Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleotide substitutions within U5 are critical for efficient reverse transcription of human immunodeficiency virus type 1 with a primer binding site complementary to tRNA(His)

Sequence analysis of integrated proviruses of human immunodeficiency virus type 1 (HIV-1) which utilize tRNA(His) to initiate reverse transcription [virus derived from pHXB2(His-AC-TGT)] revealed five additional nucleotide substitutions in the U5 and primer binding site (PBS) regions (ATGAC for CCTGT at nucleotides 152, 160, 174, 181, and 200, respectively) (Z. Zhang et al., Virology 226:306-317, 1996). We constructed a mutant proviral genome [pHXB2(His-AC-GAC)] which contained the ATGAC substitutions to test if they represented a necessary adaptation by the virus for use of tRNA(His) to initiate reverse transcription. Viruses from pHXB2(His-AC-TGT) and pHXB2(His-AC-GAC) were infectious. Sequence analysis of the U5 and PBS regions of integrated provirus from a cell culture infected with virus derived from pHXB2(His-AC-TGT) revealed a G-to-A change in CCTGT at nucleotide 181 after limited in vitro culture, suggesting that this nucleotide change represented an adaptation by the virus to efficiently utilize tRNA(His) to initiate reverse transcription. To further address this possibility, we used a specific mutation in reverse transcriptase (RT), a methionine-to-valine change in the highly conserved YMDD amino acid motif of HIV-1 RT (M184V), which has been shown in previous studies to influence the fidelity and activity of the enzyme. The M184V RT mutation was cloned into pHXB2(His-AC-GAC) and pHXB2(His-AC-TGT). Virus derived from pHXB2(His-AC-GAC) with M184V RT had slightly delayed replication compared to the virus from pHXB2(His-AC-GAC) with wild-type RT; in contrast, virus from pHXB2(His-AC-TGT) with M184V RT was severely compromised in replication. Using an endogenous reverse transcription-PCR assay to analyze the reverse transcription of viruses obtained after transfection, we found that viruses derived from pHXB2(His-AC-GAC) with the wildtype RT were slightly faster in the initiation of reverse transcription than viruses with M184V RT. The initiation of reverse transcription was delayed in viruses derived from pHXB2(His-AC-TGT) with wild-type RT and M184V RT compared to viruses derived from pHXB2(His-AC-GAC). Finally, sequence analysis of U5 and PBS regions of proviruses from pHXB2(His-AC-GAC) with wild-type RT revealed considerably more nucleotide substitutions than in viruses derived from pHXB2(His-AC-GAC) containing the M184V mutation in RT after extended in vitro culture. Our studies point to a role for these additional nucleotide substitutions in U5 as an adaptation by the virus to utilize an alternative tRNA to initiate reverse transcription.
Terahertz Time-Domain Spectroscopy of Low-Dimensional Materials and Photonic Structures

13 CHAPTER 1 . 15 1.1 DEVELOPMENT OF THZ SOURCES . 17 1.2 THZ SOURCES BASED ON ULTRAFAST LASERS . 18 1.3 NOVEL THZ SOURCES . 23 1.4 THZ SPECTROMETER . 24 1.5 OUTLINE OF THIS THESIS . 30 CHAPTER 2 . 32 2.
Frontiers in Computational Neuroscience Time and Category Information in Pattern-based Codes Eyherabide and Samengo Time and Category Information 2.2 Calculation of Mutual Information Rates Eyherabide and Samengo Time and Category Information Eyherabide and Samengo Time and Category Information Eyhe

In other cases, the patterns are spike doublets of different inter-spike interval (ISI) duration. Reich et al. (2000) presented an example of this type in primate V1; and Oswald et al. (2007) found a similar code in the electrosensory lobe of the weakly electric fish. In yet other cases, patterns are more abstract spatiotemporal combinations of spikes and silences defined in single neurons (Fellous et al., 2004) and neural populations (Nádasdy, 2000; Gütig and Sompolinsky, 2006). If different spike patterns represent different stimulus features , which aspects of the pattern are relevant to the distinction between the different features? To answer this question, previous studies have classified the response patterns into different types of categories, depending on different response aspects. The relevance of each candidate aspect was addressed using what we here define as the category information. For example, in the auditory cortex, Furukawa and Middlebrooks (2002) assessed how informative patterns were when categorized in three different ways, using the first spike latency, the total number of spikes, or the variability in the spike timing. In an even more ambitious study, Gawne et al. (1996) have not only compared the information separately transmitted by response latency and spike count, but also related these two response properties to two different stimulus features: contrast and orientation, respectively. However, these works have not addressed how the stimulus timing is represented by the response patterns. Sensory neurons represent external stimuli. In realistic conditions, different stimulus features (for example, the presence of a predator or a prey) appear at irregular times. Therefore, an efficient sensory system should not only represent the identity of each perceived stimulus, but also, its timing. Colloquially, qualitative differences between stimulus features have been called the what in the stimulus, whereas the temporal locations of the features constitute the when. Spike trains can encode both the what and the when, for example, as a sequence of spike patterns. This idea constitutes a standard view, where the timing of patterns indicates when stimulus features occur, while the pattern identities tag what stimulus features happened (Martinez-Conde et al. The information provided by the distinction between different spike patterns is here called category information. In the same manner, the information transmitted by the timing of spike patterns is here called time information. According to the standard view, the category and the time information represent the knowledge of the what and the when in the …
Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

Computational prediction of the 3D structures of molecular interactions is a challenging area, often requiring significant computational resources to produce structural predictions with atomic-level accuracy. This can be particularly burdensome when modeling large sets of interactions, macromolecular assemblies, or interactions between flexible proteins. We previously developed a protein docking program, ZDOCK, which uses a fast Fourier transform to perform a 3D search of the spatial degrees of freedom between two molecules. By utilizing a pairwise statistical potential in the ZDOCK scoring function, there were notable gains in docking accuracy over previous versions, but this improvement in accuracy came at a substantial computational cost. In this study, we incorporated a recently developed 3D convolution library into ZDOCK, and additionally modified ZDOCK to dynamically orient the input proteins for more efficient convolution. These modifications resulted in an average of over 8.5-fold improvement in running time when tested on 176 cases in a newly released protein docking benchmark, as well as substantially less memory usage, with no loss in docking accuracy. We also applied these improvements to a previous version of ZDOCK that uses a simpler non-pairwise atomic potential, yielding an average speed improvement of over 5-fold on the docking benchmark, while maintaining predictive success. This permits the utilization of ZDOCK for more intensive tasks such as docking flexible molecules and modeling of interactomes, and can be run more readily by those with limited computational resources.
Posttraumatic Stress in Parents of Children Diagnosed with Cancer: Hyperarousal and Avoidance as Mediators of the Relationship between Re-Experiencing and Dysphoria

Background Increased understanding of the relationships between different symptom clusters involved in posttraumatic stress symptoms (PTSS) could guide empirical research and clinical practice. The objective of the present study was to investigate whether hyperarousal and avoidance mediated the relationship between re-experiencing and dysphoria in parents of children diagnosed with cancer. Methods Longitudinal data from parents of children receiving cancer therapy were used. PTSS were assessed using the PTSD Checklist Civilian Version at one week (T1), two (T2) and four months (T3) after diagnosis. Mediation analyses for multiple mediators were conducted for mothers (n = 122) and fathers (n = 121), respectively. The mediation model tested the assumption that the PTSS symptom clusters hyperarousal and avoidance mediated the relationship between re-experiencing and dysphoria. Results For fathers, none of the hypothesized mediators were significant. For mothers, hyperarousal mediated the relationship between re-experiencing and dysphoria, but avoidance did not. Conclusions Results suggest that hyperarousal is important for the development of dysphoria in mothers, supporting use of interventions targeting such symptoms in the early and ongoing period following the child’s diagnosis.
WATER ABSORPTION, XRD AND FTIR ANALYSIS OF PBS-STARCH BLENDED HALLOYSITE COMPOSITES

Poly (butylene succinct) (PBS)/starch/halloysite nanotubes(HNT) composite was fabricated through solution casting using deionised water. The effect of HNT on the water absorption behavior of the composites has been studied and found to be decreasing with the increase in loading of HNT. The characterizations of the composites were carried out by the Fourier Transform Infrared spectroscopy (FTIR), X-ray diffraction (XRD). XRD and FTIR results indicated halloysite was successfully incorporated to PBS-Starch blend through solution casting method. XRD showed that the basal spacing of PBS-Starch increased because of the presence of halloysite. The UV Study shows the good shielding property of the blend Nanocomposites. From the Water absorption test, it is found that the water absorption tendency of the hybrid composites decreases regularly. Keywords: HNT, XRD, water absorption, composites. Â
On the learnability of infinitary regular sets

Abstract In this paper we extend the automaton synthesis paradigm to infinitary languages, that is, to subsets of the set Σω of all infinite sequences over some alphabet Σ. Our main result is a polynomial algorithm for learning a sub-class of the ω-regular sets from membership queries and counter-examples based on the framework suggested by Angluin (Angluin, D. (1987), Inform. and Comput.75, 87-106) for learning regular subsets of Σ*.
Channel Estimation and Training Design for Two-Way Relay Networks in Time-Selective Fading Environments

In this paper, channel estimation and training sequence design are considered for amplify-and-forward (AF)-based two-way relay networks (TWRNs) in a time-selective fading environment. A new complex-exponential basis expansion model (CE-BEM) is proposed to represent the mobile-to-mobile time-varying channels. To estimate such channels, a novel pilot symbol-aided transmission scheme is developed such that a low complex linear approach can estimate the BEM coefficients of the convoluted channels. More essentially, two algorithms are designed to extract the BEM coefficients of the individual channels. The optimal training parameters, including the number of the pilot symbols, the placement of the pilot symbols, and the power allocation to the pilot symbols, are derived by minimizing the channel mean-square error (MSE). The selections of the system parameters are thoroughly discussed in order to guide practical system design. Finally, extensive numerical results are provided to corroborate the proposed studies.
Planning Cultures in Transition: Sustainability Management and Institutional Change in Spatial Planning

This paper aims to critically review current discussions on the “reinvention” of spatial planning, postulating an all-encompassing and unproblematic shift towards new rationales, scopes, actors and instruments in planning practice. Buzzwords are, among others, “governance”, “collaborative planning” and the “communicative turn”. To overcome the somehow normative bias of these terms, the term “planning culture” is introduced to define a complex, multi-dimensional and dynamic institutional matrix combining formal and informal institutional patterns. Used in an analytical sense, it can help to better understand institutional change in spatial planning. Referring to recent conceptual debates about institutional transformation, the paper presents a six-stage model for institutional change in spatial planning, supporting it with an example from the Cologne/Bonn metropolitan region in Germany. The latter serves as an example for illustrating the institutional dynamics, but also the rigidities of planning cultural change. The paper concludes that a more thorough, “fine-grained” and empirically-grounded investigation of institutional transformation in spatial planning is necessary.
OCALA: An Architecture for Supporting Legacy Applications over Overlays

In order for overlays and new network architectures to gain real user acceptance, users should be able to leverage overlay functionality without any modifications to their applications and operating systems. We present our design, implementation, and experience with OCALA, an overlay convergence architecture that achieves this goal. OCALA interposes an overlay convergence layer below the transport layer. This layer is composed of an overlay independent sub-layer that interfaces with legacy applications, and an overlay dependent sub-layer that delivers packets to the overlay. Unlike previous efforts, OCALA enables: (a) simultaneous access to multiple overlays (b) communication between hosts in different overlays (c) communication between overlay hosts and legacy hosts (d) extensibility, allowing researchers to incorporate their overlays into OCALA. We currently support five overlays, i3, RON, HIP, DOA and OverDoSe on Linux, Windows XP/2000 and Mac OS X. We (and a few other research groups and end-users) have used OCALA for over a year with many legacy applications ranging from web browsers to remote desktop applications.
Large retail time deposits and US Treasury securities (1986‐95): evidence of a segmenting market

Argues that the similarities between US treasury securities (treasuries) and FDIC‐insured large retail certificates of deposit (CDs) should make their prices similar in an efficient market. Considers deposit pricing and substitutability between treasuries and CDs, citing previous research; and presents a study comparing their yields for three maturities using 1986‐1995 data. Presents the results and analyses further to explore the links between changes in treasury yields and lagged changes in CD yields; and upward CD yield stickiness. Finds that CD and treasury yield spreads changed from small and positive to large and negative over the period with little effect on deposit balances; and concludes that those investors who remained interested in insured balances during the early 1990s were either insensitive to interest rates or had high switching costs. Suggests that banks have used this unwillingness to migrate to non‐insured funds to decrease CD rates relative to treasuries for higher profits and asks how long this market segment will continue to accept inferior yields.
β-Estradiol Protects Against the Progression of Hypertension During Adulthood in a Mouse Model of Systemic Lupus Erythematosus

C ardiovascular disease is the leading cause of mortality in patients with systemic lupus erythematosus (SLE), a chronic autoimmune inflammatory disorder that predominantly affects women of reproductive age. The prevalence of hypertension, a major cardiovascular risk factor, is much higher in women with SLE than age-matched healthy women. 4–8 However, the factors that underlie the increased prevalence of hypertension during SLE remain unclear. Because of the partiality toward women, estrogen is commonly implicated as an important contributor to SLE disease progression. In addition, estrogens can promote humoral (antibody)-mediated immunity 9,10 that is essential for the formation of immune complexes, resulting in the tissue injury and inflammation characteristic of SLE. A role for estrogens in SLE is commonly supported by studies in experimental animal models in which removal of estrogens early in life (typically <6–8 weeks of age) delays the production of autoantibodies and the subsequent renal injury and mortality. Although these early life manipulations of estrogen suggest that they are important for the onset of SLE, the effect of estrogens on SLE in adulthood has not been widely studied, particularly with regard to their role in the development of hypertension. Understanding the influence of estrogens on cardiovascu-lar risk factors like hypertension in adulthood is important for women with SLE because autoimmunity accounts for up to 50% of premature ovarian failure, and women with SLE have increased risk for early menopause, 13 an important risk factor for hypertension and cardiovascular disease. Using an established experimental model of SLE (female NZBWF1 mice), this study was initially designed to test the hypothesis that estrogen, commonly considered an important factor in the development of SLE, has a causal role in the development of hypertension in adulthood. However, contrary to the hypothesis, the data suggest that estrogens may have an anti-inflammatory role that protects against the further development of hypertension. Animals Adult (30-week-old) female NZBWF1 (SLE) and NZW/LacJ (Ctrl) (Jackson Laboratories, Bar Harbor, ME) mice were used in this study. Abstract—Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disorder with a high prevalence of hypertension and cardiovascular disease. Because SLE predominantly affects women, estrogen is commonly implicated as a contributor to SLE disease progression. Using an established mouse model of SLE (female NZBWF1), we tested whether estrogen has a causal role in the development of hypertension in adulthood. Thirty-week-old SLE and control mice (NZW/ LacJ) underwent either a sham or ovariectomy (OVX) procedure. 17β-Estradiol …
NONLINEAR RAYLEIGH-RITZ ITERATIVE METHOD FOR SOLVING LARGE SCALE NONLINEAR EIGENVALUE PROBLEMS

A nonlinear Rayleigh-Ritz iterative (NRRIT) method for solving nonlinear eigenvalue problems is studied in this paper. It is an extension of the nonlinear Arnoldi algorithm due to Heinrich Voss. The efficiency of the NRRIT method is demonstrated by comparing with the inverse iteration method to solve a highly nonlinear eigenvalue problem arising from finite element electromagnetic simulation in accelerator modeling.
Static Optimization of Conjunctive Queries with Sliding Windows over Unbounded Streaming Information Sources

We study the problem of static optimization of conjunctive queries with sliding window joins over unbounded streaming information sources. While previous work has suggested focusing on maximizing the output rate of queries over streaming information sources, we show that in steady-state, for conjunctive queries with sliding windows over unbounded streams, all feasible plans have the same output rate. For this reason, we suggest that the goal of optimization for such queries should be to minimize resource utilization in steady state. We formulate a cost model for the problem and introduce a framework for optimization based on feasibility and resource management. We then use the model to study where to optimally place random drop boxes and how much to drop in each box in case no feasible plan exists and approximation is necessary. The goal of the approximation is to achieve the maximum throughput of the resulting tuples given the resource constraints. We find that, given a plan to approximate, the optimum placement and values are easily obtained. However, finding the best plan to approximate is not necessarily an obvious task.
Effect of bleaching treatments on microleakage of Class I restorations.

OBJECTIVE To test the effect of bleaching agents on microleakage of composite restorations. METHODS Sixty extracted human molar class I cavities were restored using Scotchbond 1 and Filtek Z250 composite according to the manufacturer's instructions. The teeth were randomly divided into four groups (n = 15 each). Group 1 was the control group, which was not bleached. Group 2 had a once-daily bleaching treatment with 20% carbamide peroxide gel for eight hours. Group 3 had a bleaching of 6% H2O2 for 30 minutes twice a day. Group 4 had a bleaching treatment once per day with 19% percarbonate gel for eight hours. The bleaching was carried out at 37 degrees C for 14 days. Nail varnish was applied on the apical portion of the teeth only, and the specimens were immersed in a 0.1% rhodamin-B-isothiocyanate for 24 hours at 37 degrees C. After thorough rinsing with tap water, the specimens were embedded in self-curing methacrylate resin. The blocks were sectioned with a water-cooled microtome saw into three to five slices. The cuts were positioned centrally through the restorations and approximately parallel to the long axis of the tooth in the mesiodistal direction. Microleakage was evaluated at the occlusal margins of the class I restorations using a stereo microscope. RESULTS Microleakage occurred in all groups. The percentage of sections showing leakage was 20% (Group 1), 11% (Group 2), 15% (Group 3), and 18% (Group 4). The statistical evaluation (Kruskal-Wallis test) showed no significant difference between groups (p = 0.537). CONCLUSION Bleaching with the materials tested has no influence on microleakage of Filtek composite bonded with Scotchbond I.
Murine fetal liver macrophages bind developing erythroblasts by a divalent cation-dependent hemagglutinin

During mammalian development the fetal liver plays an important role in hematopoiesis. Studies with the macrophage (M phi)-specific mAb F4/80 have revealed an extensive network of M phi plasma membranes interspersed between developing erythroid cells in fetal liver. To investigate the interactions between erythroid cells and stromal M phi, we isolated hematopoietic cell clusters from embryonic day-14 murine fetal liver by collagenase digestion and adherence. Clusters of erythroid cells adhered to glass mainly via M phi, 94% of which bound 19 +/- 11 erythroblasts (Eb) per cell. Bound Eb proliferated vigorously on the surface of fetal liver M phi, with little evidence of ingestion. The M phi could be stripped of their associated Eb and the clusters then reconstituted by incubation with Eb in the presence of divalent cations. The interaction required less Ca++ than Mg++, 100 vs. 250 microM for half-maximal binding, and was mediated by a trypsin- sensitive hemagglutinin on the M phi surface. After trypsin treatment fetal liver M phi recovered the ability to bind Eb and this process could be selectively inhibited by cycloheximide. Inhibition tests showed that the Eb receptor differs from known M phi plasma membrane receptors and fetal liver M phi did not bind sheep erythrocytes, a ligand for a distinct M phi hemagglutinin. We propose that fetal liver M phi interact with developing erythroid cells by a novel nonphagocytic surface hemagglutinin which is specific for a ligand found on Eb and not on mature red cells.