Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoelectrochemical synthesis of DNA microarrays

Optical addressing of semiconductor electrodes represents a powerful technology that enables the independent and parallel control of a very large number of electrical phenomena at the solid-electrolyte interface. To date, it has been used in a wide range of applications including electrophoretic manipulation, biomolecule sensing, and stimulating networks of neurons. Here, we have adapted this approach for the parallel addressing of redox reactions, and report the construction of a DNA microarray synthesis platform based on semiconductor photoelectrochemistry (PEC). An amorphous silicon photoconductor is activated by an optical projection system to create virtual electrodes capable of electrochemically generating protons; these PEC-generated protons then cleave the acid-labile dimethoxytrityl protecting groups of DNA phosphoramidite synthesis reagents with the requisite spatial selectivity to generate DNA microarrays. Furthermore, a thin-film porous glass dramatically increases the amount of DNA synthesized per chip by over an order of magnitude versus uncoated glass. This platform demonstrates that PEC can be used toward combinatorial bio-polymer and small molecule synthesis.
Study of pentoxifylline effects on motility and viability of spermatozoa from infertile asthenozoospermic males

Background: The quality of semen is one of the major parameters in male infertility. Pentoxifylline, a methylxanthine derivative, is an agent primarily used in the treatment of intermittent claudication and other vascular disorders. Studies have shown that pentoxifylline enhances the quality and quantity of sperms. In this study, we have investigated the in vitro effects of pentoxifylline on viability and motility of spermatozoa in samples of infertile oligoasthenozoospermic males. Materials and Methods: In this observer-blinded clinical trial, semen samples of 25 infertile oligoasthenozoospermic males were collected in Alzahra Educational Medical Center of Tabriz University of Medical Sciences from August 2010 to August 2012. After the isolation of spermatozoa by the swim-up method, they were randomized into four groups in ISM1 environment: The controls treated normally: Group 1 treated by pentoxifylline at a dose of 50 ΅g/ml, Group 2 treated by pentoxifylline at a dose of 100 ΅g/ml, and Group 3 treated by pentoxifylline at a dose of 200 ΅g/ml. Sperm viability and motility were compared among the groups on 45 min, 24 h, 36 h, and 48 h intervals. Results: Mean percentages of live sperms were 98.40%, 51.40%, 20.60%, and 6.00% in control group and 98.40%, 69.20%, 38.60%, and 14.60% in Group 3 on the mentioned intervals, respectively. This mean percentage decrease of live sperms was significantly lower in Group 3 comparing with that of other groups (P = 0.01). Mean percentages of motile sperms were 54%, 8.40%, 2.80%, and 0% in control group; and 54%, 16%, 4.80%, and 1.40% in Group 3 on the mentioned intervals, respectively. There was not a significant difference between the four groups in this regard (P = 0.19). Conclusion: Pentoxifylline can enhance the viability of sperm of infertile oligoasthenozoospermic males with no significant effect on its motility.
The spectrum of cardiovascular effects of dobutamine - from healthy subjects to septic shock patients

Dobutamine is the inotrope most commonly used in septic shock patients to increase cardiac output and correct hypoperfusion. Although some experimental and clinical studies have shown that dobutamine can improve systemic and regional hemodynamics, other research has found that its effects are heterogenous and unpredictable. In this review, we analyze the pharmacodynamic properties of dobutamine and its physiologic effects. Our goal is to show that the effects of dobutamine might differ between healthy subjects, in experimental and clinical cardiac failure, in animal models and in patients with septic shock. We discuss evidence supporting the claim that dobutamine, in septic shock, frequently behaves as a chronotropic and vasodilatory drug, without evidence of inotropic action. Since the side effects are very common, and the therapeutic benefits are unclear, we suggest that dobutamine should be used cautiously in septic shock. Before a definitive therapeutic decision, the efficacy and tolerance of dobutamine should be assessed during a brief time with close monitoring of its positive and negative side effects.
CynD, the Cyanide Dihydratase from Bacillus pumilus: Gene Cloning and Structural Studies

ABSTRACT The cyanide dihydratase in Bacillus pumilus was shown to be an 18-subunit spiral structure by three-dimensional reconstruction of electron micrographs of negatively stained material at its optimum pH, 8.0. At pH 5.4, the subunits rearrange to form an extended left-handed helix. Gel electrophoresis of glutaraldehyde cross-linked enzyme suggests that the fundamental component of the spiral is a dimer of the 37-kDa subunit. The gene was cloned, and the recombinant enzyme was readily expressed at high levels in Escherichia coli. Purification of the recombinant enzyme was facilitated by the addition of a C-terminal six-histidine affinity purification tag. The tagged recombinant enzyme has Km and Vmax values similar to those published for the native enzyme. This is the first cyanide dihydratase from a gram-positive bacterium to be sequenced, and it is the first description of the structure of any member of this enzyme class. The putative amino acid sequence shares over 80% identity to the only other sequenced cyanide dihydratase, that of the gram-negative Pseudomonas stutzeri strain AK61, and is similar to a number of other bacterial and fungal nitrilases. This sequence similarity suggests that the novel short spiral structure may be typical of these enzymes. In addition, an active cyanide dihydratase from a non-cyanide-degrading isolate of B. pumilus (strain 8A3) was cloned and expressed. This suggests that cynD, the gene coding for the cyanide dihydratase, is not unique to the C1 strain of B. pumilus and is not a reflection of its origin at a mining waste site.
Effect of parsley (Petroselinum crispum) intake on urinary apigenin excretion, blood antioxidant enzymes and biomarkers for oxidative stress in human subjects

Seven men and seven women participated in a randomized crossover trial to study the effect of intake of parsley (Petroselinum crispum), containing high levels of the flavone apigenin, on the urinary excretion of flavones and on biomarkers for oxidative stress. The subjects received a strictly controlled diet low in flavones and other naturally occurring antioxidants during the 2 weeks of intervention. This basic diet was supplemented with parsley providing 3·73–4·49 mg apigenin/MJ in one of the intervention weeks. Urinary excretion of apigenin was 1·59–409·09 μg/MJ per 24 h during intervention with parsley and 0–112·27 μg/MJ per 24 h on the basic diet (P < 0·05). The fraction of apigenin intake excreted in the urine was 0·58 (se 0·16) % during parsley intervention. Erythrocyte glutathione reductase (EC 1.6.4.1; GR) and superoxide dismutase (EC 1.15.1.1; SOD) activities increased during intervention with parsley (P < 0·005) as compared with the levels on the basic diet, whereas erythrocyte catalase (EC 1.11.1.6) and glutathione peroxidase (EC 1.11.1.9) activities did not change. No significant changes were observed in plasma protein 2-adipic semialdehyde residues, a biomarker of plasma protein oxidation. In this short-term investigation, an overall decreasing trend in the activity of antioxidant enzymes was observed during the 2-week study. The decreased activity of SOD was strongly correlated at the individual level with an increased oxidative damage to plasma proteins. However, the intervention with parsley seemed, partly, to overcome this decrease and resulted in increased levels of GR and SOD.
Contract-based synchronization of IP telecommunication services: a case study

Communication middleware, like J2EE and OCCAS, facilitates development and deployment of IP telecommunication services by automating various cross-cutting concerns, such as those related to messaging and security. This middleware is highly concurrent, with threads executing methods that an application programmer writes to carry out the service logic. While the middleware manages life-cycle concerns of threads, the problem of synchronizing them is left to the application programmer. Unfortunately, this synchronization code can be complex and prone to error. Moreover, it can easily obscure the service logic. Our prior work proposed solving these problems using a middleware framework to automatically synchronize concurrent service executions based on declarative synchronization contracts. This paper describes an implementation of our synchronization framework and a case study using it. The case study demonstrates the extent to which contract-based synchronization facilitates refinement of a finite-state design to code and improves design transparency. It also examines the impact on performance of the subject application. A conclusion of the case study is that contract-based synchronization could provide a foundation for automatic generation of IPT services from finite-state designs.
Ineffability in grammar

We examine that different cases of ineffability, not only in phonology and syntax, but also in morphology and semantics, and propose a typology of ineffabilities compatible with the Control component of Orgun & Sprouse (1999). Lexical gaps as well as other gaps in the morpho-syntax or the phonology are the primary source of ineffable - or absolutely ungrammatical - constructions. Further gaps arise from the need to reconcile incompatible features. Whether such instances are repaired is language dependent. Islands and other restrictions resulting from syntactic and semantic laws on scope and wh-words form the third group of ineffable cases. The upshot of our study is that neither the lexicon-based nor the semantic ineffability cases are a problem for Optimality theory, since they are located in domains of grammar for which OT's architecture cannot be held responsible.
A comparative study on the performance of interleaved converters for EV battery charging

DC-DC converters are a very important part of the Plug in Hybrid Electric Vehicles for charging. The aim is to achieve the maximum efficiency throughout the process. This paper presents a comparison of different interleaved boost converter topologies which are used in front end ac-dc conversion for EV charging. The comparison is based on various interleaved boost converter topologies which offer high efficiency, high power, and low cost. Result are presented and interpreted for three different converters to convert ac-dc and get a voltage of 430 V. From the results it was observed that bridgeless interleaved boost converter is best suited for use in charging applications of Electric Vehicles.
A study on workload-aware wavelet synopses for point and range-sum queries

In this paper we perform an extensive theoretical and experimental study on common synopsis construction algorithms, with emphasis on wavelet based techniques, that take under consideration query workload statistics. Our goal is to compare, "expensive" quadratic time algorithms with "cheap" near-linear time algorithms, particularly when the latter are not optimal and/or not workload-aware for the problem at hand. Further, we present the first known algorithm for constructing wavelet synopses for a special class of range-sum query workloads. Our experimental results, clearly justify the necessity for designing workload-aware algorithms, especially in the case of range-sum queries.
Star tracker orientation optimization using Non-dominated Sorting Genetic Algorithm (NSGA)

One of the devices used to determine the attitude of a satellite is the star tracker, whose principle of operation is based on star position measurements on a specific inertial frame, allowing precise attitude determination and control of the satellite. Due to the high sensitivity of star camera, bright objects like Sun, Earth or Moon must be avoided in the sensor's field of view. This characteristic imposes a design constraint that shall be satisfied simultaneously by all the star trackers used in the specific satellite. Considering only the Sun exclusion case, the goal of this work is to find the star tracker orientation that maximizes simultaneously the Sun exclusion angle for both sensors in a way to ensure the proper equipment operation during a typical Earth pointing satellite mission. For this optimization problem, the search space is defined by the azimuth and elevation of each star tracker in the body centered coordinate frame system. Since the engineering goal implies a vectorial objective function optimization, the method used in this work was the Non-dominated Sorting Genetic Algorithm (NSGA), which allows a multi-optimization problem solution without the scalarization approach, in order to get a few optimal solutions along the non-dominated region. In order to get diversity in the optimal solutions, simulations used six different dummy fitness functions and compared the final results.
A Test of the AdS/CFT Correspondence Using High-Spin Operators

In two remarkable recent papers, hep-th/0610248 and hep-th/0610251, the complete planar perturbative expansion was proposed for the universal function of the coupling, f ( g ), appearing in the dimensions of high-spin operators of the N = 4 SYM theory. We study numerically the integral equation derived in hep-th/0610251, which implements a resum-mation of the perturbative expansion, and ﬁnd a smooth function that approaches the asymptotic form predicted by string theory. In fact, the two leading terms at strong coupling match with high accuracy the results obtained for the semiclassical folded string spinning in AdS 5 . This constitutes a remarkable conﬁrmation of the AdS/CFT correspondence for high-spin operators, and equivalently for the cusp anomaly of a Wilson loop. We also make a numerical prediction for the third term in the strong coupling series. I.R. Klebanov dedicates this paper to the memory of his brother-in-law, Gordon E. Kato.
Fast and precise hybrid type inference for JavaScript

JavaScript performance is often bound by its dynamically typed nature. Compilers do not have access to static type information, making generation of efficient, type-specialized machine code difficult. We seek to solve this problem by inferring types. In this paper we present a hybrid type inference algorithm for JavaScript based on points-to analysis. Our algorithm is fast, in that it pays for itself in the optimizations it enables. Our algorithm is also precise, generating information that closely reflects the program's actual behavior even when analyzing polymorphic code, by augmenting static analysis with run-time type barriers. We showcase an implementation for Mozilla Firefox's JavaScript engine, demonstrating both performance gains and viability. Through integration with the just-in-time (JIT) compiler in Firefox, we have improved performance on major benchmarks and JavaScript-heavy websites by up to 50%. Inference-enabled compilation is the default compilation mode as of Firefox 9.
Validation of the Cardiosphere Method to Culture Cardiac Progenitor Cells from Myocardial Tissue

Background At least four laboratories have shown that endogenous cardiac progenitor cells (CPCs) can be grown directly from adult heart tissue in primary culture, as cardiospheres or their progeny (cardiosphere-derived cells, CDCs). Indeed, CDCs are already being tested in a clinical trial for cardiac regeneration. Nevertheless, the validity of the cardiosphere strategy to generate CPCs has been called into question by reports based on variant methods. In those reports, cardiospheres are argued to be cardiomyogenic only because of retained cardiomyocytes, and stem cell activity has been proposed to reflect hematological contamination. We use a variety of approaches (including genetic lineage tracing) to show that neither artifact is applicable to cardiospheres and CDCs grown using established methods, and we further document the stem cell characteristics (namely, clonogenicity and multilineage potential) of CDCs. Methodology/Principal Findings CPCs were expanded from human endomyocardial biopsies (n = 160), adult bi-transgenic MerCreMer-Z/EG mice (n = 6), adult C57BL/6 mice (n = 18), adult GFP+ C57BL/6 transgenic mice (n = 3), Yucatan mini pigs (n = 67), adult SCID beige mice (n = 8), and adult Wistar-Kyoto rats (n = 80). Cellular yield was enhanced by collagenase digestion and process standardization; yield was reduced in altered media and in specific animal strains. Heparinization/retrograde organ perfusion did not alter the ability to generate outgrowth from myocardial sample. The initial outgrowth from myocardial samples was enriched for sub-populations of CPCs (c-Kit+), endothelial cells (CD31+, CD34+), and mesenchymal cells (CD90+). Lineage tracing using MerCreMer-Z/EG transgenic mice revealed that the presence of cardiomyocytes in the cellular outgrowth is not required for the generation of CPCs. Rat CDCs are shown to be clonogenic, and cloned CDCs exhibit spontaneous multineage potential. Conclusions/Significance This study demonstrates that direct culture and expansion of CPCs from myocardial tissue is simple, straightforward, and reproducible when appropriate techniques are used.
Multichannel intraluminal impedance accurately detects fasting, recumbent reflux events and their clearing.

Multichannel intraluminal impedance (MII) is a new diagnostic test for gastroesophageal reflux disease (GERD). The objective of this report is to determine the accuracy of MII in detecting individual reflux events (REs) identified by pH probe and manometry, as well as their clearing in patients with severe GERD compared with normal volunteers. Ten severe GERD patients and 10 normal volunteers underwent simultaneous manometry [7 sites: gastric, lower esophageal sphincter, esophagus (4), pharynx], pH, and MII (6 sites in esophagus) for 15 min in the left and right recumbent posture while fasting. We found that patients had 30-fold more REs than normal volunteers (41 +/- 11 vs. 1.3 +/- 0.4), and 95% of all REs were detected by MII. An average 15-fold fall in impedance with liquid and fivefold rise with gas made REs and their composition easy to detect with MII. In the right recumbent posture, nearly all REs detected by MII were liquid (98%, 98/100). In contrast, all 283 REs detected by MII in the left recumbent posture were gas. Nearly all REs detected by MII were cleared (98%, 368/374). Mean acid clearing time was threefold longer (47 s) than clearing time by either manometry (15 s) or MII (13 s), primarily due to acid rereflux, i.e., additional acid REs during acid clearing. We conclude that MII is accurate in detecting REs identified by manometry and/or pH probe, their composition, and their clearing.
MicroRNA Expression Signatures during Malignant Progression from Barrett's Esophagus to Esophageal Adenocarcinoma

Barrett's esophagus is the precursor lesion of esophageal adenocarcinoma, whose progression follows sequential stages. However, the low progression rate and the inadequacy and subjective interpretation of histologic grading in predicting Barrett's esophagus progression call for more objective biomarkers that can improve risk prediction. We conducted a genome-wide profiling of 754 human microRNAs (miRNA) in 35 normal epithelium, 34 Barrett's esophagus, and 36 esophageal adenocarcinoma tissues using TaqMan real-time PCR-based profiling. Unsupervised hierarchical clustering using 294 modestly to highly expressed miRNAs showed clear clustering of two groups: normal epithelium versus Barrett's esophagus/esophageal adenocarcinoma tissues. Moreover, there was an excellent clustering of Barrett's metaplasia (without dysplasia) tissues from normal epithelium tissues. However, Barrett's esophagus tissues of different stages and esophageal adenocarcinoma tissues were interspersed. There were differentially expressed miRNAs at different stages. The majority of miRNA aberrations involved upregulation of expression in Barrett's esophagus and esophageal adenocarcinoma tissues, with the most dramatic alterations occurring at the Barrett's metaplasia stage. Known oncomiRs, such as miR-21, miR-25, and miR-223, and tumor suppressor miRNAs, including miR-205, miR-203, let-7c, and miR-133a, showed progressively altered expression from Barrett's esophagus to esophageal adenocarcinoma. We also identified a number of novel miRNAs that showed progressively altered expression, including miR-301b, miR-618, and miR-23b. The significant miRNA alterations that were exclusive to esophageal adenocarcinoma but not Barrett's esophagus included miR-375 downregulation and upregulation of five members of the miR-17-92 and its homologue clusters, which may become promising biomarkers for esophageal adenocarcinoma development. Cancer Prev Res; 6(3); 196–205. ©2013 AACR.
Cosmological Parameter Estimation Using 21 cm Radiation from the Epoch of Reionization

A number of radio interferometers are currently being planned or constructed to observe 21 cm emission from reionization. Not only will such measurements provide a detailed view of that epoch, but, since the 21 cm emission also traces the distribution of matter in the universe, this signal can be used to constrain cosmological parameters. The sensitivity of an interferometer to the cosmological information in the signal may depend on how precisely the angular dependence of the 21 cm three-dimensional power spectrum can be measured. Using an analytic model for reionization, we quantify all the effects that break the spherical symmetry of the three-dimensional 21 cm power spectrum. We find that upcoming observatories will be sensitive to the 21 cm signal over a wide range of scales, from larger than 100 to as small as 1 comoving Mpc. Next, we consider three methods to measure cosmological parameters from the signal: (1) direct fitting of the density power spectrum to the signal, (2) using only the velocity field fluctuations in the signal, and (3) looking at the signal at large enough scales that all fluctuations trace the density field. With the foremost method, the first generation of 21 cm observations should moderately improve existing constraints on cosmological parameters for certain low-redshift reionization scenarios, and a 2 yr observation with the second-generation interferometer MWA5000 in combination with the CMB telescope Planck could improve constraints on Ωw, Ωmh2, Ωbh2, Ων, ns, and αs. If the universe is substantially ionized by z ~ 12 or if spin temperature fluctuations are important, we show that it will be difficult to place competitive constraints on cosmological parameters with any of the considered methods.
Self recognition by autologous mixed lymphocyte reaction-primed cells.

Human T cells were separated with neuraminidase-treated autologous erythrocytes into auto-rosette-forming cells (ARFC) and non-ARFC (N-ARFC). These 2 subsets were examined for reactivity to autologous non-T cells. When N-ARFC were stimulated by autologous non-T cells, blastogenesis was weak; ARFC, however, proliferated vigorously. ARFC were revealed to be the major subset that responded and proliferated in autologous mixed lymphocyte reaction (AMLR). AMLR-primed cells were restimulated by autologous or allogeneic non-T cells to study self recognition in relation to HLA complex. Self recognition by AMLR-primed cells was closely related to HLA complex, and absolute identity of HLA complex was necessary to recognize allogeneic cells as self. In addition, in respect to the responder cell difference between AMLR and allogeneic MLR, the reactivity of 2 kinds of cells (i.e., AMLR-primed cells and alloreactive cells) strongly suggested that autoreactive T cells were distinguished from alloreactive T cells.