bluuebunny/crossref_metadata_2025 huggingface dataset:
Pembangunan model penilaian Massive Open Online Courses (MOOC) untuk bahasa Arab di Institusi Pengajian Tinggi
Authors: Zainuddin Ghazali , Ismail Irwan Mahazir , Ramlan Siti Rosilawati , Jaffar Mohammad Najib , Ahmad Mohammad Imran , Mohd Hamidin Norfaezah , Mohd Danuri Mohd Shahrul Nizam , Isa Sofia Noraina
Published: January 2022

Platform Massive Open Online Courses (MOOC) merupakan salah satu platform pembelajaran dalam talian yang sedang popular digunakan di pelusuk dunia terutamanya dalam Institut Pengajian Tinggi. Ia telah dijadikan salah satu platform utama sebagai proses pengajaran dan pembelajaran (PdP) di IPT Malaysia ketika pandemik covid-19 yang telah menular di seluruh dunia sejak Disember 2019. Walaupun begitu, terdapat beberapa pensyarah menyuarakan kebimbangan mereka dalam melaksanakan penilaian dalam MOOC khususnya untuk pembelajaran bahasa Arab. Justeru itu, pembangunan model penilaian MOOC untuk bahasa Arab boleh dijadikan sebagai salah satu alternatif penyelesaian. Artikel ini bertujuan untuk merungkaikan permasalahan yang kompleks, menganalisis struktur dan elemen penting untuk diterapkan dalam model penilaian MOOC. Model ini dibangunkan berpandukan kepada kesepakatan pakar seramai tujuh orang. Interpretive Structural Modelling (ISM) diaplikasikan dalam pembangunan model ini. Enam langkah utama yang terlibat dalam pembangunan model adalah bermula dengan mengenal pasti elemen-elemen yang berkaitan, mewujudkan hubungan antara pemboleh ubah, membangunkan matriks struktur interaksi kendiri (SSIM), penjanaan model daripada pendekatan ISM, pembentangan model kajian dan langkah terakhir melibatkan persembahan serta pindaan model akhir kajian. Sebanyak tujuh elemen dikenal pasti oleh barisan pakar bagi pelaksanaan penilaian MOOC untuk bahasa Arab. Elemen yang menjadi keutamaan adalah elemen menentukan jenis pentaksiran (penilaian kendiri, rakan sebaya, penilaian sumatif, formatif) bagi mengukur prestasi pelajar dan di akhiri dengan elemen menentukan syarat pensijilan bagi pelajar menamatkan kursus.
OFLOXACIN ION PAIRING WITHIN SUBMICRON EMULSION: A POTENTIAL APPROACH FOR OCULAR DELIVERY
Authors: Pandey D , Singh R , Jain S , Jain D ,   School of Pharmaceutical Sciences, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Airport Road Gandhi Nagar, Bhopal - 462 033, Madhya Pradesh, India
Published: January 2022

The aim of the work was to improve the entrapment of ofloxacin within the submicron emulsion by ion pairing with sodium deoxycholate to improve antimicrobial activity and precorneal retention. Partition coefficient of ofloxacin-sodium deoxycholate was found to be 3.788, compared to 0.113 for the drug alone. Formulation was characterized for globules size 0.143 ± 0.07 μm, viscosity 3.8 ± 0.2 cP and pH, 7.1 ± 0.3. The entrapment was 80 ± 1% for ofloxacin-sodium deoxycholate in submicron emulsion compared to 57 ± 2% for the drug alone. More than 90% drug remained after 90 days in optimized formulations and was found stable. SEM confirmed droplets size to be 200 nm and spherical. Drug released 53.16% after 24 h from optimized formulation. In vitro antimicrobial efficacy improved against S. aureus as compared to free drug. No toxicity of optimized formulation on HET-CAM test was observed. Designed formulation may hold some promise for severe ocular infections where frequent dosing is required.
RP-HPLC METHOD DEVELOPMENT AND VALIDATION FOR SIMULTANEOUS ESTIMATION OF LINAGLIPTIN AND EMPAGLIFLOZIN
Authors: Lakshmana Rao A , Prasanthi T. , Anusha E. L ,   Department of Pharmaceutical Analysis V.V. Institute of Pharmaceutical Sciences, Gudlavalleru - 521 356, Andhra Pradesh, India
Published: January 2022

A simple, accurate and precise RP-HPLC method was developed for the simultaneous estimation of the linagliptin and empagliflozin in tablet dosage form. Chromatogram was run through Kromasil 250 x 4.6 mM, 5mM column, mobile phase containing 0.1% o-phosphoric acid buffer and acetonitrile in the ratio of 60:40%v/v was pumped through column at a flow rate of 1 mL/min. The optimized wavelength was 230 nm. Retention times of linagliptin and empagliflozin were found to be 2.759 min and 2.139 min. %RSD of the Linagliptin and Empagliflozin were found to be 0.5 and 0.6 respectively. Percentage assay was obtained as 99.91% and 100.15% for linagliptin and empagliflozin, respectively. LOD, LOQ values obtained for linagliptin and empagliflozin were 0.23 μg/ml and 0.44 μg/mL and 0.70 μg/mL and 1.34 μg/mL, respectively. Thus, the current study showed that the developed RP-HPLC method is sensitive and selective for the estimation of linagliptin and empagliflozin in combined dosage form.
SYNTHESIS AND BIOLOGICAL EVALUATION OF 2-PHENYLPYRIDO[2,3-D] PYRIMIDINE DERIVATIVES AS CYCLIN-DEPENDENT KINASE (CDK) INHIBITORS
Authors: Bhagwanrao P. V , Ingole P. G. , Butle S. R ,   Panchabhai Vivek Bhagwanrao School of Pharmacy, Swami Ramanand Teerth Marathwada University, Nanded-431 606, Maharashtra, India
Published: January 2022

We report a novel scaffold of 2-phenylpyrido[2,3-d]pyrimidine derivatives designed as structural analogues of dinaciclib. Sixteen derivatives were synthesised and evaluated for their CDK2/5 inhibition activity. Compounds 4-(2-(3-methoxybenzylidene)hydrazineyl)-2-phenylpyrido[2,3-d]pyrimidine (7i) and 4-(2-(3-nitrobenzylidene)hydrazineyl)-2-phenylpyrido[2,3-d]pyrimidine (7n) show promising IC50 and kinase selectivity. These compounds also show moderate anti-proliferative activity in the colon cancer HCT116 and breast cancer MCF7 cell lines. In molecular docking studies with CDK2, compounds 7i and 7nshow binding similar to dinaciclib.
Edith Stein's Contribution to Critical Phenomenology: On Self-Formation and Value-Modification
Authors:   Emory University, Bath Rachel
Published: January 2022

One defining claim that critical phenomenologists make of the critical phenomenological method is that description no longer simply plays the role of detailing the world around the describing phenomenologist, but rather has the potential to transform worlds and persons. The transformative potential of the critical phenomenological enterprise is motivated by aspirations of social and political transformation. Critical phenomenology accordingly takes, as its starting point, descriptions of the oppressive historical social structures and contexts that have shaped our experience and shows how these produce inequitable ways of being in the world (Guenther 2020, 12). For example, critical phenomenologists have provided rich descriptions of marginalized lived experience, particularly racialized experience (Ngo, 2017; Yancy, 2017), dis-abled experience and experiences of illness (Lajoie and Douglas, 2020; Toombs, 1993), gendered experience (Beauvoir, 2009; Salamon, 2010), and so forth. What is common across these accounts is the assumption that these descriptions provide means of enacting political change. First, they illuminate the existence of oppressive structures and their effects upon us, our possibilities, and our relations. Second, through increasing awareness they begin to denaturalize the oppressive historical structures that “privilege, naturalize, and normalize certain experiences of the world while marginalizing, pathologizing, and discrediting others” (Guenther 2020, 15). Third, through strategic responses (e.g., hesitation in Alia Al-Saji’s work), they produce new possibilities of action and experience, which initiates the process of creating different ways of being in the world (Al-Saji 2014).2
Climate Collapse, Judgment Day, and the Temporal Sublime
Authors:   The Pennsylvania State University, Toadvine Ted
Published: January 2022

It is commonplace today to hear climate change identified as the single most important challenge facing humanity. Consider the headlines from COP24, the United Nations Climate Change Conference held in Poland in December 2018. U.N. Secretary-General António Guterres opened the proceedings by calling climate change “the most important issue we face” (PBS 2018). The Secretary-General’s remarks paraphrase the opening line of the U.N.’s climate change web page, which announces that “[c]limate Change is the defining issue of our time and we are at a defining moment” (United Nations n.d.). Such statements about the singular significance of climate change—the most important, the defining issue—are often followed by proclamations about what hangs in the balance, and this was the case at COP24. There, the celebrated British naturalist Sir David Attenborough warned that “collapse of our civilizations and the extinction of much of the natural world is on the horizons,” amounting to, in his words, “disaster of global scale, our greatest threat in thousands of years” (PBS 2018).
Sensitivity and Specificity of Serology, Histopathology, and Molecular Tests in the Detection of Leptospirosis from Slaughtered Cattle in Indonesia
Authors: Rahayu Asih , Prakoso Yos Adi , Desiandura Kurnia , Kristianingrum Yuli Purwandari
Published: January 2022

Leptospira spp. is a pathogenic bacteria that causes leptospirosis in humans and cattle. The World Health Organization (WHO) recommends the microscopic agglutination test (MAT) as the laboratory gold standard in the detection of leptospirosis. However, the limitation of MAT triggers the laboratory technicians to develop alternative laboratory tests against leptospirosis. The current study aimed to compare the sensitivity and specificity of histopathology special stain using modified Gram staining (MGS) and molecular test using reverse transcriptase-polymerase chain reaction (RT-PCR), compared to the MAT for Leptospira spp. detection in cattle. This study used a total of 38 serum and 38 kidney samples from the cattle slaughtered in the Sidoarjo slaughterhouse, Indonesia. The collected serum samples were tested against MAT and RT-PCR. The kidneys were processed for histopathology using MGS. The result indicated that 16 (42.10%) of the tested samples were positive against MAT, 6 (15.78%) were positive against MGS, and 18 (47.36%) were positive against RT-PCR. The RT-PCR indicated better sensitivity and lower specificity, compared to MAT and MGS. The findings revealed that the RT-PCR is an appropriate laboratory test for detecting cattle leptospirosis with better sensitivity and specificity. Therefore, this method can be suggested to substitute MAT and overcome its limitations.
Sperm Quality and Histology of the Testis and Epididymis in Chemical Castrated Male Cats with Intra-testicular Injection of Sodium Chloride Solution
Authors: Dayanti Marissa Divia , Berata I Ketut , Puja I Ketut
Published: January 2022

The high population of feral cats in Bali, Indonesia, could be a problem associated with cat welfare and the risk of zoonotic diseases. Gonadectomy or male castration is an option for population control; however, there would be more economical ways to reach this goal. Sterilization using chemicals is an alternative to the surgical method of castration as it is reasonably priced, activated in a short time, and does not affect animal activity after the chemical administration. The present study aimed to evaluate intratesticular injection of Sodium chloride as an agent of chemosterilants in male cats. In the current study, 16 healthy male cats aged nearly one year old were randomly selected. The male cats were allocated into four groups containing four cats in each. Group 1 (control) received bilateral intratesticular injection with 0.25 mL normal saline solution containing 2% Lidocaine. The cats in groups 2, 3, and 4 received bilateral intratesticular injection of 0.25 mL Sodium chloride solution containing 2% Lidocaine with a concentration of 15%, 20%, and 25%, respectively. At the end of the study (after 30 days of injection), the cats were castrated and their testes were removed for sperm quality and histopathological evaluation. The results of the present study indicated that intratesticular injection of Sodium chloride significantly decreased the motility and viability rates, and increased the abnormalities of the sperms. Histopathological studies revealed marked depletion of spermatozoa in the testes and seminiferous tubular degeneration, seminiferous tubular atrophy, and epithelial cell vacuolation. In conclusion, the injection of 20-25% solution of Sodium chloride in testes had the potential as a chemosterilant for chemical sterilization in cats.
Chemical and in vitro evaluation of Leucaena (Leucaena leucocephala) Leaves as a Substitute of Alfalfa (Medicago sativa L.) with/without Rejected Green Banana Fruits (Musa paradisiaca)
Authors: Salama Rashid Mohamed Rashid , Hanafy Mohamed Ahmed , Youssef Mervat Sayed Hassan , Archimède Harry , Sallam Sobhy Mohamed Abdallah , Soltan Yosra Ahmed , Ali Ghoneem Wafaa Mostafa
Published: January 2022

Leucaena leaves and rejected green banana fruits can be promising to cope with feed gaps in arid and semi-arid Mediterranean regions. The present study evaluated the feeding value and secondary active compounds of Leucaena leaves and rejected green banana fruits for ruminants using a semi-automated gas production (GP) system. Comparisons were made with the traditional feeds as alfalfa, and Dichanthium spp. grass hay. Analysis of HPLC was performed for the feed ingredients to characterize the main phenolic components. The in vitro evaluation was carried out for the experimental feed ingredients and diets. Four diets were formulated as the first diet consisted of alfalfa and grass hay at a ratio of 35:65 (AG), the second diet composed of alfalfa, grass hay, and green banana fruits at a ratio of 35:55:10 (AGB), third and fourth diets were prepared by replacing alfalfa in AG and AGB with Leucaena leaves to be LG and LGB, respectively. Leucaena leaves showed a high content of valuable phenolic components that have antioxidant and anti-inflammatory properties, such as gallic acid, ellagic acid, and naringenin. Moreover, Leucaena leaves and diet had higher crude protein, total phenols, and total tannins than alfalfa, which was reflected on the chemical composition of diets, and recorded the lowest total accumulative GP at 24 hours leading to low CH4 and CO2 production. Banana fruits recorded the lowest ruminal pH, ammonia concentration, and degraded neutral detergent fiber, compared to other feed ingredients, while it had the highest GP and degraded organic matter. Therefore, it is highly recommended to use Leucaena leaves in animals’ diets with/without rejected green banana fruits as an alternative feed resource with potential environmental and animal health benefits.
Gastroprotective Effect of Conocarpus Erectus Plus Omega-3 on Experimentally Induced Ulcer in Rats
Authors: Ayad Zahraa M , Alameedi Ali I. , Abbas Hassan Adheem , Al-Rubaie Laith S.G.
Published: January 2022

There has been a dearth of research on the gastroprotective effect of Conocarpus erectus in the literature so the current study was designed to estimate the ability of Conocarpus erectus (C. erectus) leaves extract alone and in combination with omega-3 regarding gastroprotective effects. A total of 30 male rats were divided into five groups (n = 6). All animals induced gastric ulcer by 80 mg/kg of naproxen orally twice a day for three consecutive days. At the same time, the animals treated orally with 175 mg/kg omega-3, 250 mg/kg C. erectus, 80 mg omega-3 + 150 mg C. erectus, 10 mg/kg of lansoprazole, and 2 ml/kg of DMSO were named T1, T2, T3, T4, and TC, respectively. The obtained results of the present study indicated the presence of flavonoids, saponin, and tannin as active ingredients in C. erectus leaves extract. Consequently, C. erectus seemed to have the potential of chelating metals in a concentration-dependent manner. Gross and histopathology findings showed the highly protective capability of C. erectus and omega-3 against ulcerative lesion, compared to the time each was used alone. The outcomes of the current study indicated that using C. erectus alone or plus omega-3 can protect the gastric mucosa from the ulceration induced by naproxen, and the chelating properties of C. erectus.
Potential of Chitosan from Shrimp Waste for Treating Staphylococcus aureus Bacteria in Skin Wound
Authors: Widnyana I Made Satya , Subekti Sri , . Kismiyati
Published: January 2022

Shrimp or crustacean waste on the skin, head, and feet has not been maximally utilized. Shrimp or crustacean waste can be processed into chitin or chitosan which can provide high added value. Chitosan is one ingredient that can be used to make skin ointments. One of the bacteria that is harmful to the skin during a wound is Staphylococcus aureus. Hence, there is a need to have a skin ointment that can inhibit these bacteria. The current study aimed to evaluate the antibacterial activity of chitosan in the ointment. Moreover, the current study planned to determine the optimum inhibitory concentration of chitosan in the ointment against Staphylococcus aureus and evaluate the physical properties of ointments. The methods used in the current study were the pH determination, organoleptic test, homogeneity test, and antibacterial activity test to examine chitosan against Staphylococcus aureus. The results showed that chitosan in ointment had a weak antibacterial activity with a value of < 5 mm inhibition zone. Chitosan with a concentration of 0.2% in ointment fulfilled the requirements of a good ointment. Its white colour as the typical colour of chitosan showed the characteristic odour of chitosan and a semi-solid form. Chitosan in the ointment has antibacterial activity that can inhibit Staphylococcus aureus bacteria.
Adding Kaffir Lime (Citrus hystrix) Leaf Essential Oil to Gelatin Coating for Extending the Shelf Life of Red Snapper Fillet
Authors: Febriana Ika , Mashithah Endang Dewi , Pramono Heru
Published: January 2022

Red Snappers contain high content protein and water which makes them highly perishable. However, they are widely processed into the fillet. One of the disadvantages of filleting is the short shelf life due to the high water content turning the fillets into an ideal media for bacteria. The edible coating protects the meat from perishability by reducing the water vapor, aroma, and lipid migration. One of the potential protein sources for coating is gelatin. The essential oil content that has a role in inhibiting bacterial growth is citronellal. The present study aimed to determine the effects of adding Kaffir limes (Citrus hystrix) leaf essential oil to a gelatin coating on the shelf life of red snappers’ fillet. An experiment was conducted using a completely randomized design with four treatment groups based on the concentration of Citrus hystrix essential oil and five replications (n = 3 per group). In this regard, the treatments were named P0 (0% of Citrus hystrix), P1 (1% of Citrus hystrix), P2 (1.5% of Citrus hystrix), and P3 (2% of Citrus hystrix). The investigated parameters included total plate count, sensory quality, and acidity. Data analysis was performed using ANOVA followed by Duncan’s multiple range test. The results showed that the addition of 1.5% and 2% Citrus hystrix essential oil decreased the number of bacteria, and led to a higher sensory quality. In conclusion, The addition of Citrus hystrix essential oil in the gelatin-coating process can be used as a method of processing the fishery products to extend the shelf life of red snappers’ fillet at room temperature and inhibit bacterial growth.
The Effect of Mycotoxins in naturally Contaminated Diet on the Pathogenicity of Escherichia coli in Broiler Chickens
Authors: Batikh Mohamed Mohamed , El-nabarawy Anwaar Mettwally , Shakal Mohamed Abdel-salam , Hegazy Abdel-Haleem Mohamed , Morsy Eman Anter
Published: January 2022

Contamination of feedstuffs with mycotoxins is considered a huge issue plaguing the poultry sector of Egypt. Therefore, the current study was conducted to examine the effect of the neglected natural mycotoxin contamination of ration on the clinicopathological picture of Escherichia coli infection in broiler chickens. A total of 240 one-day-old chicks were divided into 5 groups. The first 3 groups (1, 2, and 3) were further equally subdivided into 2 subgroups (A and B). Those in group A were fed on commercial ration treated with antimycotoxin while group B was fed on ration contaminated with mycotoxins. Groups 1, 2, and 3 were inoculated at one-day-old with E. coli O78, O128, and O157, respectively while group 4 was kept as a negative control and fed on a ration treated with antimycotoxin. Finally, group 5 was kept as positive controls and fed on a mycotoxin contaminated ration and inoculated with physiological saline. All groups contained 30 chicks. Results showed that the challenged groups fed on a ration containing mycotoxin had high mortality (23.3%) and also a high feed conversion ratio. Moreover, severe clinical symptoms, postmortem lesions, histopathological pictures, and a high rate of bacterial re-isolation were recorded. The pathological lesions were congestion of the liver, spleen, and kidneys in addition to severe pericarditis, perihepatitis, air sacullitis, ascites, and unabsorbed yolk sac. The histopathological changes included degeneration, necrosis, and liver inflammation with lymphoid depletion in the spleen and enteritis associated with sloughing of the mucosal epithelium. The obtained results were less severe in the challenged groups fed on a ration treated with antimycotoxin indicating combined action of both Escherichia coli and mycotoxins. In conclusion, the obtained results revealed that the mycotoxins even at low concentrations can augment the pathogenisity of Echerichia coli in broiler chickens.
Soil Biological Activity in some Leguminous Species on Draught Affected Degraded Western Rajasthan Sites
Authors: Chaukiyal S.P.
Published: January 2022

Ten leguminous species viz Alysicarpus longifolius, Clitoria tarnatea, Crotalaria burhia, Crotalaria medicaginea, Indigofera argentea, Indigofera linnaei, Indigofera sessiliflora, Mimosa hamata, Mucuna pruriens and Rhynchosia minima were assessed for soil biological activity and its nutrients status from some degraded Western Rajasthan soils. The rhizospheric soil was assessed for acid and alkaline phosphatase activity, dehydrogenase activity, soil organic carbon, NO3- N, NH4+ N, moisture content and relative neigbhour effects. Soil organic carbon (SOC), N03- N, NH4+ N, phosphatase, dehydrogenase activity and moisture content was observed higher than control in the rhizospheric soils of all species. Relative neighboring effect (RNE) indicates that species are not influenced by each other. However, soil pH remains around 8 and there was varying degree of RNE between and among the species. In most of the species except Indigofera argentia, I. sessiliflora and Crotalaria medicaginea all other performed well. It was observed that soil moisture played an important role in the soil biological enzyme activities. On the basis of results obtained, Mimosa hamata, Rhynchosia minima, Mucuna pruriens, Clitoria tarnatea and Crotalaria burhia performed best. Further studies are required to be carried out in this direction.
Cardiac motion estimation using multi-scale feature points
Authors: Becciu Alessandro , van Assen Hans C. , Florack Luc , Janssen Bart J. , Ter haar romeny Bart
Published: January 2022

Heart illnesses influence the functioning of the cardiac muscle and are the major causes of death in the world. Optic flow methods are essential tools to assess and quantify the contraction of the cardiac walls, but are hampered by the aperture problem. Harmonic phase (HARP) techniques measure the phase in magnetic resonance (MR) tagged images. Due to the regular geometry, patterns generated by a combination of HARPs and sine HARPs represent a suitable framework to extract landmark features. In this paper we introduce a new aperture-problem free method to study the cardiac motion by tracking multi-scale features such as maxima, minima, saddles and corners, on HARP and sine HARP tagged images.
A robust Expectation-Maximization algorithm for Multiple Sclerosis lesion segmentation
Authors: Garcia-Lorenzo Daniel , Prima Sylvain , Morrissey Sean P. , Barillot Christian
Published: January 2022

A fully automatic workflow for Multiple Sclerosis (MS) lesion segmentation is described. Fully automatic means that no user interaction is performed in any of the steps and that all parameters are fixed for all the images processed in beforehand. Our workflow is composed of three steps: an intensity inhomogeneity (IIH) correction, skull-stripping and MS lesions segmentation. A validation comparing our results with two experts is done on MS MRI datasets of 24 MS patients from two different sites.
Contrast Enhancement for Liver Tumor Identification
Authors: Nugroho Hanung adi , Ihtatho Dani , Nugroho Hermawan
Published: January 2022

In CT images, tumors located in a liver are generally identified by intensity difference between tumor and liver. The intensity of the tumor can be lower and or higher than that of the liver. However, the main problem of liver tumor detection from is related to low contrast between tumor and liver intensities. Tumor sometimes presents in a very small dimension and makes the detection even more difficult. In this work, we focus on contrast enhancement of CT images containing liver and tumor based on the histogram processing as a necessary preprocessing for liver tumor identification. Results show that using our proposed method, the contrast of the CT images can be enhanced and results in relatively accurate identification of tumors in the liver.
Open Source Software to Visualize Complex Data on Remote CEA's Supercomputing Facilities
Authors: Vivodtzev Fabien , Carrard Thierry
Published: January 2022

In order to guaranty performances of complex systems using numerical simulation, CEA is performing advanced data analysis and scientific visualization with open source software using High Performance Computing (HPC) capability. The diversity of the physics to study produces results of growing complexity in terms of large-scale, high dimensional and multivariate data. Moreover, the HPC approach introduces another layer of complexity by allowing computation amongst thousands of remote cores accessed from sites located hundreds of kilometers away from the computing facility. This paper presents how CEA deploys and contributes to open source software to enable production class visualization tools in a high performance computing context. Among several open source projects used at CEA, this presentation will focus on Visit, VTK and Paraview. In the first part we will address specific issues encountered when deploying VisIt and Paraview in a multi-site supercomputing facility for end-users. Several examples will be given on how such tools can be adapted to take advantage of a parallel setting to explore large multi-block dataset or perform remote visualization on material interface reconstructions of billions of cells. Then, the specific challenges faced to deliver Paraview’s Catalyst capabilities to end-users will be discussed. In the second part, we will describe how CEA contributes to open source visualization software and associated software development strategy by emphasizing on two recent development projects. The first is an integrated simulation workbench providing plugins for every step required to achieve numerical simulation independently on a local or a remote computer. Embedded in an Eclipse RCP environment, VTK views allow the users to perform data input using interaction or mesh preview before running the simulation code. Contributions to VTK have been made in order to smoothly integrate these technologies. The second details how recent developments at CEA have helped to visualize and to analyze results from ExaStamp, a parallel molecular dynamics simulation code dealing with molecular systems ranging from a few millions up to a billion atoms. These developments include a GPU intensive rendering method specialized for atoms and specific parallel algorithms to process molecular data sets.
Gaussian Intensity Model with Neighborhood Cues for Fluid-Tissue Categorization of Multi-Sequence MR Brain Images
Authors: Katyal Ranveer , Paneri Sahil , Kuse Manohar
Published: January 2022

This work presents an automatic brain MRI segmentation method which can classify brain voxels into one of three main tissue types: gray matter (GM), white matter (WM) and Cerebro-spinal Fluid (CSF). Intensity-model based classification of MR images has proven problematic. The statistical approach does not carry any spatial, textural and neighborhood information in it. We propose to use a computationally fast and novel feature-set to facilitate voxel wise classification based on regional intensity, texture, spatial location of voxels in addition to posterior probability estimates. Information available through T1-weighted (T1), T1-weighted inversion recovery (IR) and T2-weighted FLAIR (FLAIR) MRI sequences was also leveraged. An aggregate overlap of 90.21% for all intracranial structures was reported between the automatic classification and available expert annotation as measured by the DICE coefficient.
4D Morphological segmentation and the MICCAI LV-segmentation grand challenge
Authors: Marak László , Cousty Jean , Najman Laurent , Talbot Hugues
Published: January 2022

The goal of the Cardiac MR Left Ventricle Segmentation Challenge at MICCAI 2009 is to compare state-of-the-art LV segmentation methods. This goal is facilitated through an evaluation system and a database of cardiac cine MR images, as well as expert contours, now freely available on the internet for research purposes. This challenge is important because the analysis and the segmentation of 3D+t sequences of MR cardiac images is fastidious, time consuming and error-prone for human operators, due to the large amount of data. Conversely, automated segmentation of cardiac images is well-known to be a challenging task. This paper describes the method that our group submitted for the challenge, based on 4D discrete mathematical morphology. This method leads to discrete segmentations, i.e, binary masks (bitmaps) of the left ventricular myocardiums that are both spatially and temporally consistent.
A generic computer assisted intervention plug-in module for 3D Slicer with multiple device support
Authors: Lassó András , Tokuda Junichi , Vikal Siddharth , Tempany Clare M , Hata Nobuhiko , Fichtinger Gabor
Published: January 2022

Various frameworks and toolkits have been proposed for rapid development of computer assisted intervention (CAI) software. In this paper, we investigate how the open-source 3D Slicer application framework can be used for this purpose. We defined common requirements for CAI software to evaluate and enhance 3D Slicer for interventional applications in general. 3D Slicer is found to be an appropriate end-user deployment environment for CAI software, as its built-in functions fulfill many requirements and missing functionalities can be conveniently added. We describe the implementation of a CAI software based on extending core 3D Slicer functions. Three enhancements are described in detail: the management of workflow, DICOM image transfer, and multiple views. The resulting software fulfills general CAI requirements and supports two different MRI-guided prostate biopsy systems (each with a different imaging mode, robotic manipulator and calibration method), thereby demonstrating the usability of Slicer for implementing different CAI applications.
The graph windowed Fourier transform: a tool to quantify the gyrification of the cerebral cortex
Authors: Rabiei Hamed , Richard Frederic , Roth Muriel , Anton Jean-Luc , Coulon Olivier , Lefevre Julien
Published: January 2022

The Gyrification Index (GI) quantifies the amount of folding of a cortical surface. In this paper, we show the efficiency of spectral analysis to perform such a task, and in particular we explain how the graph windowed Fourier transform can be used as a tool to define new GIs with multiscale properties. We propose two different GIs and study their effect on a set of subjects whose cortical surfaces are modeled with triangular meshes.
Vessel tracking by connecting the dots
Authors: Szymczak Andrzej
Published: January 2022

We propose an algorithm for tracking blood vessel segments in Computed Tomographic (CT) images. Our procedure first finds core points that tend to concentrate along the centerlines of vessels. Intuitively, the core points are centers of intensity plateaus in two-dimensional slices through the input image. The starting and the end point of the desired vessel (S and E) are also considered core points. The weighted core graph is built by connecting nearby core points with edges. Edge weights are designed so that edges of large weights are unlikely to follow a vessel segment. We compute the shortest path connecting S and E in the core graph. The output is the result of applying shortcutting operations to this path.
Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching
Authors: Barbosa Daniel , Friboulet Denis , D'hooge Jan , Bernard Olivier
Published: January 2022

We present a novel method for segmentation and tracking of the left ventricle (LV) in 4D ultrasound sequences using a combination of automatic segmentation at the end-diastolic frame and tracking using both a global optical flow-based tracker and local block matching. The core novelty of the proposed algorithm relies on the recursive formulation of the block-matching problem, which introduces temporal consistency on the patterns being tracked. The proposed method offers a competitive solution, with average segmentation errors of 2.29 and 2.26mm in the training (#=15) and testing (#=15) datasets respectively.
Adaptations of MARACAS algorithm to the segmentation of the carotid bifurcation and stenosis quantification in CTA images
Authors: Zuluaga Maria A. , Orkisz Maciej , Delgado Leyton Edgar J.F. , Dore Vincent , Morales Pinzon Alfredo , Hernandez Hoyos Marcela
Published: January 2022

This paper describes a 3D CTA image segmentation method submitted to the CLS09 contest (Carotid Lumen Segmentation and Stenosis Quantification) held in conjunction with the MICCAI 2009 conference. First, images are denoised to improve image quality and posterior segmentation. Second, region-based measurements are performed to differentiate possible vessels from other structures. Then, edge-driven metrics are used to allow vessel separation from nearby structures. Using, both edge-driven and region-based metrics a filter is used to enhance the vessels. The vessels of interest are extracted by use of the provided initialization points and of a model-driven segmentation algorithm. Using the obtained result, the final stage is devoted to stenosis quantification.
Prototyping a Hybrid Cooperative and Tele-robotic Surgical System for Retinal Microsurgery
Authors: Balicki Marcin , Xia Tian , Jung Min Yang , Anton Deguet Anton , Vagvolgyi Balazs , Kazanzides Peter , Taylor Russell
Published: January 2022

This paper presents the design of a tele-robotic microsurgical platform designed for development of cooperative and tele-operative control schemes, sensor based smart instruments, user interfaces and new surgical techniques with eye surgery as the driving application. The system is built using the distributed component-based cisst libraries and the Surgical Assistant Workstation framework. It includes a cooperatively controlled EyeRobot2, a da Vinci Master manipulator, and a remote stereo visualization system. We use constrained optimization based virtual fixture control to provide Virtual Remote-Center-of-Motion (vRCM) and haptic feedback. Such system can be used in a hybrid setup, combining local cooperative control with remote tele-operation, where an experienced surgeon can provide hand-over-hand tutoring to a novice user. In another scheme, the system can provide haptic feedback based on virtual fixtures constructed from real-time force and proximity sensor information.
Fifth International Workshop on Systems and Architectures for Computer Assisted Interventions
Authors: Enquobahrie Andinet
Published: January 2022

Open interfaces/frameworks increase the pace of research and discovery by promoting collaborations within and between clinicians, biomedical engineers, and software developers. These systems usually employ modular architectures to model the complexity involved in surgical assistance systems. Hence, standards are critical to allow for cross-framework interoperability of systems, and modules. SACAI workshop aims to establish a forum for discussing systems and architectures for computer assisted discussing intervention (CAI) applications. Continuing the success of the series, the workshop will focus on open interfaces, interoperability, and standards. In addition, this year, we will discuss clinical applications and future directions of CAI systems and frameworks. The workshop will continue to include the robust discussion between industry and academia.
Auto-kNN: Brain Tissue Segmentation using Automatically Trained k-Nearest-Neighbor Classification
Authors: Vrooman Henri , Van der Lijn Fedde , Niessen Wiro
Published: January 2022

In this paper we applied one of our regularly used processing pipelines for fully automated brain tissue segmentation. Brain tissue was segmented in cerebrospinal fluid (CSF), gray matter (GM) and white matter (WM). Our algorithms for skull stripping, tissue segmentation and white matter lesion (WML) detection were slightly adapted and applied to twelve data sets within the MRBrainS13 brain tissue segmentation challenge. Skull stripping is performed using non-rigid registration of 5 atlas masks. Our tissue segmentation is based on an automatically trained kNN-classifier. Training samples were obtained by non-rigid registration of 5 manually labeled scans followed by a pruning step in feature space to remove any residual erroneously sampled tissue voxels. The kNN-classification incorporates voxel intensities from a T1-weighted scan and a FLAIR scan. The white matter lesion detection is based on an automatically determined threshold on the FLAIR scan. The application of the algorithms on the data from the MRBrainS13 Challenge showed that our pipeline produces acceptable segmentations. Average resulting Dice scores were 77.86 (CSF), 81.22 (GM), 87.27 (WM), 93.78 (total parenchyma), and 96.26 (all intracranial structures). Total processing time was about 2 hours per subject.
Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models
Authors: Van Stralen Marijn , Haak Alexander , Leung K Esther , Van Burken Gerard , Bosch Johan G.
Published: January 2022

Segmentation of 3D echocardiograms (3DEs) is still a challenging task due to the low signal-to-noise ratio, the limited field of view, and typical ultrasound artifacts. We propose to segment the left ventricular endocardial surface by using Active Appearance Models (AAMs). Separate end-diastolic (ED) and end-systolic (ES) AAMs were built from presegmented 3DEs of the CETUS training data and 25 previously acquired 3DEs, imaged using various 3DE equipment. The AAMs fully automatically segmented the 15 training sets in a leave-one-out cross validation, comparing two training populations and various initialization strategies. All segmentations took about 15 seconds per patient. The comparison on the CETUS training data shows that the AAM benefits from additional training data and more accurate initialization. The results on the CETUS training and testing data confirm good ED and ES segmentation accuracy on multi-center, multi-vendor, multi-pathology data, and corresponding EF estimation. Selection from different initialization strategies, based on the minimal residual error, and propagation of detected ED contours to initialize ES detection, contributed to more accurate segmentations in this heterogeneous population.
Active Contour-Based Segmentation of Head and Neck with Adaptive Atlas Selection
Authors: Gorthi Subrahmanyam , Duay Valérie , Bach Cuadra Meritxell , Tercier Pierre-Alain , Allal Abdelkarim S. , Thiran Jean-Philippe
Published: January 2022

This paper presents automated segmentation of structures in the Head and Neck (H&N) region, using an active contour-based joint registration and segmentation model. A new atlas selection strategy is also used. Segmentation is performed based on the dense deformation field computed from the registration of selected structures in the atlas image that have distinct boundaries, onto the patient’s image. This approach results in robust segmentation of the structures of interest, even in the presence of tumors, or anatomical differences between the atlas and the patient image. For each patient, an atlas image is selected from the available atlas-database, based on the similarity metric value, computed after performing an affine registration between each image in the atlas-database and the patient’s image. Unlike many of the previous approaches in the literature, the similarity metric is not computed over the entire image region; rather, it is computed only in the regions of soft tissue structures to be segmented. Qualitative and quantitative evaluation of the results is presented.
Affine Transformation for Landmark Based Registration Initializer in ITK
Authors: Kim Eun young , Johnson Hans , Williams Norman
Published: January 2022

This document describes an affine transformation algorithm as an additional feature for landmark based registration in ITK www.itk.org. The algorithm is based on the paper by Spath, H [1]. The author derives a set of linear equations from paired landmarks and generates an affine transform from them. The method implemented here gives more freedom in the choice of registration and/or initialization method in ITK. The submission describes ITK implementation of the algorithm.
Predicting implant stability: in vitro validation in artificial bone
Authors: Bardyn Thibaut
Published: January 2022

Primary stability of osseointegrated implants is necessary for short and long-term success of the treatment. This paper presents a method to help clinicians preoperatively assess this primary implant stability. The method combines a planning software with a in-house finite element solver. Once the clinician has chosen a position for the implant on the planning tool, a finite element analysis is automatically started and calculates the mechanical stability of the implant at this position. The process is designed to be as simple and fast as possible for an efficient clinical use. Mechanical testing material was used to validate the stability measured by the software. The novel tool presented here leads the way to a new generation of intelligent computer-assisted tools able to give a priori indication on the life span of the implant.
Carotid Lumen Segmentation and Stenosis Grading Challenge
Authors: Hameeteman K. , Freiman M. , Zuluaga M. A. , Joskowicz L. , Rozie S. , Van Gils M. J. , Van den Borne L. , Sosna J. , Berman P. , Cohen N. , Douek P. , Sanchez I. , Aissat M. , Van der Lugt A. , Krestin G. P. , Niessen W. J. , Van Walsum T.
Published: January 2022

This paper describes the Carotid Lumen Segmentation and Stenosis Grading Challenge, which was part of the workshop ``3D Segmentation in the Clinic: A Grand Challenge’’. This workshop was part of the 12th conference on Medical Image Computing and Computer Assisted Interventions, held in London in September 2009. We introduce the purpose and background of the challenge and describe the data, reference standard and evaluation measures that were used in this challenge. We also provide the results of the data that were submitted by industrial and academic research institutes.
Coronary Artery Centerline Tracking Using Axial Symmetries
Authors: Dikici Engin , O'donnell Thomas , Grady Leo , White Richard
Published: January 2022

We present a method for tracking a coronary artery centerline given a single user supplied distal endpoint. Briefly, we first isolate the aorta and compute its surface. Next, we apply a novel two-stage Hough-like election scheme to the image volume to detect points which exhibit axial symmetry (vessel centerpoints). From the axial symmetry image a graph is constructed. This graph is searched for the optimal path from the user supplied point to any point on the surface of the aorta. Our technique falls under Challenge 2 of the Coronary Artery Tracking Challenge.
A Treatment Planning System for the Small Animal Radiation Research Platform (SARRP) based on 3D Slicer
Authors: Cho Nathan , Kazanzides Peter
Published: January 2022

This paper describes the software integration of a treatment planning system (TPS), based on the open-source 3D Slicer package, with the Small Animal Radiation Research Platform (SARRP).The TPS is designed to enable researchers to replicate their clinical techniques, allow for image fusion with other imaging modalities, and provide dose computation and graphical visualization of treatment plans consisting of multiple x-ray beams and conformable arcs. The dose computation is implemented on a GPU to achieve high performance; the dose volume for a typical treatment plan can be computed in less than a minute.
Fully automatic brain segmentation using model-guided level sets and skeleton-based models
Authors: Wang Chunliang , Wang Chun , Smedby Örjan
Published: January 2022

A fully automatic brain segmentation method is presented. First the skull is stripped using a model-based level set on T1-weighted inversion recovery images, then the brain ventricles and basal ganglia are segmented using the same method on T1-weighted images. The central white matter is segmented using a regular level set method but with high curvature regulation. To segment the cortical gray matter, a skeleton-based model is created by extracting the mid-surface of the gray matter from a preliminary segmentation using a threshold-based level set. An implicit model is then built by defining the thickness of the gray matter to be 2.7 mm. This model is incorporated into the level set framework and used to guide a second round more precise segmentation. Preliminary experiments show that the proposed method can provide relatively accurate results compared with the segmentation done by human observers. The processing time is considerably shorter than most conventional automatic brain segmentation methods.
Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS)
Authors: Bernard Olivier , Heyde Brecht , Alessandrini Martino , Barbosa Daniel , Camarasu-Pop Sorina , Cervenansky Frederic , Valette Sebastien , Mirea Oana , Galli Elena , Geleijnse Marcel , Papachristidis Alexandros , Bosch Johan G. , D'hooge Jan
Published: January 2022

Real-time 3D echocardiography has already been shown to be an accurate tool for left ventricular (LV) volume assessment. However, LV border identification remains a challenging task, mainly because of the low contrast of the images combined with drop-out artifacts. Many (semi-)automatic algorithms have been proposed to segment the LV border, but a systematic and fair comparison between such methods has so far been impossible due to a lack of publicly available common database. The aim of this MICCAI challenge was to gather researchers around the field of LV segmentation in 3D cardiac ultrasound by providing a common database to compare algorithms directly. The proposed platform will allow a consistent evaluation and ranking of the current state-of-the-art segmentation solutions and will contribute to a faster clinical translation of groundbreaking technical advances. The purpose of this paper is to describe the technical aspects of the generation of the database, give an overview of the ranking strategy and the outline of the challenge itself.