Miracle-dz/UniFAR-FTUs huggingface dataset:
PARP1-driven poly-ADP-ribosylation regulates BRCA1 function in homologous recombination-mediated DNA repair.

UNLABELLED BRCA1 promotes homologous recombination-mediated DNA repair (HRR). However, HRR must be tightly regulated to prevent illegitimate recombination. We previously found that BRCA1 HRR function is regulated by the RAP80 complex, but the mechanism was unclear. We have now observed that PARP1 interacts with and poly-ADP-ribosylates (aka PARsylates) BRCA1. PARsylation is directed at the BRCA1 DNA binding domain and downmodulates its function. Moreover, RAP80 contains a poly-ADP-ribose-interacting domain that binds PARsylated BRCA1 and helps to maintain the stability of PARP1-BRCA1-RAP80 complexes. BRCA1 PARsylation is a key step in BRCA1 HRR control. When BRCA1 PARsylation is defective, it gives rise to excessive HRR and manifestations of genome instability. BRCA1 PARsylation and/or RAP80 expression is defective in a subset of sporadic breast cancer cell lines and patient-derived tumor xenograft models. These observations are consistent with the possibility that such defects, when chronic, contribute to tumor development in BRCA1+/+ individuals. SIGNIFICANCE We propose a model that describes how BRCA1 functions to both support and restrict HRR. BRCA1 PARsylation is a key event in this process, failure of which triggers hyper-recombination and chromosome instability. Thus, hyperfunctioning BRCA1 can elicit genomic abnormalities similar to those observed in the absence of certain BRCA1 functions.
Metastable states in disordered Ising magnets in mean-field approximation

The mechanism of appearance of exponentially large number of metastable states in magnetic phases of disordered Ising magnets with short-range random exchange is suggested. It is based on the assumption that transitions into inhomogeneous magnetic phases results from the condensation of macroscopically large number of sparse delocalized modes near the localization threshold. The properties of metastable states in random magnets with zero ground state magnetization (dilute antiferromagnet, binary spin glass, dilute ferromagnet with dipole interaction) has been obtained in framework of this mechanism using variant of mean-field approximation. The relations between the characteristics of slow nonequilibrium processes in magnetic phases (such as hysteresis loop form, thermo-remainent and isothermal remainent magnetizations, field-cooled and zero-field-cooled thermodynamic quantities) and thermodynamic parameters of metastable states are established.
Influence of clinical and immunological parameters on the health-related quality of life of patients with primary Sjögren's syndrome.

OBJECTIVE To evaluate health-related quality of life (HR-QoL) in patients with primary SS patients using the SF-36 questionnaire and to analyse the association between the main clinical features and the SF-36 scales. METHODS We studied 110 patients (105 women and 5 men, mean age of 56 years) with primary SS seen consecutively in the outpatient clinic of our Department. We used the population-based reference values for the Spanish version of the SF-36 health survey as control values for a healthy population. RESULTS Comparison between patients with primary SS and the control population showed lower scores in all SF-36 scales (p < 0.001). Analysis of the SF-36 scales by gender showed a significant correlation between age and the values for physical functioning (p = 0.013) and bodily pain (p = 0.016) scores. No significant differences in SF-36 scores were found when comparing patients according to the presence or absence of sicca features. Women with vaginal dryness had lower scores for social functioning (61.9 vs. 74.4) and general health (37.2 vs. 44.7) than those without, although the differences were not statistically significant (p > 0.05). Patients with extraglandular involvement had lower scores for the vitality scale (40.8 vs. 54.5 p = 0.007), social functioning (67.0 vs. 79.8, p = 0.010), bodily pain (49.5 vs. 62.5, p = 0.018) and general health (38.6 vs. 49.4 p = 0.001) than those without. CONCLUSION Patients with primary SS had clearly lower HR-QoL scores than the healthy population; with significantly lower scores in all SF-36 scales and in both summary measures. We identified several epidemiological and clinical SS features related to these lower SF-36 scores. Age at protocol correlated with physical functioning and bodily pain. Vaginal dryness was the sicca feature that most affected the HR-QoL of female SS patients, and a poor HR-QoL was also observed in those patients with a systemic expression of the disease, with pulmonary involvement being the extraglandular manifestation that most contributed to a poor HR-QoL. Our results highlight the importance of earlier diagnostic and therapeutic management of patients with primary SS, which, together with a close follow-up, may contribute to a significant improvement in their HR-QoL.
Spectrally Resolved Approach for Modeling Short Pulse Amplification in Er$^{3+}$-Doped Fibers

We study pulse propagation in Er3+-doped fiber amplifiers (EDFA) within the framework of a spectrally resolved pulse rate-propagation equations model. Our model accounts for the effects of gain dispersion, gain saturation, waveguide and chromatic dispersion, and amplified spontaneous emission. This model allows us to approximate the effects of nonlinear resonant dispersion on short pulse amplification in doped fibers, without reverting to the generalized nonlinear Schroedinger equation. Numerical results of the time-dependent power spectrum of the amplified pulse demonstrate subpicosecond pulse propagation in EDFAs
Threshold phenomena versus cell heredity in the manifestation of sex-linked genes in mammals.

The mode of action of sex-linked genes in mammals has been the subject of much discussion in recent years. This has centred round the concept that in the mammalian female, either the maternal or the paternal X-chromosome is randomly and irreversibly inactivated during development, with the result that in the female, as in the male, one X-chromosome only is active in a given cell (Lyon, 1966, and earlier papers). The Lyon Hypothesis (l.h.) is based, in part, on the mottled or striped phenotypes of heterozygotes for certain sex-linked genes affecting the coat of the mouse and other mammals: these phenotypes are regarded as a mixture of clones descended from cells in which either one or the other X-chromosome has been inactivated. As Baker (1967) rightly insists, the interpretation of a pattern as clonal must be based on known cell lineages, as without such a basis one simply postulates what should be put to the test.
Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response

Haberlea rhodopensis is a paleolithic tertiary relict species, best known as a resurrection plant with remarkable tolerance to desiccation. When exposed to severe drought stress, H. rhodopensis shows an ability to maintain the structural integrity of its photosynthetic apparatus, which re-activates easily upon rehydration. We present here the results from the assembly and annotation of the chloroplast (cp) genome of H. rhodopensis, which was further subjected to comparative analysis with the cp genomes of closely related species. H. rhodopensis showed a cp genome size of 153,099 bp, harboring a pair of inverted repeats (IR) of 25,415 bp separated by small and large copy regions (SSC and LSC) of 17,826 and 84,443 bp. The genome structure, gene order, GC content and codon usage are similar to those of the typical angiosperm cp genomes. The genome hosts 137 genes representing 70.66% of the plastome, which includes 86 protein-coding genes, 36 tRNAs, and 4 rRNAs. A comparative plastome analysis with other closely related Lamiales members revealed conserved gene order in the IR and LSC/SSC regions. A phylogenetic analysis based on protein-coding genes from 33 species defines this species as belonging to the Gesneriaceae family. From an evolutionary point of view, a site-specific selection analysis detected positively selected sites in 17 genes, most of which are involved in photosynthesis (e.g., rbcL, ndhF, accD, atpE, etc.). The observed codon substitutions may be interpreted as being a consequence of molecular adaptation to drought stress, which ensures an evolutionary advantage to H. rhodopensis.
Automatic Zoom and Pseudo Haptics to Support Semiautomatic Segmentation Tasks

This paper presents a new technique for navigating large amounts of biological image data during segmentation. Digitized microtome tissue slices of barley grains constitute the image data. Automatic zoom is dependent on mouse speed, thus enabling users to navigate an image more efficiently and with a tighter focus during segmentation. The user remains oriented and smoothly moves through the data. Furthermore, pseudo haptic feedback based on image cost map data compensates for user inaccuracies generated, for example, by shaky hands. A prototype was implemented and tested. An informal usability study revealed that users are inclined to prefer automatic zooming and pseudo haptics for semiautomatic segmentation tasks.
5-HT1A-receptor subtype mediates the effect of fluvoxamine, a selective serotonin reuptake inhibitor, on marble-burying behavior in mice.

The effect of fluvoxamine, a selective serotonin (5-HT) reuptake inhibitor, was studied in a model of anxiety and/or obsessive compulsive disorder (OCD) in mice. In the anxiety/OCD model, marble-burying behavior, marble-burying was significantly suppressed by fluvoxamine at 30 and 60 mg/kg, p.o. and the monoamine reuptake inhibitor clomipramine, at 60 mg/kg, p.o. No suppressive effect, however, was observed by the selective norepinephrine reuptake inhibitor desipramine at doses from 15 to 60 mg/kg, p.o. Suppressive effects were obtained by the serotonergic anxiolytic buspirone at 30 and 60 mg/kg, p.o. and the benzodiazepine anxiolytic diazepam at 10 mg/kg, p.o. The effect of fluvoxamine on marble-burying was slightly attenuated after repeated administration. On the other hand, both the effects of buspirone and diazepam completely disappeared after repeated administration. Effect of fluvoxamine on the marble-burying was unaffected by the 5-HT2 antagonist ritanserin. However, the 5-HT1A antagonist NAN-190 (1-(2-methoxyphenyl)-4-[4-(2-phthalimido)butyl] piperazine) inhibited the suppressive effect of fluvoxamine on the marble-burying. From these results, the 5-HT1A-receptor subtype may be involved in the suppressive effect of fluvoxamine on the marble-burying, but the 5-HT2-receptor subtype is not involved in this effect.
Clinical Manifestations and Management of Inherited Thrombophilia: Retrospective Analysis and Follow-up after Diagnosis of 238 Patients with Congenital Deficiency of Antithrombin III, Protein C, Protein S

Summary The clinical history of 238 patients with inherited thrombophilia (AT III = 94, PC = 103, PS = 41) was analyzed retrospectively at diagnosis and in the follow-up period after diagnosis. At diagnosis 129 patients (54%) had suffered from thrombosis, with a recurrence rate of 48%. The most frequent onset manifestation was deep vein thrombosis of lower limbs (58%). Thrombotic history started before 40 in 80% of the cases. Forty-nine percent of the venous thromboses were preceded by a triggering event, in most cases pregnancy (17%) and surgery (12%). After diagnosis, follow-up lasted a total of 1,113 pt-years. A policy of short-term prophylaxis during risk situations for all patients and long-term prophylaxis in symptomatic patients failed to prevent venous thrombotic episodes (diagnosed by objective methods) in 4 previously asymptomatic subjects and recurrence in 7 previously symptomatic subjects. After knowledge of the patients’ diagnosis the incidence of venous thrombosis/100 pt-years was reduced as compared before diagnosis as total episodes (onset + recurrencies) (1.0 vs 1.9), onset episodes (0.7 vs 1.3) and recurrent episodes (1.3 vs 4.8), even though the differences were not statistically significant. However most of the venous thromboses occurred at a more advanced age (67% after 40 years) and without any apparent cause (83%), at significant variance with the period preceding the diagnosis; in particular the incidence of venous thrombotic onset in patients younger than 40 passed from 1.3/100 pt-years to 0.2/100 pt-years. In 6 recurrences after diagnosis a poor compliance for antithrombotic treatment was recognized. We conclude that a policy based on knowledge of diagnosis and on the implementation of antithrombotic treatment during risk situations appears to modify the clinical outcome of deficiencies of natural anticoagulants even in the absence of long-term antithrombotic prophylaxis; in particular morbidity of young patients is significantly reduced.
Adolescents' perceptions of social status: development and evaluation of a new indicator.

OBJECTIVE Eliminating health disparities, including those that are a result of socioeconomic status (SES), is one of the overarching goals of Healthy People 2010. This article reports on the development of a new, adolescent-specific measure of subjective social status (SSS) and on initial exploratory analyses of the relationship of SSS to adolescents' physical and psychological health. METHODS A cross-sectional study of 10 843 adolescents and a subsample of 166 paired adolescent/mother dyads who participated in the Growing Up Today Study was conducted. The newly developed MacArthur Scale of Subjective Social Status (10-point scale) was used to measure SSS. Paternal education was the measure of SES. Indicators of psychological and physical health included depressive symptoms and obesity, respectively. Linear regression analyses determined the association of SSS to depressive symptoms, and logistic regression determined the association of SSS to overweight and obesity, controlling for sociodemographic factors and SES. RESULTS Mean society ladder ranking, a subjective measure of SES, was 7.2 +/- 1.3. Mean community ladder ranking, a measure of perceived placement in the school community, was 7.6 +/- 1.7. Reliability of the instrument was excellent: the intraclass correlation coefficient was 0.73 for the society ladder and 0.79 for the community ladder. Adolescents had higher society ladder rankings than their mothers (micro(teen) = 7.2 +/- 1.3 vs micro(mom) = 6.8 +/- 1.2; P =. 002). Older adolescents' perceptions of familial placement in society were more closely correlated with maternal subjective perceptions of placement than those of younger adolescents (Spearman's rho(teens <15 years) = 0.31 vs Spearman's rho(teens 15 years) = 0.45; P <. 001 for both). SSS explained 9.9% of the variance in depressive symptoms and was independently associated with obesity (odds ratio(society) = 0.89, 95% confidence interval = 0.83, 0.95; odds ratio(community) = 0.91, 95% confidence interval = 0.87, 0.97). For both depressive symptoms and obesity, community ladder rankings were more strongly associated with health than were society ladder rankings in models that controlled for both domains of SSS. CONCLUSIONS This new instrument can reliably measure SSS among adolescents. Social stratification as reflected by SSS is associated with adolescents' health. The findings suggest that as adolescents mature, SSS may undergo a developmental shift. Determining how these changes in SSS relate to health and how SSS functions prospectively with regard to health outcomes requires additional research.
Optical properties and carrier dynamics of InP quantum dots embedded in GaP

The optical properties and associated carrier dynamics of self-organized InP quantum dots embedded in a GaP matrix are presented and discussed, together with their growth and structural properties. InP deposited on GaP (001) using gas-source molecular-beam epitaxy forms Stranski-Krastanow quantum dots for an InP coverage greater than 1.8 monolayers. The size of dots is dependent on the growth conditions; supercritical InP deposition under a sufficiently high phoshine flux results in relatively small (≈20 nm) and dense (≈ 5 × 109 dots/cm2) dots with intense optical emission. The photoluminescence from the quantum dots is observed up to room temperature at about 2 eV; photoluminescence from the strained two-dimensional InP wetting layer peaks at about 2.2 eV. Modeling based on the “model-solid theory” as well as time-resolved photoluminescence indicate that the band alignment for the InP wetting layer is indirect and probably type II; this emission results from spatially indirect recombination of electrons in the GaP X valley with holes in the InP and their phonon replicas. The band alignment of InP quantum dots, however, is type I. Whereas low-temperature time-resolved photoluminescence measurements indicate a rather long carrier lifetime of about 25 ns for the wetting layer, the carrier lifetime in the quantum dots is about 2 ns, typical for type-I quantum dots. Pressure-dependent photoluminescence measurements provide further evidence for a type-I band alignment for InP/GaP QDs at normal pressure, but indicate that they become type II under hydrostatic pressures of about 1.2 GPa and are consistent with an energy difference between the lowest InP and GaP states of about 31 meV. Exploiting the visible direct-bandgap transition in the GaP system could lead to an increased efficiency of light emission in GaP-based light emitters.
Chronic intermittent hypoxia induces hypoxia‐evoked catecholamine efflux in adult rat adrenal medulla via oxidative stress

Chronic intermittent hypoxia (CIH) augments physiological responses to low partial pressures of O2 in the arterial blood. Adrenal medullae from adult rats, however, are insensitive to direct effects of acute hypoxia. In the present study, we examined whether CIH induces hypoxic sensitivity in the adult rat adrenal medulla and, if so, by what mechanism(s). Experiments were performed on adult male rats exposed to CIH (15 s of 5% O2 followed by 5 min of 21% O2; 9 episodes h−1; 8 h d−1; for 3 or 10 days) or to comparable, cumulative durations of continuous hypoxia (CH; 4 h of 7% O2 followed by 20 h of 21% O2 for 1 or 10 days). Noradrenaline (NA) and adrenaline (ADR) effluxes were monitored from ex vivo adrenal medullae. In adrenal medullae of rats exposed to CIH, acute hypoxia evoked robust NA and ADR effluxes, whereas these responses were absent in control rats or in those exposed to CH for 1 or 10 days. Hypercapnia (10% CO2; either acidic, pH 6.8, or isohydric, pH 7.4) was ineffective in eliciting catecholamine (CA) efflux from control, CIH or CH rats. Nicotine (100 μm) evoked NA and ADR effluxes in control rats, and this response was abolished in CIH but not in CH rats. Systemic administration of 2‐deoxyglucose depleted ADR content in control rats, and CIH attenuated this response, indicating downregulation of neurally regulated CA secretion. Cytosolic and mitochondrial aconitase enzyme activities decreased in CIH adrenal medullae, suggesting increased generation of superoxide anions. Systemic administration of antioxidants reversed the effect of CIH on the adrenal medulla. Rats exposed to CIH exhibited increased blood pressures and elevated plasma CA, and antioxidants abolished these responses. These observations demonstrate that CIH induces hypoxic sensing in the adult rat adrenal medulla via mechanisms involving increased generation of superoxide anions and suggest that hypoxia‐evoked CA efflux from the adrenal medulla contributes, in part, to elevated blood pressure and plasma CA.
Investigation of sparse matrix multiplication task for the PDCS “Buran”

In order to improve the efficiency of the sparse matrices multiplication task on a traditional cluster supercomputer, it is necessary to take into account different levels of parallelism when programming. To work around these problems the dataflow computing model with the dynamically formed context and the architecture of the parallel dataflow computing system can be used. The article describes the implementation of a parallel algorithm of the sparse matrices multiplication task on the parallel dataflow computing system. The experiments performed on the emulator of the system demonstrate the application perspectiveness of the dataflow computing model for this class of tasks.
Tensile properties of polypropylene/kaolin composites

Tensile properties of isotactic polypropylene filled with particulate kaolin fillers were evaluated in the composition range 0–60 wt % kaolin. Tensile modulus increased with filler concentration while breaking elongation and tensile strength decreased. The modulus increase was attributed to the restriction on the molecular mobility of the polymer imposed by kaolin particles. The decrease in elongation was also an effect of this restriction coupled with interference to stress transfer by the filler particles. Generation of discontinuity in the composite structure through formation of stress concentration points accounted for the tensile strength decrease. Morphology studies by SEM also indicated the introduction of stress concentration points by the presence of bare and nonadherent kaolin particles and their agglomerates with sharp edges in these composites.
Usefulness of Surgical Media Center as a Cataract Surgery Educational Tool

Purpose. This study retrospectively analyzed cataract surgeries to examine the usefulness of Surgical Media Center (SMC) (Abbott Medical Optics Inc.), a new cataract surgery recording device, for training of cataract surgery. Methods. We studied five hundred cataract surgeries conducted with a phacoemulsification system connected to the SMC. After surgery, the surgical procedures were reviewed, with changes in aspiration rate, vacuum level, and phaco power displayed as graphs superimposed on the surgical video. We examined whether use of SMC is able to demonstrate the differences in technique between experienced and trainee operators, to identify inappropriate phacoemulsification techniques from analyzing the graphs, and to elucidate the cause of intraoperative complications. Results. Significant differences in the time taken to reach maximum vacuum and the speed of increase in vacuum during irrigation and aspiration were observed between experienced and trainee operators. Analysis of the graphs displayed by SMC detected inappropriate phacoemulsification techniques mostly in cases operated by trainee operators. Conclusions. Using SMC, it was possible to capture details of cataract surgery objectively. This recording device allows surgeons to review cataract surgery techniques and identify the cause of intraoperative complication and is a useful education tool for cataract surgery.
Isolation of Chlamydia psittaci from naturally infected African clawed frogs (Xenopus laevis)

An inclusion-forming agent was isolated from the livers of commercially raised African clawed frogs (Xenopus laevis) involved in an epizootic of high morbidity and mortality. Original isolation was made in McCoy cells. This agent was identified as Chlamydia psittaci based on the formation of typical intracytoplasmic inclusions which developed within 48 h, were not stained by iodine, and were resistant to sulfadiazine. The isolate from one particular frog (designated as strain 178) was further studied and found to be lethal for 7-day-old embryonated chicken eggs after intra-yolk sac inoculation. This strain was demonstrated not to be pathogenic for mice when inoculated intraperitoneally. The cell culture isolate of C. psittaci was transmitted to uninfected X. laevis, causing disease and death.