Miracle-dz/UniFAR-FTUs huggingface dataset:
PaWaIC-PSAOFDTD: Particle-Wave Interaction Code With Pseudospectral Arbitrary-Order Accurate Temporal and Spatial Derivatives FDTD Technique for Helix TWT

Numerical modeling and simulations have been essential for rapid developments of vacuum electronic devices. Pseudospectral solvers have interesting capabilities to be considered, but up to now, they have not been extensively used for the modeling of vacuum tubes. In this paper, we present a novel 1-D time-domain numerical scheme which has the great aptitude of considering geometrical dispersion characteristic of helix traveling-wave tube (TWT) in time domain. This ability is interesting for one-run investigation of time-domain events such as pulse excitation of wideband tubes. The numerical model is extended to have simultaneously arbitrary order of accuracy in space and time derivations; so we achieve a code which presents a very low level of numerical dispersion error, without forcing a notable numerical calculation burden. To validate our new simulation tool, we have studied the experimental results of a TWT product, and successfully compared the results to the impulse response of the new 1-D code.
Comparison and Intercalibration of Vegetation Indices from Different Sensors for Monitoring Above-Ground Plant Nitrogen Uptake in Winter Wheat

Various sensors have been used to obtain the canopy spectral reflectance for monitoring above-ground plant nitrogen (N) uptake in winter wheat. Comparison and intercalibration of spectral reflectance and vegetation indices derived from different sensors are important for multi-sensor data fusion and utilization. In this study, the spectral reflectance and its derived vegetation indices from three ground-based sensors (ASD Field Spec Pro spectrometer, CropScan MSR 16 and GreenSeeker RT 100) in six winter wheat field experiments were compared. Then, the best sensor (ASD) and its normalized difference vegetation index (NDVI (807, 736)) for estimating above-ground plant N uptake were determined (R2 of 0.885 and RMSE of 1.440 g·N·m−2 for model calibration). In order to better utilize the spectral reflectance from the three sensors, intercalibration models for vegetation indices based on different sensors were developed. The results indicated that the vegetation indices from different sensors could be intercalibrated, which should promote application of data fusion and make monitoring of above-ground plant N uptake more precise and accurate.
Structure-Function Analysis of Staphylococcus aureus Amidase Reveals the Determinants of Peptidoglycan Recognition and Cleavage*

Background: Autolysins ensure the plasticity of bacterial cell walls, and deletion leads to impaired cell clusters. Results: High resolution structures of Staphylococcus aureus amidase AmiA shed light on peptidoglycan binding and cleavage. Conclusion: AmiA distinguishes peptidoglycan mostly by the peptide, and cleavage is facilitated by a zinc-activated water molecule. Significance: These structures will inform strategies to develop new therapeutics against MRSA. The bifunctional major autolysin AtlA of Staphylococcus aureus cleaves the bacterium's peptidoglycan network (PGN) at two distinct sites during cell division. Deletion of the enzyme results in large cell clusters with disordered division patterns, indicating that AtlA could be a promising target for the development of new antibiotics. One of the two functions of AtlA is performed by the N-acetylmuramyl-l-alanine amidase AmiA, which cleaves the bond between the carbohydrate and the peptide moieties of PGN. To establish the structural requirements of PGN recognition and the enzymatic mechanism of cleavage, we solved the crystal structure of the catalytic domain of AmiA (AmiA-cat) in complex with a peptidoglycan-derived ligand at 1.55 Å resolution. The peptide stem is clearly visible in the structure, forming extensive contacts with protein residues by docking into an elongated groove. Less well defined electron density and the analysis of surface features indicate likely positions of the carbohydrate backbone and the pentaglycine bridge. Substrate specificity analysis supports the importance of the pentaglycine bridge for fitting into the binding cleft of AmiA-cat. PGN of S. aureus with l-lysine tethered with d-alanine via a pentaglycine bridge is completely hydrolyzed, whereas PGN of Bacillus subtilis with meso-diaminopimelic acid directly tethered with d-alanine is not hydrolyzed. An active site mutant, H370A, of AmiA-cat was completely inactive, providing further support for the proposed catalytic mechanism of AmiA. The structure reported here is not only the first of any bacterial amidase in which both the PGN component and the water molecule that carries out the nucleophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidoglycan amidase complex structure of an important human pathogen.
Numerical solution of the Euler equations by finite volume methods using Runge Kutta time stepping schemes

A new combination of a finite volume discretization in conjunction with carefully designed dissipative terms of third order, and a Runge Kutta time stepping scheme, is shown to yield an effective method for solving the Euler equations in arbitrary geometric domains. The method has been used to determine the steady transonic flow past an airfoil using an O mesh. Convergence to a steady state is accelerated by the use of a variable time step determined by the local Courant member, and the introduction of a forcing term proportional to the difference between the local total enthalpy and its free stream value. 24 refs.
Intraoperative Blood Loss Predicts Hemorrhage-Related Reoperation after Orthotopic Liver Transplantation

Postoperative hemorrhage after orthotopic liver transplantation (OLT) may require early reoperative intervention. Previous studies have shown intraoperative transfusion requirement as a main determinant of reoperative intervention after OLT. The goal of this study was to develop an intraoperative hemorrhage model predicting need for reoperation after OLT. A single institution, retrospective review of adult primary OLT patients from January 2002 to 2008 was conducted. Multivariate logistical regression analysis was performed to identify predictors of reoperation due to postoperative hemorrhage. Secondary analysis was conducted on patients in the reoperation group managed with temporary open abdomen techniques. Four hundred and ten primary transplantations were performed with 59 patients (14.4%) requiring reoperation. The adjusted odds of reoperation when intraoperative blood loss (IBL) increases from 1.5 L to 10.0 L is 2.48 [95% confidence interval: (1.18, 5.31)]. IBL of 10.0 L predicts a 19.4 per cent probability of reoperation. Patients managed with open abdomen (n = 8) exhibited a significant IBL difference (16.0 L vs 6.0 L, P < 0.001) when compared with the closed abdomen cohort. Our results indicate that intraoperative blood loss is the primary predictor of reoperation after OLT and provide a hemorrhage threshold to guide postoperative management of complicated OLT patients.
Secretion of Paracrine Factors Enabling Expansion of Cumulus Cells Is Developmentally Regulated in Pig Oocytes1

Abstract To demonstrate secretion of cumulus expansion-enabling factor (CEEF) by porcine oocytes, we used an interspecies testing system. Porcine oocytes were used to condition culture medium, and the presence of CEEF was tested using mouse oocytectomized complexes (OOX), which require CEEF for expansion. Follicle-stimulating hormone-stimulated expansion and synthesis of hyaluronic acid (HA) by mouse OOX were assessed after 18 h of culture in media conditioned by porcine oocytes: 1) at different stages of maturation and 2) in which maturation was inhibited with a specific inhibitor of cdk-kinases, butyrolactone I. Fully grown (GV-germinal vesicle), late-diakinesis (LD), metaphase I (MI), and metaphase II (MII) oocytes were prepared by culture of oocyte-cumulus complexes (OCC) for 0, 22, 27, and 42 h, respectively. To block GV breakdown, porcine oocytes were cultured for 27 h in medium supplemented with butyrolactone I (50 μM). Medium conditioned by oocytes in GV, LD, and after butyrolactone I block allowed full expansion of >90% of mouse OOX, whereas oocytes in MI and MII caused disintegration of mouse OOX without cumulus mucification. To measure synthesis of HA by cumulus cells, 25 mouse OOX were cultured in the conditioned media in the presence of 2.5 μCi of d-[6-3H]glucosamine hydrochloride. After 18 h, incorporation of the [3H]glucosamine into HA was determined either in complexes (retained HA) or in medium plus complexes (total HA). Total HA accumulation by mouse OOX was not different from that of intact OCC. However, oocytes in GV, LD, and after butyrolactone I treatment enabled mouse OOX to retain significantly more HA within the complex than oocytes in MI and MII. The results indicate that secretion of factors that promote the retention of HA within the complex is developmentally regulated during oocyte maturation.
In Vitro Reconstitution of the Modulation of Drosophila Notch-Ligand Binding by Fringe*

Notch signaling plays critical roles in animal development and physiology. The activation of Notch receptors by their ligands is modulated by Fringe-dependent glycosylation. Fringe catalyzes the addition of N-acetylglucosamine in a β1,3 linkage onto O-fucose on epidermal growth factor-like domains. This modification of Notch by Fringe influences the binding of Notch ligands to Notch receptors. However, prior studies have relied on in vivo glycosylation, leaving unresolved the question of whether addition of N-acetylglucosamine is sufficient to modulate Notch-ligand interactions on its own, or whether instead it serves as a precursor to subsequent post-translational modifications. Here, we describe the results of in vitro assays using purified components of the Drosophila Notch signaling pathway. In vitro glycosylation and ligand binding studies establish that the addition of N-acetylglucosamine onto O-fucose in vitro is sufficient both to enhance Notch binding to the Delta ligand and to inhibit Notch binding to the Serrate ligand. Further elongation by galactose does not detectably influence Notch-ligand binding in vitro. Consistent with these observations, carbohydrate compositional analysis and mass spectrometry on Notch isolated from cells identified only N-acetylglucosamine added onto Notch in the presence of Fringe. These observations argue against models in which Fringe-dependent glycosylation modulates Notch signaling by acting as a precursor to subsequent modifications and instead establish the simple addition of N-acetylglucosamine as a basis for the effects of Fringe on Drosophila Notch-ligand binding.
Avotermin: A Novel Antiscarring Agent

Published literature shows that both physicians and their patients are highly concerned about scarring, even relatively minor scars and those that can be concealed by clothing. Furthermore, both patients and their physicians value any opportunities to improve or minimize scarring. While a range of treatment paradigms have been evaluated, no single therapy has been adopted as a universally accepted standard of care and, currently, there are no marketed pharmaceuticals for the prophylactic reduction of scarring. Many of the available treatments are used empirically and most have not been evaluated in robust prospective, randomized, controlled clinical trials. To address this unmet medical need, translational research into the molecular mechanisms of scarring has led to the discovery and commercial development of a new class of prophylactic medicines that promote the regeneration of normal skin and improve scar appearance. Avotermin, the first agent identified in this class, is the clinical application of human recombinant transforming growth factor β3 (TGFβ3), a key protein involved in scar-free healing observed in embryos. Controlled, double-blind, randomized phase I/II clinical studies have shown that avotermin, administered as an intradermal injection at the time of surgery, leads to both short-term and longer-term (at ≥12 months) improvements in the appearance of scars compared with placebo and standard wound care.
Effects of dietary fat content on adiposity during energy restriction in genetically obese rats.

The effects of the amount of fat provided in a restricted diet on weight loss and body composition were studied in this work. Lean male (Fa/? ) Zucker rats were fed a control diet ad libitum. Obese (fa/fa) Zucker rats were divided into three groups: one group was fed a control diet ad libitum and the other two groups were fed 75% energy-restricted diets, which provided 10 or 50% of calories as fat. After 4 weeks, energy restriction normalized body weight but not body composition in the genetically obese rats. Reductions in adipose tissue weights and adipocyte size, without changes in the cellularity, were observed. Differences only reached statistical significance in subcutaneous adipose tissue. A standard fat content in the diet induced the same fat-free mass reduction as a higher amount of this macronutrient, but a greater body fat reduction. This suggests that the restriction of dietary fat, as well as energy, is necessary to achieve dietary management in obesity.
A Longitudinal Study of the Effects of Ecological Interface Design on Skill Acquisition

Results from evaluations of interface design concepts conducted over short durations may not generalize to longer time spans. In an attempt to address this issue, this paper presents a longitudinal study of the effect of interface design on skill acquisition in which participants' quasi-dally performance was observed over an unprecedented period of six months. The research was conducted in the context of DURESS II, a real-time, interactive thermal-hydraulic process control simulation that was designed to be representative of industrial systems. The performance of two interfaces was compared, one containing physical and functional (P + F) system representations based on the principles of the ecological interface design framework, and a more traditional interface based solely on a physical (P) representation. Participants were required to perform several control tasks, including start-up, tuning, shutdown, and fault management. The results indicate that the P interface led to significantly less-consistent performance than did the P + F interface; with the former, participants occasionally took up to 2 times longer to complete the required tasks, even after 5.5 months of daily practice. There was very little difference in average performance between the two groups. These results have important implications for designing interfaces that lead to efficient performance under normal operating conditions.
Drug induction apoptosis assay as predictive value of chemotherapy response in patients with B-cell chronic lymphocytic leukemia

A large number of prognostic factors are available to help predict the course of the disease for patients with B-cell chronic lymphocytic leukemia (B-CLL). However, it is not clear the involvement of these well established prognostic factors in the clinical response of the patients with B-CLL to the chemotherapy. The possible association of the patient clinical–biological characteristics and the in vitro response to chemotherapic agents may serve to provide powerful predictive information to identify optimum treatment for patients. An apoptosis induction assay displays the patient in vitro responses to chemotherapy and the possible association with their clinical–biological characteristics. In this study, patients showed a significant better in vitro response to drugs when they were in the initial stages of the disease or with low β2 microglobulin serum level. Response to purine analogues was significantly higher in patients with long lymphocyte doubling time (LDT), few cells expressing CD38, normal karyotype or no p53 deletion, whereas there was no correspondence with ZAP-70 expression. Furthermore, a good correlation was shown between in vitro apoptosis induction assay and the patient clinical response to purine analogues. In conclusion, association between in vitro drug sensitivity and some of the markers considered as prognostic factors could help to develop personalised therapeutic regimens for patients with B-CLL.
Efficient multidimensional quantitative hypotheses generation

Finding local interrelations (hypotheses) among attributes within very large databases of high dimensionality is an acute problem for many databases and data mining applications. These include, dependency modeling, clustering large databases, correlation and link analysis. Traditional statistical methods are concerned with the corroboration of (a set of) hypotheses on a given body of data. Testing all of the hypotheses that can be generated from a database with millions of records and dozens of fields is clearly infeasible. Generating, on the other hand, a set of the most "promising" hypotheses (to be corroborated) requires much intuition and ingenuity. We present an efficient method for ranking the multidimensional hypotheses using image processing of data visualization. In the heart of the method lies the use of visualization techniques and image processing ideas to rank subsets of attributes according to the relation between them in the databases. Some of the scalability issues are solved by concise generalized histograms and by using an efficient on-line computation of clustering around a median with only five additional memory words. In addition to presenting our algorithmic methodology, we demonstrate its efficiency and performance by applying it to real census data sets, as well as synthetic data sets.
Heart rate as a predictor of mortality: the MATISS project.

OBJECTIVES This study sought to verify the independent role of heart rate in the prediction of all-cause, cardiovascular, and noncardiovascular mortality in a low-risk male population. METHODS In an Italian population-based observational study, heart rate was measured in 2533 men, aged 40 to 69 years, between 1984 and 1993. Data on cardiovascular risk factors were collected according to standardized procedures. Vital status was updated to December 1997. RESULTS Of 2533 men followed up (representing 24,457 person-years), 393 men died. Age-adjusted death rates for 5 heart rate levels showed increasing trends. The adjusted hazard rate ratios for each heart rate increment were 1.52 (95% confidence interval [CI] = 1.29, 1.78) for all-cause mortality, 1.63 (95% CI = 1.26, 2.10) for cardiovascular mortality, and 1.47 (95% CI = 1.19, 1.80) for noncardiovascular mortality. Relative risks between extreme levels were more than 2-fold for all endpoints considered. CONCLUSIONS Heart rate is an independent predictor of cardiovascular, noncardiovascular, and total mortality in this Italian middle-aged male population.
Early ear development in the embryo of the Zebrafish, Danio rerio

The zebrafish provides an important model for vertebrate inner ear development. The otic placode becomes visible at ∼16 hours (at 28.5°C) and forms a vesicle with a lumen by cavitation at ∼18 hours. Two otoliths appear in the lumen by 19.5 hours, and at about 24 hours the first sensory hair cells are seen, grouped in two small patches, one beneath each otolith, corresponding to future maculae. Staining with fluorescent phalloidin reveals 10–20 hair cells in each macula by 42 hours; between 3 days and 7 days the numbers grow to ∼80 per macula. Neurons of the statoacoustic ganglion are first visible by staining with HNK‐1 antibody at about 24 hours. Serial sections and time‐lapse films show that the neuronal precursors originate by delamination from the ventral face of the otocyst; the peak period of delamination is from 22 hours to 30 hours. The system of semicircular canals forms between 42 hours and 72 hours by outgrowth of protrusions from the walls of the otocyst to form pillars of tissue spanning the lumen. Three further clusters of hair cells also become visible in this period, forming the three cristae. Thus, by the end of the first week, all key components of the ear are present. Subsequent growth produces thousands more hair cells; additional neurons probably derive from proliferation of neuronal precursors within the ganglion. Although the timetable is species‐specific, the principles of inner ear development in the zebrafish seem to be the same as in other vertebrates. © 1996 Wiley‐Liss, Inc.
The role of psychoneuroendocrine factors on spaceflight‐induced immunological alterations

This paper summarizes previous in‐flight infections and novel conditions of spaceflight that may suppress immune function. Granulocytosis, monocytosis, and lymphopenia are routinely observed following short duration orbital flights. Subtle changes within the monocyte and T cell populations can also be noted by flow cytometric analysis. The similarity between the immunological changes observed after spaceflight and other diverse environmental stressors suggest that most of these alterations may be neuroendocrine‐mediated. Available data support the hypothesis that spaceflight and other environmental stressors modulate normal immune regulation via stress hormones, other than exclusively glucocorticoids. It will be essential to simultaneously collect in‐flight endocrine, immunologic, and infectious illness data to determine the clinical significance of these results. Additional research that delineates the neuroendocrine mechanisms of stress‐induced changes in normal immune regulation will allow clinicians in the future to initiate prophylactic immunomodulator therapy to restore immune competence altered by the stress of long‐duration spaceflight and therefore reduce morbidity from infectious illness, autoimmune disease, or malignancy.
Improved therapeutic monitoring with several interventions: a randomized trial.

BACKGROUND Medication errors are frequently related to failure to appropriately select medications or adjust for laboratory parameters. Differences between guideline recommendations and actual frequency of therapeutic laboratory monitoring are substantial. This study evaluated interventions to improve laboratory monitoring at initiation of medication therapy. METHODS This cluster-randomized trial compared 3 interventions to usual care for 10 medications in 15 primary care clinics in a health maintenance organization with an electronic medical record system. Eligible patients, identified from electronic databases, had not received recommended laboratory monitoring within 5 days after new dispensing of a study medication. Interventions were an electronic medical record reminder to the prescribing health care professional, an automated voice message to the patient, and a pharmacy team outreach to the patient. Primary outcome was completion of all recommended baseline laboratory monitoring. RESULTS A total of 961 patients participated in the study. At 25 days, 95 (48.5%) of 196 patients in the electronic medical record reminder group, 177 (66.3%) of 267 in the automated voice message group, 214 (82.0%) of 261 in the pharmacy team outreach group, and 53 (22.4%) of 237 in the usual care group had completed all recommended baseline laboratory monitoring (P<.001). After adjustments, the hazard ratios for completing laboratory monitoring compared with usual care were 2.5 (95% confidence interval, 1.8-3.5) for electronic medical record reminder, 4.1 (95% confidence interval, 3.0-5.6) for automated voice message, and 6.7 (95% confidence interval, 4.9-9.0) for pharmacy team outreach. CONCLUSIONS All 3 interventions were effective in increasing laboratory monitoring when initiating new medications in primary care. Further work is necessary to determine if these interventions improve patient outcomes.