Miracle-dz/UniFAR-FTUs huggingface dataset:
Valvular calcification and its relationship to atherosclerosis in chronic kidney disease.

BACKGROUND AND AIM OF THE STUDY Cardiovascular calcification is a common complication in patients with chronic kidney disease (CKD). The study aim was to identify the characteristics and risk factors of valvular calcification, and its relationship to atherosclerosis, in CKD. METHODS In this cross-sectional study, a total of 135 patients with CKD (mean age 52 +/- 11 years) included 58 pre-dialysis patients, 36 dialysis patients, and 41 renal transplant recipients. A control group of 58 subjects was also examined. The characteristics of valvular calcification were assessed using transthoracic echocardiography. RESULTS The combined prevalences of mitral or aortic valve calcification were 31% in pre-dialysis patients, 50% in dialysis patients, 29% in renal transplant recipients, and 12% in controls (p = 0.001). The prevalences of mitral annular calcification were 17%, 31%, 27% and 2%, respectively (p = 0.001). In multivariate analysis, the risk factors for valvular calcification in CKD were age, duration of dialysis treatment and interleukin-6 level. Mitral annular calcification proved to be five-fold more common in diabetic patients than among non-diabetics. A close association between valvular calcification and patients with or without increased carotid intima-media thickness (44% versus 15%, p < 0.001), carotid plaque (77% versus 49%, p = 0.002), calcified carotid plaque (65% versus 26%, p = 0.001), coronary artery disease (40% versus 15%, p = 0.003) and peripheral arterial disease (46% versus 9%, p < 0.001) was found. CONCLUSION Valvular calcification is common in CKD, and is closely associated with findings of intimal arterial disease. The presence of inflammation and the duration of dialysis treatment contribute to this complication. Diabetes is also a prominent risk factor for mitral annular calcification in CKD.
Comparative effects of lipopolysaccharide on newborn versus adult rat hepatocyte and nonparenchymal cell cocultures.

OBJECTIVE To examine the effects of development on the response of hepatocytes and nonparenchymal cells to an endotoxin challenge as an in vitro model of organ system dysfunction at differing developmental ages. DESIGN In vitro animal cell culture model. SETTING University teaching hospital research laboratory. SUBJECTS Adult and newborn Sprague-Dawley rats. INTERVENTIONS The method of hepatocyte and nonparenchymal cell coculture was utilized and modified to allow evaluation of cells derived from newborns. Cells were isolated from adult rats by standard perfusion technique. Hepatocytes and nonparenchymal cells were isolated from newborn rats by use of identical enzymatic degradation after fine mincing of the organ. Isolated cells were purified by density gradient. The hepatocytes were incubated in standard cell culture plates for 24 hrs before the addition of nonparenchymal cells. Hepatocytes were incubated with similar-age nonparenchymal cells. After an additional 24 hrs, serial log dilutions of lipopolysaccharide were added as a stimulus and the system was cultured an additional 24 hrs. The response of the hepatocytes was assessed by determination of 3H-leucine incorporation in acid-precipitated protein. In addition, the production of tumor necrosis factor, interleukin (IL)-1, and IL-6 by isolated nonparenchymal cells from adult and newborn rats was determined after stimulation with serial log dilutions of lipopolysaccharide by bioassay. MEASUREMENTS AND MAIN RESULTS Both adult and newborn hepatocytes cocultivated with nonparenchymal cells demonstrated a comparable and statistically significant dose response to lipopolysaccharide (p < .01). The newborn hepatocytes demonstrated a greater rate of protein synthesis than the adult hepatocytes at all concentrations of lipopolysaccharide. Tumor necrosis factor production by newborn and adult nonparenchymal cells was similar at all lipopolysaccharide doses. IL-1 production demonstrated a positive dose response to lipopolysaccharide in the adult and newborn nonparenchymal cells, with a trend (p = .17) toward greater IL-1 secretion by the adult cells. There were significant differences in IL-6 production by isolated nonparenchymal cells at lipopolysaccharide doses of 0.01, 0.1, and 10 micrograms/mL. While a similar trend was apparent in the cocultured cells, the significance was not apparent, except at the highest lipopolysaccharide dose. CONCLUSIONS The dose responses of newborn and adult hepatocytes to nonparenchymal cells stimulated with lipopolysaccharide were similar, although newborn hepatocytes appeared to have an inherently higher rate of protein synthesis compared with adult hepatocytes. Cytokine production was similar in nonparenchymal cells of both ages, although IL-1 production by stimulated newborn nonparenchymal cells appeared to be less than IL-1 production by adult nonparenchymal cells.
From Boston to Chinese parallel to deferred acceptance: theory and experiments on a family of school choice mechanisms

We characterize a parametric family of application-rejection school choice mechanisms, including the Boston and Deferred Acceptance mechanisms as special cases, and spanning the parallel mechanisms for Chinese college admissions, the largest centralized matching in the world. Moving from one extreme member to the other results in systematic changes in manipulability, stability and welfare properties. Neither the ex-post dominance of the DA over the equilibria of Boston, nor the ex-ante dominance of Boston equilibria over the DA in stylized settings extends to the parallel mechanisms. In the laboratory, participants are most likely to reveal their preferences truthfully under the DA mechanism, followed by the Chinese parallel and then the Boston mechanisms. Furthermore, while the DA is significantly more stable than the Chinese parallel mechanism, which is more stable than Boston, efficiency comparisons vary across environments.
Detection of Campylobacter in human and animal field samples in Cambodia

Campylobacter are zoonotic bacteria and a leading cause of human gastroenteritis worldwide with Campylobacter jejuni and C. coli being the most commonly detected species. The aim of this study was to detect Campylobacter in humans and livestock (chickens, ducks, pigs, cattle, water buffalo, quail, pigeons and geese) in rural households by routine culturing and multiplex PCR in faecal samples frozen before analysis. Of 681 human samples, 82 (12%) tested positive by PCR (C. jejuni in 66 samples and C. coli in 16), but none by routine culture. Children were more commonly Campylobacter positive (19%) than adult males (8%) and females (7%). Of 853 livestock samples, 106 (12%) tested positive by routine culture and 352 (41%) by PCR. Campylobacter jejuni was more frequent in chickens and ducks and C. coli in pigs. In conclusion, Campylobacter proved to be highly prevalent by PCR in children (19%), ducks (24%), chickens (56%) and pigs (72%). Routine culturing was insufficiently sensitive in detecting Campylobacter in field samples frozen before analysis. These findings suggest that PCR should be the preferred diagnostic method for detection of Campylobacter in humans and livestock where timely culture is not feasible.
Approximate entropy of respiratory patterns in panic disorder.

OBJECTIVE Considerable evidence suggests a connection between panic disorder and respiration, but the nature of the respiratory abnormalities in panic disorder remains unclear. The authors investigated the breath-by-breath complexity of respiration dynamics in panic disorder. METHOD Respiratory physiology was assessed in 40 patients with panic disorder and 31 healthy comparison subjects by using a breath-by-breath stationary system for testing cardiorespiratory function. Irregularity in the breathing pattern was determined by applying the approximate entropy index, which is an indicator of the irregularity and the "disorder" of the measure. RESULTS The patients with panic disorder showed significantly higher approximate entropy indexes than the healthy subjects for the measured respiratory parameters. Sighs contributed to the irregularity of breathing patterns but did not account for all the differences in approximate entropy between the patients with panic disorder and the comparison subjects. Anxiety state, severity of illness, and somatic and individual variables such as participation in sports and cigarette smoking did not seem to influence the results. CONCLUSIONS Patients with panic disorder showed greater entropy in baseline respiratory patterns, indicating higher levels of irregularity and complexity in their respiratory function. Greater respiratory entropy could be a factor in vulnerability to panic attacks.
Sediment transport control by check dams and open check dams in Alpine torrents

Check dams and open check dams are key structures in torrent hazard protection. Their managers must mitigate flood hazards, but now must also minimize the environmental impacts of these protection structures. This requires to improve the knowledge on the effects of check dams and open check dams on the sediment transport, and this thesis forms a contribution towards this end.The section on the current state of research reviews i) the diverse effects of check dams on sediment production and transfer; ii) descriptions of the hydraulics and sedimentation processes occurring in open check dams; and iii) woody debris production and trapping processes. This state of the art is completed with proposition of new bedload transport estimation methods, specifically developed for paved streams experiencing external supply or armour breaking.Experimental results are then provided. Firstly, flume experiments highlight the emergence of a more regular bedload transport when check dams are built in alluvial reaches. In a second stage, experiments were performed on a generic Froude scale model of an open check dam basin in order to capture the features of laterally-unconstrained, highly mobile flows. A new flow measurement and inverse-reconstruction procedure has been developed. A preliminary analysis of the results describes flows that tend toward a critical regime and the occurrence of feedback mechanisms between geomorphology and hydraulics during massive bedload deposition.
Right Ventricular Enlargement on Chest Computed Tomography: Prognostic Role in Acute Pulmonary Embolism

Background—We investigated the prognostic role of right ventricular enlargement on multidetector-row chest CT in acute pulmonary embolism (PE). Methods and Results—We studied 63 patients with CT-confirmed PE who underwent echocardiography within the ensuing 24 hours. Adverse clinical events, defined as 30-day mortality or the need for cardiopulmonary resuscitation, mechanical ventilation, pressors, rescue thrombolysis, or surgical embolectomy, were present in 24 patients. We performed off-line CT measurements of right and left ventricular dimensions (RVD, LVD) with axial and 2-dimensional reconstructed 4-chamber (4-CH) views. The proportion of patients with RVD/LVD>0.9 on the axial view was similar in patients with (70.8%) and those without adverse events (71.8%; P =0.577). In contrast, RVD/LVD>0.9 on the 4-CH view was more common in patients with (80.3%) than without (51.3%; P =0.015) adverse events. The area under the curve of RVD/LVD from the axial and 4-CH views for predicting adverse events was 0.667 and 0.753, respectively. Sensitivity and specificity of RVD/LVD>0.9 for predicting adverse events were 37.5% and 92.3% on the axial view and 83.3% and 48.7% on the reconstructed 4-CH view, respectively. RVD/LVD>0.9 on the 4-CH view was an independent predictor for adverse events (OR, 4.02; 95% CI, 1.06 to 15.19; P =0.041) when adjusted for age, obesity, cancer, and recent surgery. Conclusions—Right ventricular enlargement on the reconstructed CT 4-CH views predicts adverse clinical events in patients with acute PE. Ventricular CT measurements obtained from 4-CH views are superior to those from axial views for identifying high-risk patients.
Structural Analysis of Oligosaccharides from Lipopolysaccharide (LPS) of Escherichia coli K12 Strain W3100 Reveals a Link between Inner and Outer Core LPS Biosynthesis*

Lipopolysaccharide (LPS) from Escherichia coli K12 W3100 is known to contain several glycoforms, and the basic structure has been investigated previously by methylation analyses (Holst, O. (1999) in Endotoxin in Health and Disease (Brade, H., Opal, S. M., Vogel, S. N., and Morrison, D., eds) pp. 115–154; Marcel Dekker, Inc., New York). In order to reveal dependences of gene activity and LPS structure, we have now determined the composition of de-O-acylated LPS by electrospray ionization-Fourier transform ion cyclotron-mass spectrometry (ESI-FT-MS) and identified 11 different LPS molecules. We have isolated the major glycoforms after de-O- and de-N-acylation and obtained four oligosaccharides that differed in their carbohydrate structure and phosphate substitution. The main oligosaccharide accounted for ∼70% of the total and had a molecular mass of 2516 Da according to ESI-FT-MS. The dodecasaccharide structure (glycoform I) as determined by NMR was consistent with MS and compositional analysis. One minor oligosaccharide (5%) of the same carbohydrate structure did not contain the 4′-phosphate of the lipid A. Two oligosaccharides contained the same phosphate substitution but differed in their carbohydrate structure, one (5%) which contained an additional β-d-GlcN in 1→7 linkage on a terminal heptose residue (glycoform II) which was N-acetylated in LPS. A minor amount of a molecule lacking the terminal l-α-d-Hep in the outer core but otherwise identical to the major oligosaccharide (glycoform III) could only be identified by ESI-FT-MS of the de-O-acylated LPS. The other oligosaccharide (20%) contained an α-Kdo-(2→4)-[α-l-Rha-(1→5)]-α-Kdo-(2→4)-α-Kdo branched tetrasaccharide connected to the lipid A (glycoform IV). This novel inner core structure was accompanied by a truncation of the outer core in which the terminal disaccharide l-α-d-Hep-(1→6)-α-d-Glc was missing. The latter structure was identified for the first time in LPS and revealed that changes in the inner core structure may be accompanied by structural changes in the outer core.
Optimum concentration of bupivacaine for combined caudal--general anesthesia in children.

Caudal epidural anesthesia has become widely accepted as a means of providing postoperative pain relief and intraoperative supplementation to general anesthesia for children. To determine the best concentration of bupivacaine for combined general-caudal anesthesia in children, 122 children aged 1-8 yr scheduled for outpatient inguinal herniorrhaphy were randomized to receive, in a double-blind fashion, caudal anesthesia with bupivacaine in one of six concentrations (0.125, 0.15, 0.175, 0.2, 0.225, or 0.25%). After incision, a programmed reduction in inspired halothane resulted, if tolerated by the subject, in an inspired halothane concentration of 0.5% 10 min after incision. End-tidal halothane concentration at hernia sac ligation for subjects receiving 0.175% bupivacaine (0.55 +/- 0.03%) was less than that for subjects receiving 0.15% bupivacaine (0.75 +/- 0.05%; P less than 0.05). Subjects receiving 0.175% bupivacaine also were discharged earlier from the postanesthesia care unit (PACU) (27 +/- 1 min) than were subjects receiving 0.15% bupivacaine (38 +/- 5 min; P = 0.05). Children receiving greater than or equal to 0.2% bupivacaine tended to complain more of leg weakness after surgery; however, the difference did not reach statistical significance (39 of 67 vs. 16 of 47; P = 0.057). The incidence of complaints of leg weakness and paresthesia was positively correlated with bupivacaine concentration (r = 0.706; P = 0.05). Subjects receiving 0.125% bupivacaine had higher pain scores on arrival to the PACU than did those receiving 0.2% bupivacaine (P = 0.05); there were no other differences in pain scores. (ABSTRACT TRUNCATED AT 250 WORDS)
The open state of human topoisomerase I as probed by molecular dynamics simulation

The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a short time to induce destabilization of the local minimum, after which an unperturbed simulation has been carried out for 10 ns. The simulation shows that the protein undergoes a large conformational change due to rearrangements in the orientation of the protein domains, which however move as a coherent unit, fully maintaining their secondary and tertiary structures. Despite movements between the domains as large as 80–90 Å, the catalytic pentad remains preassembled, the largest deviation of the active site backbone atoms from the starting crystallographic structure being only 1.7 Å. Electrostatic calculation of the open protein structure shows that the protein displays a vast positive region with the active site residues located nearly at its center, in a conformation perfectly suited to interact with the negatively charged supercoiled DNA substrate.
Wild-Type Levels of Nuclear Localization and Human Immunodeficiency Virus Type 1 Replication in the Absence of the Central DNA Flap

ABSTRACT Numerous factors have been implicated in the nuclear localization of retroviral preintegration complexes. Whereas sequences in human immunodeficiency virus type 1 (HIV-1) matrix, Vpr, and integrase proteins were initially reported to function specifically in nondividing cells, other recently identified sequences apparently function in dividing cells as well. One of these, the central DNA flap formed during reverse transcription, is specific to lentiviruses. It was previously reported that flap-negative (F−) HIV-1LAI was completely defective for viral spread in the MT-4 T-cell line, yet F− HIV-1 vectors were only 2- to 10-fold defective in various single-round transduction assays. To address these different findings, we analyzed the infectivity and nuclear localization phenotypes of two highly related T-cell-tropic strains, HIV-1NL4-3 and a derivative of HIV-1HXBc2 deficient for both Vpr and Nef. In stark contrast to the previous report, F− derivatives of both strains replicated efficiently in MT-4 cells. F− HIV-1NL4-3 also spread like wild-type HIV-1NL4-3 in infected Jurkat and primary T-cell cultures. In contrast, F− HIV-1HXBc2 was replication defective in primary T cells. Results of real-time quantitative PCR assays, however, indicated that F− HIV-1HXBc2 entered primary T-cell nuclei as efficiently as its wild-type counterpart. Thus, the F− HIV-1HXBc2 growth defect did not appear to correlate with defective nuclear import. Consistent with this observation, wild-type nef restored replication to F− HIV-1HXBc2 in primary T cells. Our results indicate that the central DNA flap does not play a major role in either preintegration complex nuclear import or HIV-1 replication in a variety of cell types.
The influence of expertise on brain activation of the action observation network during anticipation of tennis and volleyball serves

In many daily activities, and especially in sport, it is necessary to predict the effects of others' actions in order to initiate appropriate responses. Recently, researchers have suggested that the action–observation network (AON) including the cerebellum plays an essential role during such anticipation, particularly in sport expert performers. In the present study, we examined the influence of task-specific expertise on the AON by investigating differences between two expert groups trained in different sports while anticipating action effects. Altogether, 15 tennis and 16 volleyball experts anticipated the direction of observed tennis and volleyball serves while undergoing functional magnetic resonance imaging (fMRI). The expert group in each sport acted as novice controls in the other sport with which they had only little experience. When contrasting anticipation in both expertise conditions with the corresponding untrained sport, a stronger activation of AON areas (SPL, SMA), and particularly of cerebellar structures, was observed. Furthermore, the neural activation within the cerebellum and the SPL was linearly correlated with participant's anticipation performance, irrespective of the specific expertise. For the SPL, this relationship also holds when an expert performs a domain-specific anticipation task. Notably, the stronger activation of the cerebellum as well as of the SMA and the SPL in the expertise conditions suggests that experts rely on their more fine-tuned perceptual-motor representations that have improved during years of training when anticipating the effects of others' actions in their preferred sport. The association of activation within the SPL and the cerebellum with the task achievement suggests that these areas are the predominant brain sites involved in fast motor predictions. The SPL reflects the processing of domain-specific contextual information and the cerebellum the usage of a predictive internal model to solve the anticipation task.
Power Supply Noise Analysis Methodology For Deep-submicron Vlsi Chip Design

This paper describes a new design methodology to analyzethe on-chip power supply noise for high-performance microprocessors.Based on an integrated package-level andchip-level power bus model, and a simulated switching circuitmodel for each functional block, this methodology offersthe most complete and accurate analysis of Vdd distributionfor the entire chip. The analysis results not only providedesigners with the inductive ¿I noise and the resistive IRdrop data at the same time, but also allow designers to easilyidentify the hot spots on the chip and ¿V across the chip.Global and local optimization such as buffer sizing, powerbus sizing, and on-chip decoupling capacitor placement canthen be conducted to maximize the circuit performance andminimize the noise.
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

The nonessential regions in bacterial chromosomes are ill-defined due to incomplete functional information. Here, we establish a comprehensive repertoire of the genome regions that are dispensable for growth of Bacillus subtilis in a variety of media conditions. In complex medium, we attempted deletion of 157 individual regions ranging in size from 2 to 159 kb. A total of 146 deletions were successful in complex medium, whereas the remaining regions were subdivided to identify new essential genes (4) and coessential gene sets (7). Overall, our repertoire covers ∼76% of the genome. We screened for viability of mutant strains in rich defined medium and glucose minimal media. Experimental observations were compared with predictions by the iBsu1103 model, revealing discrepancies that led to numerous model changes, including the large-scale application of model reconciliation techniques. We ultimately produced the iBsu1103V2 model and generated predictions of metabolites that could restore the growth of unviable strains. These predictions were experimentally tested and demonstrated to be correct for 27 strains, validating the refinements made to the model. The iBsu1103V2 model has improved considerably at predicting loss of viability, and many insights gained from the model revisions have been integrated into the Model SEED to improve reconstruction of other microbial models.