Miracle-dz/UniFAR-FTUs huggingface dataset:
VGJφ, a Novel Filamentous Phage of Vibrio cholerae, Integrates into the Same Chromosomal Site as CTXφ

ABSTRACT We describe a novel filamentous phage, designated VGJφ, isolated from strain SG25-1 of Vibrio cholerae O139, which infects all O1 (classical and El Tor) and O139 strains tested. The sequence of the 7,542 nucleotides of the phage genome reveals that VGJφ has a distinctive region of 775 nucleotides and a conserved region with an overall genomic organization similar to that of previously characterized filamentous phages, such as CTXφ of V. cholerae and Ff phages of Escherichia coli. The conserved region carries 10 open reading frames (ORFs) coding for products homologous to previously reported peptides of other filamentous phages, and the distinctive region carries one ORF whose product is not homologous to any known peptide. VGJφ, like other filamentous phages, uses a type IV pilus to infect V. cholerae; in this case, the pilus is the mannose-sensitive hemagglutinin. VGJφ-infected V. cholerae overexpresses the product of one ORF of the phage (ORF112), which is similar to single-stranded DNA binding proteins of other filamentous phages. Once inside a cell, VGJφ is able to integrate its genome into the same chromosomal attB site as CTXφ, entering into a lysogenic state. Additionally, we found an attP structure in VGJφ, which is also conserved in several lysogenic filamentous phages from different bacterial hosts. Finally, since different filamentous phages seem to integrate into the bacterial dif locus by a general mechanism, we propose a model in which repeated integration events with different phages might have contributed to the evolution of the CTX chromosomal region in V. cholerae El Tor.
Phonological Encoding in the Lexical Decision Task

In lexical decision experiments, subjects have difficulty in responding NO to non-words which are pronounced exactly like English words (e.g. BRANE). This does not necessarily imply that access to a lexical entry ever occurs via a phonological recoding of a visually-presented word. The phonological recoding procedure might be so slow that when the letter string presented is a word, access to its lexical entry via a visual representation is always achieved before phonological recoding is completed. If prelexical phonological recodings are produced by using grapheme-phoneme correspondence rules, such recodings can only occur for words which conform to these rules (regular words), since applications of the rules to words which do not conform to the rules (exception words) produce incorrect phonological representations. In two experiments, it was found that time to achieve lexical access (as measured by YES latency in a lexical decision task) was equivalent for regular words and exception words. It was concluded that access to lexical entries in lexical decision experiments of this sort does not proceed by sometimes or always phonologically recoding visually-presented words.
Pipeline timing analysis using a trace-driven simulator

We present a technique for worst-case execution time (WCET) analysis for pipelined processors. Our technique uses a standard simulator instead of special-purpose pipeline modeling. Our technique handles CPUs that execute multiple shorter instructions in parallel with long-running instructions. The results of other machine analyses, like cache analysis, can be used in our pipeline analysis. Also, results from high-level program flow analysis can be used to tighten the execution time predictions. Our primary target is embedded real-time systems, and since processor simulators are standard equipment for embedded development work, our tool will be easy to port to relevant target processors.
Impact of Art on At-Risk Students

The research study focused on the influence and impact of art education on at-risk students who have experienced or are experiencing trauma. Through support of literature, including scholarly journals and case studies, and classroom observations of the researcher’s students from an inner city school in southeast Washington, D.C., it was concluded that not only does art impact at-risk students education, but it does so, positively. The classroom observations included five principal participants in both elementary and middle school, three boys and two girls, whom all live in a housing project near their school. Information was gathered about these students through both researcher observations and personal communications with the school psychologist. In combination with the student participants, data was gathered from literature —mainly from the works of Eleanor D. Brown who has done extensive research on the effects of the arts on at-risk students who have experienced trauma and/or chaotic situations. The literature and student observations were used to support one another in a cohesive, coherent way. The literature helped to decipher some of the classroom observations and better understand the reactions and responses of students. The study revealed that art education affects students in several ways including influencing the child’s education as a whole, art as a coping mechanism, school readiness, and a child’s general wellbeing. Implications of the study are the resulting affects on art education as a whole, including policy writing and the field of arts advocacy. IMPACT OF ART EDUCATION ON AT-RISK STUDENTS iii Acknowledgements Acknowledgements are given to the friends and family of the researcher for their continued support of the process. Further acknowledgements are given to the school psychologist at Friendship Chamberlain for her contribution and involvement in giving insight into the student participants lives. IMPACT OF ART EDUCATION ON AT-RISK STUDENTS iv
Therapeutics , Targets , and Chemical Biology RNAi-Mediated Targeting of Noncoding and Coding Sequences in DNA Repair Gene Messages Ef fi ciently Radiosensitizes Human Tumor Cells

Human tumor cell death during radiotherapy is caused mainly by ionizing radiation (IR)–induced DNA double-strand breaks (DSB), which are repaired by either homologous recombination repair (HRR) or nonhomologous end-joining (NHEJ). Although siRNA-mediated knockdown of DNA DSB repair genes can sensitize tumor cells to IR, this approach is limited by inefficiencies of gene silencing. In this study, we show that combining an artificial miRNA (amiR) engineered to target 30-untranslated regions of XRCC2 (an HRR factor) or XRCC4 (an NHEJ factor) along with an siRNA to target the gene coding region can improve silencing efficiencies to achieve more robust radiosensitization than a single approach alone. Mechanistically, the combinatorial knockdown decreased targeted gene expression through both a reduction in mRNA stability and a blockade to mRNA translation. Together, our findings establish a general method of gene silencing that is more efficient and particularly suited for suppressing genes that are difficult to downregulate by amiRor siRNA-based methods alone. Cancer Res; 72(5); 1221–8. 2012 AACR.
Double Knockdown of Prolyl Hydroxylase and Factor-Inhibiting Hypoxia-Inducible Factor With Nonviral Minicircle Gene Therapy Enhances Stem Cell Mobilization and Angiogenesis After Myocardial Infarction

Background— Under normoxic conditions, hypoxia-inducible factor (HIF)-1&agr; is rapidly degraded by 2 hydroxylases: prolyl hydroxylase (PHD) and factor-inhibiting HIF-1 (FIH). Because HIF-1&agr; mediates the cardioprotective response to ischemic injury, its upregulation may be an effective therapeutic option for ischemic heart failure. Methods and Results— PHD and FIH were cloned from mouse embryonic stem cells. The best candidate short hairpin (sh) sequences for inhibiting PHD isoenzyme 2 and FIH were inserted into novel, nonviral, minicircle vectors. In vitro studies after cell transfection of mouse C2C12 myoblasts, HL-1 atrial myocytes, and c-kit+ cardiac progenitor cells demonstrated higher expression of angiogenesis factors in the double-knockdown group compared with the single-knockdown and short hairpin scramble control groups. To confirm in vitro data, shRNA minicircle vectors were injected intramyocardially after left anterior descending coronary artery ligation in adult FVB mice (n=60). Functional studies using MRI, echocardiography, and pressure-volume loops showed greater improvement in cardiac function in the double-knockdown group. To assess mechanisms of this functional recovery, we performed a cell trafficking experiment, which demonstrated significantly greater recruitment of bone marrow cells to the ischemic myocardium in the double-knockdown group. Fluorescence-activated cell sorting showed significantly higher activation of endogenous c-kit+ cardiac progenitor cells. Immunostaining showed increased neovascularization and decreased apoptosis in areas of injured myocardium. Finally, western blots and laser-capture microdissection analysis confirmed upregulation of HIF-1&agr; protein and angiogenesis genes, respectively. Conclusions— We demonstrated that HIF-1&agr; upregulation by double knockdown of PHD and FIH synergistically increases stem cell mobilization and myocardial angiogenesis, leading to improved cardiac function.
Parallel implementation of saliency maps for real-time robot vision

This paper presents a parallel implementation model for real-time video image processing of saliency maps (SMs), which are a model to predict gaze directions based on human visual attention. It can extract high visual saliency regions that differ from surroundings in scene images. In computer vision, SMs are used for various applications because of the sparse feature representation. As an implementation device, we use IMAPCAR2, which is a single instruction multiple data (SIMD) processor with 64 processing elements (PEs). The features of IMAPCAR2 are high performance, low power consumption, and easy programming using one-dimensional C (1DC) of the ANSI-C compatible. We compared the performance of a sequential model and our parallel model for all steps. The processing speed of our model was 250 times higher than that of the sequential model. We compared our model with the existing parallel model. The processing speed of our model was 5.6 times higher than that of the existing model. For real-time video image processing, we implemented our model on an IMAPCAR2 evaluation board. The processing cost was 47.5 ms for the video images of 640 × 240 pixel resolution.
Prime and composite polynomials

where each <p,(z) is a polynomial of degree greater than unity, prime or composite, we shall say that (2) is a decomposition of F(z). The first result of the present paper is that any two decompositions of a given polynomial into prime polynomials contain the same number of polynomials; the degrees of the polynomials in one decomposition are the same as those in the other, except, perhaps, for the order in which they occur. Two decompositions of F(z) into the same number of polynomials,
A Gap Reduction and Manufacturing Technique for Thick Oxide Mask Layers With Multiple-Size Sub-$mu$m Openings

This paper introduces a technique for the fabrication of thick oxide hard masks on top of a substrate with adjustable opening sizes in the sub-mum regime, while the only lithography step involved has mum-scale resolution. This thick oxide mask layer with sub-mum openings is suitable for etching deep narrow trenches in silicon using deep reactive ion etching (DRIE) tools. Openings of less than 100 nm are realized in a 1.5-mum-thick oxide layer, while the original lithographically defined feature sizes are larger than 1 mum in width. This method, combined with modified high aspect ratio DRIE recipes, shows a great potential for single-mask batch-fabrication of high frequency low-impedance single crystalline resonators on silicon-on-insulator (SOI) substrates. Dry-etched trenches with aspect ratios as high as 60:1 are fabricated in silicon using the gap reduction technique to realize 200 nm opening sizes in an oxide mask layer. Various resonator structures with sub-mum capacitive gaps are also fabricated on a SOI substrate using a single-mask process. Measurement results from high-frequency and high-quality factor (Q) all single crystal silicon resonators are presented
Persistence of Cyprinid Herpesvirus 3 in Infected Cultured Carp Cells

ABSTRACT Cyprinid herpesvirus 3 (CyHV-3), previously designated carp interstitial nephritis and gill necrosis virus or koi herpesvirus, is the cause of a worldwide mortal disease of koi and carp. Morphologically, the virus resembles herpesviruses, yet it bears a genome of 277 to 295 kbp, which is divergent from most of the genomic sequences available in GenBank. The disease afflicts fish in the transient seasons, when the water temperature is 18 to 28°C, conditions which permit virus propagation in cultured cells. Here we report that infectious virus is preserved in cultured cells maintained for 30 days at 30°C. CyHV-3-infected vacuolated cells with deformed morphology converted to normal, and plaques disappeared following shifting up of the temperature and reappeared after transfer to the permissive temperature. Viral propagation and viral gene transcription were turned off by shifting cells to the nonpermissive temperature. Upon return of the cells to the permissive temperature, transcription of viral genes was reactivated in a sequence distinguished from that occurring in naïve cells following infection. Our results show that CyHV-3 persists in cultured cells maintained at the nonpermissive temperature and suggest that viruses could persist for long periods in the fish body, enabling a new burst of infection upon a shift to a permissive temperature.
A Tool for Sheep Product Quality: Custom Microarrays from Public Databases

Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. The purpose of this study was to gain an understanding of the genomic influence on milk quality and synthesis by comparing two sheep breeds with different milking attitude (Sarda and Gentile di Puglia) using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we have generated the first annotated microarray developed for sheep with a coverage of most of the genome.
Power-Distance, Gender and Organizational Justice

A sample of Hong Kong employees was used to test the hypotheses that power-distance orientation and gender moderate the relationships between justice perceptions and the evaluation of authorities (trust in supervisor) and the organization (contract fulfillment). Results indicated that 1) the relationship between procedural justice and contract fulfillment was higher for males, 2) the relationship between procedural justice and trust in supervisor was higher for those with low power-distance orientations, and 3) the relationship between distributive justice and contract fulfillment was higher for those with low power-distance orientations. The discussion addresses the implication of including power-distance and gender variables in research on procedural and distributive justice.
Reverse link erlang capacity of time-hopping/TDMA wireless communication systems

In this paper, the performance analysis of a recently proposed multiple-access (MA) scheme for data communication via TDMA wireless channel in terms of Erlang capacity is carried out. The proposed MA scheme takes advantage of time-hopping (TH) within multiple frames of a time-division multiple-access (TDMA) system to provide access to the channel for network subscribers. First, a super-frame for the TDMA signaling is defined. Subsequently, a user is provided with an access code that is used to hop over the indicated TDMA super-frame, hereafter referred to as a TH frame. The assignment codes are those of the {0,1} family codes, recently exploited for fiber-optic code-division multiple-access (FO-CDMA) applications. It is assumed that each assignment code can guarantee no more than 1 hit in a superframe and that code synchronization exists between all users. For differential phase-shift-keying (DPSK) and M-ary frequency-shift-keying (MFSK) modulated THMA systems and when side information is available at the receiver, upper bounds on the overall symbol error rate are derived when the communication channel is impaired by slow frequency non-selective Rayleigh and Rician fading. The capacity of the proposed system is obtained in terms of Erlang/sector for reverse link and is compared to those of TDMA and CDMA systems. It is demonstrated that the power control requirement of the proposed THMA system is identical to that of a conventional TDMA system, and that the proposed system achieves an Erlang capacity identical to that of its CDMA counterpart
Communications in Mathematical Physics Geometry of Maurer-Cartan Elements on Complex Manifolds ,

The semi-classical data attached to stacks of algebroids in the sense of Kashiwara and Kontsevich are Maurer-Cartan elements on complex manifolds, which we call extended Poisson structures as they generalize holomorphic Poisson structures. A canonical Lie algebroid is associated to each Maurer-Cartan element. We study the geometry underlying these Maurer-Cartan elements in the light of Lie algebroid theory. In particular, we extend Lichnerowicz-Poisson cohomology and Koszul-Brylinski homology to the realm of extended Poisson manifolds; we establish a sufficient criterion for these to be finite dimensional; we describe how homology and cohomology are related through the Evens-Lu-Weinstein duality module; and we describe a duality on Koszul-Brylinski homology, which generalizes the Serre duality of Dolbeault cohomology.
Hormonal and Cardiac Effects of Converting Enzyme Inhibition in Rat Myocardial Infarction

To explain how converting enzyme inhibition could improve the prognosis in cardiac insufficiency, the effect of converting enzyme inhibition (CEI) by S9490–3 (Perindopril) treatment for 2 months (treated infarctions, n = 18) on hormonal plasma variables and the quantitative and qualitative changes in myocardium were studied in an experimental model of left ventricular infarction in rats (untreated infarctions, n = 18) and compared to a sham-operated control group (n = 15). Induction of myocardial infarction was associated with a transient decrease in blood pressure. CEI treatment maintained a lower blood pressure throughout the experimental period. Plasma renin concentration was not significantly increased in the untreated infarct group (155.4 ± 136.7 ng AI/ml/hr) as compared to the sham-operated group (47.6 ± 15.9 ng AI/ml/hr). Plasma aldosterone did not change in the three experimental groups. The plasma level of immunoreactive atrial natriuretic factor increased in the untreated infarct group (185 ± 245 pg/ml) as compared with the control group (76 ± 40 pg/ml) and was normalized by CEI (66 ± 60 pg/ml). Body weight was slightly decreased in both treated and untreated infarct groups, whereas the heart weight was significantly increased in the untreated group (1,540 ± 310 mg) and normalized by treatment (1,145 ± 180 mg) as compared with sham-operated controls (1,071 ± 80 mg). The combined atria and right ventricular mass was significantly increased in the untreated infarct group (660 ± 210 mg) and decreased by treatment (443 ± 106 mg) but was not completely normalized (controls, 343 ± 40 mg). Left ventricular isomyosin profiles were modified by myocardial infarction as compared with controls: V1 form decreased from 62.4 ± 9.4% in the sham-operated group to 41.6 ± 13.4% in the infarct group, and the V3 form increased from 13.0 ± 4.7% in sham-operated animals to 27.4 ± 11.8% in untreated infarct animals. CEI treatment partially, but significantly, reversed this modification of the isomyosin profile (V1, 53.0 ± 14.4%; V1,17.5 ± 8.0%). Volume density of collagen was significantly increased in the untreated infarct rats (4.14 ± 0.81% versus 2.68 ± 0.49% in controls), and this was reversed by treatment (2.95 ± 0.66%). Messenger RNA encoding for atrial natriuretic factor, measured by dot blot hybridization, was significantly increased in both the atria and the ventricles in the untreated infarct group, and treatment by CEI partially reversed this increase. Thus, myocardial infarction profoundly modified several variables of peripheral circulation and quantitative and qualitative myocardial protein expression. CEI treatment largely reversed these changes but probably did not completely normalize them.
Body Mass Index and Risk of Suicide Among One Million US Adults

Background: Body mass index (BMI) has been linked with both increased and decreased risk of suicide attempts and deaths. Methods: In a prospective cohort study of 1.1 million adults, participants reported their anthropometric and other characteristics in 1982. Participants were followed for cause-specific mortality through 2004. Results: A total of 2231 participants died of suicide during 21.6 million person-years of follow-up. Compared with a BMI of 18.5–22.9 kg/m2, adjusted hazard ratios for completed suicide were 0.99 (95% confidence interval = 0.72–1.37), 0.78 (0.69–0.88), 0.73 (0.65–0.82), 0.72 (0.62–0.83), 0.77 (0.65–0.92), and 0.55 (0.36–0.83) for BMI values <18.5, 23.0–24.9, 25.0–27.4, 27.5–29.9, 30.0–34.9, and ≥35.0 kg/m2, respectively. The relationship was consistent among men and women and across geographic regions, but was limited to married individuals (test for interaction, P = 0.009). Conclusions: The risk of death from suicide is inversely related to BMI in middle-aged and older adults.
Effects of Endocrine Disruptors on Dehydroepiandrosterone Sulfotransferase and Enzymes Involved in PAPS Synthesis: Genomic and Nongenomic Pathways

Background Sulfation plays an important role both in detoxification and in the control of steroid activity. Studies in rodents have shown that the conversion of dehydroepiandrosterone (DHEA) to DHEA-sulfate is involved in learning and the memory process. Methods The effects of a range of plasticizers and related compounds commonly encountered in the environment were evaluated kinetically against human DHEA sulfotransferase (SULT 2A1) and by reverse transcriptase-polymerase chain reaction (RT-PCR) against several enzymes involved in the synthesis of the sulfotransferase cofactor adenosine 3′-phosphate 5′-phosphosulfate (PAPS). Results We found that several of the chemicals acted as competitive inhibitors of SULT 2A1 (Ki for 4-tert-octylphenol is 2.8 μM). Additionally, after treatment of TE 671 cells with 0.005–0.5 μM 4-n-octylphenol, bis(2-ethylhexyl)phthalate, and diisodecyl phthalate, real-time RT-PCR showed dose-dependent decreases in the steady-state mRNA levels of cysteine dioxygenase type I, sulfite oxidase, and 3′-phosphate 5′-phosphosulfate synthase I. Conclusions These data suggest that environmental contaminants may exert effects on neuronal function both by direct inhibition of sulfotransferase enzymes and by interrupting the supply of PAPS, which has wider implications for endocrine disruption and xenobiotic metabolism.
Analysis of Ergot Alkaloids

The principles and application of established and newer methods for the quantitative and semi-quantitative determination of ergot alkaloids in food, feed, plant materials and animal tissues are reviewed. The techniques of sampling, extraction, clean-up, detection, quantification and validation are described. The major procedures for ergot alkaloid analysis comprise liquid chromatography with tandem mass spectrometry (LC-MS/MS) and liquid chromatography with fluorescence detection (LC-FLD). Other methods based on immunoassays are under development and variations of these and minor techniques are available for specific purposes.