Miracle-dz/UniFAR-FTUs huggingface dataset:
Conversion to organic farming: a multidimensional research object at the crossroads of agricultural and social sciences. A review

Literature on the conversion from intensive to organic farming is scarce. However, both the conversion of farmers to organic farming and of consumers to organic food are the driving forces for the development of the organic sector. In this review, we combine agricultural and social scientists’ viewpoints for a critical appraisal of literature on conversion to organic food and farming. First, a brief historical retrospective enables us to refer the scientific production to the institutional and economic context over the past decades. Secondly, we review the methods used to analyse conversion in agricultural and social sciences, and show that emphasis is most often laid upon the effects of conversion and the motivations to convert, on the basis of comparative approaches with so-called conventional agriculture. Therefore, the literature minimises the importance of transitional aspects and trajectories, and rarely approaches conversion as a longer process than its legal duration and from a wider point of view. Thirdly, we examine the paradigms of input efficiency and system redesign, which frame discussions about transitions in agriculture, beyond organics, and therefore helps shed light on sustainability issues. We suggest that analysing conversion and more generally transitions in agriculture as multidimensional issues, involving both production and social practices, entails interdisciplinary approaches and the redefinition of some central research topics.
A Simple and Practicable Approach on Implementing for the Reduced Triaxial Extension by the Conventional Triaxial Apparatus

Stress path is one of the very important factors of soil strength. It is significant to study the strength and reveal the importance of the impact of sand in different stress path conditions. Firstly, an ameliorating approach on implementing for the reduced triaxial extension by the conventional triaxial apparatus was discussed. Then, In order to study shear behaviors of the eolian sand under different stress path, two monotonic shearing tests with the conventional triaxial compression and the reduced triaxial extension stress path were performed and analyzed. The test results not only indicate that the amelioration on conventional triaxial apparatus is simple, practicable and inexpensive, but also reveal the difference of strength’s parameter between the reduced triaxial extension and conventional triaxial compression stress path. In sum, the stress path has important effect on the strength of the eolian sand.
Does Off-pump Coronary Artery Bypass Reduce Mortality, Morbidity, and Resource Utilization When Compared with Conventional Coronary Artery Bypass? A Meta-analysis of Randomized Trials

The authors undertook a meta-analysis of 37 randomized trials (3369 patients) of off-pump coronary artery bypass surgery versus conventional coronary artery bypass surgery. No significant differences were found for 30-day mortality (odds ratio [OR], 1.02; 95% confidence interval [CI], 0.58–1.80), myocardial infarction (OR, 0.77; 95%CI, 0.48–1.26), stroke (OR, 0.68; 95%CI, 0.33–1.40), renal dysfunction, intraaortic balloon pump, wound infection, rethoracotomy, or reintervention. However, off-pump coronary artery bypass surgery significantly decreased atrial fibrillation (OR, 0.58; 95%CI, 0.44–0.77), transfusion (OR, 0.43; 95%CI, 0.29–0.65), inotrope requirements (OR, 0.48; 95%CI, 0.32–0.73), respiratory infections (OR, 0.41; 95%CI, 0.23–0.74), ventilation time (weighted mean difference, −3.4 h; 95%CI, −5.1 to −1.7 h), intensive care unit stay (weighted mean difference, −0.3 days; 95%CI −0.6 to −0.1 days), and hospital stay (weighted mean difference, −1.0 days; 95%CI −1.5 to −0.5 days). Patency and neurocognitive function results were inconclusive. In-hospital and 1-yr direct costs were generally higher for conventional coronary artery bypass surgery versus off-pump coronary artery bypass surgery. Therefore, this meta-analysis demonstrates that mortality, stroke, myocardial infarction, and renal failure were not reduced in off-pump coronary artery bypass surgery surgery; however, selected short-term and mid-term clinical and resource outcomes were improved compared with conventional coronary artery bypass surgery.
Fast Measurement of Left Ventricular Mass With Real-Time Three-Dimensional Echocardiography: Comparison With Magnetic Resonance Imaging

Background—Left ventricular (LV) mass is an important predictor of morbidity and mortality, especially in patients with systemic hypertension. However, the accuracy of 2D echocardiographic LV mass measurements is limited because acquiring anatomically correct apical views is often difficult. We tested the hypothesis that LV mass could be measured more accurately from real-time 3D (RT3D) data sets, which allow offline selection of nonforeshortened apical views, by comparing 2D and RT3D measurements against cardiac MR (CMR) measurements. Methods and Results—Echocardiographic imaging was performed (Philips 7500) in 21 patients referred for CMR imaging (1.5 T, GE). Apical 2- and 4-chamber views and RT3D data sets were acquired and analyzed by 2 independent observers. The RT3D data sets were used to select nonforeshortened apical 2- and 4-chamber views (3DQ-QLAB, Philips). In both 2D and RT3D images, LV long axis was measured; endocardial and epicardial boundaries were traced, and mass was calculated by use of the biplane method of disks. CMR LV mass values were obtained through standard techniques (MASS Analysis, GE). The RT3D data resulted in significantly larger LV long-axis dimensions and measurements of LV mass that correlated with CMR better (r=0.90) than 2D (r=0.79). The 2D technique underestimated LV mass (bias, 39%), whereas RT3D measurements showed only minimal bias (3%). The 95% limits of agreement were significantly wider for 2D (52%) than RT3D (28%). Additionally, the RT3D technique reduced the interobserver variability (37% to 7%) and intraobserver variability (19% to 8%). Conclusions—RT3D imaging provides the basis for accurate and reliable measurement of LV mass.
Protein Binding of Flucloxacillin in Neonates

The isoxazolyl penicillins, including flucloxacillin, have the highest levels of plasma protein binding among the semisynthetic penicillins. Because only the free fraction of the penicillin is pharmacologically active, it would be useful to measure both protein-bound and free flucloxacillin to determine its protein binding. Until now, flucloxacillin protein binding in newborn infants has been investigated in only two studies with relatively small populations. In the present study, flucloxacillin protein binding was investigated in 56 (preterm) infants aged 3 to 87 days (gestational age, 25-41 weeks). Surplus plasma samples from routine gentamicin assays of each infant were collected and combined to obtain a sufficiently large sample for analysis. Free flucloxacillin was separated from protein-bound flucloxacillin using ultrafiltration. Reversed-phase high-performance liquid chromatography with ultraviolet detection was used to measure free flucloxacillin concentrations in ultrafiltrate and total flucloxacillin concentrations in pooled plasma. Flucloxacillin protein binding was 74.5% ± 13.1% (mean ± standard deviation) with a high variability among the infants (34.3% to 89.7%). High Pearson correlations were found between protein binding and the covariates-plasma albumin concentration (r = 0.804, P < 0.001, n = 18) and plasma creatinine concentration (r = −0.601, P < 0.001, n = 45). Statistically significant but less striking correlations were found between protein binding and gestational age, postconceptional age, body weight, and triglyceride concentration. Because of the high variability of protein binding among infants, it is difficult to devise a flucloxacillin dosage regimen effective for all infants. Individualized dosing, based on free flucloxacillin concentrations, might help to optimize treatment of late-onset neonatal sepsis, but practical obstacles will probably prevent analysis of free flucloxacillin concentrations in newborn infants on a routine basis.
The density of AMPA receptors activated by a transmitter quantum at the climbing fibre‐Purkinje cell synapse in immature rats

We aimed to estimate the number of AMPA receptors (AMPARs) bound by the quantal transmitter packet, their single‐channel conductance and their density in the postsynaptic membrane at cerebellar Purkinje cell synapses. The synaptic and extrasynaptic AMPARs were examined in Purkinje cells in 2‐ to 4‐day‐old rats, when they receive synaptic inputs solely from climbing fibres (CFs). Evoked CF EPSCs and whole‐cell AMPA currents displayed roughly linear current‐voltage relationships, consistent with the presence of GluR2 subunits in synaptic and extrasynaptic AMPARs. The mean quantal size, estimated from the miniature EPSCs (MEPSCs), was ∼300 pS. Peak‐scaled non‐stationary fluctuation analysis of spontaneous EPSCs and MEPSCs gave a weighted‐mean synaptic channel conductance of ∼5 pS (∼7 pS when corrected for filtering). By applying non‐stationary fluctuation analysis to extrasynaptic currents activated by brief glutamate pulses (5 mm), we also obtained a small single‐channel conductance estimate for extrasynaptic AMPARs (∼11 pS). This approach allowed us to obtain a maximum open probability (Po,max) value for the extrasynaptic receptors (Po,max= 0.72). Directly resolved extrasynaptic channel openings in the continued presence of glutamate exhibited clear multiple‐conductance levels. The mean area of the postsynaptic density (PSD) of these synapses was 0.074 μm2, measured by reconstructing electron‐microscopic (EM) serial sections. Postembedding immunogold labelling by anti‐GluR2/3 antibody revealed that AMPARs are localised in PSDs. From these data and by simulating error factors, we estimate that at least 66 AMPARs are bound by a quantal transmitter packet at CF‐Purkinje cell synapses, and the receptors are packed at a minimum density of ∼900 μm−2 in the postsynaptic membrane.
The Ordered Subsets Mirror Descent Optimization Method with Applications to Tomography

We describe an optimization problem arising in reconstructing three-dimensional medical images from positron emission tomography (PET). A mathematical model of the problem, based on the maximum likelihood principle, is posed as a problem of minimizing a convex function of several million variables over the standard simplex. To solve a problem of these characteristics, we develop and implement a new algorithm, ordered subsets mirror descent, and demonstrate, theoretically and computationally, that it is well suited for solving the PET reconstruction problem.
A new species of the Marphysa sanguinea complex from French waters (Bay of Biscay, NE Atlantic) (Annelida, Eunicidae)

Abstract A new species of Eunicidae, Marphysa victori sp. n. , has been identified from Arcachon Bay, Bay of Biscay, NE Atlantic. This new species, belonging to the sanguinea complex, is characterised by branchiae with long filaments from chaetigers 26–34, the presence of four types of pectinate chaetae with first ones present from chaetiger 2, a large number of both pectinate chaetae and compound spinigers, and the pygidium with only one pair of pygidial cirri. An identification key for European species of the genus Marphysa is provided.
Conjugal Transfer of Plasmid-Borne Multiple Antibiotic Resistance in Streptococcus faecalis var. zymogenes

A strain of Streptococcus faecalis var. zymogenes, designated JH1, had high-level resistance to the antibiotics streptomycin, kanamycin, neomycin, erythromycin, and tetracycline. These resistances were lost en bloc from approximately 0.1% of cells grown in nutrient broth at 45 C. The frequency of resistance loss was not increased by growth in the presence of the “curing” agents acriflavine or acridine orange, but after prolonged storage in nutrient agar 17% of cells became antibiotic sensitive. Covalently closed circular deoxyribonucleic acid (DNA) molecules were isolated from the parental strain and from antibiotic-sensitive segregants by using cesium chloride-ethidium bromide gradients. DNA molecular species were identified by using neutral sucrose gradients. Strain JH1 contained two covalently closed circular DNA species of molecular weights 50 × 106 and 38 × 106. An antibiotic-sensitive segregant, strain JH1-9, had lost the larger molecular species. A second sensitive segregant, strain JH1-5, had also lost the larger molecular species but a new molecular species of approximate molecular weight 6 × 106 was present. The antibiotic resistances that were curable from the parental strain were transferred to antibiotic-sensitive strains of S. faecalis and to strain JH1-9, during mixed incubation in nutrient broth at 37 C. Data to be described are interpreted to suggest that the transfer is by a conjugal mechanism. Analysis of the plasmid species in recipient clones showed that all had received the plasmid of molecular weight 50 × 106. Strain JH1-5 was not a good recipient. Analysis of one successful recipient clone of JH1-5 revealed that it had gained the 50 × 106 molecular weight plasmid but lost the 6 × 106 molecular weight species. These data are interpreted to mean that the multiple antibiotic resistance is borne by a transferable plasmid of 50 × 106 molecular weight, and that in clone JH1-5 this plasmid suffered a large deletion leaving only a 6 × 106 remnant which was incompatible with the complete replicon.
Adaptive controller design and disturbance attenuation for a general class of sequentially interconnected SISO linear systems with noisy output measurements

We study the adaptive controller design for a special class of MIMO system, which is composed of arbitrary but a finite number of SISO linear subsystems under noisy output measurements, S1, …, Sm, sequentially interconnected with additional feedbacks. Using the design approach as [1] and [2], we obtain a class of adaptive controllers which guarantees the boundedness of closed-loop signals with bounded exogenous disturbances, and achieves asymptotic tracking if exogenous disturbances are bounded and of finite energy. Moreover, the closed-loop system admits a guaranteed disturbance attenuation level with respect to the exogenous disturbance inputs, where the ultimate attenuation lower bound for the achievable performance level is equal to the noise intensity in the measurement channel of S1.
Calcium-Induced Conformational Transition of Trout Ependymins Monitored by Tryptophan Fluorescence

Ependymins are secretory, calcium-binding sialoproteins which are the predominant constituents of the cerebrospinal fluid of many teleost fish. A bound form of these regeneration-responsive glycoproteins is associated with collagen fibrils of the extracellular matrix. Here, the tryptophan fluorescence of ependymins was monitored at various Ca2+ concentrations. Two distinct states were identified with a relatively sharp transition at about 1 mM Ca2+. In agreement with previous circular dichroism measurements, this strongly supports the hypothesis that a calcium-induced conformational change is important for the interaction of ependymins with components of the extracellular matrix. Such interactions with constituents of various basal laminae would also explain the important roles of piscine ependymins as well as invertebrate and mammalian ependymin-related proteins for cell adhesion processes and cell migration.
An essential role for interferon gamma in resistance to Mycobacterium tuberculosis infection

Tuberculosis, a major health problem in developing countries, has reemerged in recent years in many industrialized countries. The increased susceptibility of immunocompromised individuals to tuberculosis, and many experimental studies indicate that T cell- mediated immunity plays an important role in resistance. The lymphokine interferon gamma (IFN-gamma) is thought to be a principal mediator of macrophage activation and resistance to intracellular pathogens. Mice have been developed which fail to produce IFN-gamma (gko), because of a targeted disruption of the gene for IFN-gamma. Upon infection with Mycobacterium tuberculosis, although they develop granulomas, gko mice fail to produce reactive nitrogen intermediates and are unable to restrict the growth of the bacilli. In contrast to control mice, gko mice exhibit heightened tissue necrosis and succumb to a rapid and fatal course of tuberculosis that could be delayed, but not prevented, by treatment with exogenous recombinant IFN-gamma.
Protein Kinase C Inhibitor Sotrastaurin in De Novo Liver Transplant Recipients: A Randomized Phase II Trial

Efficacy and safety of protein kinase C inhibitor sotrastaurin (STN) with tacrolimus (TAC) was assessed in a 24‐month, multicenter, phase II study in de novo liver transplant recipients. A total of 204 patients were randomized (1:1:1:1) to STN 200 mg b.i. d. + standard‐exposure TAC (n = 50) or reduced‐exposure TAC (n = 52), STN 300 mg b.i. d. + reduced‐exposure TAC (n = 50), or mycophenolate mofetil (MMF) 1 g b.i. d. + standard‐exposure TAC (control, n = 52); all with steroids. Owing to premature study termination, treatment comparisons were only conducted for Month 6. At Month 6, composite efficacy failure rates (treated biopsy‐proven acute rejection episodes of Banff grade ≥1, graft loss, or death) were 25.0%, 16.5%, 20.9% and 15.9% for STN 200 mg + standard TAC, STN 200 mg + reduced TAC, STN 300 mg + reduced TAC and control groups, respectively. Median estimated glomerular filtration rates were 84.0, 83.3, 81.1 and 75.3 mL/min/1.73 m2, respectively. Gastrointestinal events (constipation, diarrhea, and nausea), infection, and tachycardia were more frequent in STN groups. More patients in STN groups experienced serious adverse events compared with the control group (62.3–70.8% vs. 51.9%). STN‐based regimens were associated with a higher efficacy failure rate and higher incidence of adverse events with no significant difference in renal function between the groups.
Characterization of Structural Changes in Vimentin Bearing an Epidermolysis Bullosa Simplex-like Mutation Using Site-directed Spin Labeling and Electron Paramagnetic Resonance*

Mutations in intermediate filament protein genes are responsible for a number of inherited genetic diseases including skin blistering diseases, corneal opacities, and neurological degenerations. Mutation of the arginine (Arg) residue of the highly conserved LNDR motif has been shown to be causative in inherited disorders in at least four different intermediate filament (IF) proteins found in skin, cornea, and the central nervous system. Thus this residue appears to be broadly important to IF assembly and/or function. While the genetic basis for these diseases has been clearly defined, the inability to determine crystal structure for IFs has precluded a determination of how these mutations affect assembly/structure/function of IFs. To investigate the impact of mutation at this site in IFs, we have mutated the LNDR to LNDS in vimentin, a Type III intermediate filament protein, and have examined the impact of this change on assembly using electron paramagnetic resonance. Compared with wild type vimentin, the mutant shows normal formation of the coiled coil dimer, with a slight reduction in the stability of the dimer in rod domain 1. Probing the dimer-dimer interactions shows the formation of normal dimer centered on residue 191 but a failure of dimerization at residue 348 in rod domain 2. These data point toward a specific stage of assembly at which a common disease-causing mutation in IF proteins interrupts assembly.
Surface analysis of ProFile instruments by scanning electron microscopy and X-ray energy-dispersive spectroscopy: a preliminary study.

AIM The purpose of this preliminary study was to analyze surface irregularities on ProFile nickel-titanium (NiTi) rotary instruments before use, after sterilization by two different methods and after instrumentation of molar root canals. METHODOLOGY Five new ProFile NiTi rotary instruments with 0.04 taper, size 20, five instruments with 0.04 taper, size 25 and five with 0.06 taper, size 20 were analyzed by scanning electron microscopy (SEM) and X-ray energy-dispersive spectroscopy (EDS). The instruments were then divided into two groups: three of each taper and size were sterilized in a dry heat sterilizer, whilst two of each taper and size were sterilized in an autoclave. After inspection by the same techniques, the files were used to instrument six molar root canals, and again analyzed by SEM/EDS. RESULTS Together with the usual machining defects, a variable amount of material containing mainly carbon and sulphur was found on the surface of new instruments. This material was not removed by standard cleaning and sterilization procedures. The use of the files for instrumentation of root canals eliminated a considerable amount of the adhered substance, but deposits rich in calcium and phosphorus accumulated on the remaining impurities. CONCLUSIONS The adherence of dentine on surface deposits found on new ProFile instruments requires special cleaning, prior to sterilization.
Pareto-Based Multiobjective Machine Learning: An Overview and Case Studies

Machine learning is inherently a multiobjective task. Traditionally, however, either only one of the objectives is adopted as the cost function or multiple objectives are aggregated to a scalar cost function. This can be mainly attributed to the fact that most conventional learning algorithms can only deal with a scalar cost function. Over the last decade, efforts on solving machine learning problems using the Pareto-based multiobjective optimization methodology have gained increasing impetus, particularly due to the great success of multiobjective optimization using evolutionary algorithms and other population-based stochastic search methods. It has been shown that Pareto-based multiobjective learning approaches are more powerful compared to learning algorithms with a scalar cost function in addressing various topics of machine learning, such as clustering, feature selection, improvement of generalization ability, knowledge extraction, and ensemble generation. One common benefit of the different multiobjective learning approaches is that a deeper insight into the learning problem can be gained by analyzing the Pareto front composed of multiple Pareto-optimal solutions. This paper provides an overview of the existing research on multiobjective machine learning, focusing on supervised learning. In addition, a number of case studies are provided to illustrate the major benefits of the Pareto-based approach to machine learning, e.g., how to identify interpretable models and models that can generalize on unseen data from the obtained Pareto-optimal solutions. Three approaches to Pareto-based multiobjective ensemble generation are compared and discussed in detail. Finally, potentially interesting topics in multiobjective machine learning are suggested.
Probabilistic Analysis of Parallel Program with Partially Eliminated Barriers

Since barrier synchronization is a simple means to guarantee the order of data producing and data consuming, it is often used in parallel programs. However, barrier synchronization causes the processors' idle time to increase. To reduce the overhead of barrier synchronization, we have proposed an algorithm which eliminates barrier synchronizations and evaluated its validity experimentally in our previous study. In this paper, we model the behavior of parallel programs and proposed a dependency matrix to represent dependencies among processors. Using the behavioral model, we evaluated the execution time of parallel programs which have three typical dependency patterns. Based on results, we found that 1) if a processors depends on less other processors, the obtained effect of eliminating barriers is higher, 2) even if the number of directly-depended processors is the same between two dependency patterns, less indirectly-depended processors in all previous phases provide more effect of eliminating barriers.