Miracle-dz/UniFAR-FTUs huggingface dataset:
Acyclovir prophylaxis predisposes to antiviral-resistant recurrent herpetic keratitis.

PURPOSE Long-term acyclovir (ACV) prophylaxis, recommended to prevent recurrent herpes simplex virus type 1 (HSV-1) ocular disorders, may pose a risk for ACV-refractory disease due to ACV resistance. We determined the effect of ACV prophylaxis on the prevalence of corneal ACV-resistant (ACV(R)) HSV-1 and clinical consequences thereof in patients with recurrent HSV-1 keratitis (rHK). METHODS Frequencies of ACV(R) viruses were determined in 169 corneal HSV-1 isolates from 78 rHK patients with a history of stromal disease. The isolates' ACV susceptibility profiles were correlated with clinical parameters to identify risk factors predisposing to ACV(R) rHK. RESULTS Corneal HSV-1 isolates with >28% ACV(R) viruses were defined as ACV(R) isolates. Forty-four isolates (26%) were ACV-resistant. Multivariate analyses identified long-term ACV prophylaxis (≥12 months) (odds ratio [OR] 3.42; 95% confidence interval [CI], 1.32-8.87) and recurrence duration of ≥45 days (OR 2.23; 95% CI, 1.02-4.87), indicative of ACV-refractory disease, as independent risk factors for ACV(R) isolates. Moreover, a corneal ACV(R) isolate was a risk factor for ACV-refractory disease (OR 2.28; 95% CI, 1.06-4.89). CONCLUSIONS The data suggest that long-term ACV prophylaxis predisposes to ACV-refractory disease due to the emergence of corneal ACV(R) HSV-1. ACV-susceptibility testing is warranted during follow-up of rHK patients.
Selectable Marker Gene Removal and Expression of Transgene by Inducible Promoter Containing FFDD Cis-Acting elements in Transgenic Plants.

BACKGROUND Selectable marker gene (SMG) systems are critical for generation of transgenic crops. Transgenic crop production without using SMG is not economically feasible. However, SMGs are non-essential once an intact transgenic plant has been established. Elimination of SMGs from transgenic crops both increases public acceptance of GM crops and prepares gene stacking possibility for improvement of complex traits. Synthetic inducible promoters provide an efficient and flexible strategy to regulate transgene expression. OBJECTIVES This study aimed to construct a transformation vector based on Cre/loxP recombination system to enhance efficiency of SMG-free transgenic plant production followed by post-excision expression of gene of interest in transgenic plants by a pathogen inducible promoter. MATERIALS AND METHODS In pG-IPFFDD-creint-gusint construct, cre recombinase and selectable marker gene (nptII) cassettes were placed between the two loxP recognition sites in direct orientation. Seed-specific Napin promoter was used for regulation of Cre expression in transgenic seeds. In the construct, loxP flanked sequence containing nptII and recombinase cassettes, located between a pathogen inducible promoter containing FFDD cis-acting elements and β-glucuronidase coding region. The cunstuct was transformed into Nicotiana tabaccum via Agrobacterium-mediated transformation. RESULTS The results showed that both cre and nptII excision occurs in T1 progeny tobacco plants through seed-specific cre expression. The excisions were confirmed by methods activation of the gus gene, germination test on kanamycin-containing medium and molecular analysis. Inducibility of gus expression by FFDD-containing promoter in T1 leaf tissues was confirmed by histochemical Gus staining assay. CONCLUSIONS The established system is not only an efficient tool for marker gene elimination but also provides possibility for inducible expression of the transgene.
Finding the Positive in the Negative

ABSTRACT The impact of natural disasters and climate change on archaeological resources has garnered much recent attention, with impacts of sea level rise and coastal flooding being the two most often cited issues. However, damage caused by flooding of interior areas and waterways has received less consideration. In this article, we present a case study of a collaborative emergency response to a significant weather event and the ensuing impacts on archaeological resources. Our project, located in Middle Tennessee, documented severe erosion and subsequent anthropogenic disturbances to ancient Native American sites following massive flooding of the Cumberland River in 2010. While striving to mitigate this damage via systematic collection of imperiled archaeological samples, we were also able to strengthen partnerships among professional archaeologists working in different arenas (academia, state and federal agencies) and the avocational archaeological community. As these types of weather-related events become more common, published case studies of response efforts will be crucial in archaeological site management, planning, and disaster response. En tiempos recientes, el efecto del cambio climático y desastres naturales en el registro arqueología y patrimonio ha ganado mucha atención, especialmente el aumento del nivel del mar y la inundación del litoral. La destrucción en la interior por cause de la inundación fluvial ha recibido menos consideración. En este artículo, presentamos un caso involucrando un programa emergencia en respuesta a un evento climático y subsecuentes impactos al registro arqueología. Nuestro proyecto, de 2010 en el valle de Río Cumberland de Medio Tennessee, ha documentado erosión severa y cambios a sitios arqueológicos indígenas. Durante nuestros trabajos de rescate y documentación, fortalecimos las relaciones entre arqueólogos académicos, estatales y federales y la comunidad. Viendo que estos tipos de eventos de la clima están ocurriendo con más frecuencia, este modelo de estudio podría ser más importante en el manejo, planificación y respuesta al desastre.
Protective Immune Responses to a Recombinant Adenovirus Type 35 Tuberculosis Vaccine in Two Mouse Strains: CD4 and CD8 T-Cell Epitope Mapping and Role of Gamma Interferon

ABSTRACT There is an urgent need for an efficacious vaccine against tuberculosis (TB). Cellular immune responses are key to an effective protective response against TB. Recombinant adenovirus (rAd) vectors are especially suited to the induction of strong T-cell immunity and thus represent promising vaccine vehicles for the prevention of TB. We have previously reported on rAd vector serotype 35, the serotype of choice due to low preexisting immunity worldwide, which expresses a unique fusion protein of Mycobacterium tuberculosis antigens Ag85A, Ag85B, and TB10.4 (Ad35-TBS). Here, we demonstrate that Ad35-TBS confers protection against M. tuberculosis when administered to mice through either an intranasal or an intramuscular route. Histological evaluation of lung tissue corroborated the protection and, in addition, demonstrated differences between two mouse strains, with diffuse inflammation in BALB/c mice and distinct granuloma formation in C57BL/6 mice. Epitope mapping analysis in these mouse strains showed that the major T-cell epitopes are conserved in the artificial fusion protein, while three novel CD8 peptides were discovered. Using a defined set of T-cell epitopes, we reveal differences between the two mouse strains in the type of protective immune response, demonstrating that different antigen-specific gamma interferon (IFN-γ)-producing T cells can provide protection against M. tuberculosis challenge. While in BALB/c (H-2d) mice, a dominant CD8 T-cell response was detected, in C57BL/6 (H-2b) mice, more balanced CD4/CD8 T-cell responses were observed, with a more pronounced CD4 response in the lungs. These results unify conflicting reports on the relative importance of CD4 versus CD8 T-cell responses in protection and emphasize the key role of IFN-γ.
Changes in the content of health-promoting compounds and antioxidant activity of broccoli after domestic processing

The effect of water- and steam-cooking on the content of vitamin C, polyphenols, carotenoids, tocopherols and glucosinolates, as well as on the antioxidant activity of broccoli, are reported. Flavonoids, phenolic acids, vitamins C and E, β-carotene, lutein, and glucosinolates in domestically processed broccoli were quantified using high-performance liquid chromatography (HPLC) methods; total polyphenols were determined with Folin–Ciocalteu reagent. The antioxidant capacities of broccoli extracts were evaluated using the Trolox equivalent antioxidant capacity (TEAC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) methods. The results indicated that steam-cooking of broccoli results in an increase in polyphenols, as well as the main glucosinolates and their total content as compared with fresh broccoli, whereas cooking in water has the opposite effect. Steam-cooking of broccoli has no influence on vitamin C, whereas cooking in water significantly lowers its content. Both, water- and steam-cooking of broccoli results in an increase in β-carotene, lutein, and α- and γ-tocopherols as compared with fresh broccoli. Similar effects of steaming and water-cooking of broccoli on their antioxidant activity were observed.
Maximizing mutual information in general MIMO fading AWGN channels under a rank constraint

The maximization of mutual information in a general point-to-point MIMO fading channel with additive white Gaussian noise (AWGN) is considered under a rank constraint on the covariance of the vector Gaussian input. The channel is assumed to have an arbitrarily distribution with the channel state information (CSI) available at the receiver and the channel distribution information known at the transmitter. Solutions to such a problem, for instance, would enable us to investigate the tradeoff between complexity and performance while using low rank signalling as a communication strategy. A numerical algorithm is developed to compute the optimal input covariance that maximizes mutual information, which is a non-convex optimization problem, over the space of rank-constrained positive semi-definite matrices. The necessary Karush-Kuhn Tucker (KKT) conditions are solved to obtain the iterative algorithm.
Secure and Verifiable Outsourcing of Nonnegative Matrix Factorization (NMF)

Cloud computing platforms are becoming increasingly prevalent and readily available nowadays, providing us alternative and economic services for resource-constrained clients to perform large-scale computation. In this work, we address the problem of secure outsourcing of large-scale nonnegative matrix factorization (NMF) to a cloud in a way that the client can verify the correctness of results with small overhead. The input matrix protection is achieved by a lightweight, permutation-based encryption mechanism. By exploiting the iterative nature of NMF computation, we propose a single-round verification strategy, which can be proved to be effective. Both theoretical and experimental results are given to demonstrate the superior performance of our scheme.
Crystal structure of the catalytic domain of cholesterol‐α‐glucosyltransferase from Helicobacter pylori

Crystal structure of the catalytic domain of cholesterol-a-glucosyltransferase from Helicobacter pylori Sang Jae Lee, Byung Il Lee, and Se Won Suh* 1Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea 2 Cancer Cell and Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-769, Korea 3Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
Rotor Surface Ferrite Permanent Magnets in Electrical Machines: Advantages and Limitations

Permanent-magnet synchronous machines (PMSM) are gaining a foothold in a growing number of applications. However, the high cost of these machines compared with the prices of induction motors, whose production process is mature and material costs are low, limits the use of PMSMs with rare-earth permanent magnets in many potential cases. A viable design solution for a PMSM cost reduction is to use low-cost ferrite magnets instead of rare-earth ones. Nevertheless, it is challenging to apply ferrite magnets to a high-power rotor surface magnet PMSM because of their weaker magnetic properties compared with the rare-earth magnets and the risk of irreversible demagnetization. This paper aims to investigate the boundaries and limiting factors for achieving the maximum tangential stress and linear current density at a certain air gap diameter by using rotor surface ferrite magnets. The computed results are validated by a prototype, which was designed within the described boundaries.
Concerted evolution of human amylase genes

Cosmid clones containing 250 kilobases of genomic DNA from the human amylase gene cluster have been isolated. These clones contain seven distinct amylase genes which appear to comprise the complete multigene family. By sequence comparison with the cDNAs, we have identified two pancreatic amylase genes and three salivary amylase genes. Two truncated pseudogenes were also recovered. Intergenic distances of 17 to 22 kilobases separate the amylase gene copies. Within the past 10 million years, duplications, gene conversions, and unequal crossover events have resulted in a very high level of sequence similarity among human amylase gene copies. To identify sequence elements involved in tissue-specific expression and hormonal regulation, the promoter regions of the human amylase genes were sequenced and compared with those of the corresponding mouse genes. The promoters of the human and mouse pancreatic amylase genes are highly homologous between nucleotide -160 and the cap site. Two sequence elements thought to influence pancreas-specific expression of the rodent genes are present in the human genes. In contrast, similarity in the 5' flanking sequences of the salivary amylase genes is limited to several short sequence elements whose positions and orientations differ in the two species. Some of these sequence elements are also associated with other parotid-specific genes and may be involved in their tissue-specific expression. A glucocorticoid response element and a general enhancer element are closely associated in several of the amylase promoters.
TCP Friendly Rate Control (TFRC): Protocol Specification

This document specifies TCP-Friendly Rate Control (TFRC). TFRC is a congestion control mechanism for unicast flows operating in a best- effort Internet environment. It is reasonably fair when competing for bandwidth with TCP flows, but has a much lower variation of throughput over time compared with TCP, making it more suitable for applications such as telephony or streaming media where a relatively smooth sending rate is of importance.
Working Paper Series No . 11 / 261 School meal crowd out in the 1980 s

This paper explores whether state provision of school meals in the 1980s crowded out private provision by examining two UK policy reforms that dramatically reduced school meal take-up. The paper examines whether this affected children’s BMI, using a large, unique, longitudinal dataset of primary school children from 1972 – 1994. This period is characterized by –for some– relative scarcity of foods. The reforms placed further constraints on some families’ already tight food budgets, leading to nutritionists expecting children to become malnourished. The findings however, show no evidence of any such effects. In addition, I find no support for the hypothesis of intrahousehold food reallocation. As some of those affected are relatively poor, and as sample sizes are often large with fairly precise estimates, the analysis should have been able to detect any effects. With no such evidence, this suggests that the state provision of school meals was crowding out private provision of similarly nutritious packed and home lunches.
CELL DESIGN a dissertation submitted to the department of electrical and electronics engineering and the Graduate School of engineering and science of bilkent university in partial fulfillment of the requirements for the degree of doctor of philosophy

AIRBORNE CMUT CELL DESIGN Aslı Yılmaz Ph.D. in Electrical and Electronics Engineering Advisor: Prof. Dr. Hayrettin Köymen Co-Advisor: Prof. Dr. Abdullah Atalar July, 2014 All transducers used in airborne ultrasonic applications, including capacitive micromachined ultrasonic transducers (CMUTs), incorporate loss mechanisms to have reasonably wide frequency bandwidth. However, CMUTs can yield high efficiency in airborne applications and unlike other technologies, they offer wider bandwidth due to their low characteristic impedance, even for efficient designs. Despite these advantages, achieving the full potential is challenging due to the lack of a systematic method to design a wide bandwidth CMUTs. In this thesis, we present a method for airborne CMUT design. We use a lumped element circuit model and harmonic balance (HB) approach to optimize CMUTs for maximum transmitted power. Airborne CMUTs have narrowband characteristic at their mechanical part, due to low radiation impedance. In this work, we restrict the analysis to a single frequency and the transducer is driven by a sinusoidal voltage with half of the frequency of operation frequency, without any dc bias. We propose a new mode of airborne operation for CMUTs, where the plate motion spans the entire gap. We achieve this maximum swing at a specific frequency applying the lowest drive voltage and we call this mode of operation as Minimum Voltage Drive Mode (MVDM). We present equivalent circuit-based design fundamentals for airborne CMUT cells and verify the design targets by fabricated CMUTs. The performance limits for silicon membranes for airborne applications are derived. We experimentally obtain 78.9 dB//20Pa@1m source level at 73.7 kHz, with a CMUT cell of radius 2.05 mm driven by 71 V sinusoidal drive voltage at half the frequency. The measured quality factor is 120. CMUTs can achieve a large bandwidth (low quality factor level) as they can vi
A Generic Four-step Methodology For Institutional Analysis

The central hypothesis of this paper is that there may be situations in which the traditional approach to institutional analysis is of limited applicability. Such an approach, which has been called 'comparative institutional analysis', consists of comparing institutional environments and institutional arrangements in terms of specific economic or other efficiency criteria to see which one performs better. However, because of limitations to accurately predict the future performance of alternative institutional settings, comparisons are not always possible. Furthermore, in most cases the only information available is the performance of the current institutional setting. To account for this methodological deficiency, a generic methodology for institutional analysis, which consists of four steps (institutional structure, institutional efficiency, institutional choice, and institutional change), is proposed in this paper. Accordingly, the emphasis switches from evaluating alternative institutional choices to improving current scenarios. To show the validity of this methodology, some results of its application to a case study are presented. Although more research on this four-step methodology is needed, it proved to be robust when applied to the analysis of the governance of irrigated agriculture in the Peninsula of Santa Elena, Ecuador.
Trajectory Semantic Visualization

Thanks to current GPS technologies, the capture of evolving positions of individual moving objects has become technically and economically feasible. This opens new perspectives for a large number of applications (from transportation and logistics to ecology and anthropology) built on the knowledge of objects’ movements. The goal of this work is to propose a framework that supports querying and visualization of trajectory data. Trajectory data and its semantic context are modeled by the means of an application ontology, which allows the user to elaborate semantic queries. Results are rendered using an automatic matching procedure that allows the user to change the actual visualization of the data.
Comparative study of different control algorithms on Brushless DC motors

Recently, the role of a BLDC (Brushless Direct Current) motor is favoring the designers due to its higher efficiency. Most of the applications are already using BLDC motors as a replacement for AC motors and this holds true for innumerous applications, and these motors also reduce the overall system weight. The commutation of BLDC motor is done electronically; hence it is quite simple to control the torque and RPM of the motor even at much higher speed. This paper gives a brief comparative study of three different control schemes i.e Sinusoidal field oriented control (FOC), Field oriented control (FOC), Hysteresis control of a BLDC motor primarily on the aspect of output torque ripple. The study of all the three control schemes is discussed briefly and simulation of control algorithm has been performed.
Review of the methodologies and applications of scoring systems in neonatal and pediatric intensive care

Scoring systems and risk prediction rules quantitate the severity of clinical conditions and stratify patients according to a specified outcome. In intensive care medicine, the complexity and number of clinical scoring systems is increasing as their utility in both health services research and clinical medicine broadens. We anticipate that with increasing healthcare costs and competition, the demand for risk adjusted outcomes and institutional benchmarking will increase. As academicians and clinicians, it is vital to be knowledgeable regarding the methodologies and applications of these scoring and risk prediction systems to ensure their quality and appropriate utilization.
Tracing the Origin and Spread of Agriculture in Europe

The origins of early farming and its spread to Europe have been the subject of major interest for some time. The main controversy today is over the nature of the Neolithic transition in Europe: the extent to which the spread was, for the most part, indigenous and animated by imitation (cultural diffusion) or else was driven by an influx of dispersing populations (demic diffusion). We analyze the spatiotemporal dynamics of the transition using radiocarbon dates from 735 early Neolithic sites in Europe, the Near East, and Anatolia. We compute great-circle and shortest-path distances from each site to 35 possible agricultural centers of origin—ten are based on early sites in the Middle East and 25 are hypothetical locations set at 5° latitude/longitude intervals. We perform a linear fit of distance versus age (and vice versa) for each center. For certain centers, high correlation coefficients (R > 0.8) are obtained. This implies that a steady rate or speed is a good overall approximation for this historical development. The average rate of the Neolithic spread over Europe is 0.6–1.3 km/y (95% confidence interval). This is consistent with the prediction of demic diffusion (0.6–1.1 km/y). An interpolative map of correlation coefficients, obtained by using shortest-path distances, shows that the origins of agriculture were most likely to have occurred in the northern Levantine/Mesopotamian area.