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CTGA Database Search

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As the retrieval of information from the CTGA database is as important as filling data in, we paid considerable attention to provide the users with the option of performing complicated queries to obtain focused results without sacrificing the simplicity. At present, the CTGA database can be queried using any of three available modes of search:

1. Basic Search with a standard query box in which the user may enter one or more keywords.
2. Advanced Search with two standard query boxes, Boolean operators, and result sorting controls.
3. Power Search demonstrates the power of querying at CTGA. At this point, the user can employ a multitude of user-friendly search combinations according to the name of a disease or gene locus, its classification, symptoms, related gene loci, OMIM number, chromosome location, mode of inheritance, geographic location, and others. Result sorting control is also available. Certainly, the proper use of power search inevitably increases specificity and narrows down results to a focused number of relevant records.

In any of the search modes, the user issues a command that is interpreted in the CTGA server. Keyword processing occurs using the system's specialized mark-up language, Claris Dynamic Markup Language (CDML). Accordingly, results are sent to the user's browser as a standard HTML document with no requirement for any additional software. Query results include the names and corresponding OMIM numbers of genes and genetic disorders described in Arab people. By selecting a record among the results, the user accesses extensive details relating to a specific gene or genetic disorder.

Simple Search Strategies

In this section, the user would evaluate the behavior of simple search queries in the three search modes currently available at the CTGA Database. Simple queries may include single or multiple keywords.

Example 1: Searching for information on Leukemia

In Basic Search, enter the syntax leukemia in the search box then click on the SEARCH button. The search engine will search for the term leukemia throughout all fields in all records in the database and returns back with a minimum of 16 records sorted by default alphabetically according to disease/gene names (September 2006).

1. Amegacaryocytic Thrombocytopenia, Congenital
2. B-Cell CLL/Lymphoma 2
3. Breast Cancer 2 Gene
4. Down Syndrome
5. FANCA Gene
6. Leukemia, Acute Monocytic
7. Leukemia, Acute T-Cell
8. Leukemia, Chronic Myeloid
9. Leukemia Inhibitory Factor Receptor
10. Leukemia Viral BMI-1 Oncogene, Mouse, Homolog of
11. Neurofibromatosis, Type I
12. Nuclear Body Protein SP110
13. Stuve-Wiedemann Syndrome
14. Thyroid Hormone Receptor, Beta
15. V-KIT Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog
16. Werner Syndrome

In Advanced Search, enter the syntax leukemia in the top search box then click on the SEARCH button. The search engine will search for the term leukemia throughout all fields in all records in the database and returns back with a minimum of 16 records (September 2006); these exactly represent the results obtained in basic search mode. Note that in this mode the user may control the way results appear by sorting them according to disease/gene names or by corresponding OMIM Numbers.

In Power Search, enter the syntax leukemia in the Name of Genetic Disease / Gene Locus box then click on the SEARCH button. The search engine will search for the term leukemia in the Disease Name and Alternative Names fields, and not in other fields, and returns with a minimum of 10 records (September 2006). Again, the user may control the way results appear by sorting them according to disease/gene names or by corresponding OMIM Numbers.

1. B-Cell CLL/Lymphoma 2
2. Breast Cancer 2 Gene
3. Down Syndrome
4. Leukemia, Acute Monocytic
5. Leukemia, Acute T-Cell
6. Leukemia, Chronic Myeloid
7. Leukemia Inhibitory Factor Receptor
8. Leukemia Viral BMI-1 Oncogene, Mouse, Homolog of
9. Neurofibromatosis, Type I
10. Thyroid Hormone Receptor, Beta

Example 2: Searching for information on the syndactyly (webbed or conjoined fingers) symptom

In Basic Search, enter the syntax syndactyly in the search box and click on the SEARCH button. The search engine will search for the term syndactyly throughout all fields in all records in the database and returns back with a minimum of 17 records (September 2006).

1. Absence Defect of Limbs, Scalp, and Skull
2. Acrocephalopolysyndactyly Type II
3. Acrofrontofacionasal Dysostosis, Severe
4. Anophthalmos with Limb Anomalies
5. Apert Syndrome
6. Blepharophimosis with Ptosis, Syndactyly, and Short Stature
7. Cleft Hand and Absent Tibia
8. Ellis-van Creveld Syndrome
9. Nijmegen Breakage Syndrome
10. Orofaciodigital Syndrome I
11. Poland Syndrome
12. Polysyndactyly with Cardiac Malformation
13. Popliteal Pterygium Syndrome, Lethal Type
14. Right Pelvic Kidney
15. Saethre-Chotzen Syndrome
16. Silver-Russell Syndrome
17. Syndactyly, Type I, with Microcephaly and Mental Retardation

In Advanced Search, enter the syntax syndactyly in the search box and click on the SEARCH button. The search engine will search for the term syndactyly throughout all fields in all records in the database and returns back with a minimum of 17 records (September 2006); these exactly represent the results obtained in basic search mode.

In Power Search, enter the syntax syndactyly in the Symptom, Molecular Pathology, Epidemiology box and click on the SEARCH button. The search engine will search for the term syndactyly in the Description, Molecular Genetics, and Epidemiology fields, and not in other fields, and returns with a minimum of 11 records (September 2006).

1. Absence Defect of Limbs, Scalp, and Skull
2. Acrocephalopolysyndactyly Type II
3. Anophthalmos with Limb Anomalies
4. Apert Syndrome
5. Cleft Hand and Absent Tibia
6. Ellis-van Creveld Syndrome
7. Nijmegen Breakage Syndrome
8. Orofaciodigital Syndrome I
9. Popliteal Pterygium Syndrome, Lethal Type
10. Saethre-Chotzen Syndrome
11. Silver-Russell Syndrome

Example 3: Searching for information on alpha-thalassemia using its OMIM number (141800)

In Basic Search, enter the syntax 141800 in the search box then click on the SEARCH button. The search engine will search for the number 141800 throughout all fields in all records in the database and returns back with the record related to alpha-thalassemia.

In Advanced Search, enter the syntax 141800 in the top search box then click on the SEARCH button. The search engine will search for the number 141800 throughout all fields in all records in the database and returns back with the record related to alpha-thalassemia.

In Power Search, enter the syntax 141800 in the OMIM Number box then click on the SEARCH button. The search engine will search for the number 141800 in the OMIM Number field only and returns with the record related to alpha-thalassemia.

Example 4: Searching for genetic disease records in CTGA by the family name (Al-Gazali) of a corresponding investigator

In Basic Search, enter the syntax Al-Gazali in the upper search box then click on the SEARCH button. The search engine will search for the family name Al-Gazali throughout all fields in all records and returns back with a minimum of 69 records (September 2006).

In Advanced Search, enter the syntax Al-Gazali in the upper search box then click on the SEARCH button. The search engine will search for the family name Al-Gazali throughout all fields in all records and returns back with the same set of records obtained using basic search.

In Power Search, enter the syntax Al-Gazali in the Literature Search box then click on the SEARCH button. The search engine will search for the name Al-Gazali ONLY in the References field and returns with a minimum of 67 records (September 2006).

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Phrase Searching

Phrase searching is used to consider keywords as phrases. Hence, the purpose of this type of search is to look for keywords that occur side by side in a record and in the order given, whereas in simple searching, multiple keywords do not necessarily have to be next to each other. In CTGA searching, using parentheses quotes " " around search words is the way to do phrase searching.

Example 5: Searching for CTGA records by the phrase "renal agenesis"

In Basic Search, enter the syntax "Renal Agenesis" in the search box (including the "" marks) then click on the SEARCH button. The search engine will search for the phrase throughout all fields in all records in the database and returns back with a minimum of 6 records (September 2006).

1. Abdominal Muscles, Absence of, with Urinary Tract Abnormality and Cryptorchidism
2. Bifid Nose, Renal Agenesis, and Anorectal Malformations
3. Meckel Syndrome, Type 1
4. Polycystic Kidney Disease, Autosomal Recessive
5. Urogenital Adysplasia, Hereditary
6. Varadi-Papp Syndrome

In Advanced Search, enter the syntax "Renal Agenesis" in the top search box (including the "" marks) then click on the SEARCH button. The search engine will search for the phrase throughout all fields in all records in the database and returns back with the same set of records obtained by basic search.

In Power Search, enter the syntax "Renal Agenesis" (including the "" marks) in the Symptom, Molecular Pathology, Epidemiology box then click on the SEARCH button. The search engine will search for the phrase Renal Agenesis in the Description, Molecular Genetics, and Epidemiology fields only and returns with a minimum of 5 records (September 2006).

1. Abdominal Muscles, Absence of, with Urinary Tract Abnormality and Cryptorchidism
2. Polycystic Kidney Disease, Autosomal Recessive
3. Bifid Nose, Renal Agenesis, and Anorectal Malformations
4. Varadi-Papp Syndrome
5. Meckel Syndrome, Type 1

Please note that removing the " " marks from the syntax in this example will result in larger numbers of records since the CTGA search engine will not recognize the phrase Renal Agenesis as a single search term, but will search for renal and agenesis as two separate keywords.

Example 6: Searching for genetic disease records in CTGA by the full name (Andre Megarbane) of a corresponding investigator

In Basic Search, enter the syntax "Megarbane A", in the format of last name plus initials with no punctuation, in the search box (including the " " marks) then click on the SEARCH button. The search engine will search for the name Andre Megarbane throughout all fields in all records in the database and returns back with a minimum of 34 records (September 2006).

In Advanced Search, enter the syntax "Megarbane A", in the format of last name plus initials with no punctuation, in the top search box (including the " " marks) then click on the SEARCH button. The search engine will search for the name Andre Megarbane throughout all fields in all records in the database and returns back with the same set of records as obtained in basic search.

In Power Search, enter the syntax "Megarbane A", in the format of last name plus initials with no punctuation, in the Literature Search box (including the " " marks) then click on the SEARCH button. The search engine will search for the name Andre Megarbane in only the References field and returns with a minimum of 34 records (September 2006).

Example 7: Searching for records citing references from Nature Genetics journal.

In Basic Search, enter the name of the journal according to the MEDLINE abbreviation "Nat Genet" in the search box (including the " " marks) then click on the SEARCH button. The search engine will search for the term "Nat Genet" throughout all fields in all records in the database and finds 13 records (September 2006).

In Advanced Search, enter the name of the journal according to the MEDLINE abbreviation "Nat Genet" in the top search box (including the " " marks) then click on the SEARCH button. The search engine will search for the term "Nat Genet" throughout all fields in all records in the database and returns with the same set of records as in basic search.

In Power Search, enter the name of the journal according to the MEDLINE abbreviation "Nat Genet" in the Literature Search box (including the " " marks) then click on the SEARCH button. The search engine will search for the term "Nat Genet" only in the References field and finds a minimum of 13 records (September 2006).

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Wildcard Searching

By default, the CTGA search engine permits the use of the * wildcard symbol to perform truncation queries. A wildcard symbol is a special character that will match any other(s), including absence of a character.

The purpose of wildcard searching is to broaden a search strategy. It also means using a "root word" or partial term along with the wildcard character. Hence, wildcard searching is also a method for saving time in searching for keywords with common roots. While wildcard searching is a useful tool, the proper use of the root word is an essential determinant for a successful query. In other words, using common root words (e.g. parent*; for parent, parents, parental, and others) or very short terms (less than four characters long) will lead to large sets of unfocused results.

By default, the CTGA search engine recognizes prefixes and suffixes and applies wildcard searching without the need to use the * symbol. However, for wildcard substitution within keywords, it is necessary to use the * symbol.

Example 8: Searching for keywords starting with the prefix Hemo-

In Basic Search, enter the syntax Hemo (or Hemo*) in the search box (including the * marks) then click on the SEARCH button. The search engine will search for all possible keywords with the root Hemo throughout all fields in all records in the database and finds a minimum of 45 records (September 2006). Terms that are searched in this example include: Hemoglobin, Hemostasis, Hemolysis, Hemochromatosis, Hemophagocytic, Hemorrhagic, Methemoglobin, and many others.

In Advanced Search, enter the syntax Hemo (or Hemo*) in the top search box (including the * marks) then click on the SEARCH button. The search engine will search for all possible keywords with the root Hemo throughout all fields in all records in the CTGA database and returns back with the same sets of records as obtained in basic search.

In Power Search, enter the syntax Hemo (including the * mark) in the required box then click on the SEARCH button. The search engine will search for the term in the corresponding field(s) and returns with the proper set records. For example, searching for Hemo in Disease Names will result in 20 records while searching for occurrence of the term Hemo in the symptoms field will result in 30 records.

Example 9: Searching for keywords ending with the suffix -dactyly

In Basic Search, enter the syntax dactyly (or *dactyly) in the search box (including the * marks) then click on the SEARCH button. The search engine will search for all words ending with the suffix dactyly throughout all fields in all records in the CTGA database and returns back with a minimum of 55 records (September 2006). Terms that are searched in this example include: Syndactyly, Brachydactyly, Camptodactyly, Ectrodactyly, and many others.

In Advanced Search, enter the syntax dactyly (or *dactyly) in the top search box (including the * marks) then click on the SEARCH button. The search engine will search for all words ending with the suffix dactyly throughout all fields in all records in the CTGA database and returns back with the same set of records as obtained in basic search.

In Power Search, enter the syntax dactyly (or *dactyly; including the * mark) in the required box then click on the SEARCH button. The search engine will search for the term in the corresponding field(s) and returns with the proper records. For example, searching for dactyly in Disease Names will result in 21 records while searching for dactyly within the symptoms fields will result in 40 records (September 2006).

Example 10: Letter substitution to search for the keywords micro- and macrocephaly.

In Basic Search, enter the syntax M*crocephaly in the search box then click on the SEARCH button. The search engine will search for all possible combinations of the keyword (microcephaly or macrocephaly) throughout all fields in all records in the CTGA database and returns back with a minimum of 49 records (September 2006). Test this search again by entering either microcephaly or macrocephaly; results will include a minimum of 38 or 13 records, respectively.

In Advanced Search, enter the syntax M*crocephaly in the top search box then click on the SEARCH button. The search engine will return back with the same set of records as obtained in basic search.

In Power Search, enter the syntax M*crocephaly in the required box then click on the SEARCH button. The search engine will search for the term in the corresponding field(s) and returns with the proper records. For example, searching for M*crocephaly in Disease Names will result in 19 records while searching within the symptoms fields will result in 35 records (September 2006).

No difference occurred between results obtained using basic or advanced search in all examples described thus far. The main reason for this outcome is that in both modes the CTGA search engines address a query to all fields of all records in the CTGA database. However, the importance of advanced search querying in CTGA is expressed in its capacity to conduct Boolean searching, as we shall see in the following section.

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Boolean searching

Searching the CTGA Database can also be formulated according to the principles of the Boolean logic, named for the British-born Irish mathematician George Boole. Boolean searching refers to the logical relationship among search terms. Carrying out a Boolean search is not as frightening as it may sound. You simply apply the common Boolean operators to your search string to construct logical relationships among search terms:

search term BOOLEAN OPERATOR search term

By default, querying using a string of keywords in basic, advanced, or power search modes results in the implementation of the AND operator, where all keywords should occur in common records irrespective of their sequence. However, the advanced CTGA search engine surpasses the other two search modes by its capacity to process two or more keywords with 'OR' and 'NOT' Boolean connectors.

Example 11: Searching for an association between leukemia and neurofibromatosis.

In Basic Search, enter the syntax leukemia neurofibromatosis in the search box and then click the SEARCH button. By default, the AND Boolean operator is utilized and the CTGA search engine seeks records where BOTH terms occur together throughout all fields and returns back with a minimum of 1 record (September 2006).

In Advanced Search, enter the syntax leukemia in the upper search box, neurofibromatosis in the lower search box, and then click the SEARCH button. By default, the advanced CTGA search engine interprets this query using the AND Boolean operator. In other words, the search engine will search for BOTH terms occurring together throughout all fields in all records in the database and returns back with a minimum of 1 record (September 2006). Alternatively, the syntax leukemia neurofibromatosis may be entered either in the upper or lower search boxes and results in exactly similar results. The reason for this is that each of the two boxes represent a full functional basic search box.

In Power Search, enter the syntax leukemia neurofibromatosis in the required box then click on the SEARCH button. The search engine will search for BOTH keywords in the corresponding field(s) and returns with the proper records. For example, searching for leukemia neurofibromatosis in Disease Names or in the symptoms field will result in a single record (September 2006).

1. Neurofibromatosis, Type I

Remember that in example 1, a simple search for the term leukemia resulted in 16 records. Hence, one of these records also included the term neurofibromatosis.

Example 12: Searching for leukemia without any association with neurofibromatosis.

Since basic and power search do not have the option of applying the NOT operator, in Advanced Search, enter the syntax leukemia in the upper search box, neurofibromatosis in the lower search box, chose the NOT Boolean connector, and then click on the SEARCH button. The search engine will search for all records with the term leukemia excluding all records containing the term neurofibromatosis occurring throughout all fields in all records in the database and return back with a minimum of 15 records (September 2006).

1. Amegacaryocytic Thrombocytopenia, Congenital
2. B-Cell CLL/Lymphoma 2
3. Breast Cancer 2 Gene
4. Down Syndrome
5. FANCA Gene
6. Leukemia, Acute Monocytic
7. Leukemia, Acute T-Cell
8. Leukemia, Chronic Myeloid
9. Leukemia Inhibitory Factor Receptor
10. Leukemia Viral BMI-1 Oncogene, Mouse, Homolog of
11. Nuclear Body Protein SP110
12. Stuve-Wiedemann Syndrome
13. Thyroid Hormone Receptor, Beta
14. V-KIT Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog
15. Werner Syndrome

From the interpretation made in the previous example, the results obtained herein can be easily verified since 16 records had the term leukemia including one in which the term neurofibromatosis also occurred. It is also important to note that the CTGA search engine processes Boolean search in a left-to-right sequence. Hence, the syntax leukemia NOT neurofibromatosis will search for records containing the term leukemia, but excluding all those containing the term neurofibromatosis whereas the syntax neurofibromatosis NOT leukemia will search for records containing the term neurofibromatosis but not the term leukemia.

Example 13: Searching for records with either the term leukemia or the term neurofibromatosis.

Since basic and power search do not have the option of applying the OR operator, in Advanced Search, enter the syntax leukemia in the upper search box, neurofibromatosis in the lower search box, chose the OR Boolean connector, and then click on the SEARCH button. The search engine will search for all records with either terms leukemia or neurofibromatosis occurring throughout all fields in all records in the database and returns back with a minimum of 18 records (September 2006).

1. Amegacaryocytic Thrombocytopenia, Congenital
2. B-Cell CLL/Lymphoma 2
3. Breast Cancer 2 Gene
4. Dandy-Walker Syndrome
5. Down Syndrome
6. FANCA Gene
7. Leukemia, Acute Monocytic
8. Leukemia, Acute T-Cell
9. Leukemia, Chronic Myeloid
10. Leukemia Inhibitory Factor Receptor
11. Leukemia Viral BMI-1 Oncogene, Mouse, Homolog of
12. Moyamoya Disease
13. Neurofibromatosis, Type I
14. Nuclear Body Protein SP110
15. Stuve-Wiedemann Syndrome
16. Thyroid Hormone Receptor, Beta
17. V-KIT Hardy-Zuckerman 4 Feline Sarcoma Viral Oncogene Homolog
18. Werner Syndrome

The interpretation of this result is for the reason that three records in the CTGA database contain the term neurofibromatosis (September 2006) and 16 records contain the term leukemia (including one common record with neurofibromatosis).

Please note that only one Boolean operator may be used at a time in the advanced search mode of CTGA. The simultaneous selection of the OR and NOT checkboxes will activate a warning message that demands the user to switch off one of the options before using the other. The behavior of the AND, OR, and NOT Boolean operators in simple queries in the advanced CTGA search engine can be visually described using Venn diagrams.

Figure 1. Illustration of how the AND, OR, and NOT Boolean search logic works.

Boolean-based search is not only limited to simple queries as indicated in examples 11 through 13. Additionally, all examples indicated in simple, phrase, and wildcard search strategies may be clustered in a multitude of compound queries and subject them to Boolean logic.

So far, all examples described in this section demonstrated the application of Boolean logic in queries containing a maximum of two terms. Queries with three or more terms are interpreted differently in the Advanced Search mode in CTGA. The examples described in Table 5 best express the behavior of the top and bottom Advanced Search boxes. By default, a string of keywords in either the top or bottom boxes are treated with the AND Boolean operator. The same applies when the NOT operator is utilized. However, the use of the OR operator replaces the default action of the bottom box where multiple keywords are treated with the OR operator among themselves too.

Figure 2. Examples of multiple keyword queries and their results using Boolean logic in the CTGA Advanced Search mode (results as of September 2006).

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Composite Search Strategies

All search strategies described thus far included examples in which the user is searching for a keyword, a string of keywords, or phrases occurring in a defined field (power search) or anywhere in all CTGA records (basic and advanced modes). However, in certain cases querying multiple keywords, each occurring in a specific field, is the key to achieve more focused results. Actually, basic and advanced search engines in CTGA map all queried keywords similarly to all fields in all records in the database and, thus, are not very efficient tools in this situation. In the following examples, we shall see the advantage of utilizing the power search mode in CTGA database to query for multiple keywords each mapped to a specific field in CTGA records.

Example 14: Searching for all Nervous System Disorders mapped to Chromosome 1 in the Arab Populations.

In Power Search, click the button Disease Phenotype, chose “Diseases of the Nervous System” from the drop-down menu, click the Chromosome 1 button, chose the results sorting preference (optional), then click on the SEARCH button. This query results in 7 records (September 2006).

1. Charcot-Marie-Tooth Disease, Axonal, Type 2B1
2. Hypertrophic Neuropathy of Dejerine-Sottas
3. Mitochondrial Complex I Deficiency
4. Muscular Dystrophy, Congenital, 1B
5. Parkinson Disease 7, Autosomal Recessive Early-Onset
6. Parkinson Disease 9
7. Schwartz-Jampel Syndrome, Type 1

Example 15: Searching for Autosomal Recessive disorders mapped to Chromosome 4 in the population of the United Arab Emirates.

In Power Search, click the button Disease Phenotype, leave the drop-down menu unchecked to search in all disease classifications, click the Chromosome 4, Autosomal, Recessive, and United Arab Emirates checkboxes, chose the results sorting preference (optional), then click on the SEARCH button. This search results in 3 records (September 2006):

1. Autonomic Control, Congenital Failure of
2. Ellis-van Creveld Syndrome
3. Multiple Acyl-CoA Dehydrogenation Deficiency

Example 16: Searching for Gene Loci mapped to the X Chromosome in the Lebanese population.

In Power Search, click the buttons Gene Locus, Chromosome X, and Lebanon. This search will result in 3 records (September 2006):

1. OCRL Gene
2. WAS Gene
3. Zinc Finger Protein of Cerebellum, 3

Please note that in the categories Chromosome, Mode of Inheritance, and Country, it is possible to select multiple checkboxes. However, in the Record Category, search is restricted to one option at a time, either genetic disease (Disease Phenotype) or disease-causing gene (Gene Locus) since CTGA records are classified in either option at a time.

Example 17: Searching for all disorders leading to either micro- or macrocephaly and that Prof. Al-Gazali described in the United Arab Emirates.

In Power Search, enter the keywords M*crocephaly in the Symptom, Molecular Pathology, Epidemiology search box and Al-Gazali in the Literature Search box. Then click the United Arab Emirates checkbox, chose the results sorting preference (optional), and then click on the SEARCH button. This search results in 11 records (September 2006):

1. Achondroplasia
2. Arthrogryposis Multiplex Congenita
3. Cohen Syndrome
4. Down Syndrome
5. Lissencephaly I
6. Macrocephaly with Multiple Epiphyseal Dysplasia and Distinctive Facies
7. McDonough Syndrome
8. Meckel Syndrome, Type 1
9. Noonan Syndrome 1
10. Osteosclerotic Bone Dysplasia, Lethal
11. Rhizomelic Chondrodysplasia Punctata, Type 2

By combining the ease of buttons, checkboxes, and drop-down menu selections with proper term searching in power search boxes mining the CTGA database gains a further dimension. Undoubtedly, the correct use of the CTGA Power Search Engine will help any average end-user to retrieve well-focused answers.

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