This study compared two techniques, Voxel-Based Lesion Symptom Mapping (VLSM) and Voxel-Based Morphometry (VBM), to identify lesion sites associated with language impairments in 20 patients with chronic post-stroke aphasia. Both techniques found overlapping associations between auditory sentence comprehension deficits and lesions in the superior and middle temporal gyri. However, VBM identified additional regions while VLSM found more posterior and subcortical associations. The techniques also showed differences in mapping word repetition and object naming deficits. While using both techniques can increase mapping reliability, each has advantages and answering somewhat different questions.
Comparison of the effects of face mask treatment started simultaneously
and after the completion of the alternate rapid maxillary expansion and
constriction procedure
Bayesian Hierarchical Model of Width of Keratinized GingivaIOSRJM
Ā
The purpose of this paper is to offer a method for studying the treatment result of gingival recession. A parameter showing the success of the surgical treatment of gingival recessions is the keratinized gingival width. It was measured four times: at baseline, after 1 month, after 3 months and after 6 months. Every patient has data that can be described by an individual trend. Bayesian hierarchical model of the keratinized gingiva widthās increase rate is built.
Comparison of the effects of face mask treatment started simultaneously
and after the completion of the alternate rapid maxillary expansion and
constriction procedure
Bayesian Hierarchical Model of Width of Keratinized GingivaIOSRJM
Ā
The purpose of this paper is to offer a method for studying the treatment result of gingival recession. A parameter showing the success of the surgical treatment of gingival recessions is the keratinized gingival width. It was measured four times: at baseline, after 1 month, after 3 months and after 6 months. Every patient has data that can be described by an individual trend. Bayesian hierarchical model of the keratinized gingiva widthās increase rate is built.
Malposition of unerupted mandibular second premolar in children with palatall...EdwardHAngle
Ā
Objective: To test the hypotheses that (1) the distal angulation of unerupted mandibular premolar
(MnP2) is significantly greater in children with palatally displaced canines (PDC) than in those in
a control sample; and (2) delayed tooth formation is significantly more frequent in children with
both malposed MnP2 and PDC than in children with PDC only.
Materials and Methods: We examined retrospectively panoramic radiographs from 43 patients
with PDC who had no previous orthodontics. A control sample consisted of age- and sex-matched
patients. The distal angle formed between the long axis of MnP2 and the tangent to the inferior
border was measured. Dental age was evaluated using the Koch classification.
Results: A significant difference was observed between the mean inclination of the right side
MnP2 in the PDC group (75.4 degrees) and that of the control group (85.8 degrees). This difference
was highly statistically significant (P < .0001). The same evaluation was carried out for the
left side, with similar results. The average dental age was found to be delayed in patients who
showed both abnormalities (malposed MnP2 and PDC) compared with patients who showed the
PDC anomaly only.
Conclusion: Both hypotheses are retained. Statistically, PDC and MnP2 malposition are significantly
associated suggesting a common genetic etiology, despite taking place on opposite jaws.
While the presence of PDC or MnP2 anomaly has been associated with a delay in tooth formation,
we find the presence of both anomalies to show a more profound delay. Our findings suggest a
delay in tooth formation as a possible common genetic mechanism for these 2 malposition anomalies.
MEDICAL IMAGING MUTIFRACTAL ANALYSIS IN PREDICTION OF EFFICIENCY OF CANCER TH...cscpconf
Ā
Based on pressing need for predictive performance improvement, we explored the value of pretherapy
tumour histology image analysis to predict chemotherapy response. It was shown that
multifractal analysis of breast tumour tissue prior to chemotherapy indeed has the capacity to
distinguish between histological images of the different chemotherapy responder groups with
accuracies of 91.4% for pPR, 82.9% for pCR and 82.1% for PD/SD.
MEDICAL IMAGING MUTIFRACTAL ANALYSIS IN PREDICTION OF EFFICIENCY OF CANCER TH...csandit
Ā
Based on pressing need for predictive performance improvement, we explored the value of pretherapy
tumour histology image analysis to predict chemotherapy response. It was shown that
multifractal analysis of breast tumour tissue prior to chemotherapy indeed has the capacity to
distinguish between histological images of the different chemotherapy responder groups with
accuracies of 91.4% for pPR, 82.9% for pCR and 82.1% for PD/SD.
Multimode Vector Modalities of HMM-GMM in Augmented Categorization of Bioacou...ijceronline
Ā
International Journal of Computational Engineering Research (IJCER) is dedicated to protecting personal information and will make every reasonable effort to handle collected information appropriately. All information collected, as well as related requests, will be handled as carefully and efficiently as possible in accordance with IJCER standards for integrity and objectivity.
Multimode Vector Modalities of HMM-GMM in Augmented Categorization of Bioacou...ijceronline
Ā
International Journal of Computational Engineering Research (IJCER) is dedicated to protecting personal information and will make every reasonable effort to handle collected information appropriately. All information collected, as well as related requests, will be handled as carefully and efficiently as possible in accordance with IJCER standards for integrity and objectivity.
Study on Physicians Request for Computed Tomography Examinations for Patients...IRJESJOURNAL
Ā
Background and objectives: There is a lot controversy about the use of Computed tomography (CT) for patients with minor head injury. We aimed to determine the practice of guiding rules for the safety of radiation and increasing awareness of physicians about risks of ionizing radiation and find out the reasons of emergency doctors for sending head injury patients to CT scan exams. Materials and Methods: A descriptive questionnaire in the Emergency Department (ED) based study was performed to assess physicians' knowledge of radiation doses received from radiological treatments and knowledge about Clinic Decision Support rules (CDS). The questionnaire consisted of 26 questions distributed to physicians working in the emergency department in six hospitals in East Java. Finally, the data collected have been analyzed by some tests using SPSS version 15 and Smart PLS. Results: In this study 44 participants had taken part. The percentage of general knowledge and awareness that shows the response of people who work in the emergency departments was total 44 respondents, by percent 6.8% of the respondents had passably knowledge, awareness and 84.1% they were having a good knowledge and awareness and 9.1% the respondents had very good knowledge and awareness. That means almost of respondents have good knowledge and awareness. To find out if an indicator is forming a construct (latent variables) testing the convergent validity of the measurement model with a reflexive indicator assessed based on the correlation between the item score to construct scores were calculated with the help of software Smart PLS. Size reflexive considered valid if the individual has a correlation (loading) to construct (latent variables) to be measured ā„ 0.5 or the value of t-statistics should ā„1.96 (test two tailed) at a significance level of Ī± = 0.05. If one of the indicators has a leading value <0.5,><1.96, then the indicator should be discarded (dropped) because it indicates that the indicators are not good enough to measure the construct in right. The positive influence between general knowledge and awareness against to knowledge about radiation doses can be interpreted that the better general knowledge and awareness, then it will be followed by an increase in their knowledge about radiation doses. And vice versa, the worse general knowledge and awareness, then this will decrease their knowledge about radiation doses too. Conclusion: The present study has illustrated that the level of awareness and knowledge physicians who deal with ionizing radiation in CT scan units are adequate overall. There is a good influence between the diligence in applying the principles of guidance and rules stipulated by the nuclear energy in Indonesia by physicians to adjust the use of CT in the emergency department, the majority of participants who have a good awareness & knowledge, there are some of them do not have enough knowledge.
Estimation of Severity of Speech Disability Through Speech Envelopesipij
Ā
In this paper, envelope detection of speech is discussed to distinguish the pathological cases of speech disabled children. The speech signal samples of children of age between five to eight years are considered for the present study. These speech signals are digitized and are used to determine the speech envelope. The envelope is subjected to ratio mean analysis to estimate the disability. This analysis is conducted on ten speech signal samples which are related to both place of articulation and manner of articulation. Overall speech disability of a pathological subject is estimated based on the results of above analysis.
Maxillofacial Pathology Detection Using an Extended a Contrario Approach Comb...sipij
Ā
In this work, we develop a method for pathology detection of the maxillary-facial in 3D CT medical images. Our method is based on āa contrarioā approach that is a statistical region based method. To do this, we detect significant changes in regions previously delineated by a physician anatomist. We apply a decision algorithm based on fuzzy logic on the changes detected and we get a decision with a degree of uncertainty. Tests conducted on a basis of real images have shown the performance and robustness of the proposed approach.
Malposition of unerupted mandibular second premolar in children with palatall...EdwardHAngle
Ā
Objective: To test the hypotheses that (1) the distal angulation of unerupted mandibular premolar
(MnP2) is significantly greater in children with palatally displaced canines (PDC) than in those in
a control sample; and (2) delayed tooth formation is significantly more frequent in children with
both malposed MnP2 and PDC than in children with PDC only.
Materials and Methods: We examined retrospectively panoramic radiographs from 43 patients
with PDC who had no previous orthodontics. A control sample consisted of age- and sex-matched
patients. The distal angle formed between the long axis of MnP2 and the tangent to the inferior
border was measured. Dental age was evaluated using the Koch classification.
Results: A significant difference was observed between the mean inclination of the right side
MnP2 in the PDC group (75.4 degrees) and that of the control group (85.8 degrees). This difference
was highly statistically significant (P < .0001). The same evaluation was carried out for the
left side, with similar results. The average dental age was found to be delayed in patients who
showed both abnormalities (malposed MnP2 and PDC) compared with patients who showed the
PDC anomaly only.
Conclusion: Both hypotheses are retained. Statistically, PDC and MnP2 malposition are significantly
associated suggesting a common genetic etiology, despite taking place on opposite jaws.
While the presence of PDC or MnP2 anomaly has been associated with a delay in tooth formation,
we find the presence of both anomalies to show a more profound delay. Our findings suggest a
delay in tooth formation as a possible common genetic mechanism for these 2 malposition anomalies.
MEDICAL IMAGING MUTIFRACTAL ANALYSIS IN PREDICTION OF EFFICIENCY OF CANCER TH...cscpconf
Ā
Based on pressing need for predictive performance improvement, we explored the value of pretherapy
tumour histology image analysis to predict chemotherapy response. It was shown that
multifractal analysis of breast tumour tissue prior to chemotherapy indeed has the capacity to
distinguish between histological images of the different chemotherapy responder groups with
accuracies of 91.4% for pPR, 82.9% for pCR and 82.1% for PD/SD.
MEDICAL IMAGING MUTIFRACTAL ANALYSIS IN PREDICTION OF EFFICIENCY OF CANCER TH...csandit
Ā
Based on pressing need for predictive performance improvement, we explored the value of pretherapy
tumour histology image analysis to predict chemotherapy response. It was shown that
multifractal analysis of breast tumour tissue prior to chemotherapy indeed has the capacity to
distinguish between histological images of the different chemotherapy responder groups with
accuracies of 91.4% for pPR, 82.9% for pCR and 82.1% for PD/SD.
Multimode Vector Modalities of HMM-GMM in Augmented Categorization of Bioacou...ijceronline
Ā
International Journal of Computational Engineering Research (IJCER) is dedicated to protecting personal information and will make every reasonable effort to handle collected information appropriately. All information collected, as well as related requests, will be handled as carefully and efficiently as possible in accordance with IJCER standards for integrity and objectivity.
Multimode Vector Modalities of HMM-GMM in Augmented Categorization of Bioacou...ijceronline
Ā
International Journal of Computational Engineering Research (IJCER) is dedicated to protecting personal information and will make every reasonable effort to handle collected information appropriately. All information collected, as well as related requests, will be handled as carefully and efficiently as possible in accordance with IJCER standards for integrity and objectivity.
Study on Physicians Request for Computed Tomography Examinations for Patients...IRJESJOURNAL
Ā
Background and objectives: There is a lot controversy about the use of Computed tomography (CT) for patients with minor head injury. We aimed to determine the practice of guiding rules for the safety of radiation and increasing awareness of physicians about risks of ionizing radiation and find out the reasons of emergency doctors for sending head injury patients to CT scan exams. Materials and Methods: A descriptive questionnaire in the Emergency Department (ED) based study was performed to assess physicians' knowledge of radiation doses received from radiological treatments and knowledge about Clinic Decision Support rules (CDS). The questionnaire consisted of 26 questions distributed to physicians working in the emergency department in six hospitals in East Java. Finally, the data collected have been analyzed by some tests using SPSS version 15 and Smart PLS. Results: In this study 44 participants had taken part. The percentage of general knowledge and awareness that shows the response of people who work in the emergency departments was total 44 respondents, by percent 6.8% of the respondents had passably knowledge, awareness and 84.1% they were having a good knowledge and awareness and 9.1% the respondents had very good knowledge and awareness. That means almost of respondents have good knowledge and awareness. To find out if an indicator is forming a construct (latent variables) testing the convergent validity of the measurement model with a reflexive indicator assessed based on the correlation between the item score to construct scores were calculated with the help of software Smart PLS. Size reflexive considered valid if the individual has a correlation (loading) to construct (latent variables) to be measured ā„ 0.5 or the value of t-statistics should ā„1.96 (test two tailed) at a significance level of Ī± = 0.05. If one of the indicators has a leading value <0.5,><1.96, then the indicator should be discarded (dropped) because it indicates that the indicators are not good enough to measure the construct in right. The positive influence between general knowledge and awareness against to knowledge about radiation doses can be interpreted that the better general knowledge and awareness, then it will be followed by an increase in their knowledge about radiation doses. And vice versa, the worse general knowledge and awareness, then this will decrease their knowledge about radiation doses too. Conclusion: The present study has illustrated that the level of awareness and knowledge physicians who deal with ionizing radiation in CT scan units are adequate overall. There is a good influence between the diligence in applying the principles of guidance and rules stipulated by the nuclear energy in Indonesia by physicians to adjust the use of CT in the emergency department, the majority of participants who have a good awareness & knowledge, there are some of them do not have enough knowledge.
Estimation of Severity of Speech Disability Through Speech Envelopesipij
Ā
In this paper, envelope detection of speech is discussed to distinguish the pathological cases of speech disabled children. The speech signal samples of children of age between five to eight years are considered for the present study. These speech signals are digitized and are used to determine the speech envelope. The envelope is subjected to ratio mean analysis to estimate the disability. This analysis is conducted on ten speech signal samples which are related to both place of articulation and manner of articulation. Overall speech disability of a pathological subject is estimated based on the results of above analysis.
Maxillofacial Pathology Detection Using an Extended a Contrario Approach Comb...sipij
Ā
In this work, we develop a method for pathology detection of the maxillary-facial in 3D CT medical images. Our method is based on āa contrarioā approach that is a statistical region based method. To do this, we detect significant changes in regions previously delineated by a physician anatomist. We apply a decision algorithm based on fuzzy logic on the changes detected and we get a decision with a degree of uncertainty. Tests conducted on a basis of real images have shown the performance and robustness of the proposed approach.
Similar to A comparison of VLSM and VBM in a cohort of patients with post-stroke aphasia (20)
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Ā
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The systemās unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's entangled aventures in wonderlandRichard Gill
Ā
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leberās hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendelās laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four Oāclock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called āsmallā because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
A comparison of VLSM and VBM in a cohort of patients with post-stroke aphasia
1. A comparison of VLSM and VBM in a
cohort of patients with post-stroke aphasia
2. Introduction
ā¢ Studies attempting to map post-stroke cognitive or motor symptoms to lesion location have been
available in the literature for over 150 years. In the last two decades, two computational techniques
have been developed to identify the lesion sites associated with behavioural impairments. Voxel
Based Morphometry (VBM) has now been used extensively for this purpose in many different patient
populations. More recently, Voxel-based Lesion Symptom Mapping (VLSM) was developed specifically
for the purpose of identifying lesionāsymptom relationships in stroke patients, and has been used
extensively to study, among others functions, language, motor abilities and attention. However, no
studies have compared the results of these two techniques so far. In this study we compared VLSM
and VBM in a cohort of 20 patients with chronic post-stroke aphasia.
3. Materials and methods
ā¢ Participants
ā¢ Patients were tested cognitive-behavioral tests
ā¢ Imaging data acquisitionusing a 3 T Siemens Magentom Trio Tim MRI scanne and 1.5 T MRI Siemens
scanner
ā¢ Data pre-processing for VLSM and VBM
ā¢ Data analysis
5. Material and methods
2. Behavioral test
ā¢ Comprehensive Aphasia Test were analysed:
ā¢ 1) Auditory sentence comprehension: participants
were read a sentence and were asked to point to
one of four pictures which best fitted the sentence.
The task had 16 trials.
ā¢ 2) Word repetition: participants were asked to
repeat words read out by the examiner. This task
included 16 short words.
ā¢ 3) Object naming: participants were asked to name
24 pictures of objects. In all tasks, a correct answer
was given 2 points. A delayed answer or a correct
answer following self-correction was given 1 point.
In the auditory sentence comprehension and the
word repetition tasks, if the participant asked the
examiner to repeat the question, and this was
followed by a correct answer, 1 point was given as
well. Maximum possible scores and the cut-off
score for defining impaired function are presented
in Fig 1
Fig. 1. Behavioural scores for all patients in
the various language tasks. Red lines
represent the cut-off score for deļ¬ning
impaired function in each task.
6. 3. Imaging data acquisition
ā¢ Imaging was performed using a 3 T Siemens Magentom Trio Tim MRI
scanner. Four patients could not undergo a 3 T MRI scan due to
cardiac stents (n = 2) or PFO devices (n = 2) which were not 3 T
compatible. These four patients were scanned using a 1.5 T MRI
Siemens scanner (Erlangen, Germany) and the effect of using a
different scanner on the results was considered
7. Data pre-processing for VLSM
1.Lesion Identification
2.Validation:
3.Mask Creation:
4.Spatial Normalization:
VBM
ā¢ 1. Creation of masks.
ā¢ 2. Data pre-processing for VBM.
8. ā¢ Fig. 2. An overlay of all
patients' lesions. Colours
represent number of patients
with a lesion to a speciļ¬c
voxel. Warmer areas indicate
areas of greater lesion
overlap. Colour range runs
from 1 (the lowest value in the
image) to 14 (the highest
value in the image).
9. Auditory sentence comprehension
1.Common Findings:
1.Both VBM and VLSM found associations with auditory sentence
comprehension in the superior and middle temporal gyri (STG/MTG).
2.Poor performance correlated with lower gray matter (GM) voxel
intensity in the STG/MTG border and lower white matter (WM) voxel
intensity.
3.Adding age as a covariate did not alter the pattern of results.
2.Differences Between VBM and VLSM:
1.VBM extended more laterally and medially, involving the post-central
gyrus and the supramarginal gyrus (SMG).
2.VLSM extended more posteriorly, including the post-central gyrus,
superior parietal lobule, pre-central gyrus, inferior frontal gyrus (IFG),
and insula.
10. ā¢ Fig. 3. Colour maps of signiļ¬cant regions in the VBM (top); VLSM (middle);
and both methods (bottom) in the auditory sentence comprehension task
(p b 0.05, FDR correction). All voxels lesioned in at least 5% of patients are
included. Colours represent Z-scores.
11. Word Repetition:
ā¢ Overlap and Differences:Limited overlap between VBM and
VLSM in the supramarginal gyrus (SMG) and superior temporal
gyrus (STG).
ā¢ VBM highlighted larger clusters, including the insula, inferior
frontal gyrus (IFG), and pre-central gyrus.
ā¢ VLSM identified small unconnected clusters in frontal and
parietal lobes.
12. Object Naming:
1.Common Findings:
1.Both methods associated poorer performance in object naming with
the IFG, insula, STG, and SMG.
2.Differences:
1.VBM found additional associations in IFG pars triangularis/BA 45 and
subcortical regions.
2.VLSM found associations with white matter regions.
13. Analysis of Variations and Covariates:
1.VBM Analysis:
1.No significant correlations at corrected thresholds for auditory
sentence comprehension.
2.Effects of scanner type and number of voxels analyzed did not
significantly affect results.
2.VLSM Analysis:
1.No differences between analyzing 5% or 20% of damaged voxels.
2.Changes in VBM cluster sizes with different percentages of damaged
voxels.
14. Conclusions
ā¢ We compared the use of VBM and VLSM in the study of language
impairments in a cohort of chronic stroke patients. Areas where the
two techniques gave overlapping results are those areas previously
shown to be relevant for the cognitive functions tested. This suggests
that using both techniques and looking for overlaps can potentially
increase results reliability when seeking to map cognitive functions in
the brain. However, the two techniques do not produce precisely the
same results and potentially answer somewhat different questions.
Since each method has some clear advantages over the other, we
suggest that in future studies of chronic stroke patients, researchers
consider the differences between the techniques when evaluating
results and their implications.
15. Differences
ā¢ VBM extended more laterally and medially, involving the post-
central gyrus and the supramarginal gyrus (SMG).
ā¢ VLSM extended more posteriorly, including the post-central
gyrus, superior parietal lobule, pre-central gyrus, inferior frontal
gyrus (IFG), and insula.
16. Specific Voxels:
ā¢ Voxel [ā 60, ā 6, ā 6] in the anterior MTG was significant in both
analyses.
ā¢ A posterior voxel [ā 66, ā 24, 4] was significant only in VBM.
ā¢ A frontal lobe voxel [ā 30, 48, ā 8] was significant only in VLSM.
Editor's Notes
Lesion Identification:
Lesions were defined using the Regions of Interest (ROI) facility in Analyze 7.5 software.
One author manually traced lesions on T2-weighted scans in native space, consulting coregistered sequences (FLAIR, PD, and MPRAGE).
Lesion contours were drawn on the outer borders of hyper-intense regions, considering intensity changes in other modalities.
Sulci widening was included in lesion definition only if there was clear asymmetry.
Periventricular regions were defined as lesioned with clear signal intensity change and cortical extension to the periventricular space.
Areas around enlarged ventricles with normal signal intensity or symmetric periventricular white matter changes were not defined as lesioned.
Validation:
Drawn lesions were validated by a trained neurologist who was blinded to patient diagnoses.
A lesion overlap map was generated (Fig. 2) to visualize common areas of lesions.
Mask Creation:
Binary masks were created from the lesions using MRIcron.
MPRAGE images were normalized and segmented into grey matter (GM), white matter (WM), and cerebro-spinal fluid (CSF) probability maps in standard Montreal Neurological Institute (MNI) space.
The unified segmentation-normalization algorithm in Statistical Parametric Mapping software (SPM8) was used for this process.
Spatial Normalization:
Lesion masks were utilized to mask out abnormal tissue during spatial normalization.
Spatial parameter files from the normalization routine were applied to the original drawn lesions.
This resulted in spatially normalized binary lesion definitions for each patient in standard MNI stereotactic space.
These pre-processing steps are crucial for accur