Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliability of editors' subjective quality ratings of peer reviews of manuscripts.

CONTEXT Quality of reviewers is crucial to journal quality, but there are usually too many for editors to know them all personally. A reliable method of rating them (for education and monitoring) is needed. OBJECTIVE Whether editors' quality ratings of peer reviewers are reliable and how they compare with other performance measures. DESIGN A 3.5-year prospective observational study. SETTING Peer-reviewed journal. PARTICIPANTS All editors and peer reviewers who reviewed at least 3 manuscripts. MAIN OUTCOME MEASURES Reviewer quality ratings, individual reviewer rate of recommendation for acceptance, congruence between reviewer recommendation and editorial decision (decision congruence), and accuracy in reporting flaws in a masked test manuscript. INTERVENTIONS Editors rated the quality of each review on a subjective 1 to 5 scale. RESULTS A total of 4161 reviews of 973 manuscripts by 395 reviewers were studied. The within-reviewer intraclass correlation was 0.44 (P<.001), indicating that 20% of the variance seen in the review ratings was attributable to the reviewer. Intraclass correlations for editor and manuscript were only 0.24 and 0.12, respectively. Reviewer average quality ratings correlated poorly with the rate of recommendation for acceptance (R=-0.34) and congruence with editorial decision (R=0.26). Among 124 reviewers of the fictitious manuscript, the mean quality rating for each reviewer was modestly correlated with the number of flaws they reported (R=0.53). Highly rated reviewers reported twice as many flaws as poorly rated reviewers. CONCLUSIONS Subjective editor ratings of individual reviewers were moderately reliable and correlated with reviewer ability to report manuscript flaws. Individual reviewer rate of recommendation for acceptance and decision congruence might be thought to be markers of a discriminating (ie, high-quality) reviewer, but these variables were poorly correlated with editors' ratings of review quality or the reviewer's ability to detect flaws in a fictitious manuscript. Therefore, they cannot be substituted for actual quality ratings by editors.
Synergistic longitudinal PET image reconstruction

Positron emission tomography (PET) is regularly used to measure changes in physiological and molecular processes at multiple time points, for example in oncological treatment response studies or in brain activation studies. Conventionally, the datasets from these time points are used independently to reconstruct images, and post-reconstruction measurements made and compared. However, this independent dataset approach fails to consider that much of the image detail between scans remains unchanged. By exploiting this inherent similarity between the images, image reconstruction and quantification can be improved. This work proposes to achieve this by incorporating two datasets into a joint reconstruction framework, linked by a regularisation term that penalises differences between the scans. Two such penalty terms were considered, the L1-norm and a non-convex function. Optimisation of the joint objective function was sought using a one-step-late approach. For comparison of methods, a dual time point brain cancer treatment response study was simulated, including three regions of change. Longitudinally penalised reconstructions were compared to conventional maximum likelihood expectation-maximisation (MLEM), and a benchmark method that assumes perfect knowledge of areas of change and averages MLEM reconstructions where no change occurs. Results show that the proposed penalised reconstruction methods achieved a lower error level across the whole brain when compared to MLEM, and error levels comparable to the benchmark method. While the L1 penalised method lost accuracy in regions of change due to over-penalisation of large differences, the non-convex prior maintained and even improved performance in these regions compared to the benchmark method, highlighting the potential of longitudinal reconstruction methods in improving the quantification of multi-dataset PET studies.
An Accurate Conformal Fourier Transform Method for 3D Discontinuous Functions

Fourier transform of discontinuous functions are often encountered in computational electromagnetics and other areas. In this work, a highly accurate, fast conformal Fourier transform (CFT) algorithm is proposed to evaluate the finite Fourier transform of 3D discontinuous functions. A curved tetrahedron mesh combined with curvilinear coordinate transform, instead of the Cartesian grid, is adopted to flexibly model an arbitrary shape of the discontinuity boundary. This enables us to take full advantages of high order interpolation and Gaussian quadrature methods to achieve highly accurate Fourier integration results with a low sampling density. The 3D nonuniform fast Fourier transform (NUFFT) helps to keep the complexity of the proposed algorithm to that similar to the traditional 3D FFT algorithm. Therefore, the proposed CFT algorithm can achieve order of magnitude higher accuracy than 3D FFT with lower sampling density and similar computation time. The convergence is proved and verified.
Structure des populations sur un réseau hydrographique dendritique

Les reseaux hydrographiques sont caracterises par leur structure hierarchique de type dendritique (ramifie) et l'heterogeneite spatio-temporelle du milieu. En effet, l'heterogeneite de l'habitat sur les cours d'eau varie selon le temps (variations saisonnieres), la dimension longitudinale (caracteristiques physico-chimiques et courant) et la dimension laterale (connectivite entre le cours principal et les annexes hydrauliques). Ces variations des parametres environnementaux sont soit graduelles le long des branches du reseau hydrographique (gradient physico-chimique, courant), soit discretes entre les branches du reseau (diversite de l'habitat). La structure du reseau hydrographique va, par consequent, influencer la distribution, les deplacements et le flux genique des organismes infeodes aux cours d'eau. Les objectifs de cette these etaient de tester (i) l'effet de la topologie du reseau hydrographique sur la dispersion et le flux de genes, et (ii) l'effet des variations environnementales sur la distribution et les traits phenotypiques des individus lies a la dispersion. Pour repondre a ces objectifs nous avons utilise une approche empirique, en menant notre etude sur le bassin moyen de la Loire chez une espece de demoiselle, le Calopteryx splendens (Odonates : Zygopteres). Parallelement nous avons developpe un modele theorique permettant de simuler la dispersion et le flux de genes sur des reseaux hydrographiques artificiels. Ainsi nous avons mis en evidence une distribution discontinue des individus sur le cours d'eau et un cline morphologique sur le bassin de la Loire entre l'amont et l'aval. Ce cline est lie aux caracteristiques physico-chimiques de l'eau. Ces variations morphologiques n'influencent pas les capacites de dispersion, mais affectent la survie des individus. La survie et la densite sont les facteurs determinants de la dispersion chez C. splendens. Les analyses genetiques ont montre un isolement par la distance et une forte structuration genetique sur le bassin versant, mais l'absence d'entites genetiques clairement definies. Ceci peut etre explique par la presence de flux de genes entre les sous-bassins et une structure en metapopulation a l'echelle du reseau hydrographique. Ces resultats sont les premiers obtenus a l'echelle d'un bassin versant tel que la Loire sur des populations naturelles. L'etude a egalement permis de realiser le logiciel Gene-Net testant l'effet de la geometrie des reseaux hydrographiques sur la structure genetique des populations d'organismes d'eau douce.
The role of fixed and switching traps in long-term fading of implanted and unimplanted gate oxide RADFETs

Radiation-sensing field effect transistors (RADFETs) have become widely used as radiation monitors in space missions. However, partial recovery (fading) of the dosimetric parameter (threshold voltage shift) may introduce severe complexities in measured dose analysis. The evolution of charge trap density during irradiation and postirradiation annealing of implanted and unimplanted RADFETs with different gate oxide thickness was studied in detail. It was found that a surprisingly high increase of border traps and their subsequent annealing in positively biased 400 nm implanted RADFETs were the origin of substantial fading, whereas the same devices irradiated with zero bias exhibited much lower fading. Additional differences between implanted and unimplanted RADFETs irradiated and annealed with and without bias are discussed.
Hydra Peptide Project 1993–2007

A systematic screening of peptide signaling molecules (<5000 da) in Hydra magnipapillata (the Hydra Peptide Project) was launched in 1993 and at least the first phase of the project ended in 2007. From the project a number of interesting suggestions and results have been obtained. First, a simple metazoan‐like Hydra appears to contain a few hundred peptide signaling molecules: half of them neuropeptides and the rest epitheliopeptides that are produced by epithelial cells. Second, epitheliopeptides were identified for the first time in Hydra. Some exhibit morphogen‐like activities, which accord with the notion that epithelial cells are primarily responsible for patterning in Hydra. A family of epitheliopeptides was involved in regulating neuron differentiation possibly through neuron–epithelial cell interaction. Third, many novel neuropeptides were identified. Most of them act directly on muscle cells inducing contraction or relaxation. Some were involved in cell differentiation and morphogenesis. During the course of this study, a number of important technical innovations (e.g. genetic manipulations in transgenic Hydra, high‐throughput purification techniques, etc.) and expressed sequence tag (EST) and genome databases were introduced in Hydra research. They have already helped to identify and characterize novel peptides and will contribute even more to the Hydra Peptide Project in the near future.
Effect of propofol anaesthesia on the event-related potential mismatch negativity and the auditory-evoked potential N1.

BACKGROUND Studies on the effects of anaesthesia on event-related potentials and long latency auditory-evoked potentials (AEP) are sparse. Both provide information on cortical processing and may have potential as monitors of awareness. We studied the effect of propofol on the event-related potential mismatch negativity (MMN) and the long-latency AEP NI. METHODS Twenty-one patients received 1 microgram ml-1 stepped increases in the target concentration of propofol using Diprifusor until a maximum of 6 micrograms ml-1 was achieved or the patient had lost consciousness. Neurophysiological responses (MMN and N1) and the patients' level of consciousness were recorded before the administration of propofol and at a target effector site concentration of propofol of 1, 2, 3, 4, and 6 micrograms ml-1. Grand average evoked potentials were computed at baseline, before the administration of propofol (A); at the highest propofol concentration at which each patient was responsive (B); and at the concentration of propofol at which the patient became unconscious (C). RESULTS Patients lost consciousness at different target concentrations of propofol, all being unresponsive by 4 micrograms ml-1. The response to the deviant stimuli used to elicit duration-shift MMN was significantly more negative than to the standard stimuli at A (mean difference 2.58 microV, P = 0.0011) but this difference was virtually abolished at point B, before the patients lost consciousness (mean difference 0.63 microV, P = ns). The amplitude of N1 evoked by standard stimuli was negative compared with electrical baseline at both point A (mean amplitude -3.81 microV, P < 0.001) and at point B (mean amplitude -2.2 microV, P = 0.002), but was no longer significantly different to baseline at point C (mean amplitude 0.51 microV, P = ns). The change in the mean amplitude of N1 from last awake (point B) to first unconscious (point C) was also significant (mean difference in amplitude 1.69 microV, P = 0.02). CONCLUSIONS MMN is unlikely to be a clinically useful tool to detect awareness in surgical patients. In contrast, the loss of N1 may identify the transition from consciousness to unconsciousness and deserves further study.
Modeling and Simulation of Charge-Pumping Characteristics for LDD-MOSFET Devices With LOCOS Isolation

We propose a model for the so-called constant-amplitude charge-pumping (CP) characteristics, giving the Elliot Gaussian-like CP current curve (I<sub>CP</sub>-V<sub>L</sub>) of lightly doped drain (LDD) MOSFET with local oxidation of silicon (LOCOS). This method is based on modulation of the contributing active-channel area (A<sub>G</sub>) to the I<sub>CP</sub>-V<sub>L</sub> curve, depending on the position of the high and low levels of the gate signal voltage. In addition, it allows to separate and clarify the contribution of all MOSFET regions (such as the effective channel, LDD, LOCOS, and LDD subdiffusion under the LOCOS) to the amount of I<sub>CP</sub>-V<sub>L</sub> curves. We have simulated this model and compared with experimental CP data. The model shows a very good correlation with experimental I<sub>CP</sub>-V<sub>L</sub> curves, particularly for transistors with short channel gate lengths (L<sub>G</sub> ≤ 1 μm). However, as the channel gate length increases, the model matches only for rising and falling I<sub>CP</sub>-V<sub>L</sub> curve edges, corresponding to the contribution of LDD and LOCOS regions, respectively. Moreover, we have demonstrated that the deviation, which was observed between the CP model and experimental data at the maximum plateau of I<sub>CP</sub>-V<sub>L</sub> characteristics, depends on the gate pulse fall time and vanishes for large fall time. This difference has been found to behave like a geometric component, since it depends on gate length and fall time and disappears for both short gate lengths and long fall times.
Regression of sclerosis in aging by an angiotensin inhibition-induced decrease in PAI-1.

BACKGROUND Glomerular and vascular sclerosis increase with aging, and angiotensin inhibitors ameliorate progression of this injury. We investigated the potential for achieving regression of existing age-related sclerosis, and the mechanisms by which angiotensin type 1 receptor antagonist (AIIRA) may affect remodeling of this sclerosis. We focused on plasminogen activator inhibitor-1 (PAI-1) because it is directly induced by angiotensin, inhibits matrix degradation, and may thus be pivotal in remodeling. METHODS Eighteen-month-old male Sprague-Dawley rats were treated with the AIIRA losartan (N = 8, 80 mg/L, dry weight), sacrificed at age 21 and 24 months, and compared with age-matched untreated controls (N = 15). Blood pressure and renal function were monitored, and morphological, biochemical, and molecular analyses were done on aorta and kidney. RESULTS Body weight increased in both groups. Mean arterial pressure (MAP) and serum creatinine remained normal (24-month MAP 115 +/- 8 vs. 113 +/- 6 mm Hg, controls vs. AIIRA, P = NS). Aorta wall thickness ratio was reduced by AIIRA at 21 and 24 months vs. age-matched controls (21 months 0. 12 +/- 0.01 vs. 0.15 +/- 0.01, P = 0.006; 24 months 0.10 +/- 0.005 vs. 0.14 +/- 0.003, AIIRA vs. controls, respectively, P = 0.0027). The aorta wall thickness ratio after treatment with AIIRA for six months was even lower than that of 18-month control rats (P = 0.018). AIIRA reduced proteinuria versus age-matched control at 24 months (253 +/- 62 vs. 390 +/- 51 mg/24 h, P = 0.0017). AIIRA at 24 months decreased glomerulosclerosis versus age-matched control (sclerosis index, 0 to 4+ scale: 0.06 +/- 0.02 vs. 0.49 +/- 0.12, P = 0.0082) to levels even lower than the 18-month baseline (0.37 +/- 0.14, P = 0.014). Renal collagen content increased with aging and was decreased by AIIRA at 24 months (5.0 +/- 0.7 vs. 3.1 +/- 0.5% collagen, P < 0.05). Apoptosis, assessed by TUNEL, was increased in tubular and interstitial cells in aging and was reduced by AIIRA versus control and baseline, respectively (TUNEL scoring, AIIRA 24 months 0.33 +/- 0.16 vs. 1.06 +/- 0.23 and 0.80 +/- 0.05, P < 0.05). PAI-1 mRNA in kidney was decreased at 24 months in AIIRA versus age-matched controls (PAI-1/GAPDH density ratio: AIIRA 24 months 0. 34 +/- 0.05 vs. 24-month controls 0.99 +/- 0.05, P < 0.05). Increased glomerular PAI-1 immunostaining with aging was decreased by AIIRA at 24 months versus age-matched controls, even below baseline (staining score 0 to 4+, 0.57 +/- 0.15 vs. control 0.90 +/- 0.07, P < 0.05; baseline 1.05 +/- 0.02, P < 0.01). CONCLUSION We conclude that AIIRA not only slows the progression of glomerular and vascular sclerosis in aging, but can also induce regression of these processes. The mechanisms appear to involve modulation of cortical cell turnover and inhibition of PAI-1 expression.
Prevalence of the Pandemic Genotype of Vibrio parahaemolyticus in Dhaka, Bangladesh, and Significance of Its Distribution across Different Serotypes

ABSTRACT Sixty-six strains of Vibrio parahaemolyticus belonging to 14 serotypes were isolated from hospitalized patients in Dhaka, Bangladesh, from January 1998 to December 2000. Among these, 48 strains belonging to four serotypes had the pandemic genotype and possessed the tdh gene. A marker (open reading frame ORF8) for a filamentous phage previously thought to correspond to the pandemic genotype was found to have a poor correlation with the pandemic genotype.
Salmonella enterica delivers its genotoxin through outer membrane vesicles secreted from infected cells

Cytolethal‐distending toxins (CDTs) belong to a family of DNA damage inducing exotoxins that are produced by several Gram‐negative bacteria. Salmonella enterica serovar Typhi expresses its CDT (named as Typhoid toxin) only in the Salmonella‐containing vacuole (SCV) of infected cells, which requires its export for cell intoxication. The mechanisms of secretion, release in the extracellular space and uptake by bystander cells are poorly understood. We have addressed these issues using a recombinant S. Typhimurium strain, MC71‐CDT, where the genes encoding for the PltA, PltB and CdtB subunits of the Typhoid toxin are expressed under control of the endogenous promoters. MC71‐CDT grown under conditions that mimic the SCV secreted the holotoxin in outer membrane vesicles (OMVs). Epithelial cells infected with MC71‐CDT also secreted OMVs‐like vesicles. The release of these extracellular vesicles required an intact SCV and relied on anterograde transport towards the cellular cortex on microtubule and actin tracks. Paracrine internalization of Typhoid toxin‐loaded OMVs by bystander cells was dependent on dynamin‐1, indicating active endocytosis. The subsequent induction of DNA damage required retrograde transport of the toxin through the Golgi complex. These data provide new insights on the mode of secretion of exotoxins by cells infected with intracellular bacteria.
A new low power voltage controlled oscillator based on bandwidth enhancement technique

In this paper, we present a novel low power voltage-controlled-oscillator (VCO) based on bandwidth enhancement technique. The enhanced bandwidth allowed the VCO to achieve steep output waveform resulting in improved phase noise. The VCO was fabricated in 0.13 µm standard CMOS process having 6 layers of copper metallization. The oscillation frequency ranged from 4.48 to 4.82 GHz with a turning range of 7.5 %. The measured phase noise of the VCO was −119 dBc/Hz at 1 MHz offset under 4.2 mW power consumption.
Range analysis of biological cells subjected to pulsed electric fields

In modelling the electro-permeabilization processes of biological cells, several physical constants need to be measured or approximated in order to obtain realistic results from the numerical scheme approximating the theoretical model. The dynamics of the permeabilization processes due to electrical stimuli is regulated by the voltage evolution across the membrane (trans-membrane voltage-TMV). In this paper a detailed range analysis is carried out on the classical circuit model representing the cell membrane, taking into account parameters variations and/or uncertainties. Such an analysis provides the corresponding spans of the TMV and, in perspective, an accurate tool for evaluating the ranges of electrical pulses values (amplitude, rise time, duration) to be applied in order to obtain reversible or irreversible effects on the cell behaviour.
The influence of light quality on C4 photosynthesis under steady-state conditions in Zea mays and Miscanthus×giganteus: changes in rates of photosynthesis but not the efficiency of the CO2 concentrating mechanism.

Differences in light quality penetration within a leaf and absorption by the photosystems alter rates of CO(2) assimilation in C(3) plants. It is also expected that light quality will have a profound impact on C(4) photosynthesis due to disrupted coordination of the C(4) and C(3) cycles. To test this hypothesis, we measured leaf gas exchange, (13) CO(2) discrimination (Δ(13) C), photosynthetic metabolite pools and Rubisco activation state in Zea mays and Miscanthus × giganteus under steady-state red, green, blue and white light. Photosynthetic rates, quantum yield of CO(2) assimilation, and maximum phosphoenolpyruvate carboxylase activity were significantly lower under blue light than white, red and green light in both species. However, similar leakiness under all light treatments suggests the C(4) and C(3) cycles were coordinated to maintain the photosynthetic efficiency. Measurements of photosynthetic metabolite pools also suggest coordination of C(4) and C(3) cycles across light treatments. The energy limitation under blue light affected both C(4) and C(3) cycles, as we observed a reduction in C(4) pumping of CO(2) into bundle-sheath cells and a limitation in the conversion of C(3) metabolite phosphoglycerate to triose phosphate. Overall, light quality affects rates of CO(2) assimilation, but not the efficiency of CO(2) concentrating mechanism.