Detection of chromosomal aneuploidy in ancient genomes

Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.

Dental calculus in the industrial age: Human dental calculus in the Post-Medieval period, a case study from industrial Manchester

The analysis of dental calculus (mineralised dental plaque) has become an increasingly important facet of bioarchaeological research. Although microscopic analysis of microdebris entrapped within dental calculus has revealed important insights into the diet, health, and environment of multiple prehistoric populations, relatively few studies have examined the contributions of this approach to more recent historical periods. In this study, we analyze dental calculus from an English Post-Medieval, middle-class urban skeletal assemblage from Manchester, England using light microscopy. We characterize all types of microremains, observing heavily damaged starch and plant material, high quantities of fungal and yeast spores, the presence of wood particles, plant (cotton) and animal (wool) fibres, as well as limited quantities of microcharcoal and burnt debris. We observe the presence of non-native, imported plant products, including New World maize and potentially tapioca starch. We compare our results to similar studies from earlier time periods to reveal the impacts of the significant economic, social and environmental changes occurring during the Industrial period in England, including changes in food processing, food access, food storage, and air quality. We conclude by outlining important methodological considerations for the future study of Post-Medieval dental calculus and propose potential areas of future research.

Development and validation of a computer-based algorithm to identify foreign-born patients with HIV infection from the electronic medical record

OBJECTIVE

To develop and validate an efficient and accurate method to identify foreign-born patients from a large patient data registry in order to facilitate population-based health outcomes research.

METHODS

We developed a three-stage algorithm for classifying foreign-born status in HIV-infected patients receiving care in a large US healthcare system (January 1, 2001-March 31, 2012) (n = 9,114). In stage 1, we classified those coded as non-English language speaking as foreign-born. In stage 2, we searched free text electronic medical record (EMR) notes of remaining patients for keywords associated with place of birth and language spoken. Patients without keywords were classified as US-born. In stage 3, we retrieved and reviewed a 50-character text window around the keyword (i.e. token) for the remaining patients. To validate the algorithm, we performed a chart review and asked all HIV physicians (n = 37) to classify their patients (n = 957).We calculated algorithm sensitivity and specificity.

RESULTS

We excluded 160/957 because physicians indicated the patient was not HIV-infected (n = 54), "not my patient" (n = 103), or had unknown place of birth (n = 3), leaving 797 for analysis. In stage 1, providers agreed that 71/95 foreign language speakers were foreign-born. Most disagreements (23/24) involved patients born in Puerto Rico. In stage 2, 49/50 patients without keywords were classified as US-born by chart review. In stage 3, token review correctly classified 55/60 patients (92%), with 93% (CI: 84.4, 100%) sensitivity and 90% (CI: 74.3, 100%) specificity compared with full chart review. After application of the three-stage algorithm, 2,102/9,114 (23%) patients were classified as foreign-born. When compared against physician response, estimated sensitivity of the algorithm was 94% (CI: 90.9, 97.2%) and specificity 92% (CI: 89.7, 94.1%), with 92% correctly classified.

CONCLUSION

A computer-based algorithm classified foreign-born status in a large HIV-infected cohort efficiently and accurately. This approach can be used to improve EMR-based outcomes research.

Enhanced carbon pump inferred from relaxation of nutrient limitation in the glacial ocean

The modern Eastern Equatorial Pacific (EEP) Ocean is a large oceanic source of carbon to the atmosphere. Primary productivity over large areas of the EEP is limited by silicic acid and iron availability, and because of this constraint the organic carbon export to the deep ocean is unable to compensate for the outgassing of carbon dioxide that occurs through upwelling of deep waters. It has been suggested that the delivery of dust-borne iron to the glacial ocean could have increased primary productivity and enhanced deep-sea carbon export in this region, lowering atmospheric carbon dioxide concentrations during glacial periods. Such a role for the EEP is supported by higher organic carbon burial rates documented in underlying glacial sediments, but lower opal accumulation rates cast doubts on the importance of the EEP as an oceanic region for significant glacial carbon dioxide drawdown. Here we present a new silicon isotope record that suggests the paradoxical decline in opal accumulation rate in the glacial EEP results from a decrease in the silicon to carbon uptake ratio of diatoms under conditions of increased iron availability from enhanced dust input. Consequently, our study supports the idea of an invigorated biological pump in this region during the last glacial period that could have contributed to glacial carbon dioxide drawdown. Additionally, using evidence from silicon and nitrogen isotope changes, we infer that, in contrast to the modern situation, the biological productivity in this region is not constrained by the availability of iron, silicon and nitrogen during the glacial period. We hypothesize that an invigorated biological carbon dioxide pump constrained perhaps only by phosphorus limitation was a more common occurrence in low-latitude areas of the glacial ocean.

Expression of cell surface transmembrane carbonic anhydrase genes CA9 and CA12 in the human eye: overexpression of CA12 (CAXII) in glaucoma

PURPOSE

Carbonic anhydrase enzymes (CAs) are universally involved in many fundamental physiological processes, including acid base regulation and fluid formation and movement. In glaucoma patients, CA inhibitors are very effective in lowering intraocular pressure by reducing the rate of aqueous humour secretion mediated by the CAs in the ciliary epithelium. In this work, we investigated the expression and tissue distribution of two recently discovered CA genes CA9 (CAIX) and CA12 (CAXII) in fetal, neonatal, and adult human eyes with and without glaucoma.

METHODS

CAIX and CAXII expression in 16 normal and 10 glaucomatous eyes, and in cultured non-pigmented ciliary epithelial cells (NPE) from normal and glaucoma eye donors was assessed by immunostaining. In addition, northern blot hybridisation was performed to assess expression of CA4, CA9, and CA12 mRNA in cultured NPE cells from normal and glaucoma donors.

RESULTS

CAXII was localised primarily to the NPE with its expression prominent during embryonic eye development but which decreased significantly in adults. CAIX expression in the NPE was very low. The epithelium of cornea and lens occasionally expressed both enzymes at low levels during development and in adult eye, and no expression was detected in the retina. The NPE from glaucoma eyes expressed higher levels of CAXII, but not CAIX, in comparison with normal eyes. This expression pattern was retained in cultured NPE cell lines. NPE cells from a glaucoma patient showed a five-fold increase in the CA12 mRNA level with no detectable expression of CA9 mRNA. Also, no expression of the CA4 gene encoding a GPI anchored plasma membrane protein was detected on these northern blots.

CONCLUSIONS

Transmembrane CAIX and CAXII enzymes are expressed in the ciliary cells and, thus, may be involved in aqueous humour production. CA12 may be a targeted gene in glaucoma.

The effect of prinomastat (AG3340), a synthetic inhibitor of matrix metalloproteinases, on posttraumatic proliferative vitreoretinopathy

In a search for a pharmacologic adjuvant in the management of posttraumatic proliferative vitreoretinopathy (PVR), we investigated the effect of intravitreal injection of prinomastat (AG3340) on an experimental model. Posterior penetrating eye trauma was created in one eye each of 24 New Zealand white rabbits. One week after the surgery, all rabbits were randomized (1:1) to receive 0.5 mg prinomastat or the vehicle of the drug intravitreally every week for 6 weeks. The degree of PVR for each hemiretina was scored, and the two scores were summed to obtain a total eye score. The mean total eye score was 3.58 in the treatment group and 5.75 in the control group (p = 0.0307). The numbers of eyes with tractional retinal detachment in the prinomastat-treated (n = 12) and control (n = 12) groups were 3 and 9, respectively (p = 0.0391). These results suggest that intravitreally administered prinomastat has an inhibitory effect on posttraumatic PVR.

The effect of prinomastat (AG3340), a potent inhibitor of matrix metalloproteinases, on a subacute model of proliferative vitreoretinopathy

PURPOSE

To determine the efficacy of prinomastat (AG3340), a synthetic inhibitor of matrix metalloproteinase, in the treatment of experimental proliferative vitreoretinopathy (PVR) induced by intravitreal dispase injection.

METHODS

One eye each of 53 New Zealand white rabbits was injected in the vitreous cavity with 0.07 unit of dispase to induce PVR. One week after PVR induction, 53 rabbits were randomized (27:26) to receive 0.5 mg prinomastat or the vehicle of the drug (acidified water) intravitreally every two weeks. The scores of PVR severity (scale of 1-5) were graded to compare the prinomastat-treated animals with the control group.

RESULTS

The average PVR scores in the treatment and control groups were 2.62 and 3.57 respectively (p = 0.038; Wilcoxon rank sum). Clinically significant PVR with retinal detachment (PVR > or = grade 3) developed in 76% of rabbits in the control group versus 51% of rabbits treated with prinomastat.

CONCLUSIONS

Intravitreally administered prinomastat decreased development of PVR in an experimental model which made use of dispase to induce PVR.

Atypical glandular cells of undetermined significance in cervical cytologic findings

OBJECTIVE

Our purpose was to increase our understanding of the clinical significance of atypical glandular cells of undetermined origin.

STUDY DESIGN

All cytologic Papanicolaou smears were reviewed and classified within the context of the Bethesda classification system. Charts of all patients with a diagnosis of atypical glandular cells of undetermined origin were reviewed for previous medical history, diagnostic study, histologic diagnosis, and prior Papanicolaou smear abnormalities.

RESULTS

The incidence of atypical glandular cells of undetermined origin in 76,018 Papanicolaou smears was 0.196%. We reviewed 133 patient medical records with cytologic diagnoses. Eighty of these patients have had appropriate follow-up. Thirty-six (45%) of these were found to have significant histologic abnormalities, including 6 patients with cervical intraepithelial neoplasia, grades 2 and 3, and 4 invasive cancers.

CONCLUSION

The frequency of underlying serious histologic changes is much greater in atypical glandular cells than in atypical squamous cells of undetermined significance. On the basis of our results, we believe that all patients with atypical glandular cells should undergo intensive evaluation including colposcopy, cervical biopsy, and endocervical curettage. When diagnosis cannot be clearly established, patient should undergo endometrial biopsy.

An animal model for cidofovir (HPMPC) toxicity: intraocular pressure and histopathologic effects

Intravitreal cidofovir has been shown to be a long acting and highly efficacious treatment for CMV retinitis; however decrease in IOP is an adverse effect. We wanted to determine the effect of cidofovir on intraocular pressure (IOP) in the guinea pig, and rabbit eye to develop an animal model of cidofovir induced ocular hypotony and to study the histopathology of this toxicity. Twenty-eight guinea pig eyes were injected with cidofovir yielding final intravitreal concentrations of 25, 200, 625 and 2000 micrograms ml-1. Eighteen eyes of pigmented rabbits were injected with cidofovir yielding final intravitreal concentrations of 625 and 2000 micrograms ml-1. A carefully calibrated low volume displacement manometer system using a micro-transducer was used to determine the IOP measurements in the guinea pig and rabbit eyes. Histology was evaluated using light and electron microscopy. Injection of 6.25 micrograms of cidofovir intravitreally (vitreous concentration of 25 micrograms ml-1) is the highest non-toxic dose in the guinea pig; the IOP was unchanged at two and four weeks after injection with this dose; histologically the eyes were normal. A single injection of 50 micrograms of cidofovir intravitreally (vitreous concentration of 200 micrograms ml-1) caused a long lasting (9.3 mmHg) decrease in IOP (approximately 50% of baseline). At this dose there were only mild and variable histologic changes in the ciliary body and the retina. Higher doses of 156.25 micrograms and 500 micrograms of cidofovir (vitreous concentrations of 625, and 2000 micrograms ml-1, respectively) caused moderate to severe ciliary body and retinal changes. In rabbit eyes there was a mild but statistically insignificant pressure drop with doses of 875 micrograms cidofovir intravitreally (vitreous concentration of 625 micrograms ml-1); retina was within normal limits after injection with this dose, there were mild changes in the ciliary body. There was a total destruction of ciliary body and loss of nonpigmented epithelial cells with injections of 2800 micrograms of cidofovir intravitreally (vitreous concentration of 2000 micrograms ml-1): retina was relatively well preserved. The guinea pig eye shows similar reduction in IOP and ciliary body changes as are seen in the human eye after intravitreal cidofovir and also appears to have a similar dose-response curve. However, the reduction of IOP caused by cidofovir occurs in the guinea pig eye at a concentration 40 times higher than was observed in the human eye.

Demographic and psychosocial risk for alcohol use: ethnic differences

OBJECTIVE

We examined the influence of demographic variables, and social (parents and peers), attitudinal and intentions variables regarding alcohol use on actual drinking behavior among Asian and white populations.

METHOD

Asian (n = 148; 79 female, 69 male) and white (n = 132; 72 female, 60 male) college students completed a questionnaire.

RESULTS

Confirmatory factor analyses revealed that social and attitudinal factors reflected a common construct of Psychosocial Vulnerability which, in a structural equation model, was significantly predicted by ethnicity. The white population was exposed to more psychosocial risks to alcohol use compared to the Asian population. Ethnicity, however, did not directly predict either drinking intentions or drinking behavior, after the effects on Psychosocial Vulnerability were considered.

CONCLUSIONS

Our findings suggest that ethnic differences in alcohol use between Asians and whites are mainly due to different levels of exposure to risk factors. Effective prevention programs must consider, not only psychosocial factors, but also certain contextual factors such as sex and ethnicity.

Friends' influence of adolescents' adjustment to school

Adolescents may be influenced both by their friends' behaviors and by the features of their friendships. To examine both types of influence, seventh and eighth graders (N = 297) were asked in the fall of a school year to report their involvement and disruption at school. The students also described the positive and negative features of their best friendships. Teachers reported on the students' involvement, disruption, and grades. These assessments were repeated in the following spring. Students whose friends in the fall described themselves as more disruptive increased in self-reported disruption during the year. Girls' self-reported disruption was more influenced by that of their very best friend than was boys'. Students whose very best friendships had more positive features increased in their self-reported involvement during the year. Students whose friendships had more negative features increased in their self-reported disruption, but only if their friendships also had many positive features. The theoretical and practical implications of these findings, and the adequacy of different methods for estimating friends' influence, were discussed.

Clinical and histopathologic study of varicella zoster virus retinitis in patients with the acquired immunodeficiency syndrome

Varicella zoster virus retinitis in patients with the acquired immunodeficiency syndrome is known to be a devastating disease. We studied a series of six consecutive patients that sheds new light on the clinical manifestations and treatment options of this disorder. All patients had episodes of cutaneous zoster, long-term exposure to oral acyclovir, and CD4+ T lymphocyte counts less than 50 cells/mm3. Two of the six patients had simultaneous radiographically demonstrable and histologically proven varicella zoster virus encephalitis; this is an important association. Histologic examination of autopsy specimens disclosed that the retinal infection by varicella zoster virus involves the retinal pigment epithelium more heavily than the inner retina, which is consistent with the characteristic clinical impression of an outer retinal necrosis.

Perceptions of normative social pressure and attitudes toward alcohol use: changes during adolescence

The present study examined age differences in perceived normative social pressure and attitudes as well as the importance of these variables for adolescent alcohol use. Seventh, ninth and eleventh graders (N = 386) completed a questionnaire. A majority of adolescents reported that friends pressured them not to use alcohol. Ninth and eleventh graders, however, perceived their friends as pressuring less against their alcohol use than did seventh graders. While parental influence decreased with age, peer influence did not show a consistent age difference across two drinking measures. As expected, the importance of perceived benefits increased with age, while that of perceived costs of alcohol use decreased with age. The findings suggest that the perceived normative pressure varies with the age and the behavior of the adolescent.

Enhancing services for sexual-minority clients: a community mental health approach

The authors describe the efforts of a community mental health district to improve services for gay men, lesbians, and bisexuals. A Gay Services Coordinating Committee recommended that the district (1) hire more sexual-minority staff, (2) give clients the option of seeing therapists sensitive to sexual minorities, (3) provide continuing education on homosexuality, and (4) appoint a contact person to coordinate services in each unit.

Use of a murine monoclonal antibody for detection of circulating plasma DF3 antigen levels in breast cancer patients

The murine monoclonal antibody (MAb), designated DF3, reacts with a 300,000-mol wt mammary epithelial antigen. A sequential double-determinant radioimmunoassay (RIA) has been developed to monitor circulating DF3 antigen. Using this assay, we have demonstrated that 33 of 36 normal women had plasma RIA antigen levels less than 150 U/ml. In contrast, 33 of 43 patients (76%) with metastatic breast cancer had RIA DF3 antigen levels greater than or equal to 150 U/ml. The difference between these two groups was statistically significant (P less than 0.001). Similar results have been obtained with a double-determinant enzyme-linked immunoassay (EIA). Only 6 of 111 age-matched normal subjects had EIA DF3 antigens levels greater than or equal to 30 U/ml, while 42 of 58 patients (72%) with breast cancer had levels equal to or above this value. Thus, similar patterns of specificity are obtained with the EIA or RIA. The elevation of circulating DF3 antigen levels in breast cancer patients has been confirmed by transfer blot assays. MAb DF3 reactivity occurred predominantly with circulating antigens of three different molecular weights ranging from 300,000 to approximately 400,000 mol wt. We also demonstrate that patients with both primary and metastatic breast cancer who were free of detectable disease at the time of sampling have DF3 antigen levels that are similar to those obtained from normal subjects. While patients with hepatoma (27%) and ovarian carcinoma (47%) also had elevated circulating DF3 antigen levels, the results suggest that DF3 antigen levels may be useful in distinguishing breast cancer patients from those with esophageal, gastric, colorectal, pancreatic, and lung carcinomas. Furthermore, the results of the RIA, EIA, and transblot analyses demonstrate that the measurement of circulating DF3 antigen levels provides a new and potentially useful marker to follow the clinical course of patients with metastatic breast cancer.

Motor and cognitive interference effects on unimanual tapping rates

Experiments conducted on both normal and disordered populations have led to the hypothesis that the left hemisphere's specialization for language results from its control over motor activities. This control is reflected in the lateralized disruption of manual activity during cerebral time-sharing tasks. Recent studies have challenged this hypothesis, stating that the interference effects reflect both cognitive and motor mechanisms in the left hemisphere. This experiment investigates whether the left hemisphere's control over speech involves both of these components or is purely motor. The question was examined by measuring the effect of concurrent hemispheric activity on single-finger tapping rates. Forty subjects tapped under two conditions: speaking and listening. The data show there may be both motor and cognitive mechanisms involved in left-hemisphere control.