The role of citizen science in addressing grand challenges in food and agriculture research.

The power of citizen science to contribute to both science and society is gaining increased recognition, particularly in physics and biology. Although there is a long history of public engagement in agriculture and food science, the term 'citizen science' has rarely been applied to these efforts. Similarly, in the emerging field of citizen science, most new citizen science projects do not focus on food or agriculture. Here, we convened thought leaders from a broad range of fields related to citizen science, agriculture, and food science to highlight key opportunities for bridging these overlapping yet disconnected communities/fields and identify ways to leverage their respective strengths. Specifically, we show that (i) citizen science projects are addressing many grand challenges facing our food systems, as outlined by the United States National Institute of Food and Agriculture, as well as broader Sustainable Development Goals set by the United Nations Development Programme, (ii) there exist emerging opportunities and unique challenges for citizen science in agriculture/food research, and (iii) the greatest opportunities for the development of citizen science projects in agriculture and food science will be gained by using the existing infrastructure and tools of Extension programmes and through the engagement of urban communities. Further, we argue there is no better time to foster greater collaboration between these fields given the trend of shrinking Extension programmes, the increasing need to apply innovative solutions to address rising demands on agricultural systems, and the exponential growth of the field of citizen science.

Body composition and physical activity in 8-year-old children.

Body measurements and determinations were made of normal children age 8 3/4 yr. Anthropometric indices most highly correlated with percentage fat as determined by body density were the sum of four skinfolds, relative weight, and triceps skinfold thickness. Girls had a significantly higher percentage of fat than boys. Percentage fat at this age was compared to longitudinal activity scores (based on 1-day activity records) obtained from 6 months to the current age. There was no significant correlation of activity with fatness in girls. In boys, activity at 3 and 4 yr had a significant negative correlation with fatness at age 8; activity at age 8 was not correlated. Relative-leanness-fatness was better related to past than current activity. Comparison of longitudinal activity scores revealed a continuity of activity patterns for short intervals (e.g., 1 yr), but over longer periods (e.g., 4 or more yr) the effect diminished.

Properties of staircase procedures for estimating thresholds in automated perimetry.

The properties of the staircase procedure as applied in automated perimetry were examined. Two computer simulation models were used to vary different test- and patient-related parameters in clinical perimetry. One model was based on the KRAKEN computer simulation program; the other computer simulation was based on stimulus-response data sets from 11 normal subjects. The results were analyzed in terms of efficiency and accuracy. It was found that: (1) in general, there was an efficiency-accuracy trade-off; (2) increases in response fluctuation produced substantially greater errors in threshold estimates; (3) little or no improvements in accuracy were achieved by increasing the number of reversals; (4) the starting position of the staircase relative to the threshold influenced the efficiency of threshold determinations but not their accuracy; (5) a single-response error reduced the efficiency of staircases; (6) the position of a single-response error in a staircase sequence influenced the accuracy and efficiency of the threshold determination; and (7) more than one response error during a staircase sequence always resulted in a marked reduction in accuracy and/or efficiency. Current perimetric strategies appear to be at or near optimal levels, and therefore, strategies in the future may need to depart from a staircase-style procedure to achieve a significant increase in both accuracy and efficiency. Computer simulation studies can provide an effective means of evaluating perimetric test procedures and defining optimum strategies, which then can be verified clinically by subsequent testing in patient populations.

Short-term fluctuation as an estimate of variability in visual field data.

The short-term fluctuation index (SF) is one of several values that provide an indication of a patient's response reliability during an automated perimetry examination. The authors investigated the number of visual field locations used and the number of determinations per location as factors affecting the SF estimate. A computer simulation program for perimetry was used to measure the SF index for 350 normal visual fields with various levels of response fluctuation. As expected, the variability of the SF estimate decreased as the number of locations used to estimate SF increased. There was a more important finding that, for an equal number of threshold estimates, a larger number of determinations at a smaller number of locations produced greater consistency in the SF estimate (eg, ten determinations at two locations instead of two determinations at ten locations). However, it is also important to sample from a representative spatial distribution of visual field locations. These results suggest that five determinations at four locations in the visual field is optimal for most clinical perimetric testing situations.

Prenatal diagnosis of the fra(X) syndrome.

The fra(X) syndrome is one of the most common causes of mental retardation, and validation of the reliability and feasibility of making the prenatal diagnosis of this disorder is important for genetic counseling and prevention. We have received a total of 74 amniotic fluid specimens for prenatal diagnosis of fra(X) from worldwide sources. Results were obtained on 68 specimens of which 43 had a documented family history of the fra(X) syndrome. Of the 43 specimens, 23 were male and 4 were prenatally diagnosed as being affected. On the basis of the results, several conclusions follow: 1.) At least 3 different tissue culture methods should be utilized. 2.) At least 150 cells should be scored, preferably 50 from each of 3 different tissue culture methods or 100 from each method if less than 3 methods are used. 3.) While the test appears to be reliable, it should still be considered to be experimental until larger numbers are obtained with completed follow-up of cases.

Interrelationships of the hemifacial microsomia-VATER, VATER, and sirenomelia phenotypes.

The phenotypes of hemifacial microsomia-VATER, VATER, and sirenomelia patients suggest a sequence of overlapping developmental abnormalities. The malformations of 247 hemifacial microsomia (HFM) patients with one or more anomalies in other body regions were analyzed and compared with those of 255 VATER and 101 sirenomelia patients studied in the same fashion. The HFM patients were analyzed in four subgroups delineated by the number of their concomitant VATER ascertainment abnormalities (VAA). Three or more VAA occurred in 33 HFM patients who were designated to have the HFM-VATER phenotype and while no significant alteration of the HFM phenotype was found, there were notable differences in the analyses of the 20 malformation categories studied. Analyzed in separate heart and blood vessel (BV) categories, occurrences of BV defects in HFM patients with 0-1 VAA were low (4-6%) and due to anomalies other than single umbilical arteries (SUA). The BV abnormalities increased to 20% in the HFM with two VAA, HFM-VATER, and VATER phenotypes with equal occurrences of SUA and other BV anomalies. The incidence of SUA was markedly increased (64%) in the sirenomelia. Heart defects rose from 22% to 40% with the increasing VAA in individual HFM patients but were less in VATER (29%) and sirenomelia (21%) patients and were attributed to complex, conotruncal, and other early embryonic anomalies. Unilateral agenesis of paired organs systems occurred frequently and, possibly, can be attributed to an absent blood supply. Each phenotype of the sequence also had increased VAA, rib/vertebrae hypersegmentation, and monozygotic twinning. The variation in the incidences of malformations in the three phenotypes can be attributed to their relative location in the craniocranial organogenesis sequence of normal human embryologic development.

Sacrococcygeal dysgenesis association.

In the malformation analysis of 445 patients ascertained only for a sacrococcygeal malformation, a new phenotype, the sacrococcygeal dysgenesis association (SDA), was delineated in 34%. In addition, sirenomelia patients were found in 12%, the VATER association in 27%, and 27% could not be classified. Heterogeneity in the patients with sacrococcygeal malformations was identified by the differences found in their associated malformations. SDA patients have a relatively small average number (3.3) of anomalies per patient as compared with 9.3 in sirenomelia and 6.2 in VATER patients. SDA abnormalities occurred to a significant degree only in 6 of 20 designated malformation categories (vertebral, rib, pelvic, lower limb, central nervous system [CNS], renal) in contrast to 17 in VATER and 18 in sirenomelia patients. The SDA vertebral malformation pattern also differed from that of VATER/sirenomelia patients as did the high sacrococcygeal agenesis:dysgenesis ratio and low thoracolumbar vertebrae and/or rib hypersegmentations. Most significantly, SDA patients had a large number of CNS anomalies and CNS-related dysfunctions of the urinary and distal intestinal tracts but no anatomic urinary or intestinal tract malformations. This contrasted sharply with the markedly increased occurrences of anatomic abnormalities in these body regions of the sirenomelia and VATER patients. Demographic data such as patient survival, twinning and, particularly, the high (28%) incidence of maternal diabetes in the SDA further support its differentiation from VATER/sirenomelia patients.

Prenatal cytogenetic diagnosis of the fragile X chromosome: feasibility and speed of in situ clonal method in amniotic fluid cell tissue culture.

We have had experience with over 300 amniotic fluid specimens for prenatal diagnosis for the fragile X chromosome [fra(X)], and the flask method of tissue culture has been routinely utilized requiring extended tissue culture periods of 3-4 weeks. The use of the in situ clonal method of tissue culture for routine prenatal cytogenetic diagnosis of amniotic fluid cells has shortened tissue culture time and resulted in more rapid reporting; however, it has not been widely employed for fra(X) prenatal diagnosis. The simultaneous use of both methods of tissue culture has resulted in the detection of 2 cytogenetically fra(X) positive cases in amniotic fluid, with more rapid reporting and satisfactory expression of the fra(X) with the in situ clonal method. Thus, the use of the in situ clonal method of tissue culture for fra(X) prenatal diagnosis in amniotic fluid cells is feasible, faster and can serve as a more rapid cytogenetic adjunct to the newer DNA testing methods.

Prenatal cytogenetic diagnosis of the fragile X syndrome in amniotic fluid: calculation of accuracy.

We have completed over 350 prenatal diagnoses for the fragile X [fra(X)] syndrome using amniotic fluid, chorion villus specimen (CVS), fetal blood sampling and molecular methods. A total of 300 amniotic fluid specimens have been received for prenatal diagnosis of the fra(X) syndrome. There was a documented family history of fra(X) in 170/300 amniotic fluid cases, and 23/170 were correctly identified as cytogenetically fra(X) positive (16 male; 7 female). Three males were false-negative, and one female was fra(X) negative but identified as a probable carrier by RFLPs. No fra(X) positive or false-negative results were found in the absence of a fra(X) family history. Because the a priori risk for the fra(X) syndrome for each pregnancy was different and widely variable, the determination of the accuracy of the prenatal diagnosis results requires a consideration of these variables. On this basis, the calculated accuracy of prenatal cytogenetic diagnosis for the fra(X) syndrome is approximately 97%. This accuracy can be improved further with the simultaneous use of molecular methods, especially in view of recent developments.

Prenatal diagnosis of fragile X syndrome: results from parallel molecular and cytogenetic studies.

Since 1985, we have provided coordinated DNA-based and cytogenetic prenatal analysis for couples at risk for offspring afflicted with the fragile X [fra(X)] syndrome. To date, 40 pregnancies have been studied (22 males, 18 females). There were 5 males and 3 females identified to be at high risk by DNA but only 2 males and one female were demonstrated to be cytogenetically expressing the fra(X) prenatally. Of the other 3 males, one was a cytogenetic false negative (i.e. confirmed fra(X)+ at termination of pregnancy). The other 2 remain fra(X)- and are developing normally (undetected recombinants or non-penetrant male carriers). All fetuses at low risk were carried to term and are reported to be normal.

Prenatal diagnosis of the fragile X syndrome: possible end of the experimental phase for amniotic fluid.

We have had experience with 260 prenatal diagnosis cases for the fragile X syndrome [fra(X)]; amniotic fluid was received in 230. There was a documented family history of fra(X) in 148 amniotic fluid cases. Our sample includes 91 males. Eleven were correctly identified as fra(X)-positive and 2 were false-negative. Eight of 57 females were fra(X) positive and one was a false-negative. CVS were received in 21 cases with a family history of fra(X), and there were 2 positive results in females and 3 false-negative results in males which were ultimately detected by means of molecular analysis or a subsequent amniotic fluid specimen. RFLPs were utilized in 29 cases (amniotic fluid and CVS); RFLPs identified 2 false-negative cytogenetic results in CVS. Two male fetuses were found to have a high probability of being affected by means of RFLPs, but on the basis of prenatal and postnatal negative fra(X) cytogenetic results and subsequent normal growth and development, they are either unaffected transmitting males or are double recombinants. Three female fetuses were also found to be cytogenetically negative in CVS but had a 90%, 93%, and 99% probability of being affected by RFLPs. On the basis of the data, it can be concluded: 1. Amniotic fluid experience is adequate to eliminate the "experimental" designation providing the limitations are understood and an experienced laboratory is involved. 2. Chorionic villus cells for cytogenetic analysis should still be considered experimental. 3. Negative results with CVS should be confirmed by molecular methods and/or by cytogenetic analysis of another tissue. 4. Multiple approaches can maximize reliability of fra(X) prenatal diagnosis.

Kallmann syndrome associated with complex chromosome rearrangement.

We report on a male with Kallmann syndrome (KS) and an apparently balanced complex chromosome rearrangement (CCR): 46,XY,t(3; 9)(9;12)(q13.2;q21.2p13;q15). This is the first known report of a CCR in the KS and the second reported case of a definitive autosomal chromosome abnormality with KS. Possible relationships between the cytogenetic abnormality and KS are discussed.

Multiple meningiomas in a patient with constitutional ring chromosome 22.

We report on a patient with multiple congenital anomalies and ring chromosome 22 who died at age 16 years of bronchopneumonia. Autopsy documented multiple psammomatous meningiomas of the spinal dura and tentorium. Tumor tissue for cytogenetic analysis was not available. Although abnormalities of chromosome 22 in tumor tissue have been reported, to our knowledge, this is only the third report of a constitutional chromosome 22 abnormality associated with the development of meningiomas. Thus, a constitutional chromosome 22 abnormality may predispose to the development of meningiomas.

Cytogenetic diagnosis of the fragile X syndrome: efficiency, utilization, and trends.

In order to assess the impact of the increasing awareness of the fra(X) syndrome and a broader approach to fra(X) testing, we analyzed our laboratory experience for 1980-1988. In 1981-1986, there was an average of 80 cases/year (62 male; 18 female). The 103 (74 male; 29 female) cases in 1987 represent a 45% increase over the prior 3 years; this sustained in 1988 with 106 cases. The fra(X) positive yield decreased from a high of 49% in 1980 to an average of 20% (range 15-24%) in 1981-1984, 10% (range 9-11%), in 1985-1987 and 7% in 1988. The positive rate for males and females was nearly identical in both time periods. The positive yield for mentally retarded individuals with a family history of mental retardation dropped from an average of 20% for 1981-1984 and 33% for 1985-87 to 13% for 1988; however, the positive fra(X) rate for mentally retarded individuals decreased from an average of 23% in 1981-1984 to 9% in 1985-1987 and 7% in 1988. The decreasing fra(X) yield and increasing case load are directly attributable to the relaxation of criteria for referral and testing related to the referral of all mentally retarded patients, and to the perceived malpractice liability for not doing a "complete" evaluation. Although the burden for cytogenetic laboratories is considerable, the yield of positive fra(X) cases is still worthwhile, and may be maximized by the use of improved screening criteria.

Experience with multiple approaches to the prenatal diagnosis of the fragile X syndrome: amniotic fluid, chorionic villi, fetal blood and molecular methods.

We have had experience with 160 prenatal diagnosis cases for the fragile X syndrome [fra(X)] or Martin-Bell Syndrome. In 140, amniotic fluid was utilized; 98 had a documented family history of fra(X). The 94 completed cases included 4 no growth; 56 males of which 7 were fra(X)-positive and 2 false-negative; 38 females of which 5 were fra(X) positive. There was no fra(X) positive result when a family history of mental retardation was not documented as fra(X). Molecular methods (RFLPs) were utilized in 10 amniotic fluid and 5 chorionic villus specimens (CVS). Percutaneous umbilical blood sampling was used in 2 negative cases and 1 fra(X) positive case because of timing, tissue culture failure or confirmation of another method. CVS were received in 13 cases, and RFLPs were utilized in 5 of the CVS cases. There was no positive fra(X) CVS chromosome result in males, 1 positive result in a female, but 2 false negatives were detected by RFLPs. On the basis of the results, it can be concluded that cytogenetic and molecular methods are complementary and best used together and that multiple approaches can enhance the efficiency and reliability of fra(X) prenatal diagnosis.

DNA-based genetic testing in fifty fragile X families.

During the past 4 years (1985-1989), we have analyzed 171 cases in 50 fragile X [fra(X)] families by DNA linkage methods. Most (140 cases; 81%) were for carrier detection, both female (98 cases; 57%) and male (41 cases; 24%). Women who were obligate carriers of the fra(X) mutation accounted for an additional 6 "prior-to-pregnancy" cases. Four pregnancies have subsequently occurred with 3 having been successfully monitored (one male, 2 females). One pregnancy miscarried early prior to testing. Prenatal diagnoses (26 cases; 15%) accounted for the remainder of cases (15 males, 11 females). These will be discussed in the companion paper by Shapiro et al. (Am J Med Genet, 1991). A diagnosis in the cytogenetically uninformative carrier cases was reached in greater than 75% of analyses with a panel of 5 probes: 3 proximal (F9, DXS105, DXS98) and 2 distal (F8, DSX52). Five additional probes, 3 proximal (DXS10, DSX51, DSX102) and 2 distal (DSX15, DXS33), were used in cases that were resistant to analysis with the standard panel. In 60% of cases, flanking markers were identified (proximal and distal). Given this panel, only 5% of cases did not have any informative markers identified. Thus, molecular methods can provide a useful adjunct to cytogenetic analysis in most situations. An unusual association between the rare allele (A1) of DXS10 with the X chromosome carrying the fra(X) mutation was observed. This occurred in both male and female carriers in the uppermost generation tested. The basis for this association is uncertain at the present time.

Deletion of 16q with prolonged survival and unusual radiographic manifestations.

Deletion of 16q is characterized by mental retardation, microcephaly, a characteristic combination of minor facial anomalies, and broad halluces. Various break points have been described. This patient's phenotype is typical of this syndrome, but in addition, unusual radiographic findings were present. This chromosome abnormality is compatible with survival into adulthood. Expression of this phenotype does not appear to be correlated with specific break points.

Three-generation dominant transmission of the Silver-Russell syndrome.

We report on 7 patients with the Silver-Russell syndrome (SRS) in two 3-generation families. Three patients in each of the families had an undergrowth of the left side of the body when compared with the normal right side. The clinical courses were mild as compared to the severity sometimes described in sporadic cases. These patients and a review of 190 SRS cases from the literature showed that there were 23 families in which 38 patients had completely expressed SRS. In 17 of the families, multiple maternal relatives had complete or partial expressions of the SRS. Most SRS patients have been reported to occur sporadically; however, of the 197 propositi analyzed, 19% had more than one affected individual in a family and several different modes of inheritance could have been responsible. Two families (8.7%) had spontaneous dominant mutations (twins) and possible autosomal recessive transmission was present in 4 families (17.4%). Because no male-to-male transmission has yet been documented in the 21 families in the literature and the two families reported here, X-linked dominant inheritance is a possibility in 17 families (74%). Thus, although sporadic occurrences and genetic heterogeneity appear to be involved in the SRS, dominant inheritance may be a major causal factor.

The use of early simultaneous percutaneous umbilical blood sampling (PUBS) and amniocentesis for prenatal fragile X chromosome diagnosis.

Early simultaneous percutaneous umbilical blood sampling (PUBS) and amniocentesis for prenatal diagnosis were undertaken for the first time in a 17-week gestation fetus at risk for the fragile X [fra (X)] syndrome. Metaphase spreads from 300 fetal lymphocytes were examined within 5 days following PUBS, while approximately 5 weeks were required for the analysis of 148 amniocytes. The chromosomes were interpreted as normal (46,XX) and the fetus as fragile X-negative at the time of prenatal diagnosis. This was cytogenetically confirmed after delivery of a healthy term female infant. Our results suggest that early PUBS may become a useful adjunct to amniocentesis because of shorter culture time and earlier diagnosis.

Aneuploidy and the fragile X syndrome.

The possibility that female carriers of the fragile X gene(s) are at increased risk for nondisjunctional events leading to aneuploid offspring has been suggested by several investigators. To better address this question we analyzed pedigrees of 117 families in which the fragile X syndrome is segregating. The 117 pedigrees, originally collected for segregation analyses, included 236 females with offspring whose carrier status was determined by cytogenetic or pedigree analysis or by analyses using flanking DNA markers. These 236 females have had 931 offspring including one 47,XXY and 6 trisomy 21 individuals (1/155). Statistical analysis suggested that the observed rate of trisomy 21 was significantly higher than expected (Fisher's exact test, p less than or equal to 0.05). Assuming a Poisson distribution to calculate the confidence interval for the observed rate of trisomy 21 individuals, we found that the expected rate of 1.6/1000 in this sample fell outside the 99% confidence limits of our observed rate of 1/155. Additional data from a larger sample are needed to replicate these findings.