Radiographic morphology of canines tested for sexual dimorphism via convolutional-neural-network-based artificial intelligence

The permanent left mandibular canines have been used for sexual dimorphism when human identification is necessary. Controversy remains whether the morphology of these teeth is actually useful to distinguish males and females. This study aimed to assess the sexual dimorphism of canines by means of a pioneering artificial intelligence approach to this end. A sample of 13,046 teeth radiographically registered from 5838 males and 7208 females between the ages of 6 and 22.99 years was collected. The images were annotated using Darwin V7 software. DenseNet121 was used and tested based on binary answers regarding the sex (male or female) of the individuals for 17 age categories of one year each (i.e. 6-6.99, 7.7.99… 22.22.99). Accuracy rates, receiver operating characteristic (ROC) curves and confusion matrices were used to quantify and express the artificial intelligence's classification performance. The accuracy rates across age categories were between 57-76% (mean: 68%±5%). The area under the curve (AUC) of the ROC analysis was between 0.58 and 0.77. The best performances were observed around the age of 12 years, while the worst were around the age of 7 years. The morphological analysis of canines for sex estimation should be restricted and allowed in practice only when other sources of dimorphic anatomic features are not available.

Applying artificial intelligence to determination of legal age of majority from radiographic data

Forensic odontologists use biological patterns to estimate chronological age for the judicial system. The age of majority is a legally significant period with a limited set of reliable oral landmarks. Currently, experts rely on the questionable development of third molars to assess whether litigants can be prosecuted as legal adults. Identification of new and novel patterns may illuminate features more dependably indicative of chronological age, which have, until now, remained unseen. Unfortunately, biased perceptions and limited cognitive capacity compromise the ability of researchers to notice new patterns. The present study demonstrates how artificial intelligence can break through identification barriers and generate new estimation modalities. A convolutional neural network was trained with 4003 panoramic-radiographs to sort subjects into 'under-18' and 'over-18' age categories. The resultant architecture identified legal adults with a high predictive accuracy equally balanced between precision, specificity and recall. Moving forward, AI-based methods could improve courtroom efficiency, stand as automated assessment methods and contribute to our understanding of biological ageing.

BRUCELLOSIS IN TEREKEKA COUNTY, CENTRAL EQUATORIA STATE, SOUTHERN SUDAN

OBJECTIVES

To identify factors associated with Brucellosis in patients attending Terekeka Health Facility, Terekeka County, Central Equatoria State, Southern Sudan and to evaluate the utility of the rapid test kit Euracil®.

DESIGN

A facility based case-control study.

SETTING

Terekeka Health Facility, Terekeka County, Central Equatoria State, Southern Sudan.

SUBJECTS

Cases were patients presenting at the Terekeka Health Facility with clinical symptoms suggestive of Brucellosis and tested positive for Brucellosis by rapid antigen test while controls were selected from individuals attending Terekeka Health facility with health problems unrelated to brucellosis or febrile illness.

RESULTS

A total of fifty eight cases with clinical symptoms suggestive of and tested positive for Brucellosis by rapid antigen test presented. A total of 116 consented controls were recruited into the study. Males accounted for 52% of the cases and 53% of the controls. The mean age was 31 years for both groups. Cases without formal education were 84% while 40% had no source of income, 20% of the cases and 14% of the controls were cattle keepers while 5% of the cases and 13% of the controls were students. In multivariate analysis there were many factors associated with Brucellosis like consumption of raw meat, living with animals at the same place, raising of goats, farm cleaning contact, eating of aborted and wild animals. Logistic regression revealed two factors associated with the disease; consumption of raw milk (OR=3.9, P-value 0.001, 95% CI 1.6666-9.0700) was a risk factor while drinking boiled milk was protective (OR = 0.09, p-value 0.000, 95% CI, 0.1-0.2).

CONCLUSIONS

The main age-groups affected were 20-30 years with males being affected more than females. Drinking of raw milk was significantly associated with Brucellosis while drinking boiled milk was protective. There should be active public health education on the benefits of boiling milk before consumption. Further studies to elucidate the extent and epidemiology of brucellosis in humans and animals in Southern Sudan are recommended.

Dissecting the genetic history of São Tomé e Príncipe: a new window from Y-chromosome biallelic markers

Twenty biallelic Y chromosome markers were analyzed in Angolares, Forros and Tongas, three population groups from the African archipelago of São Tomé e Príncipe. While most male lineages belonged to sub-Saharan haplogroups, the component of European origin added up 23.9% in the archipelago. This contrasts with the reported absence of European mtDNA lineages, and the combined findings testify to a strong sex-biased admixture process during the long-lasting colonial period in São Tomé e Príncipe. Furthermore, the male mediated European component was clearly found to be out of proportion to the small demographic impact of the Portuguese on the islands, reflecting high variance in the reproductive success of the individuals that contributed to its peopling. The male portion of European ancestry was 33.3% in Forros, 27.3% in Tongas and approximately two-fold less, 14.5%, in Angolares. The Angolares also showed the lowest haplogroup diversity and the most reduced number of different haplogroups. The current results reinforce our previous evidence pointing to remarkable restrictions in gene flow between Angolares and other São Tomean inhabitants, in agreement with their considerable isolation and confinement to the south-eastern tip of São Tomé until recently.

Pattern of mtDNA variation in three populations from São Tomé e Príncipe

We have analysed the matrilineal genetic composition of three self-reported ethnic groups from São Tomé e Príncipe (Gulf of Guinea), an African archipelago whose settlement begun in the late fifteenth century. Sequence data from the hypervariable segments I (HVS-I) and II (HVS-II) were obtained for 30 Angolares, 35 Forros and 38 Tongas. The repertory of mtDNA lineages in São Tomé e Príncipe denoted a fully African maternal pool, primarily arisen from a Central/Southwestern substratum. The absence of any lineages of putative European descent means that the European impact at the mitochondrial pool was virtually nil. Angolares showed a clear reduction of mtDNA diversity and a slight genetic differentiation relative to Tongas or Forros, whereas the latter two groups did not present any signs of genetic boundaries between each other. The data obtained here reinforce the depiction of genetic substructuring in São Tomé e Príncipe previously derived from Y-chromosome STRs. In addition, the crossing of mtDNA and Y-STR information led to the inference that the female mediated gene flow within the archipelago was less restricted than the male, a pattern that could be framed in the cultural traditions and socio-historical interactions among the groups.

Genetic structure and origin of peopling in the Azores islands (Portugal): the view from mtDNA

The Azores islands (Portugal), uninhabited when discovered by Portuguese navigators in the fifteenth century, are located in the Atlantic Ocean 1500 km from the European mainland. The archipelago is formed by nine islands of volcanic origin that define three geographical groups: Eastern (S. Miguel and Sta. Maria), Central (Terceira, Faial, Pico, Graciosa and S. Jorge) and Western (Flores and Corvo). To improve the genetic characterisation of the Azorean population, and to clarify some aspects related to the history of settlement, a study of mtDNA was conducted in the population of the archipelago. The HVRI region was sequenced and specific RFLPs were screened in 146 samples obtained from unrelated individuals with Azorean ancestry (50 from the Eastern group, 60 from the Central group, and 37 from the Western group). Samples were classified into haplogroups based on the information obtained from both sequencing and RFLP analysis. All the analyses performed support the idea that, in the whole group of islands, the majority of mtDNA lineages originated from the Iberian Peninsula, mainly from Portugal (mainland). However contributions from other European populations, especially from Northern Europe, cannot be disregarded. The values obtained for the various diversity parameters in the Azores archipelago indicate that the Azorean population, as a whole, does not exhibit the typical characteristics of an isolated population. The analysis of genetic data by groups of islands showed that the Western group exhibited particular features. The distribution of haplogroups in the Western group is very atypical, being significantly different from what is observed in the Eastern and Central groups. Furthermore, the diversity values are, in general, lower than those observed in other populations used for comparison. African haplogroups were found in all the groups of islands. Therefore the presence of Moorish and African slaves on the islands, as reported in historical sources, is supported by the mtDNA genetic data, especially in the Eastern group. The presence of Jews in the Central group is also supported by the mtDNA data. Neither historical nor genetic data (phylogeography of mtDNA) supports the idea of a differential settlement history for the Western group; however, it is represented in the phylogenies as an isolated branch. The effect of genetic drift, induced by the reduced population size since peopling occurred, has led to a very atypical distribution of haplogroups/haplotypes in this group of islands. We cannot ignore the influence of biodemographic and genetic processes, namely founder effect, genetic drift, migration, and even recent mutational events in the mtDNA lineages of the Azorean populations. Nevertheless, a great part of the variation in the Azorean mtDNA can be explained by the settlement history.

Disease knowledge and attitudes toward predictive testing and prenatal diagnosis in families with Machado-Joseph disease from the Azores Islands (Portugal)

OBJECTIVE

Machado-Joseph disease (MJD) reaches its highest prevalence world-wide in the Azores, thus constituting a public health problem in these islands. The aim of the study was thus to (1) determine the level of knowledge about the disease; (2) estimate the expected level of request for predictive testing, and (3) analyse the intentions of at-risk individuals concerning their reproductive decisions.

METHODS

A questionnaire on these points was distributed to 42 affected and 36 at-risk individuals.

RESULTS

As expected, the educational level of the respondents was significantly associated with the level of knowledge about the disease. The survey indicated that 83.3% of the at-risk individuals would make use of predictive test and that 77.8% would make use of prenatal diagnosis. Of the latter, 36.1% would terminate pregnancy if confronted with a positive result for the fetus.

CONCLUSIONS

The level of knowledge about MJD in the Azorean families is considered to be fair. Although the actual behavior can prove to be different from the intentions put forward by at-risk individuals based solely on the results of this study we can estimate that the request for a predictive test would be quite high. The intentions expressed by at-risk individuals seem to indicate that the prenatal diagnosis will have an effect on their reproductive decisions. Results obtained certify the importance of implementing genetic testing for MJD in the Azores.

Natural selection at the MJD locus: phenotypic diversity, survival and fertility among Machado-Joseph Disease patients from the Azores

Machado-Joseph Disease (MJD) is an autosomal dominant neurodegenerative disorder of adult onset, associated with the expansion of a (CAG)n tract in the coding region of the causative gene, localized on 14q32.1. Machado-Joseph Disease shows non-Mendelian features typical of other triplet repeat disorders, including clinical heterogeneity, variable age at onset and anticipation. Three phenotypes have been proposed (clinical types 1, 2 and 3). Type 1 is associated with early age at onset and a high repeat number of the CAG sequence, and Types 2 and 3 have later onset and lower numbers of CAG repeats. This paper investigates whether there is selection against the MJD gene, acting through differential survival. nuptiality and fertility associated with clinical type and age at onset. The study sample comprised 40 MJD patients from the Azores (Portugal) having fully documented reproductive histories and known dates of death. The proportion of married patients of each clinical type increased from 0.22 among Type 1 patients, to 0.40 in Type 2 and 0.95 in Type 3. Age at onset and length of survival were also associated with marital status, with the married cases having later mean age at onset and longer mean survival time. In the whole sample, clinical type was associated with fertility, with significantly fewer children born to Type 1 patients. Among married patients clinical type was not associated with age at marriage, reproductive span or number of children. No reduction of fertility was detected among married patients in whom the onset of MJD was below the age of 50. The authors' interpretation of these results is that the high-repeat CAG haplotypes associated with early age at onset and clinical Type 1 are selected against through reduced survival and fertility. The fertility component of selection is mediated by nuptiality rather than marital fertility.

Population genetics of four PKLR intragenic polymorphisms in Portugal and São Tomé e Príncipe (Gulf of Guinea)

Four intragenic PKLR polymorphisms [1705A/C, 1738C/T. T10/19, and (ATT)n microsatellite] were studied in normal population samples of Central Portugal and São Tomé e Príncipe, a small archipelago located in the Gulf of Guinea, West Africa. For all loci, the observed genotype distributions do not deviate from Hardy-Weinberg equilibrium. The allele frequencies found in the Portuguese population are similar to those previously described in Caucasian populations. Mother-child pair analysis for the (ATT)n microsatellite does not show deviations to the Mendelian rules. In São Tomé e Príncipe the biallelic polymorphisms 1705A/C, 1738C/T, and T10/19 presented inverse allelic frequencies when compared with the Portuguese population. Two new alleles were found at the (ATT)n microsatellite. Significant statistical differences were found between both populations. The results showed that São Tomeans had higher haplotype diversity and lower linkage disequilibrium among the polymorphic sites. The PKLR intragenic polymorphisms, commonly used in haplotype analysis with the gene mutations in PK-deficient patients, can thus be successfully employed in anthropological genetics.

Evidence for population sub-structuring in São Tomé e Príncipe as inferred from Y-chromosome STR analysis

Seven Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 have been analysed in population samples of Angolares, Forros and Tongas, three ethnic groups from the African archipelago of São Tomé e Príncipe (Gulf of Guinea). Complete typings were obtained for 103 chromosomes, which belonged to 79 different haplotypes. The mean heterozygosity per locus in the overall São Tomean sample was 0.566, with the highest value found among Forros and the lowest among Angolares. Angolares also showed the lowest level of haplotype diversity. On average, the mean pairwise difference between two random haplotypes from Angolares, Forros and Tongas was 4.69, 6.74 and 6.23 repeats, respectively. The genetic distances were found to be statistically significant between Angolares and Forros or Tongas. In accordance, AMOVA revealed that the percentage of variation attributable to differences among groups was only significant when we distinguished between Angolares and non-Angolares. Globally, these results indicate that, with respect to the pool of male lineages of São Tomé e Príncipe, some genetic sub-structuring does exist, basically determined by the Angolares ethnic group.

A new PKLR gene mutation in the R-type promoter region affects the gene transcription causing pyruvate kinase deficiency

Mutations in the PKLR gene responsible for pyruvate kinase (PK)-deficient anaemia are mainly located in the coding regions: 11 are in the splicing sites and, recently, three mutations have been described in the promoter region. We now report a novel point mutation A-->G on nucleotide 72, upstream from the initiation codon of the PKLR gene, in four Portuguese PK-deficient patients. This new regulatory mutation occurs within the most proximal of the four GATA motifs (GATA-A element) in the R-type promoter region. In two patients who were homozygous for this mutation, a semiquantitative reverse transcription polymerase chain reaction (PCR) procedure was used to evaluate the amount of R-PK mRNA transcript in the reticulocytes. The mRNA level was about five times lower than in normal controls, demonstrating that the PKLR gene transcription is severely affected, most probably because the -72A-->G point mutation disables the binding of the erythroid transcription factor GATA-1 to the GATA-A element. Supporting these data, the two patients homozygous for the -72A-->G mutation had severe haemolytic anaemia and were transfusion dependent until splenectomy. Two other patients who were compound heterozygous for this mutation and the previously described missense mutation 1456C-->T had a mild condition.

PK-LR gene mutations in pyruvate kinase deficient Portuguese patients

In nine unrelated Portuguese patients with pyruvate kinase (PK) deficient anaemia, whose symptoms ranged from a mild chronic haemolytic anaemia to a severe anaemia presenting at birth and requiring multiple transfusions, the PK-LR gene mutations were identified and correlated with their phenotypes. Five different mutations were identified, three of them for the first time: a missense mutation 1670G --> C on exon 12 and two 5' splice donor site (GT) mutations on intron 8 [IVS8(+2)T --> G] and intron 10 [IVS10(+1)G --> C]. Two previously described missense mutations, 1456C --> T and 993C --> A, were also found. The genotype/phenotype correlation showed that patients with two missense mutations or with a missense mutation and a splicing mutation had a mild haemolytic anaemia. The three patients with severe anaemia, who were transfusion dependent until splenectomy, were homozygous for the splicing site mutations IVS10(+1)G --> C or IVS8(+2)T --> G.

Origins of a mutation: population genetics of Machado-Joseph disease in the Azores (Portugal)

Machado-Joseph disease (MJD) is an autosomal dominant neurodegenerative disorder of adult onset. In the islands of the Azores (Portugal), MJD reaches the highest prevalence reported worldwide. It has been postulated that it is highly represented in the Azorean population as a result of a founder effect. To test this hypothesis, we reconstructed the ascending genealogies of the 32 Azorean families presently identified as harboring the disease (103 patients), using parish records as the main source of data. These patients were originally from the islands of São Miguel, Terceira, Graciosa, and Flores. The genealogies of the two main Azorean American families (Machado and Joseph) were also reconstructed. To identify the links between the MJD families, we calculated the kinship coefficient between the proponents of these genealogies. The family from Terceira was linked to three different MJD families from Flores through common ancestors. No kinship was observed between the MJD families from São Miguel and families from any other island. Links between the two Azorean American families and Azorean MJD families were found. The founders present in more than one ascendance were identified. Their chronological and geographic distribution indicates that more than one MJD mutation was introduced in the Azores, probably by settlers coming from the Portuguese mainland. The molecular evidence to date corroborates these results, because two distinct haplotypes have been established, one on the island of São Miguel and the other on Flores. Therefore molecular biology studies confirm the accuracy of the conclusions drawn from the genealogical evidence supporting the absence of a founder effect for MJD in the Azorean population.

Causes of death in Machado-Joseph disease: a case-control study in the Azores (Portugal)

BACKGROUND

Machado-Joseph disease (MJD) is an autosomal dominant cerebellar ataxia of adult onset with a high prevalence in the islands of Azores (Portugal). The genetic epidemiological studies presently under way in these islands are based on the genealogical reconstruction of the affected families, thus partially depending on the reference of patients using family history. A considerable effort has been made to obtain genealogies that are as complete as possible, making use of different types of data. The utility of the death causes contained in the death registers of the patients with MJD was determined in this study.

OBJECTIVES

To estimate the extent to which the cause of death reported in the death register can confirm other reports of an individual's status for the disease (ie, oral information), and to determine the accuracy of the death certificates in listing MJD in patients whose disease was clinically diagnosed.

DESIGN

Case-control study.

METHODS

The death registers of 113 patients with MJD (82 whose disease was identified by history and 31 whose disease was clinically diagnosed) were examined and compared with those of controls matched by sex and date and place of death.

RESULTS

There were significant differences in the causes of death between cases and controls, both for those whose disease was identified by history (chi(2) = 51.69, P < .001) and for those whose disease was identified by examination (chi(2) = 27.78, P = .004). However, the cause of death was in accord with the presence of the disease in only 40% of the cases reported as being identified only by family history. In the cases in which the disease was clinically diagnosed, only nearly 38% of the registers provided reliable information as to MJD being the direct cause of death.

CONCLUSIONS

The fact that only nearly 40% of the patients with clinically confirmed MJD had a cause of death compatible with MJD precludes the use of cause of death as a means of identifying affected individuals in the Azorean MJD pedigrees.

A tale of two islands: population history and mitochondrial DNA sequence variation of Bioko and São Tomé, Gulf of Guinea

The hypervariable segment I of the control region of the mtDNA was sequenced in 45 unrelated individuals from Bioko and 50 from São Tomé, two islands in the Gulf of Guinea that have had very different settlement patterns: Bioko was colonized around 10000 BP, while São Tomé was first settled by the Portuguese, who brought African slaves to the island. Two different patterns of sequence variation are evident and are also clearly a consequence of their very different demographic histories. The Bubi present a low genetic diversity and it is likely that the island was colonized by a small number of individuals with small later migration. São Tomeans might be considered a subset of a mainland African population relocated to the island. They present high genetic diversity with a high number of sequences being shared with many continental populations. This study, with knowledge of the population history in island populations, strengthens the genetic approach to unravel past demographic events.

Prevalence, geographic distribution, and genealogical investigation of Machado-Joseph disease in the Azores (Portugal)

Machado-Joseph disease (MJD) is an autosomal, dominantly inherited neurodegenerative disorder of adult onset. The prevalence of MJD reaches its highest values in the islands of the Azores. A research program was undertaken to study the origin and spread of the mutant gene in the Azorean populations. Here, we present the first results of such a study. The Azorean MJD patients are grouped in 34 families and are distributed on 4 of the 9 Azore islands. Values of prevalence, carrier rate, and number of individuals at risk are reported. The genealogies of the patients were reconstructed to identify the founders. An analysis of the geographic distribution of the birthplaces of the patients compared with the birthplaces of the founders revealed the existence of areas that are clusters for both, thus defining crucial sites for the origin of the disease. Preliminary results on the number of links between the affected families show that 64.7% of them have at least one link with another MJD family. So far, a single source for the introduction of the mutant gene in the Azores has not been identified.

Birth, marriage and death in illegitimacy: a study in northern Portugal

In populations in which the frequency of illegitimacy is high, illegitimates and legitimates may be subjected to different demographic and social pressures, with social and genetic consequences. A rural population from north-east Portugal is studied and variables from birth, marriage and death records are compared according to the legitimacy of the individuals. The analysis shows important differential demographic patterns in infant and child mortality and in migration prior to and related to marriage, especially in women. Some changes over time and gender differences are also evident.

Influence of industrialisation on marital behaviour in Beduído (Estarreja), Portugal

From marriage records of a Northern Portuguese parish for 1900-80, endogamy and exogamy rates were calculated for birthplace and residence in order to analyse the effect of industrialisation on the population structure after 1940. Marriages that were endogamous relative to birthplace decreased between 1940-49 (58.9%) and 1988 (20.5%), while exogamy increased. Exogamous marriages in which people came from outside the municipality (51.92%) were greater than those of the surrounding region (42.04%). After industrialisation, the pattern of marriages changed for residence, with an increase in the number of individuals who came from the district to work in the factories and married. Industrialisation advanced the start of exogamy which, for most Portuguese populations, began later, in the 1960s.

Genetic structure of the Azores: marriage and inbreeding in Flores

Flores is one of the smallest and most westerly islands of the Atlantic archipelago of the Azores. This preliminary account of the population's demography and genetic structure uses dispensations to contract consanguineous marriages taken from the Roman Catholic marriage registers in order to estimate mean inbreeding rates in the population over the period 1860-1980. Comparisons are made with inbreeding rates on the Portuguese mainland and elsewhere in Western Europe, and reasons suggested to explain the rather high rates of inbreeding encountered on Flores.