Miracle-dz/UniFAR-FTUs huggingface dataset:
Photophysical Properties of Fluorescent DNA-dyes Bound to Single- and Double-stranded DNA in Aqueous Buffered Solution¶

Abstract The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye–DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA stains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4′,6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye–DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye–DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA–cyanine dye complexes were small. Broadening of dye–ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye–dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.
A setup for gamma ray sources localization using coded apertures and CdTe detectors

We describe a setup which consists of two CdTe based gamma cameras with coded apertures and a video camera. The system is used for the localization of radioactive sources via triangulation. By adjusting the mask-to-detector distance the maximum Fully Coded Field of View (FCFV) is 92.72 degrees. The System Point Spread Function (SPSF), the Angular Resolution (AR) and the Point Source Location Accuracy (PSLA) are investigated using experimental data and simulations.
Efficacy of Tenofovir in Patients with Lamivudine Failure Is Not Different from That in Nucleoside/Nucleotide Analogue-Naïve Patients with Chronic Hepatitis B

ABSTRACT We evaluated the efficacy of tenofovir disoproxil fumarate (TDF) in patients with lamivudine failure (LAM-F) in comparison with that in nucleoside/nucleotide analogue (NA)-naïve patients with chronic hepatitis B (CHB). The criteria for inclusion were being NA naïve or having previous LAM-F and receiving TDF therapy for at least 6 months. Biochemical and virological tests were performed at the baseline, at 3-month intervals in the first year, and every 6 months thereafter. The primary outcome measure for efficacy was a complete virological response (CVR), defined as an HBV DNA level of <20 IU/ml. CVR rates were calculated by Kaplan-Meier analysis, and a multivariate Cox proportional-hazard model was generated in order to find predictive factors independently associated with the time to a CVR. We included 197 patients in the study (136 males; mean age, 43 ± 12 years; 105 patients were NA naïve). Sixty-five patients had hepatitis B e antigen (HBeAg)-positive CHB. The median duration of TDF treatment was 29 (range, 6 to 52) months. Seventy-one patients (77%) in the LAM-F group were treated with TDF add-on therapy. The CVR rates of the NA-naïve and LAM-F groups were comparable in HBeAg-negative (94% versus 96% at month 36, P = 0.10) and HBeAg-positive patients (67% versus 83% at month 36, P = 0.48). According to the multivariate Cox regression model, only HBeAg positivity (hazard ratio [HR], 0.39; 95% confidence interval [CI], 0.26 to 0.59; P < 0.001) and a high baseline HBV DNA level (HR, 0.44; 95% CI, 0.29 to 0.67; P < 0.001) had a significant influence on the time to a CVR. The similar cumulative CVR rates during the follow-up show that TDF has comparable efficacy in lamivudine-experienced and NA-naïve patients, and the presence of resistance mutations did not alter the response rates.
The achievement goal and self-determination theories as predictors of dispositional flow in young athletes

The purpose of this study was to analyse from the perspective of the achievement goal theory and the self-determination theory some variables which could help to promote positive motivation and to improve dispositional flow in adolescent athletes. A sample of 413 young athletes (from 12 to 16 years of age) completed the Perceived Motivational Climate in Sport Questionnaire-2, Perception of Success Questionnaire, Sport Motivation Scale and Dispositional Flow Scale. The results of the struc- tural equation modeling indicated that the perceived motivational climates positively predicted corresponding dispositional goal orientations. Task- involving climate and task orientation positively predicted self-determined motivation, while ego-involving climate negatively predicted it. Task and ego-involving climates, task and ego orientations and self-determined motivation positively predicted dispositional flow. Task dimensions showed more prediction power over the dispositional flow than the ego dimensions. The findings are discussed with regard to enhancing athletes' motivation and dispositional flow.
Signal transduction through Ras‐GTPase and Ca2+/ calmodulin‐dependent protein kinase II contributes to development of diabetes‐induced renal vascular dysfunction

This study examined the role of Ca2+/calmodulin‐dependent protein kinase II (CaMKII) and Ras‐GTPase in the development of abnormal reactivity to vasoactive agents in the renal artery of diabetic rats. The vasoconstrictor response induced by norepinephrine (NE), endothelin‐1 (ET‐1) or angiotensin II (Ang II) was significantly increased whereas vasodilator response to carbachol, histamine or sodium nitroprusside (SNP) was not altered in the renal artery segments of the streptozotocin (STZ)‐diabetic rats. Chronic intraperitoneal administration of KN‐93 (5 mg/kg/ alt diem), an inhibitor of CaMKII or FPTIII (1.5 mg/kg/ alt diem), an inhibitor of Ras‐GTPase, produced significant normalization of the altered agonist‐induced vasoconstrictor responses without affecting blood glucose levels. All the inhibitors were administered for four weeks starting from day one of diabetes induction. Inhibition of Ras‐GTPase or CaMKII did not affect the agonist‐induced vasoconstrictor and vasodilator responses in the non‐diabetic control animals. These data suggest that inhibition of signal transduction involving CaMKII and Ras‐GTPase can prevent development of diabetes‐induced abnormal vascular reactivity in the renal artery. Copyright © 2005 John Wiley & Sons, Ltd.
The Hazards of Starting the Cigarette Smoking Habit

It is necessary to understand the determinants of the hazards of starting smoking in developing effective policies and programs to reduce the number of smokers. In this paper, we develop a split-sample duration model of the decision to start smoking. For the empirical estimation, we use data from the 2002 Canadian tobacco use monitoring survey. The hazard rate of starting smoking peaks sharply at age 15 and quickly declines thereafter. Our parametric estimates provide evidence that gender, education level, marital status and household size are important determinants of the smoking habit. We also find that increased cigarettes price has an impact on picking up the habit, but not on the initiation age. Thus, the results highlight the importance of cigarette taxes in influencing the likelihood of smoking.
On maximum sector bounds for absolute stability of single-input single-output systems

We consider the classical problem of absolute stability, i.e. stability of a linear time-invariant system in feedback with a memoryless time-varying sector bound non-linearity. We derive necessary and sufficient conditions for the existence of periodic motion. For the special case of symmetric sector bounds, this condition yields the minimum sector bounds for which the system can sustain periodic motion. By guaranteeing the absence of periodic motion we derive non-conservative sufficient conditions for absolute stability for arbitrary sector bounds. We demonstrate by numerical examples the application of our results.
Mitochondrial translocation of p53 modulates neuronal fate by preventing differentiation-induced mitochondrial stress.

AIMS Apoptosis regulatory proteins, such as p53, play a pivotal role in neural differentiation, through mechanisms independent of cell death. In addition, p53 has been identified as an important regulator of mitochondrial survival response, maintaining mitochondrial DNA (mtDNA) integrity and oxidative protection. The aim of this study was to determine the role of mitochondrial p53 in organelle damage and neural differentiation. RESULTS Our results show that mitochondrial apoptotic events such as reactive oxygen species production, mitochondrial membrane permeabilization, and cytochrome c release are typical of early-stage mouse neural stem cell differentiation, which occurs 3-18 h after induction of differentiation, with no evidence of cell death. In addition, decreased mtDNA content, lipidated LC3 (LC3-II), colocalization of mitochondria and LC3-II puncta, and mitochondria-associated Parkin are consistent with activation of mitophagy. Importantly, at early stages of neural differentiation, p53 was actively translocated to mitochondria and attenuated mitochondrial oxidative stress, cytochrome c release, and mitophagy. Forced mitochondrial translocation of p53 increased neurogenic potential and neurite outgrowth. INNOVATION AND CONCLUSION In conclusion, our results reveal a novel role for mitochondrial p53, which modulates mitochondrial damage and apoptosis-related events in the context of neural differentiation, thus enhancing neuronal fate.
CONVEX POLYHEDRA WITHOUT SIMPLE CLOSED GEODESICS

In 1905, in his famous article “Sur les lignes géodésiques des surfaces convexes” [1] H. Poincaré posed a question on the existence of at least three geometrically different closed geodesics without self-intersections on any smooth convex two-dimensional surface (2-surface) M homeomorphic to the two-dimensional sphere (2-sphere) S2. Each such geodesic splits the surface M into two domains homeomorphic to 2-discs, and it is naturally to call it simple geodesic. In 1917, G.D. Birkhoff proved [2] the existence of at least one closed simple geodesic on M (in the late 20s he extended the result to the multidimensional case [3]). Nowadays this geodesic is called the (Birkhoff) “equator”. The presence of the Birkhoff equator serves as a basis for proving the existence of infinitely many (non-simple) closed geodesics on the considered surface. This very recent result has been established by V. Bangert [4] and J. Franks [5] in 1991-1992. In 1929 L.Luysternik and L.Shnirel’man gave a proof [6] of the existence of three closed simple geodesics, which led to a solution of the Poincaré problem. It follows from a result of Jacobi, who integrated geodesic flows on an ellipsoid (see [7], [8]), that on an ellipsoid whose semi-axes are distinct and close to 1 there are only three different closed simple geodesics. Therefore, the estimate “three” in the theorem of LyusternikShnirel’man is sharp. The complete proof of the Lyusternic-Shnirel’man theorem has been recently obtained in [9] and in [10] (see also the survey [11] on this subject, where a sketch of the proof is given). One can raise the Poincaré question also for convex polyhedra in R homeomorphic to the 2sphere S2. Geodesic flows on Euclidean polyhedra is also an old subject that goes back as far as 1906 (see [12] and [13]). It turns out that in this case, in contrast to what might be expected from what has been said above, there are convex polyhedra completely free of simple closed geodesics on their surfaces and, in a sense, such polyhedra constitute the majority in the class of all convex polyhedra (see theorems 1, 2 below). The existence of these polyhedra is due, of course, to the fact that a geodesic cannot, by definition, pass through a vertex of a polyhedron. The situation here is the same as that for a billiard trajectory in a polygon: when reaching the vertex, the billiard particle does not “know” which direction it should move afterwards. A similar situation holds when the particle moves freely on the polyhedron surface (i.e., along a geodesic): if the particle reaches a vertex then its path is broken off and hence the trace of the particle is not deemed a
Access distribution in automated microscopy system

The purpose of the paper is to define the requirements to information security system in telemedicine and its realization in automated microscopy system. The researchers designed adaptive graphical interfaces for different types of users and developed a complex of measures that ensures reliability of the system against external attacks and confidentiality of patients' personal information. Specialized graphical interfaces make image analysis to be easy and effective to use.
Intrastromal corneal ring segments in a patient with previous laser in situ keratomileusis.

PURPOSE Intrastromal corneal ring segments (ICRS; Intacs) were inserted in a patient with residual myopia of -3.375 D (spherical equivalent) 10 months after laser in situ keratomileusis (LASIK). METHODS A standard intrastromal corneal ring segment implantation technique was used with the addition of intraoperative ultrasonic pachymetry in 4 quadrants at the 7-mm zone to insure adequate stromal thickness for segment insertion. RESULTS Four months after ICRS surgery and 14 months after LASIK, the patient had uncorrected visual acuity of 20/20 and a cycloplegic refraction of plano -1.00 x 23 degrees. CONCLUSION Implantation of intrastromal corneal ring segments in an eye with previous LASIK resulted in additional corneal flattening with a decrease in residual myopia and improved uncorrected visual acuity.
CML66, a broadly immunogenic tumor antigen, elicits a humoral immune response associated with remission of chronic myelogenous leukemia

This report describes a tumor-associated antigen, termed CML66, initially cloned from a chronic myelogenous leukemia (CML) cDNA expression library. CML66 encodes a 583-aa protein with a molecular mass of 66 kDa and no significant homology to other known genes. CML66 gene is localized to human chromosome 8q23, but the function of this gene is unknown. CML66 is expressed in leukemias and a variety of solid tumor cell lines. When examined by Northern blot, expression in normal tissues was restricted to testis and heart, and no expression was found in hematopoietic tissues. When examined by quantitative reverse transcription–PCR, expression in CML cells was 1.5-fold higher than in normal peripheral blood mononuclear cells. The presence of CML66-specific antibody in patient serum was confirmed by Western blot and the development of high titer IgG antibody specific for CML66 correlated with immune induced remission of CML in a patient who received infusion of normal donor lymphocytes for treatment of relapse. CML66 antibody also was found in sera from 18–38% of patients with lung cancer, melanoma, and prostate cancer. These findings suggest that CML66 may be immunogenic in a wide variety of malignancies and may be a target for antigen-specific immunotherapy.
CREB and cAMP response element‐mediated gene expression in the ischemic brain

Cerebral ischemia triggers robust phosphorylation of cAMP response element‐binding protein (CREB) and CRE‐mediated gene expression in neurons. Glutamate receptor activation and subsequent calcium influx may activate CREB shortly after ischemia. CREB activation leads to expression of genes encoding neuroprotective molecules, such as the antiapoptotic protein Bcl‐2, and contributes to survival of neurons after ischemic insult. Recent studies have suggested that CREB may be involved in acquisition of ischemic tolerance, a phenomenon that occurs after sublethal ischemic stress. CREB activation is also involved in the survival of newborn neurons in the dentate gyrus of the hippocampus after ischemia. Therefore, CREB‐related therapeutics may be promising for brain protection and endogenous neurogenesis and could promote functional recovery in ischemic stroke patients. This minireview summarizes our current understanding for the role of CREB in regulating CRE‐mediated gene expression during cerebral ischemia.
Gene-Targeted Mice Lacking the Trex1 (DNase III) 3′→5′ DNA Exonuclease Develop Inflammatory Myocarditis

ABSTRACT TREX1, originally designated DNase III, was isolated as a major nuclear DNA-specific 3′→5′ exonuclease that is widely distributed in both proliferating and nonproliferating mammalian tissues. The cognate cDNA shows homology to the editing subunit of the Escherichia coli replicative DNA polymerase III holoenzyme and encodes an exonuclease which was able to serve a DNA-editing function in vitro, promoting rejoining of a 3′ mismatched residue in a reconstituted DNA base excision repair system. Here we report the generation of gene-targeted Trex1−/− mice. The null mice are viable and do not show the increase in spontaneous mutation frequency or cancer incidence that would be predicted if Trex1 served an obligatory role of editing mismatched 3′ termini generated during DNA repair or DNA replication in vivo. Unexpectedly, Trex1−/− mice exhibit a dramatically reduced survival and develop inflammatory myocarditis leading to progressive, often dilated, cardiomyopathy and circulatory failure.
Application of the adaptive wavelet transform for analysis of blood flow oscillations in the human skin

An original method for the analysis of oscillations of cutaneous blood flow has been developed, which makes use of laser Doppler flowmetry (LDF) data and is based on the continuous wavelet transform and adaptive wavelet theory. The potential of the method has been demonstrated in experiments with the response of microcirculatory bed to the local linearly-increasing heating of a skin spot. The use of adaptive wavelet transform for analysis of peripheral blood flow oscillations enables one to process short (5 min) LDF signals in a wide frequency range (0.009–2 Hz). The major advantage of the method proposed, as compared to traditional wavelet analysis, has been shown to be a significant reduction of ‘border effects’. This makes possible a correct low-frequency component analysis of much shorter LDF signals compared to those used in traditional wavelet processing.
A 60-µW, 98-dB SNDR and 100-dB Dynamic Range Continuous Time Delta Sigma Modulator for Biological Signal Processing in 0.18-µm CMOS

This paper presents the design of a high performance micro power modified 3 rd order Continuous Time Delta Sigma Modulator intended for digitizing biomedical signals. A distributed feed forward topology is used in order to achieve efficient operation and also the modulator makes use of a Noise Shaping Enhancement (NSE) technique for increasing the performance of the modulator. gm over ID method is opted for design of the low power analog cells. The modulator operates on the 50 kHz signal bandwidth with sampling frequency of 3.2 MHz and shows 102 dB Signal to Noise + Distortion Ratio (SNDR) in the presence of a wide variety of circuit non-ideal effect including noise in the system level and 98 dB SNDR in the circuit level. This corresponds to an Effective Number of Bits (ENOB) 16 Bits. The modulator dissipation is 60 µw so the modulator is suitable for use in low power low cost biomedical instrument.
Distribution of drb genes coding for Dr binding adhesins among uropathogenic and fecal Escherichia coli isolates and identification of new subtypes

The Dr family of related adherence structures, some fimbriated and others afimbriated, bind to decay-accelerating factor molecules on human cells. Dr is associated with recurring urinary tract infection (UTI), but the distribution of Dr subtypes among uropathogenic Escherichia coli causing UTI among otherwise healthy women has yet to be described. A total of 787 UTI and fecal E. coli isolates from college women were screened for the presence of Dr sequences (drb). Fifteen percent of UTI strains were drb positive, compared to 5% of fecal strains. The adhesin (E gene) subtype of each drb-positive strain was determined by type-specific PCR followed by restriction enzyme analysis. Among 78 drb-positive strains, we found 14 (18%) afaE1, 1 (1.3%) afaE2, 1 (1.3%) afaE3, 9 (12%) draE, 9 (12%) draE-afaE3 hybrid, 1 (1.3%) daaE, 32 (41%) afaE5, 4 (5.1%) F131 E gene-like, and 7 untypeable strains. All untypeable E genes were cloned and sequenced, revealing four additional new classes of E genes, including two similar to the previously identified nonfimbrial E series. While a great range of diversity exists among the E genes, restriction fragment length polymorphism analysis demonstrated that all of these drb operons share a highly conserved gene structure. The most common subtype, afaE5, occurred three times as often among UTI than fecal strains. Over half of the drb-positive strains and 80% of those positive for afaE5 have the same virulence signature (positive for aer, kpsMT, ompT, and fim), suggesting an association of this profile with UTI pathogenesis.
Rab 11 proteins in health and disease

Comprising over 60 members, Rab proteins constitute the largest branch of the Ras superfamily of lowmolecular-mass G-proteins. This protein family have been primarily implicated in various aspects of intracellular membrane trafficking processes. On the basis of distinct subfamily-specific sequence motifs, many Rabs have been grouped into subfamilies. The Rab11 GTPase subfamily comprises three members: Rab11a, Rab11b and Rab25/Rab11c, which, between them, have been demonstrated to bind more than 30 proteins. In the present paper, we review the function of the Rab11 subfamily. We describe their localization and primary functional roles within the cell and their implication, to date, in disease processes. We also summarize the protein machinery currently known to regulate or mediate their functions and the cargo molecules which they have been shown to transport. Rab proteins Rab proteins constitute the largest group of the Ras superfamily of small G-proteins with over 60 members identified in humans [1]. These 20–25 kDa proteins function as master regulators of intracellular membrane trafficking, serving pivotal roles in processes such as vesicle formation and budding, motility, tethering and fusion [1]. Rabs function as molecular switch proteins, cycling between GDP-bound (inactive/off) and GTP-bound (active/on) states in response to accessory proteins known as GEFs (guanine-nucleotideexchange factors) and GAPs (GTPase-activating proteins) [1]. In their active states, Rabs interact with downstream effector proteins which elicit their biological functions. When active, Rab proteins localize to the cytosolic face of membranous compartments where they are anchored by two geranylgeranyl groups covalently linked to two C-terminal cysteine residues. Each particular Rab protein displays its own signature localization pattern, and this localization is inherently linked to the physiological function of that Rab. In the present paper, we review the function of Rab11a, Rab11b and Rab25 (occasionally called Rab11c), a subfamily of Rabs that are known to function in a variety of fundamental intracellular trafficking processes and have been identified as important players in the cellular basis of an ever-increasing number of human disorders. Rab11: discovery and characterization Rab11 is a blanket term that is often used to describe three distinct Rab11 subfamily members (Rab11a, Rab11b and