Miracle-dz/UniFAR-FTUs huggingface dataset:
Nessi: a python network simulator for fast protocol development

A new and simple network simulator Nessi is described in this paper. While other simulators focus on minimizing the simulation time, Nessi tries to minimize the development time and the difficulties to implement a new simulation model. As such, it is mainly oriented toward educational use, where it enables students to implement or modify simulation models of protocols with minimal overhead. A second application of Nessi is for verification and performance evaluation of new protocols, where it allows the developer to easily explore different options. Nessi comes with an easy to use graphical interface that allows the user to interactively monitor the behavior of a simulation, to modify simulation parameters and to plot results
Lysosomal membrane response of earthworm, Eisenia fetida, to arsenic contamination in soils

Earthworm (Eisenia fetida) were exposed to sandy soils contaminated with arsenate (0.01–0.3 μmol g−1) for 28 days. Lysosomal membrane stability was used as a biomarker to determine the applicability of neutral‐red retention times (NRRTs) for arsenic (As) toxicity to earthworm in soils. Total As and As speciation were analyzed to evaluate dose–response relationship between As accumulation and NRRTs and to observe the role of As metabolism in earthworms on a subcellular level toxicity. Significant decrease of NRRTs was found with the increasing As concentration in soils (ANOVA, P < 0.05). Adverse effects on earthworm survival and growth did not occur when exposed to 0.1 and 0.05 μmol g−1 at 14 and 28 days, respectively, whereas NRRTs showed significant reduction from the control, as was readily bioconcentrated in the reduced form of As(III) in earthworms and clear dose–response relationships were found for As body burden and NRRTs. Therefore, it is possible to conclude that As has an adverse effect on lysosomal membrane of coelomocytes, and NRRT assay is a potentially applicable method to assess As toxicity as an early warning tool. Also, sequestered As in the form of As(III)‐thiol complex can be expected to cause an adverse effect on lysosomal membrane stability. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
The Involvement of the Anterolateral Ligament in Rotational Control of the Knee

Background: Rotational control of the knee is crucial for knee stability. The anterolateral ligament (ALL) has been identified as a potentially important structure involved in rotational control of the knee. Purpose/Hypothesis: The purpose of this study was to determine, utilizing a navigation system, the involvement of the anterior cruciate ligament (ACL), the iliotibial band (ITB), and the ALL in tibial internal rotational control of the knee. The hypothesis was that the ALL would be involved in rotational control of the knee at varying degrees of knee flexion. Study Design: Controlled laboratory study. Methods: Twelve fresh-frozen cadaveric knees were tested in internal rotation at 20° and 90° of flexion and then subsequently tested using a simulated pivot-shift test consisting of coupled axial rotation at 30° of flexion. Serial sectioning of the ACL, ALL, and ITB was performed. On the contralateral knee, sectioning was performed in the reverse order. Measurements were collected using a surgical navigation system before and after each sectioning. Results: After ACL sectioning, an incision of the ALL induced a significant increase in internal rotation (+19.2% [P = .0002] at 20°; +21.8% [P = .0029] at 90°) and in coupled axial rotation (+43.0%; P = .0035) compared with the intact knee as well as a significant increase in internal rotation at 90° (+13.4%; P = .009) and in coupled axial rotation (+30.8%; P = .0124) compared with the ACL-deficient knee. After ITB sectioning, an additional ALL section caused a significant increase in internal rotation (+39.0% [P = .002] at 20°; +63.0% [P = .0147] at 90°) and in coupled axial rotation (+59.7%; P = .0003) compared with the intact knee as well as a significant increase in internal rotation at 90° (+14.8%; P = .0067) in comparison to the ITB-deficient knee. Conclusion: The ALL is involved in rotational control of the knee at varying degrees of knee flexion and during a simulated pivot shift. Concomitant to an ACL or ITB transection, sectioning the ALL further increased rotational laxity. Clinical Relevance: This laboratory study demonstrated that the ALL provides rotational control of the knee in combination with the ACL and/or ITB.
Mekong Hydropower Development

Pending decisions may unleash lower Mekong dam construction, despite management challenges and troubling environmental and social impacts. The Mekong River is one of the world's last large rivers remaining mostly undammed. But China is constructing a series of eight hydropower projects on the upper Mekong. Although there are currently no dams across the mainstream channel (not including the tributaries) in the Lower Mekong Basin (LMB), nevertheless, in September 2010, the Lao People's Democratic Republic petitioned the Mekong River Commission (MRC) to begin the formal process of approving the first of 11 proposed dams across the lower Mekong (see the figure) (1). Although such a cascade would provide substantial power, it would likely reduce biodiversity and ecosystem service values of the LMB, while undercutting the livelihood and food security of millions of people. Decisions on this initial proposal expected over the coming months by the MRC countries may contribute to promoting high-impact hydropower development or to a movement toward integrated, transboundary river-basin management that could serve as a model for other rivers.
A generative model for concurrent image retrieval and ROI segmentation

This paper proposes a probabilistic generative model that concurrently tackles the problems of image retrieval and detection of the region-of-interest (ROI). By introducing a latent variable that classifies the matches as true or false, we specifically focus on the application of geometric constrains to the keypoint matching process and the achievement of robust estimates of the geometric transformation between two images showing the same object. Our experiments in a challenging image retrieval database demonstrate that our approach outperforms the most prevalent approach for geometrically constrained matching, and compares favorably to other state-of-the-art methods. Furthermore, the proposed technique concurrently provides very good segmentations of the region of interest.
A local based approach for path planning of manipulators with a high number of degrees of freedom

This paper presents an alternative to the Potential Field Method of computing local collision-free motions for general manipulators. The main distinction is that we separate the description of the task from constraints of anti-collision. This enables to control accurately all relevant measures of the problem. A task is expressed by the minimization of a function plus eventually some geometric constraints, whereas anti-collision is translated into very simple linear constraints through the methods of the velocity dampers and the tangent separating planes. This approach is applied to the control of manipulators with a high number of degrees of freedom, using hierarchical descriptions of the environment and the robots. This is illustrated by two realizations, path planning for a ten link manipulator in the cluttered environment of a nuclear plant reactor, and cooperative tasks between two six degree of freedom robots. In the end we discuss how to incorporate the action of a global planner in this general framework.
Bio‐distribution and in vivo antioxidant effects of cerium oxide nanoparticles in mice

Cerium oxide nanoparticles have oxygen defects in their lattice structure that enables them to act as a regenerative free radical scavenger in a physiological environment. We performed a comprehensive in vivo analysis of the biological distribution and antioxidant capabilities of nanoceria administered to mice perorally (PO), intravenously (IV), or intraperitoneally (IP) by dosing animals weekly for 2 or 5 weeks with 0.5 mg kg−1 nanoceria. Next, we examined if nanoceria administration would decrease ROS production in mice treated with carbon tetrachloride (CCl4). Our results showed that the most extensive and cumulative nano‐deposition was via IV and IP administered while PO administration showed mice excreted greater than 95% of their nanoceria within 24 h. Organ deposition for IV and IP mice was greatest in the spleen followed by the liver, lungs, and kidneys. Elimination for all administration routes was through feces. Nanoceria administration showed no overt toxicity, however, WBC counts were elevated with IV and IP administration. Our in vivo studies show that nanoceria administration to mice with induced liver toxicity (by CCl4) showed similar findings to mice treated with N‐acetyl cystine (NAC), a common therapeutic to reduce oxidative stress. Taken together, our studies show that nanoceria remains deposited in tissues and may decrease ROS, thereby suggesting that cerium oxide nanoparticles may be a useful antioxidant treatment for oxidative stress. © 2011 Wiley Periodicals, Inc. Environ Toxicol 2013.
Compensation of unmodeled puma manipulator dynamics

Forces unmodeled by Lagrange-Euler dynamics restrict the trajectory tracking accuracy of dynamics based PUMA manipulator control laws. The ability of unmodeled force compensation techniques to eliminate those restrictions, enabling dynamics based PUMA controllers to accurately track a high speed trajectory, has been identified. Implementation of nonlinear velocity dependent friction compensation in the feedforward loop significantly improves controller efficacy. A combination of feedforward and feedback compensation techniques permits tracking accuracy sufficient for gross motion control of a PUMA manipulator without additional instrumentation. The effectiveness of proposed modern control theories can now be compared to an experimentally determined manipulator control performance baseline.
Toxicologic and immunologic effects of perinatal exposure to the brominated diphenyl ether (BDE) mixture DE‐71 in the Sprague‐Dawley rat

Brominated diphenyl ethers (BDEs) are persistent environmental contaminants found in human blood, tissues, and milk. To assess the impact of the commercial BDE mixture DE‐71 on the developing immune system in relation to hepatic and thyroid changes, adult (F0) rats were exposed to DE‐71 by gavage at doses of 0, 0.5, 5, or 25 mg/kg body weight (bw)/d for 21 weeks. F0 rats were bred and exposure continued through gestation, lactation and postweaning. F1 pups were weaned and exposed to DE‐71 by gavage from postnatal day (PND) 22 to 42. On PND 42, half of the F1 rats were assessed for toxicologic changes. The remaining F1 rats were challenged with the T‐dependent antigen keyhole limpet hemocyanin (KLH) and immune function was assessed on PND 56. Dose‐dependent increases in total BDE concentrations were detected in the liver and adipose of all F0 and F1 rats. In F0 rats, increased liver weight, hepatocellular hypertrophy, and decreased serum thyroxine (T4) were characteristic of DE‐71 exposure. In F1 rats perinatal DE‐71 exposure caused a nondose‐dependent increase in body weight and dose‐dependent increases in liver weight and hepatocellular hypertrophy. Serum T3 and T4 levels were decreased. In spleen from DE‐71 exposed rats the area occupied by B cells declined while the area occupied by T cells increased; however, cellular and humoral immune responses to KLH challenge were not altered. Thus hepatic and thyroid changes in rats exposed perinatally to DE‐71 were associated with altered splenic lymphocyte populations, an effect which has been linked to hypothyroidism. © 2011 Wiley Periodicals, Inc. Environ Toxicol, 2013.
A hybrid graph-based and non-linear late fusion approach for multimedia retrieval

Nowadays, multimedia retrieval has become a task of high importance, due to the need for efficient and fast access to very large and heterogeneous multimedia collections. An interesting challenge within the aforementioned task is the efficient combination of different modalities in a multimedia object and especially the fusion between textual and visual information. The fusion of multiple modalities for retrieval in an unsupervised way has been mostly based on early, weighted linear, graph-based and diffusion-based techniques. In contrast, we present a strategy for fusing textual and visual modalities, through the combination of a non-linear fusion model and a graph-based late fusion approach. The fusion strategy is based on the construction of a uniform multimodal contextual similarity matrix and the non-linear combination of relevance scores from query-based similarity vectors. The proposed late fusion approach is evaluated in the multimedia retrieval task, by applying it to two multimedia collections, namely the WIKI11 and IAPR-TC12. The experimental results indicate its superiority over the baseline method in terms of Mean Average Precision for both considered datasets.
Classification of polycyclic aromatic hydrocarbons based on mutagenicity in lung tissue through DNA microarray

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental pollutants produced in the combustion of organic matter. Exposure to PAHs raises the risk of lung cancer and inflammatory and allergic disorders such as asthma. DNA microarray technologies have been applied to research on toxicogenomics in the recent years. To evaluate the mutagenicity of PAHs and constituents of environmental pollutants in lung tissue, including metabolic activation, human alveolar epithelial type II cells (A549) were treated with nonmutagenic PAH pyrene and with the mutagenic PAHs benzo‐[a]‐pyrene, 1‐nitropyrene, or 1,8‐dinitropyrene. Comparison of genome‐wide microarray expression profiles between a nonmutagenic and a mutagenic PAH‐treated group revealed that xenobiotic response genes such as CYP1B1 were commonly upregulated in two groups and that DNA damage induced genes, especially p53‐downstream genes such as p21 (CDKN1A) were upregulated only in the mutagenic PAH‐treated group. Pretreatment with cytochrome P450 inhibitor α‐naphthoflavone or p53 inhibitor pifithrin‐α inhibited the benzo‐[a]‐pyrene‐induced p21 expression. These data suggest that when PAHs enter the cells, lung epithelium induces PAH metabolic activating enzymes, and then the DNA damages‐recognition signal is converged with p53 downstream genes. This metabolic activation and DNA damage is induced in lung epithelium, and the mutagenicity of PAHs can be classified by DNA microarray expression profiles. © 2011 Wiley Periodicals, Inc. Environ Toxicol 28:652–659, 2013.
Use of sign intramedullary nailing in open tibia and femur fractures at Moi Teaching and Referral Hospital, Eldoret, Kenya

Background: Interlocking intramedullary nailing is the current method of choice for fixation of both open and closed tibia and femur fractures. This has been associated with excellent results. Objective: To assess the functional outcome of SIGN intramedullary nailing in the management of open tibia and femur fractures managed at Moi Teaching and Referral Hospital. Design: A retrospective analytical study between February 2005 and December, 2008. Setting: Moi Teaching and Referral Hospital, Eldoret. Subjects: All patients with open tibia and femur fractures who presented at the Moi Teaching and Referral Hospital and had fracture stabilized by SIGN intramedullary nailing during the study period. Results: Forty three open fractures in forty one patients were treated using SIGN intramedullary nailing in the fracture stabilization. Thirty seven (90.2%) of the patients were males while 4 (9.8%)were females. Two (4.9%) patients had bilateral tibial fractures. The average age of the patients was 37 with a range of 14 to 61 years. Road traffic accidents were the leading cause of injury followed by gunshot injuries. Other causes included falls and assault. All patients received surgical antibiotic and tetanus prophylaxis. Antibiotic therapy was maintained post operatively up to a period of two weeks. Patients were discharged with evident satisfactory wound healing and ability to walk on crutches. Irrespective of the fracture configuration, patients were advised to remain non weight bearing for the first 6 weeks. Thirty seven (90.2%) patients turned up for follow up. Sixteen per cent had superficial infections which responded to antibiotic treatment and dressings. Four (11%) had deep infection (3 femur and 1 tibia), 1 in Gustillo IIIB, 2 Gustillo IIIA and 1 Gustillo II. Exchange nailing was done in three patients and one patient had the nail removed and fracture fixed with an external fixator. Conclusion: This study shows good results of intramedullary nailing for grade I, II and IIIA-fractures. We recommend treatment of these injuries by adequate debridement followed by immediate or delayed intramedullary nailing.
Impairment of the mitochondrial oxidative phosphorylation system and oxidative stress in liver of crucian carp (Carassius auratus L.) exposed to microcystins

Hepatotoxic microcystins (MCs) are produced by cyanobacteria in diverse water bodies and the pathophysiology includes induction of reactive oxygen species and adenosine triphosphate (ATP) depletion in cells. In this study, we evaluated MCs induced changes in the oxidative phosphorylation (OXPHOS) system in mitochondria of crucian carp liver. Fish were subdivided into two groups that were intraperitoneally injected with two doses of MCs (50 and 200 MC‐LReq μg/kg bw) and were sacrificed at 1, 3, 12, 24, and 48 h postinjection. The activities of five enzyme complexes of electron transport chain and mRNA expression of mitochondrial‐encoded genes (cox1, cox2, cox3, and atp6) were significantly reduced in a time‐dependent pattern after injection. There were also changes in mitochondrial ultrastructure, decreases in ATPase activities and reduction in antioxidant level after MCs exposure. Disorder in the OXPHOS system and decreased activities of antioxidative enzymes might contribute to bioenergy deficiency and consequent hepatocyte damage induced by MCs. © 2011 Wiley Periodicals, Inc. Environ Toxicol 29: 30–39, 2014.
Attention But Not Awareness Modulates the BOLD Signal in the Human V1 During Binocular Suppression

Activity in the primary visual cortex is modulated by attention to an object, but not by whether the object is visible. Although recent psychophysical studies indicate that visual awareness and top-down attention are two distinct processes, it is not clear how they are neurally dissociated in the visual system. Using a two-by-two factorial functional magnetic resonance imaging design with binocular suppression, we found that the visibility or invisibility of a visual target led to only nonsignificant blood oxygenation level–dependent (BOLD) effects in the human primary visual cortex (V1). Directing attention toward and away from the target had much larger and robust effects across all study participants. The difference in the lower-level limit of BOLD activation between attention and awareness illustrates dissociated neural correlates of the two processes. Our results agree with previously reported V1 BOLD effects on attention, while they invite a reconsideration of the functional role of V1 in visual awareness.
Concentration‐dependent induction of reactive oxygen species, cell cycle arrest and apoptosis in human liver cells after nickel nanoparticles exposure

Due to advent of nanotechnology, nickel nanoparticles (Ni NPs) are increasingly recognized for their utility in various applications including catalysts, sensors and electronics. However, the environmental and human health effects of Ni NPs have not been fully investigated. In this study, we examined toxic effects of Ni NPs in human liver (HepG2) cells. Ni NPs were prepared and characterized by X‐ray diffraction, transmission electron microscopy and dynamic light scattering. We observed that Ni NPs (size, ∼28 nm; concentration range, 25–100 μg/mL) induced cytotoxicity in HepG2 cells and degree of induction was concentration‐dependent. Ni NPs were also found to induce oxidative stress in dose‐dependent manner evident by induction of reactive oxygen species and depletion of glutathione. Cell cycle analysis of cells treated with Ni NPs exhibited significant increase of apoptotic cell population in subG1 phase. Ni NPs also induced caspase‐3 enzyme activity and apoptotic DNA fragmentation. Upregulation of cell cycle checkpoint gene p53 and bax/bcl‐2 ratio with a concomitant loss in mitochondrial membrane potential suggested that Ni NPs induced apoptosis in HepG2 cells was mediated through mitochondrial pathway. This study warrants that applications of Ni NPs should be carefully assessed as to their toxicity to human health. © 2013 Wiley Periodicals, Inc. Environ Toxicol 30: 137–148, 2015.
Results of Anterior Cruciate Ligament Reconstruction With Patellar Tendon Autografts: Objective Factors Associated With the Development of Osteoarthritis at 20 to 33 Years After Surgery

Background: Few studies exist that report objective radiographic and physical examination results at >20 years after anterior cruciate ligament (ACL) reconstruction. Hypothesis: The risk of osteoarthritis (OA) at >20 years after surgery would be statistically significantly higher if an increased severity of factors was present. Study Design: Cohort study; Level of evidence, 2. Methods: Between 1982 and 1994, 1428 knees met the inclusion criteria of being primary ACL surgery, having no existing OA or other ligamentous laxity, and having no known graft tear. Prospective data analyzed included demographics; meniscus and articular cartilage status; ratings of bilateral standing posteroanterior weightbearing, lateral, and Merchant view radiographs; KT-1000 arthrometer measurements; and range of motion measurements. Radiographs were graded for joint space narrowing, sclerosis, and osteophytes according to International Knee Documentation Committee (IKDC) criteria. Multivariate and univariate logistic models were used to determine the effect of potential predictors on the odds of having radiographic evidence of OA. IKDC and Cincinnati Knee Rating System (CKRS) subjective surveys were conducted. Results: A minimum 20-year objective follow-up was obtained for 423 knees at a mean of 22.5 ± 2.1 years postoperatively. If a patient lacked normal extension or flexion at discharge, the odds of lacking normal extension or flexion at follow-up were 19.7 and 7.97, respectively (P < .001). Radiographic ratings were normal for 35.2%, nearly normal for 36.2%, abnormal for 20.1%, and severely abnormal for 8.5%. Multivariate analysis showed that the predictive factors for the presence of OA in the long-term were medial meniscectomy, older age at surgery, and less than normal knee extension at discharge. The odds ratios for statistically significant factors for the presence of any OA at follow-up were 2.02 for knee extension loss at discharge, 2.98 for medial meniscectomy, 1.65 for lateral meniscectomy, 1.06 for age at follow-up, 1.62 for chronic injury type, and 2.17 for articular cartilage damage. The IKDC and CKRS subjective scores were progressively and statistically significantly lower as the level of OA was greater. Conclusion: The prevalence rate of developing moderate to severe OA at >20 years after ACL reconstruction was 28.6%. Significant factors predictive of OA in the long-term were older age at surgery, medial meniscectomy, and knee extension loss.
Iron Oxide Based Nanoparticles for Multimodal Imaging and Magnetoresponsive Therapy.

Magnetoresponsive Therapy Nohyun Lee, Dongwon Yoo, Daishun Ling,†,‡,⊥ Mi Hyeon Cho, Taeghwan Hyeon,*,†,‡ and Jinwoo Cheon* †Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 151-742, Korea ‡School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Korea Department of Chemistry, Yonsei University, Seoul 120-749, Korea School of Advanced Materials Engineering, Kookmin University, Seoul 136-702, Korea Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China