Miracle-dz/UniFAR-FTUs huggingface dataset:
An investigation of the BSSE effect on the evaluation of Ab Initio interaction energies for cisplatin-water complexes

In this article the role played by the effective core potential (Pt atom) on the evaluation of basis set superposition error (BSSE) and interaction energies for the complex between cisplatin ([Pt(NH3)2Cl2]) and water was investigated. Eight distinct spatial monomer orientations in the cisplatin-water complex were considered with the counterpoise procedure being employed to calculate the BSSE. The BSSE effect on potential energy curves, required for the determination of Lennard-Jones parameters, is also discussed. The calculations were performed at the HF, DFT (BLYP, B3LYP, BP86, PBE, PW91 functional) and MP2 level with Pople's split valence and Dunning's correlated consistent basis sets.
Design aspects of poly(alkylcyanoacrylate) nanoparticles for drug delivery

Poly(alkylcyanoacrylate) (PACA) nanoparticles were first developed 25 years ago taking advantage of the in vivo degradation potential of the polymer and of its good acceptance by living tissues. Since then, various PACA nanoparticles were designed including nanospheres, oil-containing and water-containing nanocapsules. This made possible the in vivo delivery of many types of drugs including those presenting serious challenging delivery problems. PACA nanoparticles were proven to improve treatments of severe diseases like cancer, infections and metabolic disease. For instance, they can transport drugs accross barriers allowing delivery of therapeutic doses in difficult tissues to reach including in the brain or in multidrug resistant cells. This review gives an update on the more recent developments and achievements on design aspects of PACA nanoparticles as delivery systems for various drugs to be administered in vivo by different routes of administration.
Nursing home-associated pneumonia, hospital-acquired pneumonia and ventilator-associated pneumonia: the contribution of dental biofilms and periodontal inflammation.

Evidence is building that dental plaque and inflammatory periodontal disease may contribute to the initiation and/or progression of certain lung diseases. Pneumonia is an acute infection of the lung, demonstrating the following respiratory signs and symptoms: cough; shortness of breath; increased respiratory rate; sputum production; and chest pain. Pneumonia may also induce nonspecific systemic symptoms, including fever, fatigue, muscle aches, and lack of appetite. Although pneumonia can be caused by viruses or fungi, bacteria are the most frequent cause of this infection and are the most easily treatable.
Moving object segmentation in surveillance video based on adaptive mixtures

This paper presents an adaptive mixtures-based method for segmenting moving objects in surveillance video with pixel-wise accuracy. The proposed method employs a Gaussian mixture model (GMM) to represent the intensity change of a pixel over time. The GMM consists of a background component and one or more moving object component(s). The parameters of the GMM are estimated by using an adaptive algorithm that is a non-parametric and data-driven approach. The components in the GMM are subsequently classified into a background and moving objects according to their weights in the GMM. Experimental results demonstrate that the proposed method can successfully and robustly segment the moving objects in surveillance video.
USING FAULT MODELS IN STATE OBSERVERS METHODOLOGY FOR CRACK DETECTION IN CONTINUOS SYSTEMS

Abstract. Nowadays a major factor of interest in industries in relationship to development of new techniques for detection and localization of faults it is the concern with the security of their systems. There is need for supervising and monitoring in order to detect and correct any fault as fast as possible. It is verified actually, that some determined parameters of the systems may vary during the process, due to the specific characteristics or the natural wearing of its components. It is known that even in well-designed systems the occurrence of cracks in some components can cause economic losses or lead to dangerous situations. With the help of the state observers methodology one can reconstruct the unmeasured states of the system, since that it is observable, becoming possible in this way to estimate the measures for locations of difficult access. The technique of state observers consists in developing a model for the system under analysis and comparing the estimate of outcome with the measured one, the difference between these two resulting in a residue that is used for analysis. In this work a bank of signals associated to a model of crack was assembled in order to follow its progress. The data acquired from the computational simulations in a cantilever beam discretized by means of the technique of finite elements, had been sufficiently satisfactory, validating the proposed methodology
Exercise-test Tc-99m tetrofosmin SPECT in patients with chronic ischemic left ventricular dysfunction: direct comparison with Ti-201 reinjection.

BACKGROUND This study was designed to compare the results of exercise-rest technetium-99m tetrofosmin single photon emission computed tomography (SPECT) with those of thallium-201 reinjection at rest after exercise-redistribution imaging in the same patients with chronic ischemic left ventricular (LV) dysfunction. METHODS Within 1 week, 33 patients with chronic myocardial infarction and LV dysfunction underwent exercise-rest tetrofosmin SPECT and Tl-201 reinjection at rest after exercise-redistribution imaging. In each patient, regional tetrofosmin and Tl-201 activity was quantitatively measured in 22 myocardial segments. Regional LV function was assessed in corresponding segments by echocardiography. RESULTS Agreement in the evaluation of regional perfusion status between tetrofosmin and Tl-201 imaging was observed in 78% of the 726 total segments, with a kappa value of 0.61. In segments with normal function at echocardiography (n = 436), no difference between Tl-201 and tetrofosmin uptake was observed. In hypokinetic segments (n = 138), exercise tetrofosmin uptake was lower (P < .01) as compared with exercise Tl-201 activity, whereas no difference was observed between tetrofosmin uptake at rest as compared with Tl-201 activity on redistribution and reinjection images. In segments with severe functional impairment (akinetic or dyskinetic, n = 152), tetrofosmin uptake on exercise images was reduced (P < .01) as compared with exercise Tl-201 activity; furthermore, tetrofosmin uptake at rest was lower (P < .01) as compared with Tl-201 activity on both redistribution and reinjection images. In these segments, concordance in the detection of myocardial viability between tetrofosmin and Tl-201 imaging was observed in 138 (91%) of the 152 segments, with a kappa value of 0.77. CONCLUSIONS In patients with chronic coronary artery disease and LV dysfunction quantitative exercise-rest tetrofosmin and Tl-201 reinjection SPECT provide similar information in the assessment of perfusion status and in the detection of myocardial viability.
Scaling theory for the optical properties of semicontinuous metal films.

The optical properties of thin semicontinuous metal films are calculated within the framework of the scaling theory of percolation. The effective ac conductivity is calculated over a length scale determined by the optical frequency. The relevant length scale depends on the frequency through the anomalous diffusion relation. At finite frequencies the ac conductivity fluctuates over the surface of the film, resulting in fluctuations of the local optical response. These fluctuations are described by a broad bimodal distribution. The optical response of the whole film is then calculated by averaging the local contributions, using the above distribution function. We find that the intercluster capacitance is essential in understanding the optical response of a percolating film. Numerical calculations based on this model show excellent agreement with experimental data over the entire range of surface coverages.
BAYESIAN ADAPTIVE DOSE-FINDING BASED ON EFFICACY AND TOXICITY

A description of the conventional paradigm for early phase clinical evaluation of a new agent is given, followed by a list of this paradigm’s logical and practical flaws. This is provided initially to motivate the use of phase I-II clinical trial designs. The main body of the paper consists of a review of several practical Bayesian phase I-II designs for sequentially adaptive dose-finding based on efficacy and toxicity. These include designs taking two general approaches. The first approach uses elicited efficacy–toxicity probability pair trade-offs as decision criteria. Designs accommodating bivariate binary and trinary outcomes are discussed, as well as an elaboration that uses patient covariates to choose individualized doses. The second approach uses elicited joint utilities of ordinal (efficacy, toxicity) outcomes as a decision criterion, also including adaptive randomization to improve performance. Several illustrative applications of the methods are provided.
Model guided diffeomorphic demons for atlas based segmentation

Using an atlas, an image can be segmented by mapping its coordinate space to that of the atlas in an anatomically correct way. In order to find the correct mapping between the two different coordinate spaces e.g. diffeomorphic demons registration can be applied. The demons algorithm is a popular choice for deformable image registration and offers the possibility to perform computationally efficient non-rigid (diffeomorphic) registration. However, this registration method is prone to image artifacts and image noise. Therefore it has been the main objective of the presented work to combine the efficiency of diffeomorphic demons and the stability of statistical models. In the presented approach a statistical deformation model that describes "anatomically correct" displacements vector fields for a specific registration problem is used to guide the demons registration algorithm. By projecting the current displacement vector field, which is calculated during any iteration of the registration process, into the model space a regularized version of the vector field can be computed. Using this regularized vector field for the update of the deformation field in the subsequent iteration of the registration process the demons registration algorithm can be guided by the deformation model. The proposed method was evaluated on 21 CT datasets of the right hip. Measuring the average and maximum segmentation error for all 21 datasets and all 120 test configurations it could be demonstrated that the newly proposed algorithm leads to a reduction of the segmentation error of up to 13% compared to using the conventional diffeomorphic demons algorithm.
Clinicopathologic findings and prognosis of chronic inflammatory demyelinating polyneuropathy

Objective: To evaluate the clinicopathologic features and prognostic factors of 100 patients with chronic inflammatory demyelinating polyneuropathy (CIDP). Methods: Comparison of clinical and biopsy findings with functional score evaluated an average of 6 years after referral. Results: CIDP followed a relapsing course in 14% of the patients and a progressive course in 45%. After progressive onset, little change was noted during follow-up in the others. Five patients had symptomatic involvement of the CNS. Teased fiber preparations of nerve biopsy specimens showed that 68 patients had purely demyelinative lesions, 20 had mixed axonal and demyelinative lesions, and 5 had predominantly axonal lesions. Axonal loss was a common finding, with 47% of the patients retaining less than half of the normal density of fibers. Inflammatory infiltrates, found in 18 samples, were prominent only in 4. Of the 83 patients evaluated an average of 6 years after onset, 56 were in good condition; 24 had deteriorated and failed to respond to treatment, including 9 patients who died as a consequence of their neurologic deficit. Progressive course, CNS involvement, high proportion of fibers showing active demyelination on nerve biopsy, and axonal loss overall correlated with higher disability. Conclusion: Axonal loss is the major long-term pejorative prognostic factor in CIDP.
An image restoration method based on sparse constraint

In this paper, proposed an image restoration method which base on the sparse constraint. Based on the principle of Compressed Sensing, the observed image is transformed into the wavelet domain, and then converted the image restoration problem to a convex set unrestricted optimization problem by limiting the number of non-zero elements of the wavelet domain, using the gradient projection method for solving the optimization problem to achieve the restoration of the input image. Experiments show that the method presented has the fast convergence and good robustness compared to the traditional total variation regularization restoration method.
Single point mutations in various domains of a plant plasma membrane H(+)‐ATPase expressed in Saccharomyces cerevisiae increase H(+)‐pumping and permit yeast growth at low pH.

In plants, the proton pump‐ATPase (H(+)‐ATPase) of the plasma membrane is encoded by a multigene family. The PMA2 (plasma membrane H(+)‐ATPase) isoform from Nicotiana plumbaginifolia was previously shown to be capable of functionally replacing the yeast H(+)‐ATPase, provided that the external pH was kept above pH 5.5. In this study, we used a positive selection to isolate 19 single point mutations of PMA2 which permit the growth of yeast cells at pH 4.0. Thirteen mutations were restricted to the C‐terminus region, but another six mutations were found in four other regions of the enzyme. Kinetic studies determined on nine mutated PMA2 compared with the wild‐type PMA2 revealed an activated enzyme characterized by an alkaline shift of the optimum pH and a slightly higher specific ATPase activity. However, the most striking difference was a 2‐ to 3‐fold increase of H(+)‐pumping in both reconstituted vesicles and intact cells. These results indicate that point mutations in various domains of the plant H(+)‐ATPase improve the coupling between H(+)‐pumping and ATP hydrolysis, resulting in better growth at low pH. Moreover, the yeast cells expressing the mutated PMA2 showed a marked reduction in the frequency of internal membrane proliferation seen with the strain expressing the wild‐type PMA2, indicating a relationship between H(+)‐ATPase activity and perturbations of the secretory pathway.
A Diagnosis Method that Matches Class Diagrams in a Learning Environment for Object-Oriented Modeling

This paper describes the diagnostic method developed in a learning environment for object-oriented modeling called Diagram. This method compares the studentpsilas diagram with an expertpsilas diagram in order to find the differences between these two diagrams. The principles of our algorithm rely on graph matching methods and algorithms. The diagrams are schematized in characteristic structural patterns. These structures are compared by using similarity functions, and similarity scores are computed for each couple of structures. Finally, univalent and multivalent matches are qualified, according to a taxonomy of differences. An example is given on a real studentpsilas diagram. The algorithm is implemented in Java under Eclipse environment. It has been tested on several problems of increasing complexity, with students diagrams collected in real class situation. The results of the off-line experimentations are presented and discussed.
Assessment of grid-scale energy storage potential within the MISO footprint

Current state legislated renewable portfolio standards (RPS) within the MISO footprint equate to an average requirement of approximately 13 percent of generated electricity by 2025 to come from renewable sources, primarily from wind (which requires an additional 16.2 GW of wind to the existing 10 GW). Typical wind patterns produce higher energy at times when electricity demand is low. Wind generation is also variable and has to be balanced with other resources in order to maintain system reliability. As significant amounts of variable generation resources are added to the transmission grid, the system complexities associated with balancing generation and demand increase. This paper explores grid-scale energy storage potential within the MISO footprint when large amounts of variable generation are added to the system.
Diverse Mechanisms of Neuronal Protection by Nimodipine in Experimental Rabbit Brain Ischemia

The purpose of this study was to verify the possible involvement of nimodipine-sensitive calcium channels in ischemic Ca2+ influx to hippocampal neurons to assess their role in nimodipine neuroprotection. We induced 15-minute global cerebral ischemia in pentobarbital-anesthetized and relaxed rabbits, which had been implanted with a transhippocampal dialysis probe, by intrathoracic artery occlusion combined with hypotension. Apart from electroencephalographic and morphologic observations, changes in the extracellular concentrations of calcium, amino acids, and blood-brain barrier permeability to fluorescein were detected by microdialysis of the hippocampus. Nimodipine was applied either intravenously or locally to the hippocampus before, during, and after ischemia. Application of nimodipine locally or systemically, which had no effect on extracellular amino acids, enhanced recovery and normalization of the electroencephalographic activity and protected hippocampal neurons from early morphologic changes. Intravenous nimodipine reduced the ischemia-evoked drop of extracellular Ca2+ and completely prevented postischemic leakage of the blood-brain barrier, whereas local nimodipine infusion did not modify these ischemic disturbances. Our results suggest that nimodipine-sensitive Ca2+ channels play a minor role in the ischemic calcium influx to hippocampal neurons. Nimodipine, apart from a potent vasotropic action, may also directly protect brain neurons by intracellular calcium antagonism rather than by inhibition of calcium influx. (Stroke 1990;21(suppl IV):IV-108-IV-110)
Regulatory factors acting at the bacteriophage Mu middle promoter

Lytic development of bacteriophage Mu proceeds through three phases of transcription: early, middle, and late. Initiation of middle transcription from Pm requires the phage-encoded activator, Mor. An examination of the sequences surrounding the promoter revealed possible binding sites for Mu proteins A and c, as well as for Escherichia coli integration host factor. Promoter fragments containing 5' and 3' deletions were fused to the lacZ reporter gene and assayed for activity after induction of a Mu prophage or a plasmid-borne mor gene. Sequences upstream of position -62 and downstream of +10 were dispensable for promoter activity. In DNase I footprinting with both crude extract and purified protein, Mor protected Pm sequences from position -56 to -33. Mutations disrupting the dyad symmetry of the terminator of early transcription overlapping the Mor binding site did not reduce promoter activity, suggesting that the symmetry per se is not required for Mor binding or Pm activation. Purified Mu lysogenic repressor (c) also bound to Pm, overlapping the Mor binding site. Production of large amounts of repressor in vivo reduced Mor-dependent promoter activity nearly 10-fold. Promoters with mutations in the repressor binding site showed a reduction in this repressor-mediated inhibition of Pm activity.
Range Size, Habitat use, and Dial Activity of Feral Hogs on Reclaimed Surface-Mined lands in East Texas

During the last decade, surface lignite mines in eastern Texas have experienced damage by feral hogs (Sus scrofa) to reclaimed areas. Specifi cally, feral hogs have caused damage to plants used in reclamation. In addition to vegetative losses, erosion control problems and water quality impacts have been noted. Big Brown Lignite Mine in Freestone County, Texas, had tried to control feral hogs through year-long trapping, which proved expensive. We hypothesized that hogs were using reclaimed areas only at night and seasonally. If so, knowledge of travel lanes into the mine and seasonal use would help concentrate trapping efforts and reduce costs. To determine travel lanes and season use, we radio-monitored 6 male and 10 female feral hogs from January 1998 to January 1999 at Big Brown Mine. We determined annual range size and habitat selection using a geographic information system. Contrary to our hypothesis, we found feral hogs remained on reclaimed lands. We observed that male feral hogs had a signifi cantly (P < 0.02) larger mean annual range (15.8 km 2 ) than did female hogs (6.5 km 2 ), and hogs of both sexes preferred reclaimed wildlife areas and non-mined riparian corridors on the mine site, which had higher screening cover than other vegetation types. We found free water to be another important landscape feature that infl uenced hog movements. We observed that feral hogs moved greater distances from free water and screening cover during night hours. Feral hogs also traveled greater distances from both free water and screen cover during winter and spring than during summer or fall (P < 0.001). Based on the information obtained from our study, we recommend vegetation management (mowing of tall grass areas where hogs hide during daylight hours) be implemented to reduce hog impacts that occur mostly during night at the mine site. Reducing vegetative cover around water sources may also reduce hog impacts.
Extrapolation of Missing Craniofacial Skeletal Structure via Statistical Shape Models Project # 1 Seminar Report , EN . 600 . 646 Spring 2014

The goal of this project is to design and implement a method for extrapolating missing anatomical craniofacial skeletal structure with the use of a statistical shape model (SSM) of the human cranium. The procedure of interest is craniofacial transplantation, which is the process of transplanting a donor’s craniofacial soft tissue, and possibly bone structure, onto a patient that has been subject to some severe craniofacial deformation. Figure 1 shows preoperative and postoperative views of a transplant recipient. By reliably estimating the “original” skeletal structure of the patient, it is hoped that the surgical planning process may be enhanced, leading to more positive surgical outcomes. The papers by Benazzi, et al. [3] and Kazhdan, et al. [9] propose different methods of surface reconstruction; it is hoped that they may be applied for our purposes in this project.
AEG-1/MTDH-activated autophagy enhances human malignant glioma susceptibility to TGF-β1-triggered epithelial-mesenchymal transition

Autophagy is a tightly regulated process activated in response to metabolic stress and other microenvironmental changes. Astrocyte elevated gene 1 (AEG-1) reportedly induces protective autophagy. Our results indicate that AEG-1 also enhances the susceptibility of malignant glioma cells to TGF-β1-triggered epithelial-mesenchymal transition (EMT) through induction of autophagy. TGF-β1 induced autophagy and activated AEG-1 via Smad2/3 phosphorylation in malignant glioma cells. Also increased was oncogene cyclin D1 and EMT markers, which promoted tumor progression. Inhibition of autophagy using siRNA-BECN1 and siRNA-AEG-1 suppressed EMT. In tumor samples from patients with malignant glioma, immunohistochemical assays showed that expression levels of TGF-β1, AEG-1, and markers of autophagy and EMT, all gradually increase with glioblastoma progression. In vivo siRNA-AEG-1 administration to rats implanted with C6 glioma cells inhibited tumor growth and increased the incidence of apoptosis among tumor cells. These findings shed light on the mechanisms underlying the invasiveness and progression of malignant gliomas.