUSIONS Fibrosis can develop in the HA-RD model. There is an upregulation of select MMPs that may modulate the wound healing process following RD.
Indirect fluorescent antibody testing of cerebrospinal fluid for diagnosis of equine protozoal myeloencephalitis.

OBJECTIVE To assess the use of CSF testing with an indirect fluorescent antibody test (IFAT) for diagnosis of equine protozoal myeloencephalitis (EPM) caused by Sarcocystis neurona. SAMPLE POPULATION Test results of 428 serum and 355 CSF samples from 182 naturally exposed, experimentally infected, or vaccinated horses. PROCEDURE EPM was diagnosed on the basis of histologic examination of the CNS. Probability distributions were fitted to serum IFAT results in the EPM+ and EPM-horses, and correlation between serum and CSF results was modeled. Pairs of serum-CSF titers were generated by simulation, and titer-specific likelihood ratios and post-test probabilities of EPM at various pretest probability values were estimated. Post-test probabilities were compared for use of a serum-CSF test combination, a serum test only, and a CSF test only. RESULTS Post-test probabilities of EPM increased as IFAT serum and CSF titers increased. Post-test probability differences for use of a serum-CSF combination and a serum test only were < or = 19% in 95% of simulations. The largest increases occurred when serum titers were from 40 to 160 and pre-test probabilities were from 5% to 60%. In all simulations, the difference between pre- and post-test probabilities was greater for a CSF test only, compared with a serum test only. CONCLUSIONS AND CLINICAL RELEVANCE CSF testing after a serum test has limited usefulness in the diagnosis of EPM. A CSF test alone might be used when CSF is required for other procedures. Ruling out other causes of neurologic disease reduces the necessity of additional EPM testing.
Dictyostelium discoideum Dgat2 Can Substitute for the Essential Function of Dgat1 in Triglyceride Production but Not in Ether Lipid Synthesis

ABSTRACT Triacylglycerol (TAG), the common energy storage molecule, is formed from diacylglycerol and a coenzyme A-activated fatty acid by the action of an acyl coenzyme A:diacylglycerol acyltransferase (DGAT). In order to conduct this step, most organisms rely on more than one enzyme. The two main candidates in Dictyostelium discoideum are Dgat1 and Dgat2. We show, by creating single and double knockout mutants, that the endoplasmic reticulum (ER)-localized Dgat1 enzyme provides the predominant activity, whereas the lipid droplet constituent Dgat2 contributes less activity. This situation may be opposite from what is seen in mammalian cells. Dictyostelium Dgat2 is specialized for the synthesis of TAG, as is the mammalian enzyme. In contrast, mammalian DGAT1 is more promiscuous regarding its substrates, producing diacylglycerol, retinyl esters, and waxes in addition to TAG. The Dictyostelium Dgat1, however, produces TAG, wax esters, and, most interestingly, also neutral ether lipids, which represent a significant constituent of lipid droplets. Ether lipids had also been found in mammalian lipid droplets, but the role of DGAT1 in their synthesis was unknown. The ability to form TAG through either Dgat1 or Dgat2 activity is essential for Dictyostelium to grow on bacteria, its natural food substrate.
Sarbanes‐Oxley compliance and violation: an empirical study

Purpose - The purpose of this paper is to empirically examine the corporate governance and financial characteristics of firms under the new Sarbanes-Oxley (SOX) accounting regime. Design/methodology/approach - The paper first compares a comprehensive set of characteristics across firms in two states of SOX Section 404 status–Compliance and Violation. It then tests for determinants of SOX compliance in a logistic regression setting. Findings - Several differences between compliance groups in terms of equity ownership, board structure, and executive compensation schemes are reported. However, it appears that firms found to be in violation of SOX are not systematically worse when it comes to common measures of corporate governance. The financial structure and soundness of the groups of firms are very similar. The strongest determinant of Section 404 compliance is firm size. Originality/value - This result supported anecdotal evidence that compliance with SOX is achieved primarily by firms that can afford it. Further, the paper highlights an important policy issue: Is SOX really differentiating firms in terms of corporate governance or in terms of size?
Virtual classroom system with improved student feedback

Student feedback in traditional virtual classrooms is usually limited to intentional feedback. Information pertaining to the actual mental state (bored, interested, content, confused), gathered from facial expressions and gestures is lost. The paper focuses on methods to increase student feedback without placing unnecessary or excessive strain on available resources such as bandwidth, memory and processing power. The method uses indirect (facial actions from student video) and direct (answers to questions and opinions) feedback to estimate the student's state. These estimates are then used to prioritise video transmission/updating from student to teacher. An experimental system is currently being developed and implemented using the Java Multimedia Framework (JMF)
Insulin‐like growth factor II mRNA‐binding protein 3: A novel prognostic biomarker for oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is caused by multiple factors, including carcinogen exposure. Insulin‐like growth factor II mRNA‐binding protein 3 (IMP3) is highly expressed in various cancer cells but is rarely expressed in normal cells. We investigated whether IMP3 can be used as a prognostic biomarker for OSCC.
New microarchitecture challenges in the coming generations of CMOS process technologies (keynote address)(abstract only)

Over the last 15 years, CMOS scaling simplified the task of the microprocessor architect. With each new process technology, frequency increased by -50%, and transistor density increase by 100 percent. Also, the improvements in manufacturing technology (larger wafers and higher yields) allowed for increasing die sizes without increasing cost. Projections of die sizes of 1 square inch or higher were common. However, the end of these easy times is in sight, and several new challenges are facing the architect. Die size is no longer going to be limited by equipment or manufacturing cost, but rather by power. To date the approach has been to lower voltage with each process generation. But as voltage is lowered, leakage current and energy increase, contributing to higher power. And the problems extend beyond power dissipation to power delivery/distribution and increasing power density. This talk will first look at the historical trends of CMOS process technology in the context of past microprocessors. It will then look at the implications of continued CMOS scaling, as described above, and the new challenges they pose. Microarchitecture techniques that have exacerbated the power problem will also be covered. Finally, the talk will describe some of the microarchitecture directions that may lead to more power-efficient and cost-efficient microprocessors.
Classification of Human B-ZIP Proteins Based on Dimerization Properties

B-ZIP transcription factors (98) are exclusively eukaryotic proteins that bind to sequence-specific double-stranded DNA as homodimers or heterodimers to either activate or repress gene transcription (34). We have examined both of the recently published DNA sequences of the human genome (51, 95) and identified 56 genes that contain the B-ZIP motif. Three sequences were identical, giving a total of 53 unique B-ZIP domains with the potential to form 2,809 dimers. This creates the possibility for a tremendous range of transcriptional control (23, 50, 52). While significant effort has been directed at identifying dimerization partners of B-ZIP proteins, the full complement of dimerization partners remains to be elucidated. This review highlights two topics: (i) the known structural rules that regulate leucine zipper dimerization specificity and (ii) experimental data addressing mammalian B-ZIP dimerization partners. We have annotated the leucine zippers of all human B-ZIP domains, highlighting amino acids in the a, d, e, and g positions that appear critical for leucine zipper dimerization specificity. These data were used to group B-ZIP proteins into 12 families with similar dimerization properties: (i) those that strongly favor homodimerization within the family (PAR, CREB, Oasis, and ATF6), (ii) those that have the ability to both homodimerize and heterodimerize with similar affinities (C/EBP, ATF4, ATF2, JUN, and the small MAFs), and (iii) those that favor heterodimerization with other families (FOS, CNC, and large MAFs).
Applying market mechanisms to facilitate interpersonal information exchange

Requesting and sharing information through computer-mediated technology is an integral part of our lives in this information age. However, when deciding whether or not and how to engage in information exchanges, parties involved often have different needs and constraints. In addition, they are often unaware of each others' needs and constraints. Such asymmetry in motivation and information leads to suboptimal allocation of attention and time and contributes to the growing problems of information overload, costly interruptions and missed opportunities. A potential solution is to employ market mechanisms to support information exchange. Markets are institutions that allow individuals to trade goods and services efficiently. Applying markets to information exchange, askers can use pricing to signal the importance of the information exchange and compensate the answerers for their time. Answerers can use pricing mechanisms to filter incoming requests, reducing interruption costs and information overload. This dissertation studies the strengths and weaknesses of using economic markets for interpersonal information exchange. Are there costs in incorporating markets into our everyday information exchanges? How do we design these markets to maximize the benefits of market forces while minimizing the costs? Part 1 of the dissertation examines whether or not economic markets can indeed improve welfare for people involved. Part 2 studies the use of markets for question and answer (Q&A) services, a specific, but a popular type of interpersonal information exchange. Part 3 elucidates how using economic markets for information exchange may affect interpersonal relationships.
Long-term immunity in cats vaccinated with an inactivated trivalent vaccine.

OBJECTIVE To evaluate duration of immunity in cats vaccinated with an inactivated vaccine of feline panleukopenia virus (FPV), feline herpesvirus (FHV), and feline calicivirus (FCV). ANIMALS 17 cats. PROCEDURE Immunity of 9 vaccinated and 8 unvaccinated cats (of an original 15 vaccinated and 17 unvaccinated cats) was challenged 7.5 years after vaccination. Specific-pathogen-free (SPF) cats were vaccinated at 8 and 12 weeks old and housed in isolation facilities. Offspring of vaccinated cats served as unvaccinated contact control cats. Virus neutralization tests were used to determine antibody titers yearly. Clinical responses were recorded, and titers were determined weekly after viral challenge. RESULTS Control cats remained free of antibodies against FPV, FHV, and FCV and did not have infection before viral challenge. Vaccinated cats had high FPV titers throughout the study and solid protection against virulent FPV 7.5 years after vaccination. Vaccinated cats were seropositive against FHV and FCV for 3 to 4 years after vaccination, with gradually declining titers. Vaccinated cats were protected partially against viral challenge with virulent FHV. Relative efficacy of the vaccine, on the basis of reduction of clinical signs of disease, was 52%. Results were similar after FCV challenge, with relative efficacy of 63%. Vaccination did not prevent local mild infection or shedding of FHV or FCV. CONCLUSIONS Duration of immunity after vaccination with an inactivated, adjuvanted vaccine was > 7 years. Protection against FPV was better than for FHV and FCV. CLINICAL IMPLICATIONS Persistence of antibody titers against all 3 viruses for > 3 years supports recommendations that cats may be revaccinated against FPV-FHV-FCV at 3-year intervals.
A Distributed Data Processing Perspective on Industrial Real-Time Systems

Changeability is becoming a competitive factor for manufacturing companies in today's dynamic markets. Service-oriented architectures (SOAs) achieve high adaptability but usually lack the required real-time guarantees. This thesis applies principles from distributed data processing systems to SOAs in industrial manufacturing. The automation workflow is described as a network of service instances and the data flow between them. Using domain specific heuristics, the system derives distributed execution plans with verifiable real-time guarantees. These principles are realized within a real-world demonstrator.
Decomposition of new venture growth into firm age, survey period and vintage effects

Firm data are accumulated on a yearly basis. In view of the linear relationship of firm age + foundation year = survey year, the fluctuations of firm data classified by age and period cannot be decomposed into age, period and cohort (foundation year) effects. Three decomposition methods are briefly reviewed and applied to Japanese data on new ventures founded since 1995. Regarding sales and employment growth, the age effect is the largest with a downward trend, and the cohort effect is negligible. Regarding labour productivity, the age effect indicates upward movements, and the cohort effect is negligible. The reason of the negligible cohort effect is discussed.
Zinc porphyrin: A fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer

FRET between the zinc porphyrin (ZnP) chromophore in zinc-substituted cytochrome c (Zn-cyt c) and an Alexa Fluor dye attached to specific surface sites was used to characterize Zn-cyt c unfolding. The use of ZnP as a fluorescent acceptor eliminates the need to doubly label the protein with exogenous dyes to perform FRET experiments in which both donor and acceptor fluorescence is monitored. The requirement for attachment of only one dye also minimizes perturbation to the protein. This sensitive technique allowed for the determination of distances between the label placed at six different sites and ZnP through a range of denaturant concentrations. Fitting of the data to a three-state model provides distances in the unfolding intermediate. The use of ZnP as a fluorescent acceptor of energy in FRET has a significant potential for application to a range of other systems including heme-binding proteins and proteins to which a covalently attached heme tag may be added.
Academic Writing Within An Online Learning Environment: Assessing The Impact Of Peer Evaluation On Lesson Planning, Execution & Assessment

Peer evaluation, as a learning strategy, is commonly used among educators in an attempt to promote higher performance goals and improved teaching and learning outcomes through the sharing of complementary proficiencies for a familiar intent. It is commonly viewed as a technique for raising the bar' through exposing educators to alternative perspectives. Within the online learning environment, there is a high degree of isolation among educators involved in the delivery of the same course. Although individuals interact in established teacher forums about administrative issues, a forum is not provided where interaction about teaching content, delivery and conceptualization of critical concepts can be explored and discussed. As such, the provision of a forum for collaboration among peers involved in different aspects of course delivery within the online learning environment is believed to address the issue of isolated instruction while also providing support and evaluation as to the effectiveness of teaching strategies employed. The aim of the research is to investigate the impact of an established peer partnership between 14 colleagues working in pairs geared towards assessing feedback and discussions on lesson planning, execution and assessment processes. It seeks to ascertain its usefulness as a strategy to be incorporated into the teaching of English for Academic Purposes within an online learning environment. The study seeks to provide actionable direction for peer evaluation and collaboration, as a teaching and learning tool, through the mapping, assessing and evaluation of the processes involved.
The Current State of Liver Transplantation in the United States

This article is a review of the salient points and a future prospective based on the 2014 Organ Procurement and Transplantation Network (OPTN)/Scientific Registry of Transplant Recipients (SRTR) liver donation and transplantation data report recently published by the American Journal of Transplantation. Emphasis of our commentary and interpretation is placed on data relating to waitlist dynamics, organ utilization rates, the impact of recent advances in the treatment of hepatitis C, and the increases in end‐stage renal disease among liver transplant candidates. Finally, we share our vision on potential areas of innovation that are likely to significantly improve the field of liver transplantation in the near future.
A Scalable Backward Chaining-Based Reasoner for a Semantic Web

— In this paper we consider knowledge bases that organize information using ontologies. Specifically, we investigate reasoning over a semantic web where the underlying knowledge base covers linked data about science research that are being harvested from the Web and are supplemented and edited by community members. In the semantic web over which we want to reason, frequent changes occur in the underlying knowledge base, and less frequent changes occur in the underlying ontology or the rule set that governs the reasoning. Interposing a backward chaining reasoner between a knowledge base and a query manager yields an architecture that can support reasoning in the face of frequent chang-es. However, such an interposition of the reasoning introduces uncertainty regarding the size and effort measurements typically exploited during query optimization. We present an algo-rithm for dynamic query optimization in such an architecture. We also introduce new optimization techniques to the back-ward-chaining algorithm. We show that these techniques together with the query-optimization reported on earlier, will allow us to actually outperform forward-chaining reasoners in scenarios where the knowledge base is subject to frequent change. Finally, we analyze the impact of these techniques on a large knowledge base that requires external storage.
SPED – Public Digital Bookkeeping System: influence in the economic-financial results declared by companies

By deploying the Public Digital Bookkeeping System (SPED), tax administration seeks to increase the subjective perception of risk between taxpayers and reduce the tax gap. The objective of this research is to verify whether the implementation of Accounting SPED had an influence on the economic and financial results declared by companies (gross revenue and net profit). The null hypothesis of the research - the lack of relationship between these variables - was tested through the regression model with panel data. The sample was selected from the 500 largest companies listed in the database Best and Biggest, by Exame Melhores e Maiores magazine. The data collected comprise financial statements of these companies on the calendar years 2004 to 2009. Regression models were estimated using random effects, with unbalanced panels. The Accounting SPED showed significance in all regression models of gross revenue and net profit, allowing the rejection of the null hypothesis of no relationship between these variables. Finally, according to the analysis models of tax evasion exposed in the literature review, considering that the Accounting SPED increases the effectiveness and efficiency of auditing mechanisms of the tax administration, an increase on the economic and financial results declared by companies of the sample was expected, which was confirmed in research.