Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.

We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing data sets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.

A chromosome-level genome assembly for the smoky rubyspot damselfly (Hetaerina titia).

Smoky rubyspot damselflies (Hetaerina titia Drury, 1773) are one of the most commonly encountered odonates along streams and rivers on both slopes of Central America and the Atlantic drainages in the United States and southern Canada. Owing to their highly variable wing pigmentation, they have become a model system for studying sexual selection and interspecific behavioral interference. Here, we sequence and assemble the genome of a female smoky rubyspot. Of the primary assembly (i.e. the principle pseudohaplotype), 98.8% is made up of 12 chromosomal pseudomolecules (2N = 22A + X). There are 75 scaffolds in total, an N50 of 120 Mb, a contig-N50 of 0.64 Mb, and a high arthropod BUSCO score [C: 97.6% (S: 97.3%, D: 0.3%), F: 0.8%, M: 1.6%]. We then compare our assembly to that of the blue-tailed damselfly genome (Ischnura elegans), the most complete damselfly assembly to date, and a recently published assembly for an American rubyspot damselfly (Hetaerina americana). Collectively, these resources make Hetaerina a genome-enabled genus for further studies of the ecological and evolutionary forces shaping biological diversity.

Tumors of the Urogenital Tract.

Neoplasia has been reported to involve the majority of the urinary system of the horse, with tumors affecting the kidneys and bladder most comprehensively described. Primary tumors of the external genitalia are relatively common in the horse and are easily identified on clinical examination while primary tumors of the upper urogenital tract are uncommon. This article will highlight the common tumors, their clinical presentations, and discuss potential medical and surgical treatment options available. The less common neoplasms will be mentioned but not discussed in depth.

Managing Concealable Sexual Health Stigma Through Disclosure.

Individuals with concealable stigma continually decide whether, and if so, how to disclose to others. These complex decision-making processes are evident across various stigmatized sexual health contexts, including sexually transmitted diseases and infections, LGBTQ+ identities, and sexual trauma, among others. One context that has received less attention within communication scholarship is difficulty orgasming among women. Due to the stigma associated with this experience, women are often reluctant to disclose their orgasm difficulties to others, especially their sexual and/or relational partners. However, the motivations women have for, and the factors they consider prior to disclosure have yet to be identified. Building upon extant sexual health communication, concealable stigma, and disclosure research, this study used semi-structured interviews (N = 31) to examine how women disclose orgasm difficulties within their sexual and/or romantic relationships. Our findings highlight several motivations women have for (non)disclosure, and various contextual and situational factors that complicate their disclosure processes. This study contributes to our theoretical understanding of the disclosure processes model (DPM) and the disclosure of concealable (sexual health) stigma. This study also offers practical insights for improving disclosure and experiences with stigma within this context.

Developing Measures for and Testing the Theory of Communicative Disenfranchisement (TCD) in the Context of Chronic Pain.

The post-positivist articulation of the theory of communicative disenfranchisement (TCD) asserts that people subjected to disenfranchising talk (DT; talk that discredits, silences, and stereotypes) experience proximal consequences (PCs; reduced agency, perceived credibility, and ability to exercise rights and privileges) and make negative inferences about others' future interactional goals (negative goal inferences [NGIs]). Through the mediators of PCs and NGIs, DT is theorized to lead to more distal health and well-being outcomes. This article developed measures of DT, PCs, and NGIs to test the TCD's post-positivist model in the context of chronic pain. Items were developed and refined in a pilot study. Then, in two validation studies, exploratory and confirmatory factor analyses were conducted and health and well-being outcomes were assessed. Findings offer initial empirical support for the reliability and convergent, divergent, and predictive validity of the DT, PCs, and NGIs measures, as well as the model proposed in the post-positivist articulation of the TCD.

A review of epidemiological models of Clostridioides difficile transmission and control (2009-2021).

Clostridioides difficile is the leading cause of infectious diarrhea and one of the most common healthcare-acquired infections worldwide. We performed a systematic search and a bibliometric analysis of mathematical and computational models for Clostridioides difficile transmission. We identified 33 publications from 2009 to 2021. Models have underscored the importance of asymptomatic colonized patients in maintaining transmission in health-care settings. Infection control, antimicrobial stewardship, active testing, and vaccination have often been evaluated in models. Despite active testing and vaccination being not currently implemented, they are the most commonly evaluated interventions. Some aspects of C. difficile transmission, such community transmission and interventions in health-care settings other than in acute-care hospitals, remained less evaluated through modeling.

Surgical removal of intra-articular loose bodies from the cervical articular process joints in 5 horses.

OBJECTIVE: To describe the surgical removal of intra-articular loose bodies (LBs) from the cervical articular process joints (APJs) in five horses and to describe the outcome of the surgery. STUDY DESIGN: Short case series. ANIMALS: Five client-owned horses with naturally occurring LBs within the cervical APJs. METHODS: Medical records were reviewed of horses that were diagnosed with LBs of the cervical APJs on computed tomography (CT), where the LBs were subsequently removed surgically. Details of case selection and surgical technique were reviewed along with postoperative complications and clinical outcome. Histopathology was performed on LBs in some cases. RESULTS: Surgery was performed on six APJs in five horses. Of the 14 LBs identified with CT, 13 were successfully removed from the C4/C5, C5/C6 and C6/C7 articulations. No surgical complications were encountered, and clinical signs of cervical dysfunction improved in all horses. All clinical cases returned to ridden work by 6 months post surgery. Histopathologic examination revealed the removed structures to be osteochondral or chondral loose bodies consisting of cartilaginous proliferation with or without ossification and central necrosis. CONCLUSIONS: Surgical removal of LBs is achievable from the cervical APJs and can result in the resolution of cervical pain. This procedure offers a new treatment option for management of selected horses with cervical pain, following thorough assessment and CT imaging.

Targeted re-sequencing confirms the importance of chemosensory genes in aphid host race differentiation.

Host-associated races of phytophagous insects provide a model for understanding how adaptation to a new environment can lead to reproductive isolation and speciation, ultimately enabling us to connect barriers to gene flow to adaptive causes of divergence. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on legume species and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. As host choice produces assortative mating, understanding the underlying mechanisms of choice will contribute directly to understanding of speciation. As host choice in the pea aphid is likely mediated by smell and taste, we use capture sequencing and SNP genotyping to test for the role of chemosensory genes in the divergence between eight host plant species across the continuum of differentiation and sampled at multiple locations across western Europe. We show high differentiation of chemosensory loci relative to control loci in a broad set of pea aphid races and localities, using a model-free approach based on principal component analysis. Olfactory and gustatory receptors form the majority of highly differentiated genes and include loci that were already identified as outliers in a previous study focusing on the three most closely related host races. Consistent indications that chemosensory genes may be good candidates for local adaptation and barriers to gene flow in the pea aphid open the way to further investigations aiming to understand their impact on gene flow and to determine their precise functions in response to host plant metabolites.

Revealing the Demographic History of the European Nightjar (Caprimulgus europaeus).

A species' demographic history gives important context to contemporary population genetics and a possible insight into past responses to climate change; with an individual's genome providing a window into the evolutionary history of contemporary populations. Pairwise sequentially Markovian coalescent (PSMC) analysis uses information from a single genome to derive fluctuations in effective population size change over the last ~5 million years. Here, we apply PSMC analysis to two European nightjar (Caprimulgus europaeus) genomes, sampled in Northwest and Southern Europe, with the aim of revealing the demographic history of nightjar in Europe. We successfully reconstructed effective population size over the last 5 million years. Our analysis shows that in response to global climate change, the effective population size of nightjar broadly increased under stable warm periods and decreased during cooler spans and prolonged glacial periods. PSMC analysis on the pseudo-diploid combination of the two genomes revealed fluctuations in gene flow between ancestral populations over time, with gene flow ceasing by the last-glacial period. Our results are tentatively suggestive of divergence in the European nightjar population, with timings consistent with differentiation being driven by restriction to different refugia during periods of glaciation. Finally, our results suggest that migratory behaviour in nightjar likely evolved prior to the last-glacial period, with long-distance migration seemingly persisting throughout the Pleistocene. However, further genetic structure analysis of individuals from known breeding sites across the species' contemporary range is needed to understand the extent and origins of range-wide differentiation in nightjar.

Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine.

Re-introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re-introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134-year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation-introduction-induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re-introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus <1 contemporary generation), the loss of genetic diversity per generation is greater across the contemporary bottleneck. Historically, the flycatcher population was genetically structured; however, extinction on four of five islands has resulted in a homogeneous contemporary population. We conclude that severe historical bottlenecks can leave a large footprint in terms of sheer quantity of genetic diversity lost. However, severely depleted genetic diversity does not render a species immune to further genetic erosion upon re-introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re-introduction-induced bottlenecks.

Desmitis of the accessory ligament of the deep digital flexor tendon in the forelimb: A retrospective case study of 91 horses.

BACKGROUND: Desmitis of the accessory ligament of the deep digital flexor tendon (ALDDFT) is a commonly reported injury. Despite the commonality of this injury, the literature is limited to small case series, with the reported success following treatment varying from 18% to 75%. OBJECTIVES: To identify the prognosis and factors associated with a return to work following ALDDFT injury. STUDY DESIGN: Retrospective case series. METHODS: Medical records of horses from four equine hospitals (January 2000 and December 2018) with a diagnosis of desmitis of ALDDFT were reviewed. Data retrieved included case detail, use, history, lameness treatment and follow-up. Success was defined as returning to work. Backward stepwise logistic regression was used to identify variables significantly associated with return to work. RESULTS: Ninety-one horses were included. The mean age was 13.5 years (standard deviation 4.9 years). Thirty-four percent (28/91) of horses were sound at the initial presentation. Sixty-eight percent (62/91) of horses were managed using controlled exercise alone, 28% (29/91) were treated with intra-lesional injection, therapeutic ultrasound, extracorporeal shockwave therapy or desmectomy of the ALDDFT and 3% (3/91) were euthanased without treatment. Sixty-four percent (54/85) of horses returned to work. Horses that were lame at follow-up were less likely to return to work (odds ratio [OR] 107.93, 95% confidence interval [CI] 20.06-580.61, p < 0.001) than those that returned to soundness. Identification of adhesions on ultrasonography was also associated with having reduced odds for return to work when compared to horses without adhesions (OR 0.10, 95% CI 0.01-0.76, p = 0.03). MAIN LIMITATIONS: Retrospective nature of the study, the potential of selection bias with regards to follow-up. CONCLUSION: Sixty-four percent (54/85) of horses returned to work following injury of the ALDDFT. Persistence of lameness and adhesion formation were significantly associated with a poor outcome.

Validation of a novel clinical tool for monitoring distal limb stiffness.

Objective: To validate a novel technique to measure limb stiffness in a clinical setting. Animals: Three horses and three ponies owned by the Royal Veterinary College. Procedures: Limb stiffness indices for both forelimbs were first derived using the gold standard of kinematic analysis. Using the same animals, limb stiffness indices were then calculated using portable floor scales to record weight and an electrogoniometer to record changes in metacarpophalangeal joint angle. The two techniques were then assessed for correlation and repeatability. Results: The repeatability of limb stiffness measurement using the novel clinical tool was considered to be good based on a small coefficient of variation (5.70%). The correlation of limb stiffness as derived by both methods was high (r = 0.78, p < 0.01). Limb stiffness was positively correlated with the mass of the subject (r = 0.85, p < 0.01), with heavier horses having greater limb stiffness. Clinical relevance: This study has compared a novel method to measure distal forelimb stiffness non-invasively in a clinical setting to kinematic analysis in six equids. It has demonstrated that limb stiffness increases in a linear fashion with body mass consistent with the role of forelimbs providing energy storage. Because in vivo limb stiffness has been shown previously to alter with injury to the superficial digital flexor tendon, it is hypothesized that this technique will offer a practical technique for the clinician to assess limb stiffness in clinical cases. Further study will be necessary to determine its clinical usefulness in such cases.

Osteochondral fragmentation of the cervical articular process joints; prevalence in horses undergoing CT for investigation of cervical dysfunction.

BACKGROUND: Computed tomography (CT) imaging of the cervical spine of mature horses under general anaesthesia is becoming increasingly accessible. Osteochondral fragmentation (OF) of the cervical articular process joints (APJs) has been identified on CT imaging; the prevalence, clinical features and significance of this finding are currently unknown. OBJECTIVES: To describe the prevalence and clinical features of a population of horses with CT evidence of OF within the cervical APJs. STUDY DESIGN: Retrospective, descriptive case series. METHODS: The study population consisted of all horses undergoing CT imaging of the entire cervical spine between April 2016 and December 2019 at Liphook Equine Hospital for investigation of clinical signs localised to this region. CT scans were examined for evidence of OF within the APJs and additional case features were recorded. RESULTS: A total of 55 horses underwent CT imaging during the study period. OF was identified in 13 horses, giving a CT prevalence of 24% in the study population. OF occurred in a range of ages, breeds and uses of equine, presenting with varied clinical signs. It was identified at every level of the neck. Additional cervical pathology was identified in 11/13 OF cases. MAIN LIMITATIONS: Retrospective analysis of a clinical caseload with a lack of clinically normal controls or post mortem confirmation of imaging findings. Low case numbers. CONCLUSIONS: OF within the cervical APJs is recognised on CT imaging in horses with cervical dysfunction. Fragments are commonly identified in combination with additional cervical pathology. Further investigation is required to confirm their clinical significance and develop potential treatment options where necessary.

Maternal Mediterranean Diet Adherence and Its Associations with Maternal Prenatal Stressors and Child Growth.

Background: Psychosocial and physiologic stressors, such as depression and obesity, during pregnancy can have negative consequences, such as increased systemic inflammation, contributing to chronic disease for both mothers and their unborn children. These conditions disproportionately affect racial/ethnic minorities. The effects of recommended dietary patterns in mitigating the effects of these stressors remain understudied. Objectives: We aimed to evaluate the relations between maternal Mediterranean diet adherence (MDA) and maternal and offspring outcomes during the first decade of life in African Americans, Hispanics, and Whites. Methods: This study included 929 mother-child dyads from the NEST (Newborn Epigenetics STudy), a prospective cohort study. FFQs were used to estimate MDA in pregnant women. Weight and height were measured in children between birth and age 8 y. Multivariable linear regression models were used to examine associations between maternal MDA, inflammatory cytokines, and pregnancy and postnatal outcomes. Results: More than 55% of White women reported high MDA during the periconceptional period compared with 22% of Hispanic and 18% of African American women (P < 0.05). Higher MDA was associated with lower likelihood of depressive mood (ß = -0.45; 95% CI: -0.90, -0.18; P = 0.02) and prepregnancy obesity (ß = -0.29; 95% CI: -0.57, -0.0002; P = 0.05). Higher MDA was also associated with lower body size at birth, which was maintained to ages 3-5 and 6-8 y-this association was most apparent in White children (3-5 y: ß = -2.9, P = 0.02; 6-8 y: ß = -3.99, P = 0.01). Conclusions: If replicated in larger studies, our data suggest that MDA provides a potent avenue by which effects of prenatal stressors on maternal and fetal outcomes can be mitigated to reduce ethnic disparities in childhood obesity.

NDVI imaging within space exploration plant growth modules - A case study from EDEN ISS Antarctica.

The concept of using informative wavelength imagery to monitor plant health and ecosystem stability from space is derived from the deployment of Landsat and the development of the Normalized Difference Vegetative Index, or NDVI. NDVI presents the relative reflectance of the Near IR from plant leaves as a measure of relative plant health in terrestrial habitats and landscapes. However, the use of NDVI and NDVI-like imagery is rapidly evolving toward higher spatial resolution and more localized assessments of plant health, such as the use of drone imagery to monitor outdoor farms, and the use of mounted cameras within indoor growing facilities. With the advancement of plant growth systems in support of human space exploration, especially to the moon and Mars, remote assessment of plant health within exploration habitats becomes a critical element for development. This project examines the deployment of NDVI-like capabilities within a planetary analog greenhouse on the Antarctic ice shelf. The EDEN ISS Antarctica project provides a case study on the practical use of specific wavelength imagery to monitor plant health within space exploration environments. GoPro cameras, modified to dual bandpass capabilities, provided Single Image NDVI analyses for a year within the EDEN ISS Future Exploration Greenhouse at the Neumayer Station III in Antarctica. Images were acquired on site, analyzed remotely, and archived for the entire duration of the deployment through a combination of back-room science activities and operational communications with the Neumayer Station III. The results provide insights into the potential use of specific imaging wavelengths to enhance crop production in space exploration.

Immunohistochemical evaluation of necrotic malignant melanomas.

We evaluated 35 cases of malignant melanomas with substantial necrosis immunostained with S-100, HMB-45, Melan-A, tyrosinase, PNL2, and microphthalmia transcription factor (MITF). Staining patterns were evaluated in viable and necrotic areas of the tumors. S-100 was the most sensitive marker (97%) in the viable tumors, but necrotic areas demonstrated nonspecific staining. Viable tumors stained variably for HMB-45 (25 [71%]), Melan-A (28 [80%]), tyrosinase (30 [86%]), and PNL2 (23 [66%]). Necrotic areas focally reacted to the same antibodies. The necrotic areas that retained immunoreactivity for these markers corresponded to areas where the outline of the tumor cells could still be recognized as ghost cells on the H&E-stained section. Areas that showed complete coagulative necrosis were negative for melanoma markers. MITF variably stained in the viable tumors but was completely negative in necrotic areas. Our study demonstrated that a combination of antibodies to HMB-45, tyrosinase, and PNL2 detected melanocytic differentiation in necrotic areas in 80% of cases.

Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster.

Bright-red colors in vertebrates are commonly involved in sexual, social, and interspecific signaling [1-8] and are largely produced by ketocarotenoid pigments. In land birds, ketocarotenoids such as astaxanthin are usually metabolically derived via ketolation of dietary yellow carotenoids [9, 10]. However, the molecular basis of this gene-environment mechanism has remained obscure. Here we use the yellowbeak mutation in the zebra finch (Taeniopygia guttata) to investigate the genetic basis of red coloration. Wild-type ketocarotenoids were absent in the beak and tarsus of yellowbeak birds. The yellowbeak mutation mapped to chromosome 8, close to a cluster of cytochrome P450 loci (CYP2J2-like) that are candidates for carotenoid ketolases. The wild-type zebra finch genome was found to have three intact genes in this cluster: CYP2J19A, CYP2J19B, and CYP2J40. In yellowbeak, there are multiple mutations: loss of a complete CYP2J19 gene, a modified remaining CYP2J19 gene (CYP2J19(yb)), and a non-synonymous SNP in CYP2J40. In wild-type birds, CYP2J19 loci are expressed in ketocarotenoid-containing tissues: CYP2J19A only in the retina and CYP2J19B in the beak and tarsus and to a variable extent in the retina. In contrast, expression of CYP2J19(yb) is barely detectable in the beak of yellowbeak birds. CYP2J40 has broad tissue expression and shows no differences between wild-type and yellowbeak. Our results indicate that CYP2J19 genes are strong candidates for the carotenoid ketolase and imply that ketolation occurs in the integument in zebra finches. Since cytochrome P450 enzymes include key detoxification enzymes, our results raise the intriguing possibility that red coloration may be an honest signal of detoxification ability.

Ecological effects of the invasive giant madagascar day gecko on endemic mauritian geckos: applications of binomial-mixture and species distribution models.

The invasion of the giant Madagascar day gecko Phelsuma grandis has increased the threats to the four endemic Mauritian day geckos (Phelsuma spp.) that have survived on mainland Mauritius. We had two main aims: (i) to predict the spatial distribution and overlap of P. grandis and the endemic geckos at a landscape level; and (ii) to investigate the effects of P. grandis on the abundance and risks of extinction of the endemic geckos at a local scale. An ensemble forecasting approach was used to predict the spatial distribution and overlap of P. grandis and the endemic geckos. We used hierarchical binomial mixture models and repeated visual estimate surveys to calculate the abundance of the endemic geckos in sites with and without P. grandis. The predicted range of each species varied from 85 km2 to 376 km2. Sixty percent of the predicted range of P. grandis overlapped with the combined predicted ranges of the four endemic geckos; 15% of the combined predicted ranges of the four endemic geckos overlapped with P. grandis. Levin's niche breadth varied from 0.140 to 0.652 between P. grandis and the four endemic geckos. The abundance of endemic geckos was 89% lower in sites with P. grandis compared to sites without P. grandis, and the endemic geckos had been extirpated at four of ten sites we surveyed with P. grandis. Species Distribution Modelling, together with the breadth metrics, predicted that P. grandis can partly share the equivalent niche with endemic species and survive in a range of environmental conditions. We provide strong evidence that smaller endemic geckos are unlikely to survive in sympatry with P. grandis. This is a cause of concern in both Mauritius and other countries with endemic species of Phelsuma.

An examination of auditory processing and affective prosody in relatives of patients with auditory hallucinations.

Research on auditory verbal hallucinations (AVHs) indicates that AVH schizophrenia patients show greater abnormalities on tasks requiring recognition of affective prosody (AP) than non-AVH patients. Detecting AP requires accurate perception of manipulations in pitch, amplitude and duration. Schizophrenia patients with AVHs also experience difficulty detecting these acoustic manipulations; with a number of theorists speculating that difficulties in pitch, amplitude and duration discrimination underlie AP abnormalities. This study examined whether both AP and these aspects of auditory processing are also impaired in first degree relatives of persons with AVHs. It also examined whether pitch, amplitude and duration discrimination were related to AP, and to hallucination proneness. Unaffected relatives of AVH schizophrenia patients (N = 19) and matched healthy controls (N = 33) were compared using tone discrimination tasks, an AP task, and clinical measures. Relatives were slower at identifying emotions on the AP task (p = 0.002), with secondary analysis showing this was especially so for happy (p = 0.014) and neutral (p = 0.001) sentences. There was a significant interaction effect for pitch between tone deviation level and group (p = 0.019), and relatives performed worse than controls on amplitude discrimination and duration discrimination. AP performance for happy and neutral sentences was significantly correlated with amplitude perception. Lastly, AVH proneness in the entire sample was significantly correlated with pitch discrimination (r = 0.44) and pitch perception was shown to predict AVH proneness in the sample (p = 0.005). These results suggest basic impairments in auditory processing are present in relatives of AVH patients; they potentially underlie processing speed in AP tasks, and predict AVH proneness. This indicates auditory processing deficits may be a core feature of AVHs in schizophrenia, and are worthy of further study as a potential endophenotype for AVHs.

Associations of ATR and CHEK1 single nucleotide polymorphisms with breast cancer.

DNA damage and replication checkpoints mediated by the ATR-CHEK1 pathway are key to the maintenance of genome stability, and both ATR and CHEK1 have been proposed as potential breast cancer susceptibility genes. Many novel variants recently identified by the large resequencing projects have not yet been thoroughly tested in genome-wide association studies for breast cancer susceptibility. We therefore used a tagging SNP (tagSNP) approach based on recent SNP data available from the 1000 genomes projects, to investigate the roles of ATR and CHEK1 in breast cancer risk and survival. ATR and CHEK1 tagSNPs were genotyped in the Sheffield Breast Cancer Study (SBCS; 1011 cases and 1024 controls) using Illumina GoldenGate assays. Untyped SNPs were imputed using IMPUTE2, and associations between genotype and breast cancer risk and survival were evaluated using logistic and Cox proportional hazard regression models respectively on a per allele basis. Significant associations were further examined in a meta-analysis of published data or confirmed in the Utah Breast Cancer Study (UBCS). The most significant associations for breast cancer risk in SBCS came from rs6805118 in ATR (p=7.6 x 10(-5)) and rs2155388 in CHEK1 (p=3.1 x 10(-6)), but neither remained significant after meta-analysis with other studies. However, meta-analysis of published data revealed a weak association between the ATR SNP rs1802904 (minor allele frequency is 12%) and breast cancer risk, with a summary odds ratio (confidence interval) of 0.90 (0.83-0.98) [p=0.0185] for the minor allele. Further replication of this SNP in larger studies is warranted since it is located in the target region of 2 microRNAs. No evidence of any survival effects of ATR or CHEK1 SNPs were identified. We conclude that common alleles of ATR and CHEK1 are not implicated in breast cancer risk or survival, but we cannot exclude effects of rare alleles and of common alleles with very small effect sizes.