Miracle-dz/UniFAR-FTUs huggingface dataset:
Impaired Fibrinolytic Capacity and Tissue Plasminogen Activator Release in Patients with Restenosis after Percutaneous Transluminal Coronary Angioplasty (PTCA)

Summary To assess the role of the fibrinolytic system in the pathogenesis of restenosis after percutaneous transluminal coronary angioplasty (PTCA), we determined the components of this system in a retrospective study, including 16 patients with restenosis (gr. A) and 19 patients with long-term success (gr. B). In both groups at baseline fibrinolytic activity (FA) is unchanged, whereas tissue plasminogen activator antigen (tPA-Ag) is significantly increased (gr. A: 147.0%; gr. B: 139.8%; p <0.01). Fibrinolytic capacity (FC) and tPA-Ag release are significantly reduced in the restenosis group (FC: 46.5%, p <0.05; tPA-Ag release: 48.3%, p <0.01) compared to normal controls as well as to gr. B (FC: 84.3%, p <0.05; tPA-Ag release: 79.0%, p <0.05). Relating to the contact activation system, F XII (79.5%, p <0.05) is significantly, and F XI (82.3%) is clearly reduced in gr. A. Protein C (PC) is significantly elevated in gr. B (117.5%, p <0.05). There is a negative correlation between plasminogen activator inhibitor (PAI 1) and HDL-cholesterol (r = 0.37, p <0.05). It appears, that there is a typical pattern of defective fibrinolysis in patients with restenosis after PTCA and that this might be a pathogenetic factor in the development of restenosis.
Characterization of the umu-complementing operon from R391

In addition to conferring resistances to antibiotics and heavy metals, certain R factors carry genes involved in mutagenic DNA repair. These plasmid-encoded genes are structurally and functionally related to the chromosomally encoded umuDC genes of Escherichia coli and Salmonella typhimurium. Three such plasmid operons, mucAB, impCAB, and samAB, have been characterized at the molecular level. Recently, we have identified three additional umu-complementing operons from IncJ plasmid R391 and IncL/M plasmids R446b and R471a. We report here the molecular characterization of the R391 umu-complementing operon. The nucleotide sequence of the minimal R plasmid umu-complementing (rum) region revealed an operon of two genes, rumA(R391) and rumB(R391), with an upstream regulatory signal strongly resembling LexA-binding sites. Phylogenetic analysis revealed that the RumAB(R391) proteins are approximately equally diverged in sequence from the chromosomal UmuDC proteins and the other plasmid-encoded Umu-like proteins and represent a new subfamily. Genetic characterization of the rumAB(R391) operon revealed that in recA+ and recA1730 backgrounds, the rumAB(R391) operon was phenotypically indistinguishable from mucAB. In contrast, however, the rumAB(R391) operon gave levels of mutagenesis that were intermediate between those given by mucAB and umuDC in a recA430 strain. The latter phenotype was shown to correlate with the reduced posttranslational processing of the RumA(R391) protein to its mutagenically active form, RumA'(R391). Thus, the rumAB(R391) operon appears to possess characteristics that are reminiscent of both chromosome and plasmid-encoded umu-like operons.
Erratum: Dependency Parsing of Turkish

The suitability of different parsing methods for different languages is an important topic in syntactic parsing. Especially lesser-studied languages, typologically different from the languages for which methods have originally been developed, pose interesting challenges in this respect. This article presents an investigation of data-driven dependency parsing of Turkish, an agglutinative, free constituent order language that can be seen as the representative of a wider class of languages of similar type. Our investigations show that morphological structure plays an essential role in finding syntactic relations in such a language. In particular, we show that employing sublexical units called inflectional groups, rather than word forms, as the basic parsing units improves parsing accuracy. We test our claim on two different parsing methods, one based on a probabilistic model with beam search and the other based on discriminative classifiers and a deterministic parsing strategy, and show that the usefulness of sublexical units holds regardless of the parsing method. We examine the impact of morphological and lexical information in detail and show that, properly used, this kind of information can improve parsing accuracy substantially. Applying the techniques presented in this article, we achieve the highest reported accuracy for parsing the Turkish Treebank.
Boron nitride nanomaterials : from fabrication to characterization

Boron nitride nanotubes [BNNTs) and ultra thin BN sheets are two of the most important next generation nanomaterials. The synthesis and study of them are of both fundamental interest and technological importance. Improved methods of fabricating BNNTs and ultra thin BN sheets are presented in this thesis together with studies that characterize their properties and indicate potential applications. The production of high purity BNNTs in large quantities has been a major obstacle inhibiting the broad study and application of BNNTs. A new approach, involving a liquid boron [B] ink, has been developed to produce higher purity and larger quantities of BNNTs. In the new method, the ball milled B particles are homogeneously mixed with ethanol and metal nitrate in an ultrasonic bath. The ink-like liquid mixture, or B ink, is annealed in nitrogen containing gas to synthesize 0.5g of high purity BNNTs at one time. This significant invention has brought the practical application of BNNTs one step closer. As an example, bulk sized (not film shaped) BNNT reinforced polyurethane (PU) composites have been produced. The growth of nanotube films on various substrates and surfaces is vital for a range of applications. However, unlike the sophisticated carbon nanotube (CNT) film production, patterned growth of BNNTs over large areas had not previously been achieved. The new B ink method also overcomes this obstacle by providing a simple but powerful way to grow BNNT films on different substrates. It is demonstrated that the ink can be directly painted/brushed, sprayed, or even Inkjet printed on different substrates with any desired pattern and the ink layer is converted to a film of high density BNNTs by the annealing. This is the first method capable of growing BNNTs on non-flat or complex surfaces. Because the coating method involves direct growth of nanotubes, the BNNT films have strong adhesion to the substrate, which is very desirable for practical applications and a number of potential applications of such coatings are demonstrated. The larger quantities and particularly the higher purity of the BNNTs grown have enabled new properties of BNNTs to be discovered. For example, for the first time, single deep ultraviolet [DUV) emission at 225nm (5.51eV) has been found from BNNTs with a cylindrical multiwall structure and diameters smaller than lOnm. This finding suggests that BNNTs can work as nanoscale DUV light emitters opening up potential applications in miniaturized optic and optoelectronic devices as well as in biomedical analysis and treatment, in addition, many intriguing anti-wetting properties have been demonstrated for
The S2 state of the oxygen-evolving complex of photosystem II explored by QM/MM dynamics: spin surfaces and metastable states suggest a reaction path towards the S3 state.

One of the key steps in photosynthetic solar-energy conversion performed by plants, algae, and cyanobacteria is the splitting of water into molecular oxygen and hydrogen equivalents. [1] To achieve this challenging task photosynthetic organisms use a protein complex that remained almost unchanged during the evolution in the last two and a half billion years: the photosystem II (PSII). The reaction proceeds by the accumulation of four oxidizing equivalents on the {Mn4CaO5} cluster through five (S0–S4) oxidation states that are sequentially attained during water splitting (Kok cycle). [2] The deep understanding of the way nature has found to perform this difficult task efficiently has a great relevance not only for biology but also for inspiring the development of biomimetic artificial systems that can be used to store solar energy in an environmentally friendly way. [3] Atomic details of the structure of the oxygen-evolving complex (OEC) of PSII have been revealed by extended X-ray absorption fine structure (EXAFS) experiments and by X-ray crystallography at increasing resolution levels. [4] However, the accurate position of the {Mn4CaO5} cluster atoms and its ligands emerged only when a X-ray structure at 1.9 A resolution became accessible. [5] However, the effect of a possible X-ray photo-reduction, in particular on the characterization of the Kok’s state described by this structure and on the unrealistic bond lengths between the oxygen atom O5 and the two manganese ions Mn1 and Mn4, is matter of debate. [6] Additionally, important contributions to the structure refinement came from theoretical studies. [6b,7]
IIp45 Inhibits Cell Migration through Inhibition of HDAC6*

IIp45 (aka MIIP) is a newly discovered gene whose protein product inhibits cell migration. HDAC6 is a class IIb deacetylase that specifically deacetylates α-tubulin, modulates microtubule dynamics, and promotes cell migration. A yeast two-hybrid assay using IIp45 as bait identified HDAC6 protein as a binding partner of IIp45. This physical interaction of the two functionally antagonistic proteins was confirmed by glutathione S-transferase pulldown assay and co-immunoprecipitation assay in human cells. Serial deletion constructs of HDAC6 were used to characterize the interaction of HDAC6 and IIp45, and this analysis found that the two catalytic domains of HDAC6 protein are required for IIp45 binding. We examined the protein expression patterns of IIp45 and HDAC6 in glioma tissues. Elevated protein levels of HDAC6 were found in high grade glioma samples, in contrast to the decreased protein expression of IIp45. The potential negative regulation of HDAC6 expression by IIp45 was confirmed in cell lines with altered IIp45 expression by constitutive overexpression or small interfering RNA knockdown. Protein turnover study revealed that overexpression of IIp45 significantly reduces the intracellular protein stability of endogenous HDAC6, indicating a possible mechanism for the negative regulation of HDAC6 by IIp45. Results from the HDAC activity assay demonstrated that overexpressed IIp45 effectively decreases HDAC6 activity, increases acetylated α-tubulin, and reduces cell migration. The increased cell migration resulting from siIIp45 knockdown was significantly reversed by co-transfection of siHDAC6. Thus, we report here for the first time a novel mechanism by which IIp45 inhibits cell motility through inhibition of HDAC6.
Thiocyanate degradation by pure and mixed cultures of microorganisms

A mixed culture and a pure bacterial strain (BMV8) were isolated from a bioreactor for thiocyanate treatment. Both cultures removed 5 mM of thiocyanate from the medium in 36 hours. The mixed culture was able to tolerate concentrations up to 60 mM. The efficiency of thiocyanate degradation decreased when the cells were immobilized.
Meningococcal Group C and W135 Immunological Hyporesponsiveness in African Toddlers

ABSTRACT A phase II clinical study was conducted in African toddlers (aged 12 to 23 months), with subjects receiving either investigational meningococcal group A conjugate (PsA-TT), meningococcal ACWY polysaccharide (PsACWY), or Haemophilus influenzae type b (Hib-TT) vaccine. Ten months following vaccination, the 3 study groups were further randomized to receive a dose of PsA-TT, a 1/5 dose of PsACWY, or a dose of Hib-TT vaccine. Group A serum bactericidal antibody (SBA) results have been reported previously, with PsA-TT demonstrating superior immunogenicity versus PsACWY vaccine. Immunogenicity for serogroups W135 and C was assessed by SBA assay to investigate the impact of multiple doses in this age group. Blood samples were taken prior to vaccination, 28 days and 40 weeks post-primary vaccination, and 7 and 28 days post-booster vaccination with a 1/5 dose of PsACWY. Subjects who had previously received a full dose of PsACWY had W135 SBA geometric mean titers (GMTs) of 26.1 and 4.4 at 7 and 28 days post-booster vaccination with a 1/5 PsACWY dose, respectively, whereas the W135 SBA GMTs of naïve subjects at these time points following vaccination with a 1/5 dose of PsACWY were 861.1 and 14.6, respectively. Similar differences were observed for serogroup C, with SBA GMTs of 99 and 5.9 at 7 and 28 days post-booster vaccination with a 1/5 dose of PsACWY, respectively, for naïve subjects, compared to 4.1 and 3.2 for previously vaccinated subjects. Immunologic hyporesponsiveness for groups C and W135 was observed following a full dose of PsACWY vaccine at 12 to 23 months of age and a 1/5 dose of PsACWY 10 months later compared to the case for PsACWY-naïve subjects receiving a 1/5 dose of PsACWY vaccine.
Phylogenetic Analysis and Structural Predictions of Human Adenovirus Penton Proteins as a Basis for Tissue-Specific Adenovirus Vector Design

ABSTRACT The penton base is a major capsid protein of human adenoviruses (HAdV) which forms the vertices of the capsid and interacts with hexon and fiber protein. Two hypervariable loops of the penton are exposed on the capsid surface. Sequences of these and 300 adjacent amino acid residues of all 51 HAdV and closely related simian adenoviruses were studied. Adjacent sequences and predicted overall secondary structure were conserved. Phylogenetic analysis revealed clustering corresponding to the HAdV species and recombination events in the origin of HAdV prototypes. All HAdV except serotypes 40 and 41 of species F exhibited an integrin binding RGD motif in the second loop. The lengths of the loops (HVR1 and RGD loops) varied significantly between HAdV species with the longest RGD loop observed in species C and the longest HVR1 in species B. Long loops may permit the insertion of motifs that modify tissue tropism. Genetic analysis of HAdV prime strain p17′H30, a neutralization variant of HAdV-D17, indicated the significance of nonhexon neutralization epitopes for HAdV immune escape. Fourteen highly conserved motifs of the penton base were analyzed by site-directed mutagenesis of HAdV-D8 and tested for sustained induction of early cytopathic effects. Thus, three new motifs essential for penton base function were identified additionally to the RGD site, which interacts with a secondary cellular receptor responsible for internalization. Therefore, our penton primary structure data and secondary structure modeling in combination with the recently published fiber knob sequences may permit the rational design of tissue-specific adenoviral vectors.
Fluorescence labeling of the photosensory unit of Deinococcus radiodurans bacteriophytochrome for Förster resonance energy transfer studies

Phytochromes are red-light sensing proteins of bacteria, algae, plants, and fungi. A central feature of the function of phytochromes is a light-induced conversion between a red absorbing (Pr) state and a far-red absorbing state (Pfr). The photosensory unit (CBD-PHY) of Deinococcus radiodurans bacteriophytochrome is a dimeric protein consisting of a C-terminal chromophore binding (CBD) domain and a phytochromeassociated (PHY) domain. Recent crystal and solution structures of CBD-PHY have shown that the separation between the two PHY domains increases when the protein is converted from Pr to Pfr state as a result of red-light absorption. Forster resonance energy transfer (FRET) based measurements were designed in this work to be used as an alternative, non-invasive, and cost-efficient way for probing the PHY domain separation in Pr and Pfr. CBDPHY engineered with cysteine insertions at the ends of the PHY domains (E373/CC/G374) and one surface cysteine substituted with serine (C93S) was expressed in E. coli strain BL21 (DE3) cells and purified with high-pressure liquid chromatography. A maleimide-based labeling scheme was developed for attaching a FRET donor (D) – acceptor (A) pair (Alexa Fluor 488 – Alexa Fluor 546) to the cysteine insertions. Steadystate fluorescence emission spectra, fluorescence decays, and steady-state and time-resolved fluorescence anisotropies were measured for determining FRET efficiencies and corresponding D-A distances in Pr and Pfr. Emission spectrum of DA-labeled CBD-PHY in Pr and Pfr revealed FRET-associated intensity changes in both D and A emission. Surprisingly, FRET signal was absent from time-resolved results. Furthermore, none of the measurement techniques revealed a difference between Pr and Pfr, and there was discrepancy between D-A distances determined from steady-state results and those evaluated from earlier solution structures. Multiple explanations can be proposed for the unexpected results. It is evident that further development of protein labeling protocols is still needed. There is also a possibility that the system is more complicated than what was initially expected because of processes such as quenching of the dyes or FRET between the dyes and biliverdin molecules bound to the CBD-domains.
Beta 2-microglobulin is selectively associated with H-2 and TL alloantigens on murine lymphoid cells

We have used a rabbit antiserum prepared against purified rat beta2- microglobulin to immunoprecipitate molecules from lysates of radioiodinated murine thymocytes and splenocytes. All the molecules that are reactive with this serum have subunits of 44,000 and 12,000 and can be identified as H-2 and TL antigens. Thus, the anti-beta2mu serum can deplete lysates of the majority of the TL and H-2 atigens which can be subsequently recognized by alloantisera. If TL and H-2 are precipitated from the lysates before the addition of anti-beta2mu, no beta2mu-reactive molecules remain. Our results indicate that Ia antigens cannot be depleted from the lysates with anti-beta2mu. The studies also suggest that TL and H-2 heavy chains can exist as both monomers and dimers. These observations are discussed with regard to previous studies concerning the native structure of H-2 and TL antigens.
Indoor Localization by Fusing a Group of Fingerprints Based on Random Forests

Indoor localization based on SIngle Of Fingerprint (SIOF) is rather susceptible to the changing environment, multipath, and non-line-of-sight (NLOS) propagation. Building SIOF is also a very time-consuming process. Recently, we first proposed a GrOup Of Fingerprints (GOOF) to improve the localization accuracy and reduce the burden of building fingerprints. However, the main drawback is the timeliness. In this paper, we propose a novel localization framework by Fusing A Group Of fingerprinTs (FAGOT) based on random forests. In the offline phase, we first build a GOOF from different transformations of the received signals of multiple antennas. Then, we design multiple GOOF strong classifiers based on Random Forests (GOOF-RF) by training each fingerprint in the GOOF. In the online phase, we input the corresponding transformations of the real measurements into these strong classifiers to obtain multiple independent decisions. Finally, we propose a Sliding Window aIded Mode-based (SWIM) fusion algorithm to balance the localization accuracy and time. Our proposed approaches can work better in an unknown indoor scenario. The burden of building fingerprints can also be reduced drastically. We demonstrate the performance of our algorithms through simulations and real experimental data using two Universal Software Radio Peripheral (USRP) platforms.
Lipschitz Stability of an Inverse Boundary Value Problem for a Schrödinger-Type Equation

In this paper we study the inverse boundary value problem of determining the potential in the Schrodinger equation from the knowledge of the Dirichlet-to-Neumann map, which is commonly accepted as an ill-posed problem in the sense that, under general settings, the optimal stability estimate is of logarithmic type. In this work, a Lipschitz-type stability is established assuming a priori that the potential is piecewise constant with a bounded known number of unknown values.
The Effectiveness of Emotionally Focused Couples Therapy on Sexual Satisfaction and Marital Adjustment of Infertile Couples with Marital Conflicts

Background The purpose of this investigation is to determine the efficacy of emotionally focused couples therapy (EFT-C) on enhancement of marital adjustment in infertile couples. Materials and Methods This was a semi-experimental study with a pre- and post-test design. We selected 30 infertile couples (60 subjects) by purposive sampling. Couples were randomly assigned to two groups, sample and control. Each group consisted of 15 couples who had marital maladjustment and low sexual satisfaction. Couples answered the marital adjustment and sexual satisfaction questionnaires at baseline after which the sample group received 10 sessions of EFT-C. Results Results of pre-test and post-test showed that EFT-C significantly impacted marital adjustment and sexual satisfaction. Conclusion EFT-C had a significant effect on enhancement of satisfaction, cohesion and affectional expression. This approach impacted physical and emotional sexual satisfaction of infertile couples.
An energy-conscious transport protocol for multi-hop wireless networks

We present a transport protocol whose goal is to reduce power consumption without compromising delivery requirements of applications. To meet its goal of energy efficiency, our transport protocol (1) contains mechanisms to balance end-to-end vs. local retransmissions; (2) minimizes acknowledgment traffic using receiver regulated rate-based flow control combined with selected acknowledgements and in-network caching of packets; and (3) aggressively seeks to avoid any congestion-based packet loss. Within a recently developed ultra low-power multi-hop wireless network system, extensive simulations and experimental results demonstrate that our transport protocol meets its goal of preserving the energy efficiency of the underlying network.
Precision spectroscopy of AdS / CFT

We extend recent remarkable progress in the comparison of the dynamical energy spectrum of rotating closed strings in AdS5 ×S 5 and the scaling weights of the corresponding non-near-BPS operators in planar N = 4 supersymmetric gauge theory. On the string side the computations are feasible, using semiclassical methods, if angular momentum quantum numbers are large. This results in a prediction of gauge theory anomalous dimensions to all orders in the ‘t Hooft coupling λ. On the gauge side the direct computation of these dimensions is feasible, using a recently discovered relation to integrable (super) spin chains, provided one considers the lowest order in λ. This oneloop computation then predicts the small-tension limit of the string spectrum for all (i.e. small or large) quantum numbers. In the overlapping window of large quantum numbers and small effective string tension, the string theory and gauge theory results are found to match in a mathematically highly nontrivial fashion. In particular, we compare energies of states with (i) two large angular momenta in S 5 , and (ii) one large angular momentum in AdS5 and S 5 each, and show that the solutions are related by an analytic continuation. Finally, numerical evidence is presented on the gauge side that the agreement persists also at higher (two) loop order.