Investigating the role of Copy Number Variants in Specific Language Impairment and identification of new candidate genes

Specific language impairment (SLI) is a complex neurodevelopmental disorder defined as an unexpected failure to develop normal language abilities for no obvious reason. Copy number variants (CNVs) are an important source of variation in the susceptibility to neuropsychiatric disorders. Therefore, a CNV study within SLI families was performed to investigate the role of structural variants in SLI. Among the identified CNVs, we focused on CNVs on chromosome 15q11-q13, recurrently observed in neuropsychiatric conditions, and a homozygous exonic microdeletion in ZNF277. Since this microdeletion falls within the AUTS1 locus, a region linked to autism spectrum disorders (ASD), we investigated a potential role of ZNF277 in SLI and ASD. Frequency data and expression analysis of the ZNF277 microdeletion suggested that this variant may contribute to the risk of language impairments in a complex manner, that is independent of the autism risk previously described in this region. Moreover, we identified an affected individual with a dihydropyrimidine dehydrogenase (DPD) deficiency, caused by compound heterozygosity of two deleterious variants in the gene DPYD. Since DPYD represents a good candidate gene for both SLI and ASD, we investigated its involvement in the susceptibility to these two disorders, focusing on the splicing variant rs3918290, the most common mutation in the DPD deficiency. We observed a higher frequency of rs3918290 in SLI cases (1.2%), compared to controls (~0.6%), while no difference was observed in a large ASD cohort. DPYD mutation screening in 4 SLI and 7 ASD families carrying the splicing variant identified six known missense changes and a novel variant in the promoter region. These data suggest that the combined effect of the mutations identified in affected individuals may lead to an altered DPD activity and that rare variants in DPYD might contribute to a minority of cases, in conjunction with other genetic or non-genetic factors.

Ruminant rhombencephalitis-associated Listeria monocytogenes alleles linked to a multilocus variable-number tandem-repeat analysis complex

Listeria monocytogenes is among the most important food-borne pathogens and is well adapted to persist in the environment. To gain insight into the genetic relatedness and potential virulence of L. monocytogenes strains causing central nervous system (CNS) infections, we used multilocus variable-number tandem-repeat analysis (MLVA) to subtype 183 L. monocytogenes isolates, most from ruminant rhombencephalitis and some from human patients, food, and the environment. Allelic-profile-based comparisons grouped L. monocytogenes strains mainly into three clonal complexes and linked single-locus variants (SLVs). Clonal complex A essentially consisted of isolates from human and ruminant brain samples. All but one rhombencephalitis isolate from cattle were located in clonal complex A. In contrast, food and environmental isolates mainly clustered into clonal complex C, and none was classified as clonal complex A. Isolates of the two main clonal complexes (A and C) obtained by MLVA were analyzed by PCR for the presence of 11 virulence-associated genes (prfA, actA, inlA, inlB, inlC, inlD, inlE, inlF, inlG, inlJ, and inlC2H). Virulence gene analysis revealed significant differences in the actA, inlF, inlG, and inlJ allelic profiles between clinical isolates (complex A) and nonclinical isolates (complex C). The association of particular alleles of actA, inlF, and newly described alleles of inlJ with isolates from CNS infections (particularly rhombencephalitis) suggests that these virulence genes participate in neurovirulence of L. monocytogenes. The overall absence of inlG in clinical complex A and its presence in complex C isolates suggests that the InlG protein is more relevant for the survival of L. monocytogenes in the environment.

EFFICIENT EVALUATION OF RANKING PROCEDURES WHEN THE NUMBER OF UNITS IS LARGE WITH APPLICATION TO SNP IDENTIFICATION

Simulation-based assessment is a popular and frequently necessary approach to evaluation of statistical procedures. Sometimes overlooked is the ability to take advantage of underlying mathematical relations and we focus on this aspect. We show how to take advantage of large-sample theory when conducting a simulation using the analysis of genomic data as a motivating example. The approach uses convergence results to provide an approximation to smaller-sample results, results that are available only by simulation. We consider evaluating and comparing a variety of ranking-based methods for identifying the most highly associated SNPs in a genome-wide association study, derive integral equation representations of the pre-posterior distribution of percentiles produced by three ranking methods, and provide examples comparing performance. These results are of interest in their own right and set the framework for a more extensive set of comparisons.

Risk factors for invasive aspergillosis in neutropenic patients with hematologic malignancies

Risk factors for invasive aspergillosis (IA) are incompletely identified and may undergo changes due to differences in medical practice. A cohort of 189 consecutive, adult patients with neutropenia hospitalized in the hemato-oncology ward of the University hospital Berne between 1995 and 1999 were included in a retrospective study to assess risk factors for IA. In total, 45 IA cases (nine proven, three probable, 33 possible), 11 patients with refractory fever and 133 controls were analyzed. IA cases had more often acute leukemia or myelodysplastic syndrome (MDS) (88 vs 38%, P < 0.001) and a longer duration of neutropenia (mean 20.6 vs 9.9 days, P < 0.001). They also had fewer neutropenic episodes during the preceding 6 months (mean 0.42 vs 1.03, P < 0.001), that is, confirmed (82%) and probable (73%) IA occurred most often during the induction cycle. A short time interval ( < or = 14 days) between neutropenic episodes increased the risk of IA four-fold (P = 0.06). Bacteremia, however, was not related to the number of preceding neutropenic episodes. Therefore, neutropenic patients with leukemia or MDS have the highest risk of IA. The risk is highest during the first induction cycle of treatment and increases with short-time intervals between treatment cycles.

Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group

Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovis isolates that are representative of the most frequent spoligotype in the Iberian Peninsula, SB0121. VNTR typing targeted nine loci: ETR-A (alias VNTR2165), ETR-B (VNTR2461), ETR-D (MIRU4, VNTR580), ETR-E (MIRU31, VNTR3192), MIRU26 (VNTR2996), QUB11a (VNTR2163a), QUB11b (VNTR2163b), QUB26 (VNTR4052), and QUB3232 (VNTR3232). We found a high degree of diversity among the studied isolates (discriminatory index [D] = 0.9856), which were split into 65 different MIRU-VNTR types. An alternative short-format MIRU-VNTR typing targeting only the four loci with the highest variability values was found to offer an equivalent discriminatory index. Minimum spanning trees using the MIRU-VNTR data showed the hypothetical evolution of an apparent clonal group. MIRU-VNTR analysis was also applied to the isolates of 176 animals from 15 farms infected by M. bovis SB0121; in 10 farms, the analysis revealed the coexistence of two to five different MIRU types differing in one to six loci, which highlights the frequency of undetected heterogeneity.

Are Today’s Medical School Graduates Performing the Same Number of Medical Procedures Compared to Graduates Ten Years Ago? A case for Simulation?

INTRODUCTION: Medical schools are charged with providing both a strong basic science and clinical curriculum for their students. In most institutions instruction in performing the core clinical procedures is part of the curriculum, but because of many constraints do medical students practice these procedures as many times as medical students in the past? Several studies have concluded that medical students today feel incompetent to perform basic clinical procedures at the time of graduation. [See PDF for complete abstract]

Male Dominance in the New Zealand Longfin Eel Population of a New Zealand River: Probable Causes and Implications for Management

The endemic New Zealand longfin eel Anguilla dieffenbachi (hereafter, longfin eel), is overfished, and in southern South Island, New Zealand, rivers have recently become predominated by males. This study examined length and age at sexual differentiation in male eels in the Aparima River catchment (area, 1,375 km(2); mean flow, 20 m(3.)s(-1)) and the sex ratio and distribution of eels throughout the catchment. Longfin eels differentiated into males mostly at lengths from 300 to 460 mm and ages from 10 to 25+ years. Females were rare: Of 738 eels examined for sexual differentiation, 466 were males and 5 were females, and a few others, not examined, were large enough to be female. These counts suggest a male : female ratio among differentiated longfin eels of 68:1. Of 31 differentiated shortfin eels A. australis, less common in the Aparima River, 26 were females. Male longfin eels were distributed throughout the main stern and tributaries; undifferentiated eels were more prevalent in lower and middle reaches and in the main stem than in upper reaches and tributaries. In other studies, male longfin eels predominated commercial catches in the Aparima and four other southernmost rivers, by 2.4:1 to 13.6:1 males to females. The Aparima River had the most skewed sex ratio. Longfin eel catches from the Aparima River will become more male predominated because few sublegal-size females were present. The length-frequency distributions of eels in the present samples and in the commercial catches were truncated just above minimum legal size (about 460 mm), showing that few females escape the fishery. Historically, females predominated these rivers. The recent change in sex ratio is attributable partly to selective harvest of females, and partly to changes in the structure of the population from fishing, such that differentiation into males has been favored. Longevity, delayed sexual maturity, semel-parity, and endemism with restricted range make the longfin eel particularly vulnerable to overfishing.

Efficient estimation of the total number of acini in adult rat lung

Pulmonary airways are subdivided into conducting and gas-exchanging airways. An acinus is defined as the small tree of gas-exchanging airways, which is fed by the most distal purely conducting airway. Until now a dissector of five consecutive sections or airway casts were used to count acini. We developed a faster method to estimate the number of acini in young adult rats. Right middle lung lobes were critical point dried or paraffin embedded after heavy metal staining and imaged by X-ray micro-CT or synchrotron radiation-based X-rays tomographic microscopy. The entrances of the acini were counted in three-dimensional (3D) stacks of images by scrolling through them and using morphological criteria (airway wall thickness and appearance of alveoli). Segmentation stopper were placed at the acinar entrances for 3D visualizations of the conducting airways. We observed that acinar airways start at various generations and that one transitional bronchiole may serve more than one acinus. A mean of 5612 (±547) acini per lung and a mean airspace volume of 0.907 (±0.108) μL per acinus were estimated. In 60-day-old rats neither the number of acini nor the mean acinar volume did correlate with the body weight or the lung volume.

Estimating the Reproduction Number of Ebola Virus (EBOV) During the 2014 Outbreak in West Africa

The 2014 Ebola virus (EBOV) outbreak in West Africa is the largest outbreak of the genus Ebolavirus to date. To better understand the spread of infection in the affected countries, it is crucial to know the number of secondary cases generated by an infected index case in the absence and presence of control measures, i.e., the basic and effective reproduction number. In this study, I describe the EBOV epidemic using an SEIR (susceptible-exposed-infectious-recovered) model and fit the model to the most recent reported data of infected cases and deaths in Guinea, Sierra Leone and Liberia. The maximum likelihood estimates of the basic reproduction number are 1.51 (95% confidence interval [CI]: 1.50-1.52) for Guinea, 2.53 (95% CI: 2.41-2.67) for Sierra Leone and 1.59 (95% CI: 1.57-1.60) for Liberia. The model indicates that in Guinea and Sierra Leone the effective reproduction number might have dropped to around unity by the end of May and July 2014, respectively. In Liberia, however, the model estimates no decline in the effective reproduction number by end-August 2014. This suggests that control efforts in Liberia need to be improved substantially in order to stop the current outbreak.

The Hundred Most-Cited Publications in Orthopaedic Knee Research

BACKGROUND: Despite its limitations, citation analysis remains one of the best currently available tools for quantifying the impact of articles. Bibliometric studies list the "best-sellers" in a single location, and they have been published frequently in many fields during recent years. The purpose of the present study was to report the qualities and characteristics of citation classics in orthopaedic knee research. METHODS: The database of the Institute for Scientific Information (ISI) was utilized for identification of articles published from 1945 to March 2014. All knee articles that had been published in sixty-five orthopaedic and twenty-nine rheumatology journals and that had been cited at least 200 times were identified. The top 100 were selected for further analysis of authorship, source journal, number of citations, citation rate (both since publication and in 2013), geographic origin, article type, and level of evidence. RESULTS: The publication dates of the 100 most-cited articles ranged from 1948 to 2007, with the greatest number of articles published in the 1980s. Citations per article ranged from 2640 to 287. All articles were published in eleven of the ninety-four journals. The leading countries of origin were the U.S. followed by the U.K. and Sweden. The two main focus areas were sports traumatology and degenerative disease. The number of citations per article was also greatest for articles published in the 1980s. Basic research articles were cited more quickly, but not more often, than clinical articles. Most articles represented Level-IV evidence, followed by Levels II, III, and I. CONCLUSIONS: This bibliometric study is likely to include a list of intellectual milestones in orthopaedic knee research. It is apparent that a high level of evidence is not mandatory for an article to gain a large number of citations. Bibliometric reports provide a reflection of the quality of cited research published in a specific field and should therefore provoke thinking within the scientific community.

Increased number of non-degranulated mast cells in pancreatic ductal adenocarcinoma but not in acute pancreatitis.

Increasing evidence indicates that tumor microenvironment (TME) is crucial in tumor survival and metastases. Inflammatory cells accumulate around tumors and strangely appear to be permissive to their growth. One key stroma cell is the mast cell (MC), which can secrete numerous pro- and antitumor molecules. We investigated the presence and degranulation state of MC in pancreatic ductal adenocarcinoma (PDAC) as compared to acute ancreatitis (AP). Three different detection methods: (a) toluidine blue staining, as well as immunohistochemistry for (b) tryptase and (c) c-kit, were utilized to assess the number and extent of degranulation of MC in PDAC tissue (n=7), uninvolved pancreatic tissue derived from tumor-free margins (n=7) and tissue form AP (n=4). The number of MC detected with all three methods was significantly increased in PDAC, as compared to normal pancreatic tissue derived from tumor-free margins (p<0.05). The highest number of MC was identified by c-kit, 22.2∓7.5 per high power field (HPF) in PDAC vs 9.7∓5.1 per HPF in normal tissue. Contrary to MC in AP, where most of the detected MC were found degranulated, MC in PDAC appeared intact. In conclusion, MC are increased in number, but not degranulated in PDAC, suggesting that they may contribute to cancer growth by permitting selective release of pro-tumorogenic molecules.

Competitive fitness in coronaviruses is not correlated with size or number of double-membrane vesicles under reduced-temperature growth conditions.

Positive-stranded viruses synthesize their RNA in membrane-bound organelles, but it is not clear how this benefits the virus or the host. For coronaviruses, these organelles take the form of double-membrane vesicles (DMVs) interconnected by a convoluted membrane network. We used electron microscopy to identify murine coronaviruses with mutations in nsp3 and nsp14 that replicated normally while producing only half the normal amount of DMVs under low-temperature growth conditions. Viruses with mutations in nsp5 and nsp16 produced small DMVs but also replicated normally. Quantitative reverse transcriptase PCR (RT-PCR) confirmed that the most strongly affected of these, the nsp3 mutant, produced more viral RNA than wild-type virus. Competitive growth assays were carried out in both continuous and primary cells to better understand the contribution of DMVs to viral fitness. Surprisingly, several viruses that produced fewer or smaller DMVs showed a higher fitness than wild-type virus at the reduced temperature, suggesting that larger and more numerous DMVs do not necessarily confer a competitive advantage in primary or continuous cell culture. For the first time, this directly demonstrates that replication and organelle formation may be, at least in part, studied separately during infection with positive-stranded RNA virus. IMPORTANCE The viruses that cause severe acute respiratory syndrome (SARS), poliomyelitis, and hepatitis C all replicate in double-membrane vesicles (DMVs). The big question about DMVs is why they exist in the first place. In this study, we looked at thousands of infected cells and identified two coronavirus mutants that made half as many organelles as normal and two others that made typical numbers but smaller organelles. Despite differences in DMV size and number, all four mutants replicated as efficiently as wild-type virus. To better understand the relative importance of replicative organelles, we carried out competitive fitness experiments. None of these viruses was found to be significantly less fit than wild-type, and two were actually fitter in tests in two kinds of cells. This suggests that viruses have evolved to have tremendous plasticity in the ability to form membrane-associated replication complexes and that large and numerous DMVs are not exclusively associated with efficient coronavirus replication.

8p23 beta-defensin copy number determination by single-locus pseudogene-based paralog ratio tests risk bias due to low-frequency sequence variations.

BACKGROUND The copy number variation (CNV) in beta-defensin genes (DEFB) on human chromosome 8p23 has been proposed to contribute to the phenotypic differences in inflammatory diseases. However, determination of exact DEFB CN is a major challenge in association studies. Quantitative real-time PCR (qPCR), paralog ratio tests (PRT) and multiplex ligation-dependent probe amplification (MLPA) have been extensively used to determine DEFB CN in different laboratories, but inter-method inconsistencies were observed frequently. In this study we asked which one is superior among the three methods for DEFB CN determination. RESULTS We developed a clustering approach for MLPA and PRT to statistically correlate data from a single experiment. Then we compared qPCR, a newly designed PRT and MLPA for DEFB CN determination in 285 DNA samples. We found MLPA had the best convergence and clustering results of the raw data and the highest call rate. In addition, the concordance rates between MLPA or PRT and qPCR (32.12% and 37.99%, respectively) were unacceptably low with underestimated CN by qPCR. Concordance rate between MLPA and PRT (90.52%) was high but PRT systematically underestimated CN by one in a subset of samples. In these samples a sequence variant which caused complete PCR dropout of the respective DEFB cluster copies was found in one primer binding site of one of the targeted paralogous pseudogenes. CONCLUSION MLPA is superior to PRT and even more to qPCR for DEFB CN determination. Although the applied PRT provides in most cases reliable results, such a test is particularly sensitive to low-frequency sequence variations preferably accumulating in loci like pseudogenes which are most likely not under selective pressure. In the light of the superior performance of multiplex assays, the drawbacks of such single PRTs could be overcome by combining more test markers.

The 100 Most Influential Publications in Cervical Spine Research

STUDY DESIGN Bibliometric study of current literature. OBJECTIVE To identify and analyze the 100 most cited publications in cervical spine research. SUMMARY OF BACKGROUND DATA The cervical spine is a dynamic field of research with many advances made within the last century. However, the literature has never been comprehensively analyzed to identify and compare the most influential articles as measured by the number of citations. METHODS All databases of the Thomson Reuters Web of Knowledge were utilized in a two-step approach. First, the 150 most cited cervical spine studies up to and including 2014 were identified using four keywords. Second, all keywords related to the cervical spine found in the 150 studies (n = 38) were used to conduct a second search of the database. The top 100 most cited articles were hereby selected for further analysis of current and past citations, authorship, geographic origin, article type, and level of evidence. RESULTS Total citations for the 100 studies identified ranged from 173 to 879. They were published in the time frame 1952 to 2008 in a total of 30 different journals. Most studies (n = 42) were published in the decade 1991 - 2000. Level of evidence ranged from 1 to 5 with 39 studies in the level 4 category. 13 researchers were first author more than once and 9 researchers senior author more than once. The two step approach with a secondary widening of search terms yielded an additional 27 studies, including the first ranking article. CONCLUSIONS This bibliometric study is likely to include some of the most important milestones in the field of cervical spine research of the last 100 years. LEVEL OF EVIDENCE 3.

The hundred most cited articles in bariatric surgery

BACKGROUND Many studies quantitatively analyzing scientific papers have appeared in the last 2 years. Citation analysis is a commonly used bibliometric method. In spite of some limitations, it remains a good measure of the impact an article has on a specific field, specialty, or a journal. The aim of this study was to analyze the qualities and characteristics of the 100 most cited articles in the field of bariatric surgery. METHODS The Thomson Reuters Web of Knowledge was used to list all bariatric surgery-related articles (BSRA) published from 1945 to 2014. The top 100 most cited BSRA in 354 surgical and high impact general journals were selected for further analysis. RESULTS Most of the articles were published in the 2000s (60%). The top 100 most cited were published in 17 of the 354 journals. Leading countries were USA followed by Canada and Australia. Most of the articles published (76%) were clinical experience articles. The most common level of evidence was IV (42%). CONCLUSIONS Many of the milestone papers in bariatric surgery have been included in this bibliometric study. A huge increase in research activity during the last decade is clearly visible in the field. It is apparent that the number of citations of an article is not related to its level of evidence; a fact that is increasingly being emphasized in surgical research.