Qatar Foundation Annual Research Forum Volume 2013 Issue 1

One important type of speech sound disorders is articulation and phonological disorders that affect children of age between 2-8 years. All normally developing children follow a unique developmental timetable, table 1 in which they acquire articulation and phonological skills to correctly pronounce both consonants and vowels to make the sound patterns of their respective language. Previous statistics, table 2 show that the number of Arab children, in the age group 2-8 years, who suffer from articulation and phonological disorders, is significant. To be able to test, assess, and evaluate the effect of therapy on these disorders, there is need to conduct research and development that would culminate in the availability of speedy, versatile and interesting computerized tools for use by Speech and Language Therapist, SLPs in standardized test, assessment, and evaluation of articulation and phonology disorders among the children, figure 1. There are prerequisites to the development of these tools such as the development of a suitable phonetic and phonological vocabulary (see table 3) of Modern Standard Arabic, MSA that is spoken by such children and which will meet the test and assessment requirements for speech disorders. The vocabulary could then be used to create a speech corpus for children with normal speech who are in the same age group as the children with disordered speech. Such speech corpus could then be used as a frame of reference to set the standards and norms for children speech. The standards and norms can be used by SLPs to compare normal children against children suspected of having the disorder. The speech corpus could also be used by researchers to develop limited vocabulary, speaker-independent phonetic speech recognizers that would help SLPs during speech therapy and evaluation. To meet the ultimate goal of finally producing efficient and versatile computerized tools to assist SLPs in their mundane tasks of handling articulation and phonological deficits among children in an efficient manner, we envisage a project with the following objectives in mind: 1) develop a comprehensive articulation and phonology vocabulary that represent all the sounds of MSA spoken by the children in all their important articulation and phonological contexts, and 2) use the vocabulary to create a norm speech corpus that represent the articulation of all sounds for children with healthy speech production. The corpus should include significant quantities of speaker-dependent data for a significant number of children with normal speech and would be segmented, labeled and transcribed according to the standards used for such tasks. The development of test and assessment vocabulary and the creation of the speech corpus from such vocabulary are the prerequisites for any investigation on articulation and phonology disorders. Firstly they would help the research community to study the disorders and secondly, after the development of suitable computerized tools, they assist the SLPs to test, assess, and evaluate the effect of treatment for articulation and phonological disorders among children. In this article, we present the status of the research and outline a roadmap to achieve our objectives and ultimate goal.

Autism spectrum disorders (ASD) are a group of neuro-developmental disabilities, which, in many cases, is characterized by severe impairments in communication skills, social interaction, psychomotor coordination, behavioral control and emotional stability often accompanied by deficits in cognition, attention and sensory processing. According to a recent study conducted by Dr. Fouad Alshaban (Shafallah Medical Genetics Center, Doha, Qatar), the accurate prevalence rate of autism-spectrum disorders in Qatar is still uncertain. However, there is a general concern that it might be increasing in the last few years. The symptoms of ASDs are typically present before age 3 years, but frequently a formal diagnosis take longer to be established, which may compromises the efficacy of developmental and life-quality improving strategies. In most countries of the world the scenario is not much different. It has been shown that autism-associated neuroligin-3 mutations disrupt tonic endocannabinoid signaling in animals. Endocaanabinoids are neuromodulators produced by the brain, which act upon the same receptors and neuronal circuits affected by exogenous cannabinoids from the plant Cannabis sativa. This system is central for brain homeostatic activity control, learning, social interaction, memory formation and emotional modulation, among several neuronal and physiological functions. Here we present our proposal to use primates and valproate-treated rodents (an animal model for autism) in order to deepen our knowledge about the involvement of defects in endocannabinoid system as etiological factors capable of generating behavioral and cognitive aspects related to human autism. The reasoning behind the use of two species is to facilitate the conceptual bridge between the findings obtained in valproate-treated rodents and the understanding of the importance of the endocannabinoid system for social interaction and emotional behavior in primates. At first, this combination has the potential to point out possible pharmacological treatments based on modulation of the endocannabinoid system and in the identification of biomarkers in rodents. Secondly, this knowledge can help to develop, and to ethically justify, the creation of primate models for the study of pharmacologically treatable aspects related to human behavior that cannot be studied in rodents. In Brazil we have the privilege to work with non-human primates in a high-standard, naturalistic facility, the Primatology Center of the University of Brasilia (in the capital of Brazil). Therefore, we are taking advantage of this capability to test new hypotheses relating endocannabinoid signaling defects with autism symptoms and eventually generate a non-human primate animal model that, in one hand, may help on the discovery of molecular markers for early diagnosis and, on the other hand, may help the development of pharmacological tools to treat important symptoms of ASD. We want to share and discuss our ongoing project in this meeting as part of an effort to foster found raising and potential collaborations between our group and research groups from Qatar.

The interest in bone and softtissue replacement achieves rapid advances throughout the last decades. Injured bone has a unique ability to regenerate which leads to complete anatomic and physiologic repair. However, not every bony defect can beself-repaired. Repair of large osseous defects caused by neoplasms, cysts, trauma, infection, congenital diseases and surgical intervention are major problems in oral and maxillofacial field. The current approach is to use bone and bone substitutes for filling such defects. The aims of filling such osseous defects are to preserve the morphologic contour, restoration of the mechanical strength and function, elimination of the dead space to reduce postoperative infection, and the prevention of ingrowths of soft tissue. When conditions are favorable for regeneration of bone, such goals can be achieved without the need for grafting techniques. However, in many large lesions or in the absence of favorable conditions in small defects, the morphological contour is not completely restored and the bone remains weak. Different grafting materials have been introduced into the field in the last decade. The profound limitations of biological grafts have prompted the use of synthetic materials as an alternative to autogenous and allogenic bone grafts.In the present invention, we succeeded in manufacturing of a novel biomaterial in the field of bone healing. Our novel biomaterial synthesized from bovine serumalbumin using our newly developed technology (sub-critical water technology). The biomaterial showed a variety of mechanical properties and biodegradability that allowed for its application in the biomedical field and in particular as an alloplastic bone substitute. In our way to validate the applicability of our novel biomaterial, we co-operated with the department of Oral and Maxillofacial Surgery Faculty of Dentistry, Al Minia University, to evaluate our material as an alloplastic bone substitute through animal test. The results revealed satisfactory results when used as a bone grafting material in surgically created bone defects in the rabbit models. The obtained results showed that these novel materials have the following properties: Biocompatibility, Nontoxic and nonirritant, Act as a haemostatic agent and maintained the blood clot inside the defect, Osteoconductive property, Biodegradability property,easily manipulated and handled.The most important findings from the obtained results revealed that these novel materials have the ability to accelerate bone healing specially at the early stages following implementation of the material. Part of the work was patented in Japan with patent number 2005-028066 and published in high impact factor scientific journals worldwide 1, 2,3, 4, 5 . In the presnt work the most new obtained data concerning biocompatibility and animal test will be presented

The sensitivity of magnetic resonance (MR) to diffusion has long been exploited as a method for investigating molecular motions in complex systems. The recognition that MR can be made sensitive to the details of anisotropic diffusion in structured materials led to the formulation of the problem as a tensor (DTI) rather than a scalar. New directions exploiting MR diffusion imaging techniques can yield essential new information previously not accessible with other imaging modalities as potential cancer biomarkers. We investigated the feasibility of applying DTI for in-vivo fiber tractography of the prostate. We carried out retrospective study of men with biopsy proven prostate cancer. All patients had undergone prostate MRI with an endorectal coil on a 1.5 T MRI scanner. Diffusion weighted images were acquired with a single shot echo-planar acquisition, with six diffusion sensitizing directions. Preliminary fiber track data was generated as in Fig. 1 using Diffusion Toolkit and displayed with TrackVis (trackvis.org). This data was then used to identify multiple hand drawn regions of interest (ROI) over areas of pathologically proven tumor, the central gland and the normal peripheral zone of the gland. For quantitative analysis, we introduced a track density parameter, which is the number of tracks in a given ROI divided by its volume, as a normalized measure of the tracks passing through the ROI. The values were statistically analyzed and correlated with the staging. One of the key goals of the study is to apply this method to analyze post radiation treatment cases where other modalities fail to yield contrast necessary to distinguish cancerous tissue from necrosis. The main challenge of fiber tractography, however, is the existence of multiple-fiber orientations within an imaging voxel which renders the diffusion tensor model inadequate. The practical limitations imposed by the requirement for a wide spectral sampling of the diffusion spectrum in q-space, can be met if these impulse diffusion gradients are replaced with chirped oscillatory gradients. In this abstract, asymmetrical chirped diffusion sensitizing gradients are shown to yield an efficient sampling of q space in a manner that asymptotically approaches the spectral coverage afforded by delta function diffusion sensitizing gradients. The asymmetrical nature of the gradients is an extension of the method recently proposed by Laun et al.[1] that allows the diffusion experiment to preserve the phase information and hence reconstruct the exact shape of the underlying structural restrictions -see Fig. 2. The challenge is the consequent reduction in diffusion sensitivity as one probes higher frequency dynamics. This problem is addressed by restricting the gradient power to a spectral bandwidth corresponding to the diffusion spectral range of the underlying restrictive geometry. Simultaneous imaging of diffusion at microscopic resolution and at temporally resolvable diffusion time-scales thus becomes possible in-vivo. Fig. 2: Inverse imaging of a triangular restriction using asymmetrical diffusion encoding gradients [1] F. B. Laun, T. A. Kuder, W. Semmler and B. Stieltjes, Phys. Rev. Lett. 107, 048012 (2011).

Autism spectrum disorder (ASD) is a clinically and etiologically heterogeneous condition with high prevalence amongst all world populations. Due to the life long morbidity, ASD poses a profound world-wide public health challenge. Despite its obviously high heritability, a genetic cause is only identified in a small fraction of patients due to its complex etiologic heterogeneity. Recently, whole genome sequencing (WGS) emerged as a powerful tool for variant discovery due to its comprehensive and uniform coverage and is expected to be beneficial for studying ASD. We used WGS to examine 20 families with ASD, mainly from Qatar, as well as from a few other Arabic countries, to detect de novo or rare inherited genetic variants predicted to be of pathogenic significance. All probands were diagnosed with ASD by at least an ADI-R (Autism Diagnostic Interview-revised) evaluation, in addition to other screening or confirmatory tools and were recruited from the Shafallah Center for Children with Special Needs. Due to the nature of the ascertainment source, all probands had associated intellectual impairment. In all probands known causes of ASD were excluded, fragile X syndrome by PCR and Southern blott, Rett syndrome (for females) by Sanger resequencing and MLPA and Copy Number Variations (CNV) by SNP genotyping on an Illumina 1M-Duo SNP chips. Among all probands, we identified deleterious de novo mutations in six (30%) families and inherited X-linked in two families (10%). We did not identify any inherited autosomal dominant mutations, but identified putative inherited autosomal recessive varations in three families (15%). The deleterious de novo variants were found in five previously unrecognized autosomal genes, and in one known autosomal ASD gene. The inherted X-linked variations were found in ASD risk genes. We are interested in deeper examination of the putative variations with autosomal recessive pattern of inheritance, since the parents of 60% of the probands are consanguineous. The deeper examination will employ the study of knock-out and knock-in mouse models and different in silico and in vitro protein modeling studies. These results so far suggest that WGS of a trio coupled with thorough bioinformatic analyses provide a powerful diagnostic tool in ASD. It is also a potent methodology for gene discovery in ASD, which may provide the basis for genetic testing for early diagnosis and early targeted intervention with a final goal of better outcome.

Exome sequencing was used to study genetic variation in the Qatari population. We sequenced 100 healthy Qataris (50X average depth, with >80% of sites at >10x depth) representing the 3 major Qatari genetic subpopulations (Q1 - Bedouin, Q2 - Persian/South Asian, Q3 - African). A total of ~174,000 high quality variants were identified, of which 1306 were predicted to cause loss of function (frameshift/stop-gain/splice/start-loss) in 1102 unique genes. Of these, 471 (36%) were novel Qatari variants (absent from public databases) of which 43 were observed in 2 or more individuals, suggesting a population allele frequency =1%. 54 of 471 loss of function mutations affected genes in the OMIM database with a confirmed disease-causing status. Of these, 30 occurred in genes known to cause severe autosomal recessive disease. Of interest, some of these mutation had allele frequencies of up to 8% in Qataris. We further focused on the subset that were nonsense mutations (n=671/1306). These occurred in 616 of 1102 unique genes and resulted in a median truncated protein length of 54.3%. 237 of 671 nonsense mutations were novel to Qataris, suggesting that a significant number of variants from this population are yet to be sampled and covered in public databases. When nonsense alleles were considered in the 3 separate Qatari subpopulations, the Q3 population displayed the highest number of nonsense alleles per individual (mean: 40.7, range: 28-55), consistent with the highest genome diversity due to African ancestry. Surprisingly, despite having the lowest number of heterozygous nonsense mutations (mean: 22.8, range: 16-31), the Q1 subpopulation had at least 20% more homozygous nonsense mutations (range: 2-15, mean: 6.7) per individual than either Q2 or Q3, consistent with the high levels of consanguinity in this population. Specifically, the Q1 had significantly higher allele frequencies than the rest of the world for 2 autosomal recessive disease genes, including 1 individual homozygous for a nonsense mutation in POMT1 which causes muscular dystrophy, and 4 individuals heterozygous for a mutation that truncates the Holoprocencephaly-causing TGIF1 gene to 7.5% full length. Additionally, the population as a whole had higher allele frequencies for 6 other autosomal-recessive-disease-causing mutations, bearing significant health implications for the Qatari population in particular, and for this highly consanguineous region of the world in general.

[Background] Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) worldwide, and is a major cause of pelvic inflammatory disease, infertility, and ectopic pregnancy. A recent study has found larger than expected prevalence of CT in Qatar, with a prevalence of about 5% among women attending primary health-care centers. The driver of such higher than expected prevalence is not clear. We examined whether the lack of screening programs for CT could contribute to explaining this level of prevalence. [Method] We constructed a mathematical model to examine the public health impact of different CT treatment approaches. The model was parameterized by the prevalence of CT in Qatar along with state of the art empirical evidence of CT natural history and transmission. The population was divided into different risk and age groups, and a mixing matrix was introduced to describe the mixing between these groups. The impact of treatment was assessed at endemic equilibrium. Univariate sensitivity analyses were conducted. [Results] Nearly 63% of CT infections in the population were asymptomatic. A symptomatic treatment approach, where 90% of symptomatic cases were treated, reduced CT prevalence by only 6.5%. An opportunistic screening program, where 20% of the population was screened annually for CT, reduced the prevalence by 36%. Routine screening program, where 50% of the population was screened annually for CT, reduced the prevalence by 93%. The large impact of screening on CT transmission was driven not only by the diagnosis of asymptomatic infections and treating them, but also by reducing effectively the duration of the infectious period during which infected persons can transmit the infection to other individuals. [Discussion] Our results suggest that a key contributor to the higher than expected prevalence of CT in Qatar, is the non-availability of CT-specific screening programs to detect and treat asymptomatic CT infection, such as those available in West Europe and North America. Current programs that focus on treatment of syndromic cases are missing the majority of cases. The undiagnosed infections are driving further transmissions, and a larger CT prevalence. Opportunistic targeted screening could be a meaningful starting point for CT screening programs in Qatar, with potentially routine Pap smear testing as an entry point. Our findings indicate the utility of developing STI-specific programs in Qatar as part of the large expansion of health care services in this country. Detecting CT infections and linking them with appropriate treatment channels could alleviate an unnecessary disease burden and its consequences in the population.

Acute respiratory failure is one of the major causes for concern in intensive care units (ICU). It is a condition that occurs when fluid builds up in the air sacs in the lungs. When this happens the lungs cannot release oxygen into the blood and get rid of carbon dioxide from the body. The lack of oxygen in the blood will cause the organs to malfunction and in severe cases could lead to failure of vital organs such as heart and brain. Patients with acute respiratory failure are usually supported by the mechanical ventilator. The goal of mechanical ventilation is to ensure adequate ventilation, which involves a magnitude of gas exchange that leads to the desired blood level of carbon dioxide, and adequate oxygenation, which involves a blood concentration of oxygen that will ensure proper function of vital organs. A plausible reference lung volume pattern, which corresponds to an optimal patient outcome, is specified by clinical personnel and the task of automated mechanical ventilation is to apply appropriate input pressure so that the output from the system is able to track the given reference voulme pattern. One of the main challenges in mechanical ventilation that needs to be carefully considered is that the applied pressure cannot be arbitrarily large since large applied pressure could potentially damage the lungs, and hence, worsen patients outcome. Another challenge in designing an efficient control algorithm for mechanical ventilation is that the parameters characterizing the dynamics of the lungs, that is, the lung resistances and lung compliances, vary from patient to patient as well as within the same patient under different conditions. Furthermore, the volume of each compartment of the lungs cannot be directly measured and only the total volume of the lungs is available. Therefore, a robust control methodology, which only uses output information and limited applied pressure, is needed in order to design an efficient control algorithm for automated mechanical ventilation. In this research work, we propose an output-feedback sliding mode control methodology for a nonlinear multicompartment respiratory system with amplitude and integral input constraints. The amplitude input constraint is needed to ensure that the applied pressure is not too large, as not to damage the lungs, while the integral input constraint enforces the upper bound on the amount of work done by the ventilator. The proposed controller only uses output information (i.e., the total volume of the lungs) and automatically adjusts the applied input pressure so that the system is able to track a given reference volume pattern in the presence of parameter uncertainty (i.e., modeling uncertainty of the lung resistances and lung compliances) and system disturbances. A Lyapunov-based approach is presented for the stability analysis of the system and the proposed control framework is applied to a two compartment lung model to show the efficacy of the proposed control method.

Background: Myeloproliferative Neoplasms (MPNs) are clonal hematopoietic disorders, classified into three different phenotypes Polycythemia Vera (PV), Essential Thrombocytosis (ET) and Primary Myelofibrosis (PMF). This disorder is associated with the presence Jak2V617F mutation in 90% of PV and 50% of ET and PMF patients as well as other mutations such as Jak2 exon 12 and MPL. However, there are still significant numbers of MPNs cases that are negative to most common genetic anomalies and many mutations are still unknown Aim: To identify and elucidate genetic defects causing MPNs that could serve as disease biomarker. Methods: 7 MPN patients and healthy individuals from 3 consanguineous families were consented into the study. Peripheral blood samples were collected from 6 patients and 4 healthy individuals. Further, genomic DNA was extracted and used for multiplex PCR amplification of 190 amplicons targeting 739 cancer associated mutations in 604 loci from 46 key cancer genes, using the Ion AmpliSeq™ Kit. Next Generation Sequencing (NGS) was performed through the Ion Torrent Personal Genome Machine using the 318 chip and was analyzed with the Torrent Suite Software (Full list of mutations targeted can be found at http://www.bcm.edu/geneticlabs/index.cfm?pmid=21681). Mutation details were obtained from the Catalogue Of Somatic Mutations In Cancer (COSMIC) database. A human genome (hg) 19 DNA sequence (http://www.ncbi.nlm.nih.gov/refseq/rsg/) was used as references for this panel of genes. The nomenclature of mutations is based on the convention recommended by the Human Genome Variation Society (http://www.hgvs.org/mutnomen/). The confirmation of NGS data was performed using RQ-PCR or Sanger sequencing and Jak2 exon 12 mutations were studied. Results: Out of four PV patients, three were positive for the JAK2 V617F mutation. One patient had mutations in PDGFRA 838-840delGLA, APC Q1285fs, NPM1 Splice Site Loss and PTEN S10N. The second patient had mutations in KIT M541L, KDR Q472H, TP53 P72R, while the third patient had PI3KCA I391M, KIT M541L, KDR Q472H and P53 P72R mutations. The fourth patient was negative to the JAK2 V617F mutation, but showed PDGFR A838-840delGLA and SMARCB1 T72K mutations. Out of three ET patients, one patient was positive for JAK2 V617F, SMARCB1 T72K, IDH1 K115Q and PDGFRA 838-840delGLA mutations. Two patients were negative for the JAK2 V617F and MPL mutations, one patient had mutations in PDGFRA 838-840delGLA, APC Q1285fs and SMAD4 198-200delPAL, while the other patient had mutations in CDKN2A S73R, APC Q1285fs and PDGFRA 838-840delGLA. Furthermore, the PDGFRA 838-840delGLA and APC Q1285fs mutations were also found in healthy individuals. Conclusion: This study was able to identify a list of deleterious somatic mutations such as missense and frame shift mutations, in-frame deletions, splice loss sites and Single Nucleotide Variation (SNV) in MPNs patients and healthy individuals. Our preliminary results suggest that the MPNs patients in Qatar have complex mutations. Evidences show that there exists a possibility of the disease arising out of the accumulation of genetic alteration and not as the consequence of a single genetic event. This could possibly be due to the high rate of consanguineous marriages in Qatar i.e. the "Founder Effect".

Calcineurin-NFAT Signaling Pathway Mediates NHE1 Induced Cardiac Hypertrophy Mohamed Mlih, Fatima Mraiche College of Pharmacy, Qatar University, Doha, Qatar In the myocardium, the Na+/H+ exchanger isoform 1 (NHE1), a plasma membrane protein that regulates intracellular pH has been shown to be critical in the development of cardiac hypertrophy. Inhibition of NHE1 activity/expression has previously been demonstrated to produce cardioprotective effects. Recent reports have reported that transgenic mice overexpressing active NHE1 developed spontaneous cardiac hypertrophy in association with elevated levels of osteopontin (OPN). Osteopontin is a secreted protein involved in many physiological pathways including bone formation, immune response, vascularization and cardiac hypertrophy. The physiological pathway in which active NHE1 induces OPN expression in the heart remains unknown. Recently, NHE1 was described as a key regulator of the calcineurin-NFAT pathway. The calcineurin-NFAT pathway is a hypertrophic pathway induced by intracellular increase in calcium concentration that induces NFAT translocation to the nucleus. In the nucleus, NFAT interacts with the transcription factor GATA-4 and together activate hypertrophic gene. Our hypothesis is that NHE1 through the calcineurin/Nfat pathway induces OPN expression leading to cardiac hypertrophy. To verify this hypothesis , rat cardiomyoblasts (H9c2 cells) were infected with activate NHE1 adenovirus in the presence and absence of a calcineurin inhibitor, FK506 . H9c2 cells infected with active NHE1 showed an increase of NHE1 activity (NHE1: 376.5%) and exhibit a 1.6 fold increase in cell area compared to the control, which was attenuated in the presence of FK506. Our preliminary results show that NHE1 activation increases osteopontin protein expression. In addition, H9c2 cells infected with active NHE1 also demonstrate a significant activation of the transcription factor GATA-4 (NHE1: 149% ±28% , p<0.05). The activation of GATA-4 induced by active NHE1 is inhibited by FK506 treatment. In conclusion, NHE1 through the calcineurin/NFAT pathway induces cardiac hypertrophy in H9c2 cells. This new finding will give us a better understanding of signaling pathway mediating NHE1 induced cardiac hypertrophy and allow us to identify alternative therapeutic targets for the treatment heart failure.