Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of SOG1, a plant-specific transcriptional regulator, in the DNA damage response

Plants are inescapably exposed to environmental stress because of their sessile lifestyle. Such stress induces the production of reactive oxygen species (ROS), which are in turn a source of genotoxic stress. ROS are also generated intrinsically during photosynthesis in the chloroplasts. Furthermore, plants are affected by the UV component of sunlight, which damages their genomes. To protect their genomic integrity from DNA damage, plants activate a DNA damage response (DDR) system that regulates cell cycle arrest, DNA repair, and programmed cell death. Although plants have orthologs of several of the DDR factors that are found in animals, certain critical animal DDR factors, notably the tumor suppressor p53 and the DDR kinases CHK1 and CHK2, have not been found in plants. In this mini-review, we summarize the functions and regulatory mechanism of Arabidopsis thaliana SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a plant-specific transcription factor that plays a central role in the DDR. The characteristics of SOG1 are similar to those of animal p53, even though the proteins’ amino acid sequences are unrelated. We suggest that plants acquired the central transcriptional factor SOG1 as a functional homolog of p53 during the evolution of their DDR system.
Machine Perfusion Versus Cold Storage for the Preservation of Kidneys Donated After Cardiac Death: A Multicenter, Randomized, Controlled Trial

Objective:Hypothermic machine perfusion may improve outcome after transplantation of kidneys donated after cardiac death (DCD), but no sufficiently powered prospective studies have been reported. Because organ shortage has led to an increased use of DCD kidneys, we aimed to compare hypothermic machine perfusion with the current standard of static cold storage preservation. Methods:Eighty-two kidney pairs from consecutive, controlled DCD donors 16 years or older were included in this randomized controlled trial in Eurotransplant. One kidney was randomly assigned to machine perfusion and the contralateral kidney to static cold storage according to computer-generated lists created by the permuted block method. Kidneys were allocated according to standard rules, with concealment of the preservation method. Primary endpoint was delayed graft function (DGF), defined as dialysis requirement in the first week after transplantation. All 164 recipients were followed until 1 year after transplantation. Results:Machine perfusion reduced the incidence of DGF from 69.5% to 53.7% (adjusted odds ratio: 0.43; 95% confidence interval 0.20–0.89; P = 0.025). DGF was 4 days shorter in recipients of machine-perfused kidneys (P = 0.082). Machine-perfused kidneys had a higher creatinine clearance up to 1 month after transplantation (P = 0.027). One-year graft and patient survival was similar in both groups (93.9% vs 95.1%). Conclusions:Hypothermic machine perfusion was associated with a reduced risk of DGF and better early graft function up to 1 month after transplantation. Routine preservation of DCD kidneys by hypothermic machine perfusion is therefore advisable.
The Human Tumor Suppressor ARF Interacts with Spinophilin/Neurabin II, a Type 1 Protein-phosphatase-binding Protein*

The INK4a gene, one of the most often disrupted loci in human cancer, encodes two unrelated proteins, p16INK4a and p14ARF (ARF) both capable of inducing cell cycle arrest. Although it has been clearly demonstrated that ARF inhibits cell cycle via p53 stabilization, very little is known about the involvement of ARF in other cell cycle regulatory pathways, as well as on the mechanisms responsible for activating ARF following oncoproliferative stimuli. In search of factors that might associate with ARF to control its activity or its specificity, we performed a yeast two-hybrid screen. We report here that the human homologue of spinophilin/neurabin II, a regulatory subunit of protein phosphatase 1 catalytic subunit specifically interacts with ARF, both in yeast and in mammalian cells. We also show that ectopic expression of spinophilin/neurabin II inhibits the formation of G418-resistant colonies when transfected into human and mouse cell lines, regardless of p53 and ARF status. Moreover, spinophilin/ARF coexpression in Saos-2 cells, where ARF ectopic expression is ineffective, somehow results in a synergic effect. These data demonstrate a role for spinophilin in cell growth and suggest that ARF and spinophilin could act in partially overlapping pathways.
Absolute Oral Bioavailability and Metabolic Turnover of β-Sitosterol in Healthy Subjects

The metabolic turnover, absolute oral bioavailability, clearance, and volume of distribution for β-sitosterol were measured in healthy subjects. [14C]β-Sitosterol was used as an isotopic tracer to distinguish pulse doses from dietary sources and was administered by both oral and intravenous routes. The administered doses of [14C]β-sitosterol were in the region of 3 to 4 μg, sufficiently low as not to perturb the kinetics of β-sitosterol derived from the diet. Because the plasma concentrations of [14C]β-sitosterol arising from such low doses were anticipated to be very low, the ultrasensitive isotope ratio analytical method of accelerator mass spectrometry was used. The limit of quantification for [14C]β-sitosterol was approximately 0.1 pg/ml, the oral absolute bioavailability was just 0.41%, clearance was 85 ml/h, volume of distribution was 46 L, and the turnover was 5.8 mg/day. Given the steady-state concentrations of β-sitosterol (2.83 μg/ml), then the dietary load was calculated to be approximately 1400 mg/day.
Epstein‐Barr virus BZLF1 trans‐activator specifically binds to a consensus AP‐1 site and is related to c‐fos.

Two regions of the Epstein‐Barr virus BZLF1 trans‐activator protein have sequence similarity to the c‐fos protein. Part of the similarity corresponds to the region of c‐fos which is similar to the DNA binding domain of c‐jun and GCN‐4. The structure of the exon which contains this region in c‐fos and BZLF1 is also highly conserved between the two genes. Complete BZLF1 protein and a C terminal fragment were prepared either as purified fusion proteins or by in vitro translation from a BZLF1 cDNA. Gel retardation and DNase footprinting assays using these proteins show that BZLF1 is a sequence specific DNA binding protein capable of binding to a target sequence which contains a consensus AP‐1 site.
Micropuncture and cannulation studies of fluid composition and transport in the ductuli efferentes testis of the rat: comparisons with the homologous metanephric proximal tubule

Luminal fluids were collected in vivo by micropuncture and cannulation from the rete testis, efferent ducts and ductus epididymidis of the rat to determine the composition of efferent duct fluids and the rates of reabsorption of water and solutes by the efferent ducts. The concentration of spermatozoa increased by a factor of about 25 from 2.42 x 10(4) microliters‐1 in the fluid from the rete testis to 6.00 x 10(5) microliters‐1 in fluid at the end of the efferent ducts, indicating that 96.2% of the fluid leaving the testis is reabsorbed from the lumen of the efferent ducts. Most of this reabsorption (70.9% or 33.4 microliters h‐1) occurs in the region between the rete testis and the middle of the coni vasculosi, with only 25.1% (11.8 microliters h‐1) occurring between the coni and the beginning of the ductus epididymidis. However, reabsorption across the epithelium occurs at about the same rate in both regions, with the proximal region reabsorbing 17.2 microliters cm‐2 h‐1 (70.9% of fluid entering the region) and the distal region reabsorbing 12.2 microliters cm‐2 h‐1 (86.1% of fluid entering the region). Consequently, the fluid reabsorption rate for the whole efferent duct system (15.6 microliters cm‐2 h‐1) is similar to the values for individual regions. The principal solutes in luminal fluids from the efferent ducts are Na+ (137‐144 mM) and Cl‐ (113‐130 mM). The estimated sum contribution of Na+, Cl‐ and K+ to the osmotic pressure of luminal fluids was approximately 80% at each site sampled in the efferent ducts. The osmotic pressure of luminal fluid samples (301‐307 mosmol kg‐1) did not vary significantly along the ducts or differ significantly from that of blood plasma. The results demonstrate that there is a net reabsorption in the efferent ducts of nearly all the testicular output of water and inorganic electrolytes, and most of the protein, and that, in comparison, the ductus epididymidis is a negligible site of net fluid reabsorption. The results indicate that the ductus epididymidis, rather than the efferent ducts, is the site of accumulation of high concentrations of specific organic compounds like inositol. The efferent ducts are similar to the homologous proximal tubules of the metanephric kidney in that the luminal electrolyte composition (principal solutes Na+ and Cl‐) and osmotic pressure remain relatively stable and that fluid reabsorption is close to isotonic and occurs at the same rate as the reabsorption of Na+.
Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis

The ability of Mycobacterium tuberculosis to adapt to different environments in the infected host is essential for its pathogenicity. Consequently, this organism must be able to modulate gene expression to respond to the changing conditions it encounters during infection. In this paper we begin a comprehensive study of M. tuberculosis gene regulation, characterizing the transcript levels of 10 of its 13 putative sigma factor genes. We developed a real‐time RT‐PCR assay using a family of novel fluorescent probes called molecular beacons to quantitatively measure the different mRNAs. Three sigma factor genes were identified that have increased mRNA levels after heat shock, two of which also responded to detergent stress. In addition, we also identified a sigma factor gene whose mRNA increased after mild cold shock and a second that responded to conditions of low aeration.
Frequency, risk factors, anatomy, and course of unilateral neglect in an acute stroke cohort

Objective: To delineate the frequency, course, risk factors, and neuroanatomy of hemispatial neglect in a large stroke cohort. Methods: One thousand two hundred eighty-one patients with acute stroke were enrolled in a multicenter trial of an anticoagulant. Presence and severity of neglect were assessed with the NIH Stroke Scale (NIHSS) neglect item, assessing tactile extinction and visuospatial neglect at entry, daily for 1 week, and at 3 months. Head CT scans were obtained on day 7, and infarct location and size were characterized. Results: Neglect was common at presentation, occurring in 43% of right brain-lesioned (RBL) patients and 20% of left brain-lesioned (LBL) patients (p < 0.001). At 3 months, neglect was present in 17% of RBL patients and in 5% of LBL patients (p < 0.001). In RBL patients, neglect was most frequently associated with lesions involving the (in descending order) temporal, parietal, frontal, occipital lobes, basal ganglia, and thalamus. Neglect was more common and persistent with cortical than with subcortical lesions. Increasing age was associated with increased risk of neglect in RBL patients, whereas gender and handedness did not significantly affect neglect frequency. Conclusions: This series confirms that hemispatial neglect may occur with damage to several supratentorial structures but is most common and persistent with lesions of the right temporoparietal cortex. Increasing age is associated with neglect, particularly after right brain lesions. Gender and handedness do not exert a marked effect on the likelihood of the occurrence of neglect.
Biomedical signal processing with time-varying CML model

Brain electrical signals, one of the typical biomedical signals, is accepted to be produced by the nonlinear dynamic system. In brain electrical signal, both EEG and ERP signal is consider as chaotic signal. In this paper, a new time variation based coupled map lattice(CML) model is put forward to research the nonlinear character of the ERP signal under specified tasks. To further investigate the ERP model and discover new information, the time variation largest Lyapunov exponent (LLE) is developed. Both simulated EEG and acquired ERP experiments were used to test. And the results show that the brain chaos changes corresponding to the changes of attention task. There is an optimum scopes size of cues in the visual attention information processing.
Soave transanal one-stage endorectal pull-through in the treatment of Hirschsprung′s disease of the child above two-year-old: A report of 20 cases

Background: The definitive treatment of Hirschsprung′s disease is the removal of the aganglionic bowel by a pull-through surgery. In most cases, this surgery is performed in infancy or in the neonatal period as presentation in older children and adulthood is uncommon. Materials and Methods: It is a retrospective study of 20 patients above two-year-old who underwent a transanal Soave one-stage endorectal pull-through procedure for Hirschsprung′s disease between January 2002 and December 2010. Results: Twenty patients were recruited in this study. Fourteen were males and six were females. Patient ages ranged from 2 to 14 years (median age: five years and three months). All patients presented with persistent constipation and abdominal distension. Two of them had an intestinal obstruction that required colostomy. Ten patients (50%) had a recto-sigmoid Hirschsprung′s disease. All patients were operated on using a Soave one-stage endorectal pull-through procedure. The laparoscopy was necessary during the pull-through in three cases. The average duration of the intervention was 240 minutes. That represents almost the double of the duration of the same procedure in newborns and infants in our department (130 minutes). Early postoperative complications included one case of anastomosis leakage and one case of intussusception. Late postoperative complications were perineum irritation in five cases (25%), anal stenosis in four cases (20%) and enterocolitis in one case (5%). None of our patients developed fecal incontinence. Soiling was reported in four cases (20%). There was no death. Conclusion: Soave transanal one-stage endorectal pull-through is safely feasible in children of more than two years of age. Laparoscopy may be necessary whenever there are difficulties in the pull-through.
Repetitive transcranial magnetic stimulation reduces cortisol concentrations in bulimic disorders

Background In people with bulimic eating disorders, exposure to high-calorie foods can result in increases in food craving, raised subjective stress and salivary cortisol concentrations. This cue-induced food craving can be reduced by repetitive transcranial magnetic stimulation (rTMS). We investigated whether rTMS has a similar effect on salivary cortisol concentrations, a measure of hypothalamic–pituitary–adrenal axis (HPAA) activity. Method We enrolled twenty-two female participants who took part in a double-blind randomized sham-controlled trial on the effects of rTMS on food craving. Per group, eleven participants were randomized to the real or sham rTMS condition. The intervention consisted of one session of high-frequency rTMS delivered to the left dorsolateral prefrontal cortex (DLPFC). Salivary cortisol concentrations were assessed at four time points throughout the 90-min trial. To investigate differences in post-rTMS concentrations between the real and sham rTMS groups, a random-effects model including the pre-rTMS cortisol concentrations as covariates was used. Results Salivary cortisol concentrations following real rTMS were significantly lower compared with those following sham rTMS. In this sample, there was also a trend for real rTMS to reduce food craving more than sham rTMS. Conclusions These results suggest that rTMS applied to the left DLPFC alters HPAA activity in people with a bulimic disorder.
Landscape synergy in evolutionary multitasking

Over the years, the algorithms of evolutionary computation have emerged as popular tools for tackling complex real-world optimization problems. A common feature among these algorithms is that they focus on efficiently solving a single problem at a time. Despite the availability of a population of individuals navigating the search space, and the implicit parallelism of their collective behavior, seldom has an effort been made to multitask. Considering the power of implicit parallelism, we are drawn to the idea that population-based search strategies provide an idyllic setting for leveraging the underlying synergies between objective function landscapes of seemingly distinct optimization tasks, particularly when they are solved together with a single population of evolving individuals. As has been recently demonstrated, allowing the principles of evolution to autonomously exploit the available synergies can often lead to accelerated convergence for otherwise complex optimization tasks. With the aim of providing deeper insight into the processes of evolutionary multitasking, we present in this paper a conceptualization of what, in our opinion, is one possible interpretation of the complementarity between optimization tasks. In particular, we propose a synergy metric that captures the correlation between objective function landscapes of distinct tasks placed in synthetic multitasking environments. In the long run, it is contended that the metric will serve as an important guide toward better understanding of evolutionary multitasking, thereby facilitating the design of improved multitasking engines.
Rearrangement of integrated viral DNA sequences in mouse cells transformed by simian virus 40

The organization of viral DNA sequences in several cell lines derived from a primary colony of simian virus 40 (SV40)-transformed mouse cells was analyzed to examine the origin of the various distinctive patterns of SV40 sequence arrangement present in transformed cells. This analysis revealed a complex arrangement of viral sequences in the uncloned transformed cells but simplified arrangements in cloned derivatives of the primary transformant. The cell lines studied had certain SV40 sequence arrangements in common, but the cloned lines had lost some parental arrangements and acquired new arrangements. These results indicate that the arrangement of viral sequences in some SV40-transformed cells is not fixed but that alterations occur after integration, creating a heterogeneous population of transformants. In the process, expression of viral genes may be altered. Possible causes for and implications of this genetic instability are discussed.
Microwave Ablation: Comparison of Simultaneous and Sequential Activation of Multiple Antennas in Liver Model Systems.

PURPOSE To compare microwave ablation zones created by using sequential or simultaneous power delivery in ex vivo and in vivo liver tissue. MATERIALS AND METHODS All procedures were approved by the institutional animal care and use committee. Microwave ablations were performed in both ex vivo and in vivo liver models with a 2.45-GHz system capable of powering up to three antennas simultaneously. Two- and three-antenna arrays were evaluated in each model. Sequential and simultaneous ablations were created by delivering power (50 W ex vivo, 65 W in vivo) for 5 minutes per antenna (10 and 15 minutes total ablation time for sequential ablations, 5 minutes for simultaneous ablations). Thirty-two ablations were performed in ex vivo bovine livers (eight per group) and 28 in the livers of eight swine in vivo (seven per group). Ablation zone size and circularity metrics were determined from ablations excised postmortem. Mixed effects modeling was used to evaluate the influence of power delivery, number of antennas, and tissue type. RESULTS On average, ablations created by using the simultaneous power delivery technique were larger than those with the sequential technique (P < .05). Simultaneous ablations were also more circular than sequential ablations (P = .0001). Larger and more circular ablations were achieved with three antennas compared with two antennas (P < .05). Ablations were generally smaller in vivo compared with ex vivo. CONCLUSION The use of multiple antennas and simultaneous power delivery creates larger, more confluent ablations with greater temperatures than those created with sequential power delivery.
Computed Basis Functions for 2-D Edge Elements

The nonconforming voxel finite-element method (NVFEM) models material boundaries in a staircase fashion. Recently, a technique called the computed basis function (CBF) method was introduced to reduce the errors arising from this, but it was applied only to scalar fields. Here, the CBF method is developed for vector fields that are represented with 2-D edge elements. The method is tested by solving the vector wave equation for problems involving perfectly conducting or dielectric obstacles. Results show that NVFEM enhanced with CBF can achieve the same accuracy as NVFEM with between 6 and 10 times fewer unknowns, with no reduction in the sparsity of the global FE matrix.
Sharp Ca2+ Nanodomains beneath the Ribbon Promote Highly Synchronous Multivesicular Release at Hair Cell Synapses

Hair cell ribbon synapses exhibit several distinguishing features. Structurally, a dense body, or ribbon, is anchored to the presynaptic membrane and tethers synaptic vesicles; functionally, neurotransmitter release is dominated by large EPSC events produced by seemingly synchronous multivesicular release. However, the specific role of the synaptic ribbon in promoting this form of release remains elusive. Using complete ultrastructural reconstructions and capacitance measurements of bullfrog amphibian papilla hair cells dialyzed with high concentrations of a slow Ca2+ buffer (10 mm EGTA), we found that the number of synaptic vesicles at the base of the ribbon correlated closely to those vesicles that released most rapidly and efficiently, while the rest of the ribbon-tethered vesicles correlated to a second, slower pool of vesicles. Combined with the persistence of multivesicular release in extreme Ca2+ buffering conditions (10 mm BAPTA), our data argue against the Ca2+-dependent compound fusion of ribbon-tethered vesicles at hair cell synapses. Moreover, during hair cell depolarization, our results suggest that elevated Ca2+ levels enhance vesicle pool replenishment rates. Finally, using Ca2+ diffusion simulations, we propose that the ribbon and its vesicles define a small cytoplasmic volume where Ca2+ buffer is saturated, despite 10 mm BAPTA conditions. This local buffer saturation permits fast and large Ca2+ rises near release sites beneath the synaptic ribbon that can trigger multiquantal EPSCs. We conclude that, by restricting the available presynaptic volume, the ribbon may be creating conditions for the synchronous release of a small cohort of docked vesicles.