A Practical Site-specific Method for the Detection of Bulky DNA Damages

Helix-distorting DNA damages block RNA and DNA polymerase, compromising cell function and fate. In human cells, these damages are removed primarily by nucleotide excision repair (NER). Here, we describe damage-sensing PCR (dsPCR), a PCR-based method for the detection of these DNA damages. Exposure to DNA damaging agents results in lower PCR signal in comparison to non-damaged DNA, and repair is measured as the restoration of PCR signal over time. We show that the method successfully detects damages induced by ultraviolet (UV) radiation, by the carcinogenic component of cigarette smoke benzo[a]pyrene diol epoxide (BPDE) and by the chemotherapeutic drug cisplatin. Damage removal measured by dsPCR in a heterochromatic region is less efficient than in a transcribed and accessible region. Furthermore, lower repair is measured in repair-deficient knock-out cells. This straight-forward method could be applied by non-DNA repair experts to study the involvement of their gene-of-interest in repair. Furthermore, this method is fully amenable for high-throughput screening of DNA repair activity.

Autoimmune amelogenesis imperfecta in patients with APS-1 and coeliac disease

Ameloblasts are specialized epithelial cells in the jaw that have an indispensable role in tooth enamel formation-amelogenesis1. Amelogenesis depends on multiple ameloblast-derived proteins that function as a scaffold for hydroxyapatite crystals. The loss of function of ameloblast-derived proteins results in a group of rare congenital disorders called amelogenesis imperfecta2. Defects in enamel formation are also found in patients with autoimmune polyglandular syndrome type-1 (APS-1), caused by AIRE deficiency3,4, and in patients diagnosed with coeliac disease5-7. However, the underlying mechanisms remain unclear. Here we show that the vast majority of patients with APS-1 and coeliac disease develop autoantibodies (mostly of the IgA isotype) against ameloblast-specific proteins, the expression of which is induced by AIRE in the thymus. This in turn results in a breakdown of central tolerance, and subsequent generation of corresponding autoantibodies that interfere with enamel formation. However, in coeliac disease, the generation of such autoantibodies seems to be driven by a breakdown of peripheral tolerance to intestinal antigens that are also expressed in enamel tissue. Both conditions are examples of a previously unidentified type of IgA-dependent autoimmune disorder that we collectively name autoimmune amelogenesis imperfecta.

Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection

INTRODUCTION

Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Because of the overwhelming use of SARS-CoV-2 reverse transcription (RT)-PCR tests worldwide, the availability of test kits has become a major bottleneck and the need to increase testing throughput is rising. We aim to overcome these challenges by pooling samples together, and performing RNA extraction and RT-PCR in pools.

METHODS

We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of eight samples in large-scale clinical tests.

RESULTS

We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of eight samples showed that test results were not significantly affected. Implementing the eight-sample Dorfman pooling to test 26 576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput.

DISCUSSION

Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations.

The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria

Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characterize the prevalence and evolutionary conservation of IRs across 20 proteobacterial strains. We first identified IRs in Escherichia coli K-12 substr MG1655 and showed that they are overabundant. We next aimed to test whether this overabundance is reflected in the conservation of IRs over evolutionary time scales. To this end, for each perfect IR identified in E. coli MG1655, we collected orthologous sequences from related proteobacterial genomes. We next quantified the evolutionary conservation of these IRs, that is, the presence of the exact same IR across orthologous regions. We observed high conservation of perfect IRs: out of the 234 examined orthologous regions, 145 were more conserved than expected, which is statistically significant even after correcting for multiple testing. Our results together with previous experimental findings support a model in which imperfect IRs are corrected to perfect IRs in a preferential manner via a template switching mechanism.

A description of inappropriate hospital stays in selected in-patient services: a study of cases receiving social work services

The number of discharges (63,303) from a university-affiliated medical center in Israel were reviewed. Eight percent of cases in three departments rcceivcd social work services. Patients experiencing inappropriate hospital stay (discharge delay) and who received social work services were characterized and compared with social work clients not experiencing delay. Discharge delay patients differed from other social work clients on key sociodemographic variables. Patients admitted because of "injury" were significantly more likely to experience delay than patients admitted because of "illness." "Waiting for community/institutional resources" was the most common reason for delay and discharge to an institutional setting increased the likelihood of delayed discharge. High risk factors were department-specific and should be studied in context. Results suggested the limited but positive impact of hospital-community collaborative strategies in reducing the incidence of delay over time.

Does the coronary care unit improve prognosis of patients with acute myocardial infarction? A thrombolytic era study

AIMS

The purpose of our study was to examine and compare the prognosis of acute myocardial infarction patients hospitalized in an intensive coronary care unit and in an internal medicine ward, in the era of reperfusion therapy, and to identify factors associated with the observed outcomes.

METHODS AND RESULTS

Patients hospitalized for acute myocardial infarction during the period 1994-1997 at the Sheba Medical Center, Tel Hashomer, Israel (n=2114), were grouped according to the hospital department in which they were treated: the intensive coronary care unit (n=1443, 68.3%) or an internal medicine ward (n=671, 31.7%). Baseline characteristics, comorbidity, hospital course, use of procedures and 30-day mortality were compared between the groups. Stepwise logistic regression was used to identify the factors associated with 30-day mortality. Crude 30-day mortality rates were 5.4% among all patients hospitalized in the intensive coronary care unit compared with 15.9% for all patients in an internal medicine ward (P<0.001); in a subgroup of patients aged 70 years and above these rates were 11.0% and 21.0%, respectively (P<0. 001). Among the independent predictors of the 30-day mortality identified in multivariate analysis was treatment only in an internal medicine ward (odds ratio: 1.48; 95% confidence interval: 1. 00-2.18). Reperfusion therapy was independently associated with a 53% reduction in 30-day mortality.

CONCLUSIONS

Our findings emphasize the importance of the treatment of acute myocardial infarction in the setting of intensive coronary care units in the thrombolytic era, in order to ensure early access to advanced diagnostic and therapeutic options for all patients, including the elderly.

The dynamics of patient visits to a public hospital ED: a statistical model

Using a public hospital's computerized database, we formulated a statistical model to explain emergency department (ED) patient volume for better staffing and resource allocation. All patients visiting the ED over a 3-year period were included in this retrospective study. Each observation described the total daily number of referrals and was defined by the following variables: day of the week, month of the year, holiday/ weekday, relative order in a 3-year sequence, and number of visits to the ED on that day. The statistical method used to build the model was analysis of covariance. Periodicity in average number of daily visits existed for each of the seasonal factors that were examined, repeating every year during the study period. Based on a graphic analysis, the model was defined and explained 65% of the variance during the 3-year study, with a relatively low standard deviation of error. A statistically significant correlation existed between time-related factors and the number of visits to the ED. This statistical model may prove to be of value for planning emergency services, which operate under stressful, unpredictable situations.

A reduction in the number of unwanted pregnancies among female army draftees through a controlled intervention

OBJECTIVE

To assess the possibility of reducing the risk of unwanted pregnancy through a controlled intervention program that was based on a sex education workshop.

DESIGN

Educational intervention study.

SETTING

Newly drafted women in a central absorption army base in Israel.

PATIENT(S)

One thousand seven hundred ninety-three female draftees in the Israeli Defence Force.

INTERVENTION(S)

A 2-day workshop on sex education at the beginning of army service.

MAIN OUTCOME MEASURE(S)

Rate of unwanted pregnancy.

RESULT(S)

After 2 years of follow-up, there were approximately 40% fewer unwanted pregnancies among women with a lower socioeconomic and intellectual profile.

CONCLUSION(S)

Structured intervention programs may reduce significantly the rate of unwanted pregnancy in young women.

Principal components analysis of therapeutic orientations of doctoral programs in clinical psychology

A principal components analysis was conducted on a data set that consisted of ratings of therapeutic orientations reported by directors of clinical psychology training programs in 96 clinical psychology programs in the U.S. Two principal components emerged, which contrasted (1) behavioral vs. psychoanalytic approaches and (2) humanistic vs. conditioning approaches. A plotting of factor scores revealed relatively clear separation among programs primarily identified with either behavioral or psychoanalytic/humanistic approaches. The majority of training programs, however, clustered around the midpoint on both underlying factor dimensions, an indication of the adoption of multiple approaches in training.