Miracle-dz/UniFAR-FTUs huggingface dataset:
Consequences of low birthweight on urinary excretion of DNA markers of oxidative stress in young men

Objective. Low birthweight (LBW) has been associated with an increased risk of development of type 2 diabetes in adult life. Both type 1 and type 2 diabetes mellitus are characterized by increased oxidative stress. The purpose of this study was to investigate whether young healthy adults born with LBW showed differences in oxidative stress under normal conditions and during the added challenge of a physiological Intralipid infusion. Material and methods. Urinary excretion of DNA markers of oxidative stress were analyzed by LC‐MS/MS in 19 men (aged 19 years) with LBW and in 19 age matched, normal birthweight (NBW) controls pre‐ and post a 3‐fold increase of plasma free fatty acids. Results. Mean excretion rates of 8‐oxo‐guanine (8oxoGua), 8‐oxo‐guanosine (8oxoGuo), 8‐oxo‐2′deoxyguanosine (8oxodG), and 1,N6‐ethenodeoxyadenosine (εdA) did not statistically differ between subjects with LBW and NBW (66.9 versus 73.9 nmol/15 h, 17.8 versus 18.5 nmol/15 h, 11.9 versus 14.4 nmol/15 h and 44.0 versus 43.2 pmol/15 h, respectively). Furthermore, Intralipid infusion did not affect excretion of DNA adducts in LBW or NBW subjects. Statistically significant correlations were found between body mass index and urinary excretion of 8oxoGua (r = 0.64, p = 0.003) and 8oxoGuo (r = 0.64, p = 0.003) in the LBW group only. Conclusions. These findings suggest that oxidative stress may be a consequence of diabetes and is not, or at least only partly, involved in the early pathogenesis of type 2 diabetes.
The Computational Sprinting Game Songchun Fan

Computational sprinting is a class of mechanisms that boost performance but dissipate additional power. We describe a sprinting architecture in which many, independent chip multiprocessors share a power supply and sprints are constrained by the chips’ thermal limits and the rack’s power limits. Moreover, we present the computational sprinting game, a multi-agent perspective on managing sprints. Strategic agents decide whether to sprint based on application phases and system conditions. The game produces an equilibrium that improves task throughput for data analytics workloads by 4-6× over prior greedy heuristics and performs within 90% of an upper bound on throughput from a globally optimized policy.
Deterministic Synchronization Algorithms and Convergence Rates

In this paper, we study distributed deterministic algorithms to be used for synchronization in networks whose topologies may be time-varying. The problem is formulated as products of row-stochastic matrices which is a well-studied area in the mathematics literature. We derive the general conditions for synchronization and the existence of a common norm for an expanded set of row-stochastic matrices. This relation helps us understand why synchronization can be achieved by averaging the received data when there exist nodes that share information with others in the network. We then extend our results to time-varying and interval matrices, and study the convergence rates
Constraining cosmological parameters using Sunyaev-Zel'dovich cluster surveys

We discuss how future cluster surveys can constrain cosmological parameters with particular reference to the properties of the dark energy component responsible for the observed acceleration of the universe by probing the evolution of the surface density of clusters as a function of redshift. We explain how the abundance of clusters selected using their Sunyaev-Zel'dovich effect can be computed as a function of the observed flux and redshift taking into account observational effects due to a finite beam-size. By constructing an idealized set of simulated observations for a fiducial model, we forecast the likely constraints that might be possible for a variety of proposed surveys which are assumed to be flux limited. We find that Sunyaev-Zel'dovich cluster surveys can provide vital complementary information to those expected from surveys for supernovae. We analyse the impact of statistical and systematic uncertainties and find that they only slightly limit our ability to constrain the equation of state of the dark energy component.
Evolution of poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors. From concept to clinic.

Poly(ADP-ribose) polymerase-1 (PARP-1) has been an actively pursued drug discovery target for almost 3 decades. Often referred to as the “guardian angel of DNA”, this abundant nuclear enzyme has been the focus of over 20 medicinal chemistry programs in a wide range of therapeutic areas encompassing stroke, cardiac ischemia, cancer, inflammation, anddiabetes (Figure 1). Despite the great therapeutic potential for this target and the tremendous academic and industrial efforts dedicated to it, only recently have PARP-1 inhibitors made headway in clinical trials. Recent results from several PARP-1 inhibitors in phase II clinical trials for cancer therapyhave attracted the attentionofnationalmedia.Of the several potential therapeutic indications for PARP-1 inhibitors, the two major areas that hold the most promise are ischemia and cancer. This review is structured to provide the readers with a brief summary of the rationale for PARP-1 as a therapeutic target, to explain the PARP-1 inhibitor pharmacophore, and to provide an update on the progress of the PARP-1 drug discovery programs. This Perspective will offer a historical account of the critical PARP-1 publications that instilled the interest of the biopharmaceutical industry in the late 1980s and early 1990s. Furthermore, I will discuss why PARP-1 received somuch attention in the late 1990s and early 2000s followed by the slight decline in themedicinal chemistry efforts today (Figure 1). The major PARP-1 medicinal chemistry programs will be highlighted focusing on the lead generation, lead optimization, candidate selection, and clinical progress.Many aspects of the biological functions of PARP-1 fall outside the scope of this medicinal chemistry review. For this reason, the reader should refer to the following citations for a review of the PARP family of enzymes, the biological functions of poly(ADP-ribose), PARP-1 and intracellular signaling, PARP and DNA repair, PARP and epigenetics, PARP and angiogenesis, and the role of PARP-1 in inflammation. The 30 years of medicinal chemistry on this topic have also afforded some excellent medicinal chemistry reviews, most of which predated the disclosure of clinical candidate structures and recent clinical trial results.
Magnetic Resonance Imaging Using Gadolinium-Based Contrast Agents

Abstract The purpose of this article was to review the basic properties of available gadolinium-based magnetic resonance contrast agents, discuss their fundamental differences, and explore common and evolving applications of gadolinium-based magnetic resonance contrast throughout the body excluding the central nervous system. A more specific aim of this article was to explore novel uses of these gadolinium-based contrast agents and applications where a particular agent has been demonstrated to behave differently or be better suited for certain applications than the other contrast agents in this class.
Prevalence of Helicobacter pylori infection and risk of upper gastrointestinal ulcer in patients with rheumatoid arthritis in Japan

We evaluated the prevalence of Helicobacter pylori infection and the association of H. pylori infection and/or nonsteroidal anti-inflammatory drug (NSAID) use with upper gastrointestinal (UGI) ulcers in a cohort of Japanese patients with rheumatoid arthritis (RA). Using the clinical database of the cohort of RA patients and the serum titers of H. pylori antibody, 1815 patients were analyzed. Clinical data were successfully collected for 1529 patients over 2 years, and the history of NSAID use and the occurrence of newly diagnosed UGI ulcer were ascertained by patient self-reports and confirmed by their medical records. A total of 871 patients (49.3%) were H. pylori antibody-positive. Rates of positivity for H. pylori in patients with and without NSAID use were 47.5% and 54.7%, respectively (odds ratio = 0.75, 95% confidence intervals [CI]: 0.58–0.96). The incidence of newly diagnosed UGI ulcer was 0% in the H. pylori−/NSAID− group, 1.24% in the H. pylori−/NSAID+ group, 1.06% in the H. pylori+/NSAID− group, and 3.46% in the H. pylori+/NSAID+ group. The odds ratios of H. pylori infection and NSAID for the occurrence of new UGI ulcers after adjusting for age and sex were 2.97 (95% CI: 1.19–7.38) and 4.31 (95% CI: 0.57–32.4), respectively. Although the prevalence of H. pylori antibody was low in patients with RA compared with that in healthy Japanese individuals, H. pylori infection was a significant risk factor for UGI ulcer in patients with RA.
[The Federal Health Survey: response, composition of participants and non-responder analysis].

The first German Health Survey was carried out from October 1997 to March 1999. In the survey, 7,124 subjects of a representative sample of the residential population aged between 18 and 79 years were interviewed and medically examined. The response rate was 61.4%; 0.4% of the sample participated only partly in the study. Moreover, 16.0% of the non-respondents filled in a short questionnaire. This results in (although partly limited) information from 77.8% of the sample. The sample also comprises aliens living in Germany. More than 15% of the non-respondents could not be addressed to participate in the study because they were never reached personally. According to the statements in the short questionnaire, non-respondents and respondents differ in particular items such as e.g. education. The differences between the individual answers concerning the important question of the general health status can be classified as negligible. Weighting factors were calculated to arrive at representative information on the 18 to 79 year-old population.
RELATIVE IMPORTANCE OF OPTICAL FIBER EFFECTIVE AREA AND ATTENUATION IN SPAN LENGTH OPTIMIZATION OF ULTRA-LONG 100 GBPS PM-QPSK SYSTEMS

We investigate the performance of very long submarine 100 Gbps PM-QPSK WDM systems as a function of the span length, attenuation and effective area (Aeff) of optical fiber. It is determined that the optimal span length is independent of fiber Aeff and is longer for fibers with ultra-low attenuation. We show that for two fibers with the same performance in a 50 km span system, the fiber with lower attenuation will perform better in systems with longer spans, enabling higher margin, longer reach, or increased spectral efficiency with fewer repeaters.
Models for U.S. State Government Strategic Information Systems Planning (SISP)

Although efficiency of state services depends increasingly on information systems, there is a dearth of theory to explain their management in government (Fountain, 2001; Caudle, 1996; National Commission on State and Local Public Service, 1993). Multidisciplinary research discussed and presented here demonstrates the lack of workable SISP models for state government. Success of SISP in the private sector suggests that appropriate models could help bridge the gap between state resources and citizen needs (Dufner, Holley and Reed, 2002). New theoretical models of SISP, based on data covering 50 states (Government Performance Project, 2001), are introduced. Plans for research on using the models to understand the role of IS in leveraging resources for state government elder services are presented and discussed.
Oligonucleotides Containing Pyrazolo[3,4-d]Pyrimidines: 8-Aza-7-deazaadenines With Bulky Substituents in the 2- or 7-Position

The synthesis of the 2′-deoxyadenosine analogues 1b, 2b, and 3c modified at the 7- and/or 2-position is described. The effect of 7-chloro and 2-methylthio groups on the duplex stability is evaluated. For that, the nucleosides 1b, 2b, and 3c were converted to the corresponding phosphoramidites 15, 19, and 22, which were employed in the solid-phase oligonucleotide synthesis. In oligonucleotide duplexes, compound 1b forms stable base pairs with dT, of which the separated 1b- dT base pairs contribute stronger than that of the consecutive base pairs. Compound 2b shows universal base pairing properties while its N8 isomer 3c forms duplexes with lower stability.
Predicting tyrosine phosphorylation from site-modification network

Phosphorylation plays a great role in regulating variety of cellular processes. Identification of the tyrosine phosphorylation is helpful for understanding the post-translational modifications regulation processes. Although a number of computational approaches have been developed, most of them only consider local sequence information, and currently few studies are concerned about the site with in situ PTM information, which refers to different types of PTMs occurring on the same modification site. In this study, we introduce a novel method (SMNBI) based on a site-modification network, which is constructed by integrating the site with in situ PTM information to predict tyrosine phosphorylation. In order to verify the effectiveness of our SMNBI method, we compare it with Protein-based collaborative filtering (ProteinCF). The results clearly show the superior performance of the SMNBI. Furthermore, to verify the importance of the site-modification network, we compare it with SVM and Bayesian decision theory based on local sequence information. These results demonstrate the site-modification network is useful for predicting tyrosine phosphorylation.
Relationship between renal artery stenosis and intrarenal damage in autopsy subjects with stroke.

BACKGROUND In patients with cardiovascular disease (CVD), renal dysfunction is a risk factor for the prognosis, but substantial evidence is still lacking about the relationship between clinical characteristics and renal histology. The aim of our study was to evaluate the relationship between the extent of renal parenchymal damage, renal artery stenosis (RAS) and clinical characteristics in autopsy subjects with stroke. METHODS During the 17-year period 1980-1997, 2167 subjects were autopsied at the National Cardiovascular Center. We studied retrospectively all the autopsy cases aged 40 years and older who had a history of stroke. Thus, 346 subjects remained and they were classified into two groups. Thirty-six subjects had RAS (group A). Three hundred and ten subjects had no RAS, and we randomly chose 102 subjects among them (group B). We evaluated renal parenchymal damage using a semi-quantitative chronic damage score. RESULTS The average overall chronic damage score was significantly higher in the stenosed kidneys of group A than in the non-stenosed kidneys of group B (9.0+/-2.6 vs 7.0+/-2.7). The contralateral kidneys of group A had a tendency to have milder renal damage than stenosed kidneys. Furthermore, the total score was higher in the subjects with hypertension, diabetes mellitus, proteinuria, renal insufficiency and CVD than in the subjects without such complications. The total score had a significant association with RAS, proteinuria, renal insufficiency, CVD and weight of the kidney. CONCLUSIONS In autopsy subjects with stroke, we demonstrated that co-existing renal parenchymal damage was more severe in the subjects with RAS, hypertension, diabetes mellitus, proteinuria and renal insufficiency than those without such complications. The presence of RAS, impaired renal function and proteinuria was closely correlated with the severity of renal parenchymal damage.
TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION

Classic questions about trait evolution—including the directionality of character change and its interactions with lineage diversification—intersect in the study of plant breeding systems. Transitions from self‐incompatibility to self‐compatibility are frequent, and they may proceed within a species (“anagenetic” mode of breeding system change) or in conjunction with speciation events (“cladogenetic” mode of change). We apply a recently developed phylogenetic model to the nightshade family Solanaceae, quantifying the relative contributions of these two modes of evolution along with the tempo of breeding system change, speciation, and extinction. We find that self‐incompatibility, a genetic mechanism that prevents self‐fertilization, is lost largely by the cladogenetic mode. Self‐compatible species are thus more likely to arise from the isolation of a newly self‐compatible population than from species‐wide fixation of self‐compatible mutants. Shared polymorphism at the locus that governs self‐incompatibility shows it to be ancestral and not regained within this family. We demonstrate that failing to account for cladogenetic character change misleads phylogenetic tests of evolutionary irreversibility, both for breeding system in Solanaceae and on simulated trees.
Analysis of Expert Reasoning in Hardware Diagnosis

Abstract We present an analysis of expert reasoning in the domain of computer hardware diagnosis. The methods used in the study include directed interviews, observation and techniques of protocol analysis. The task investigated was the diagnosis of a complex piece of computer hardware. The initial symptoms are usually insufficient to determine the cause of a fault, requiring the acquisition of more data. Many thousands of pieces of data may be sought, but there is only enough time to obtain a few. We found that the experts use strategies to focus and obtain only the most relevant of this data. In addition, they use models of the hardware containing the diagnostically useful information. The strategies used are both powerful and efficient. Although they are specialized and save time and effort in performing the task, they are also general enough to apply to the majority of the problems encountered, including novel faults. As a test of these ideas, a prototype expert system was implemented. It is a model of problem solving and serves as a test of the adequacy of the knowledge described to perform diagnosis.
Cloning and sequencing of the blood meal‐induced late trypsin gene from the mosquito Aedes aegypti and characterization of the upstream regulatory region

A 4.1 kb genomic clone of the late trypsin gene from the mosquito Aedes aegypti was isolated, mapped and subcloned. A1.6 kb subclone, corresponding to 1.1 kb of upstream regulatory region and 0.5 kb of coding region, was sequenced. The gene has no introns within the coding region. The 5 end of the mature mRNA was mapped using primer extension analysis. A TATA box consensus sequence (TATAAA) was found at position —31 from the 5 end of the mature mRNA. A cluster of five repeat sequences homologous to the yeast GCN4 DNA binding site was found within 200 nucleotides upstream of the cap site. GCN4 is required for derepression mediated control of general amino acid biosynthesis in response to amino acid starvation in yeast. It activates the transcription of at least twenty different genes coding for enzymes involved in amino acid biosynthesis. The presence of this cluster of consensus sequences suggests that a protein similar to GCN4 might regulate expression of the late trypsin gene in the mosquito. Southern blot analysis of genomic DNA indicates that late trypsin is a single copy gene.
Product Strategy for Innovators in Markets with Network Effects

This paper examines four alternative product strategies available to an innovating firm in markets with network effects: single-product monopoly, technology licensing, product-line extension, and a combination of licensing and product-line extension. We address three questions. First, what factors affect the attractiveness of each of the four product strategies? Second, under what conditions will any particular strategy dominate the others? Third, what is the impact of licensing fees on the profitability of a licensing strategy? We show that offering a product line utilizes consumer heterogeneity to increase the total user base and is superior to free licensing when the innovator's cost of producing a low-quality product is low and network effects are weak. However, because of the advantage of licensing in generating a larger installed base, free licensing can dominate line extension when network effects are strong, even if the innovator suffers no cost disadvantage compared to the competitor. We also show that paid licensing trumps free licensing when the clone product has a high quality or a low cost, regardless of network effect. Finally, strong network effects make a lump-sum fee more profitable than a royalty fee (or a combination of both) because a royalty fee reduces the licensee's production.
Production , Manufacturing and Logistics A primal – dual algorithm for the economic lot-sizing problem with multi-mode replenishment

0377-2217/$ see front matter 2008 Elsevier B.V. A doi:10.1016/j.ejor. 2008.04. 043 * Tel. : +1 662325 9220; fax: +1 662325 7012. E-mail address: sde47@ise.msstate. edu The classical economic lot-sizing problem assumes that a single supplier and a single transportation mode are used to replenish the inventory. This paper studies an extension of this problem where several suppliers and transportation modes are available. The decision-making process in this case involves identifying (i) the timing for an order; (ii) the choice of shipment modes; and (iii) the order size for each mode. The problem is defined as a network flow problem with multiple setups cost function and additional side constraints. This study provides an MIP formulation for the problem. We also provide an additional formulation of the problem by redefining its decision variables and show that the dual of the corresponding LP-relaxation has a special structure. We take advantage of the structure of the dual problem to develop a primal–dual algorithm that generates tight lower and upper bounds. Computational results demonstrate the effectiveness of the algorithm. 2008 Elsevier B.V. All rights reserved.
Mesh decomposition using motion information from animation sequences

In computer graphics, mesh decomposition is a fundamental problem and it can benefit many applications. In this paper, we propose a novel mesh decomposition algorithm using motion information derived from a given animation sequence. The proposed algorithm first use principal component analysis (PCA) to construct a compact representation of a given animation sequence. Next, from this representation, we derive several motion parameters including motion complexity and similarity. Finally, we decompose a given mesh into sub‐meshes using derived motion information and subdivide the triangles along the cutting paths for the smoother borders between the mesh parts. Our experimental results show that this new decomposition scheme can bring the benefit of good compression ratios on animation sequences. Copyright © 2005 John Wiley & Sons, Ltd.
Realistic 3D Mesh Compression Based on Predicted Angle-Normal Images

In this paper, we propose angle-normal images to reduce the number of normal component channels from three to two and present predicting the angle-normal images by the reconstructed geometry images. We implement the scheme on realistic meshes. Experimental results verify effectiveness of the proposed scheme. For geometry image codec, the proposed scheme outperforms up 1.78 dB PSNR gains, and average 0.57 dB PSNR gains. For normal image codec, the proposed scheme outperforms up 2.03 dB PSNR gains, and average 1.31 dB PSNR gains.