Roles of homologous recombination in response to ionizing radiation-induced DNA damage.

PURPOSE: Ionizing radiation induces a vast array of DNA lesions including base damage, and single- and double-strand breaks (SSB, DSB). DSBs are among the most cytotoxic lesions, and mis-repair causes small- and large-scale genome alterations that can contribute to carcinogenesis. Indeed, ionizing radiation is a 'complete' carcinogen. DSBs arise immediately after irradiation, termed 'frank DSBs,' as well as several hours later in a replication-dependent manner, termed 'secondary' or 'replication-dependent DSBs. DSBs resulting from replication fork collapse are single-ended and thus pose a distinct problem from two-ended, frank DSBs. DSBs are repaired by error-prone nonhomologous end-joining (NHEJ), or generally error-free homologous recombination (HR), each with sub-pathways. Clarifying how these pathways operate in normal and tumor cells is critical to increasing tumor control and minimizing side effects during radiotherapy. CONCLUSIONS: The choice between NHEJ and HR is regulated during the cell cycle and by other factors. DSB repair pathways are major contributors to cell survival after ionizing radiation, including tumor-resistance to radiotherapy. Several nucleases are important for HR-mediated repair of replication-dependent DSBs and thus replication fork restart. These include three structure-specific nucleases, the 3' MUS81 nuclease, and two 5' nucleases, EEPD1 and Metnase, as well as three end-resection nucleases, MRE11, EXO1, and DNA2. The three structure-specific nucleases evolved at very different times, suggesting incremental acceleration of replication fork restart to limit toxic HR intermediates and genome instability as genomes increased in size during evolution, including the gain of large numbers of HR-prone repetitive elements. Ionizing radiation also induces delayed effects, observed days to weeks after exposure, including delayed cell death and delayed HR. In this review we highlight the roles of HR in cellular responses to ionizing radiation, and discuss the importance of HR as an exploitable target for cancer radiotherapy.

Perinatal outcomes of 221,709 singleton and twin pregnancies after the use of donor versus partner sperm.

OBJECTIVE: To study the association of donor sperm on perinatal outcomes of livebirths conceived via in vitro fertilization (IVF) when compared with partner sperm. DESIGN: Retrospective cohort study SETTING: National Human Fertilisation and Embryology Authority assisted reproductive technology registry PATIENTS: All live born singletons and twins conceived through IVF with or without intracytoplasmic sperm injection in the United Kingdom between 1991 and 2016 INTERVENTION(S): Donor sperm compared to partner sperm MAIN OUTCOME MEASURE(S): Perinatal outcomes were assessed. The primary outcomes were preterm and very preterm birth; low, very low, high, and very high birthweight; Secondary outcomes were congenital anomaly and health baby. These were assessed for singletons and twins separately. RESULTS: For singleton livebirths, compared to partner sperm, those conceived with donor sperm were at reduced odds of very preterm (odds ratio [OR], 0.76; 95% confidence interval [CI], 0.63-0.91; adjusted OR [aOR], 0.80; 95% CI, 0.66-0.96), and preterm (OR, 0.90; 95% CI, 0.83-0.98; aOR, 0.93; 95% CI, 0.85-1.01) birth. For birthweight outcomes, donor sperm showed a reduced odds of low (OR, 0.83; 95% CI, 0.76-0.91; aOR, 0.86; 95% CI, 0.78-0.94) and an increased odds of high (OR, 1.15; 95% CI, 1.07-1.23; aOR, 1.09; 95% CI, 1.01-1.17) birthweight. There was no confirmed difference in the odds ratios of very low (OR, 0.88; 95% CI, 0.74-1.06; aOR, 0.94; 95% CI, 0.78-1.13) or very high (OR, 1.21; 95% CI, 1.04-1.40; aOR, 1.15; 95% CI, 0.98-1.34) birthweight. Liveborn twins conceived with donor sperm, compared to partner sperm, were at reduced odds of very low (OR, 0.76; 95% CI, 0.66-0.88; aOR, 0.83; 95% CI, 0.72-0.96) and low (OR, 0.87; 95% CI, 0.81-0.93; aOR, 0.91; 95% CI, 0.85-0.98) birthweight. There was a suggestion of a reduced odds of very preterm (OR, 0.81; 95% CI, 0.70-0.95; aOR, 0.86; 95% CI, 0.74-1.01) and preterm (OR, 0.93; 95% CI, 0.86-1.01; aOR, 0.96; 95% CI, 0.88-1.04) birth. There was considerable uncertainty around the ORs for high (OR, 0.73; 95% CI, 0.31-1.72; aOR, 0.72; 95% CI, 0.29-1.80) and very high (OR, 1.02; 95% CI, 0.39-2.67; aOR, 1.34; 95% CI, 0.50-3.60) birthweight. CONCLUSION: Although unmeasured confounding remains a possibility, as paternal age, body mass index, and smoking status were unavailable for analysis, women, couples, service providers can be reassured that IVF livebirths conceived with donor sperm have no greater chance of adverse outcomes when compared to partner sperm.

Extracellular vesicle secretion is tissue-dependent ex vivo and skeletal muscle myofiber extracellular vesicles reach the circulation in vivo.

Extracellular vesicles (EVs) are biomarkers and modifiers of human disease. EVs secreted by insulin-responsive tissues like skeletal muscle (SkM) and white adipose tissue (WAT) contribute to metabolic health and disease but the relative abundance of EVs from these tissues has not been directly examined. Human Protein Atlas data and directly measuring EV secretion in mouse SkM and WAT using an ex vivo tissue explant model confirmed that SkM tissue secretes more EVs than WAT. Differences in EV secretion between SkM and WAT were not due to SkM contraction but may be explained by differences in tissue metabolic capacity. We next examined how many EVs secreted from SkM tissue ex vivo and in vivo are myofiber-derived. To do this, a SkM myofiber-specific dual fluorescent reporter mouse was created. Spectral flow cytometry revealed that SkM myofibers are a major source of SkM tissue-derived EVs ex vivo and EV immunocapture indicates that ∼5% of circulating tetraspanin-positive EVs are derived from SkM myofibers in vivo. Our findings demonstrate that 1) SkM secretes more EVs than WAT, 2) many SkM tissue EVs are derived from SkM myofibers, and 3) SkM myofiber-derived EVs reach the circulation in vivo. These findings advance our understanding of EV secretion between metabolically active tissues and provide direct evidence that SkM myofibers secrete EVs that can reach the circulation in vivo.

Outcomes of pregnancies using donor sperm compared with those using partner sperm: systematic review and meta-analysis.

BACKGROUND: Registry data from the Human Fertilisation and Embryology Authority (HFEA) show an increase of 40% in IUI and 377% in IVF cases using donor sperm between 2006 and 2016. OBJECTIVE AND RATIONALE: The objective of this study was to establish whether pregnancies conceived using donor sperm are at higher risk of obstetric and perinatal complications than those conceived with partner sperm. As more treatments are being carried out using donor sperm, attention is being given to obstetric and perinatal outcomes, as events in utero and at delivery have implications for long-term health. There is a need to know if there is any difference in the outcomes of pregnancies between those conceived using donor versus partner sperm in order to adequately inform and counsel couples. SEARCH METHODS: We performed a systematic review and meta-analysis of the outcomes of pregnancies conceived using donor sperm compared with partner sperm. Searches were performed in the OVID MEDLINE, OVID Embase, CENTRAL and CINAHL databases, including all studies published before 11 February 2019. The search strategy involved search terms for pregnancy, infant, donor sperm, heterologous artificial insemination, donor gametes, pregnancy outcomes and perinatal outcomes. Studies were included if they assessed pregnancies conceived by any method using, or infants born from, donor sperm compared with partner sperm and described early pregnancy, obstetric or perinatal outcomes. The Downs and Black tool was used for quality and bias assessment of studies. OUTCOMES: Of 3391 studies identified from the search, 37 studies were included in the review and 36 were included in the meta-analysis. For pregnancies conceived with donor sperm, versus partner sperm, there was an increase in the relative risk (RR) (95% CI) of combined hypertensive disorders of pregnancy: 1.44 (1.17-1.78), pre-eclampsia: 1.49 (1.05-2.09) and small for gestational age (SGA): 1.42 (1.17-1.79) but a reduced risk of ectopic pregnancy: 0.69 (0.48-0.98). There was no difference in the overall RR (95% CI) of miscarriage: 0.94 (0.80-1.11), gestational diabetes: 1.49 (0.62-3.59), pregnancy-induced hypertension (PIH): 1.24 (0.87-1.76), placental abruption: 0.65 (0.04-10.37), placenta praevia: 1.19 (0.64-2.21), preterm birth: 0.98 (0.88-1.08), low birth weight: 0.97 (0.82-1.15), high birthweight: 1.28 (0.94-1.73): large for gestational age (LGA): 1.01 (0.84-1.22), stillbirth: 1.23 (0.97-1.57), neonatal death: 0.79 (0.36-1.73) and congenital anomaly: 1.15 (0.86-1.53). WIDER IMPLICATIONS: The majority of our findings are reassuring, except for the mild increased risk of hypertensive disorders of pregnancy and SGA in pregnancies resulting from donor sperm. However, the evidence for this is limited and should be interpreted with caution because the evidence was based on observational studies which varied in their quality and risk of bias. Further high-quality population-based studies reporting obstetric outcomes in detail are required to confirm these findings.

Distinct roles of structure-specific endonucleases EEPD1 and Metnase in replication stress responses.

Accurate DNA replication and segregation are critical for maintaining genome integrity and suppressing cancer. Metnase and EEPD1 are DNA damage response (DDR) proteins frequently dysregulated in cancer and implicated in cancer etiology and tumor response to genotoxic chemo- and radiotherapy. Here, we examine the DDR in human cell lines with CRISPR/Cas9 knockout of Metnase or EEPD1. The knockout cell lines exhibit slightly slower growth rates, significant hypersensitivity to replication stress, increased genome instability and distinct alterations in DDR signaling. Metnase and EEPD1 are structure-specific nucleases. EEPD1 is recruited to and cleaves stalled forks to initiate fork restart by homologous recombination. Here, we demonstrate that Metnase is also recruited to stalled forks where it appears to dimethylate histone H3 lysine 36 (H3K36me2), raising the possibility that H3K36me2 promotes DDR factor recruitment or limits nucleosome eviction to protect forks from nucleolytic attack. We show that stalled forks are cleaved normally in the absence of Metnase, an important and novel result because a prior study indicated that Metnase nuclease is important for timely fork restart. A double knockout was as sensitive to etoposide as either single knockout, suggesting a degree of epistasis between Metnase and EEPD1. We propose that EEPD1 initiates fork restart by cleaving stalled forks, and that Metnase may promote fork restart by processing homologous recombination intermediates and/or inducing H3K36me2 to recruit DDR factors. By accelerating fork restart, Metnase and EEPD1 reduce the chance that stalled replication forks will adopt toxic or genome-destabilizing structures, preventing genome instability and cancer. Metnase and EEPD1 are overexpressed in some cancers and thus may also promote resistance to genotoxic therapeutics.

Cortical and subcortical functional specificity associated with response inhibition.

Is motor response inhibition supported by a specialised neuronal inhibitory control mechanism, or by a more general system of action updating? This pre-registered study employed a context-cueing paradigm requiring both inhibitory and non-inhibitory action updating in combination with functional magnetic resonance imaging to test the specificity of responses under different updating conditions, including the cancellation of actions. Cortical regions of activity were found to be common to multiple forms of action updating. However, functional specificity during response inhibition was observed in the anterior right inferior frontal gyrus. In addition, fronto-subcortical activity was explored using a novel contrast method. These exploratory results indicate that the specificity for response inhibition observed in right prefrontal cortex continued downstream and was observed in right hemisphere subcortical activity, while left hemisphere activity was associated with right-hand response execution. Overall, our findings reveal both common and distinct correlates of response inhibition in prefrontal cortex, with exploratory analyses supporting putative models of subcortical pathways and extending them through the demonstration of lateralisation.

Impairment of manual but not saccadic response inhibition following acute alcohol intoxication.

BACKGROUND: Alcohol impairs response inhibition; however, it remains contested whether such impairments affect a general inhibition system, or whether affected inhibition systems are embedded in, and specific to, each response modality. Further, alcohol-induced impairments have not been disambiguated between proactive and reactive inhibition mechanisms, and nor have the contributions of action-updating impairments to behavioural 'inhibition' deficits been investigated. METHODS: Forty Participants (25 female) completed both a manual and a saccadic stop-signal reaction time (SSRT) task before and after a 0.8g/kg dose of alcohol and, on a separate day, before and after a placebo. Blocks in which participants were required to ignore the signal to stop or make an additional 'dual' response were included to obtain measures of proactive inhibition as well as updating of attention and action. RESULTS: Alcohol increased manual but not saccadic SSRT. Proactive inhibition was weakly reduced by alcohol, but increases in the reaction times used to baseline this contrast prevent clear conclusions regarding response caution. Finally, alcohol also increased secondary dual response times of the dual task uniformly as a function of the delay between tasks, indicating an effect of alcohol on action-updating or execution. CONCLUSIONS: The modality-specific effects of alcohol favour the theory that response inhibition systems are embedded within response modalities, rather than there existing a general inhibition system. Concerning alcohol, saccadic control appears relatively more immune to disruption than manual control, even though alcohol affects saccadic latency and velocity. Within the manual domain, alcohol affects multiple types of action updating, not just inhibition.

Low- and High-LET Ionizing Radiation Induces Delayed Homologous Recombination that Persists for Two Weeks before Resolving.

Genome instability is a hallmark of cancer cells and dysregulation or defects in DNA repair pathways cause genome instability and are linked to inherited cancer predisposition syndromes. Ionizing radiation can cause immediate effects such as mutation or cell death, observed within hours or a few days after irradiation. Ionizing radiation also induces delayed effects many cell generations after irradiation. Delayed effects include hypermutation, hyper-homologous recombination, chromosome instability and reduced clonogenic survival (delayed death). Delayed hyperrecombination (DHR) is mechanistically distinct from delayed chromosomal instability and delayed death. Using a green fluorescent protein (GFP) direct repeat homologous recombination system, time-lapse microscopy and colony-based assays, we demonstrate that DHR increases several-fold in response to low-LET X rays and high-LET carbon-ion radiation. Time-lapse analyses of DHR revealed two classes of recombinants not detected in colony-based assays, including cells that recombined and then senesced or died. With both low- and high-LET radiation, DHR was evident during the first two weeks postirradiation, but resolved to background levels during the third week. The results indicate that the risk of radiation-induced genome destabilization via DHR is time limited, and suggest that there is little or no additional risk of radiation-induced genome instability mediated by DHR with high-LET radiation compared to low-LET radiation.

Translational research in radiation-induced DNA damage signaling and repair.

Radiotherapy is an effective tool in the fight against cancer. It is non-invasive and painless, and with advanced tumor imaging and beam control systems, radiation can be delivered to patients safely, generally with minor or no adverse side effects, accounting for its increasing use against a broad range of tumors. Tumors and normal cells respond to radiation-induced DNA damage by activating a complex network of DNA damage signaling and repair pathways that determine cell fate including survival, death, and genome stability. DNA damage response (DDR) proteins represent excellent targets to augment radiotherapy, and many agents that inhibit key response proteins are being combined with radiation and genotoxic chemotherapy in clinical trials. This review focuses on how insights into molecular mechanisms of DDR pathways are translated to small animal preclinical studies, to clinical studies of naturally occurring tumors in companion animals, and finally to human clinical trials. Companion animal studies, under the umbrella of comparative oncology, have played key roles in the development of clinical radiotherapy throughout its >100-year history. There is growing appreciation that rapid translation of basic knowledge of DNA damage and repair systems to improved radiotherapy practice requires a comprehensive approach that embraces the full spectrum of cancer research, with companion animal clinical trials representing a critical bridge between small animal preclinical studies, and human clinical trials.

Immune Modulation as an Effective Adjunct Post-exposure Therapeutic for B. pseudomallei.

Melioidosis is caused by the facultative intracellular bacterium Burkholderia pseudomallei and is potentially fatal. Despite a growing global burden and high fatality rate, little is known about the disease. Recent studies demonstrate that cyclooxygenase-2 (COX-2) inhibition is an effective post-exposure therapeutic for pulmonary melioidosis, which works by inhibiting the production of prostaglandin E2 (PGE2). This treatment, while effective, was conducted using an experimental COX-2 inhibitor that is not approved for human or animal use. Therefore, an alternative COX-2 inhibitor needs to be identified for further studies. Tolfenamic acid (TA) is a non-steroidal anti-inflammatory drug (NSAID) COX-2 inhibitor marketed outside of the United States for the treatment of migraines. While this drug was developed for COX-2 inhibition, it has been found to modulate other aspects of inflammation as well. In this study, we used RAW 264.7 cells infected with B pseudomallei to analyze the effect of TA on cell survival, PGE2 production and regulation of COX-2 and nuclear factor- kappaB (NF-ĸB) protein expression. To evaluate the effectiveness of post-exposure treatment with TA, results were compared to Ceftazidime (CZ) treatments alone and the co-treatment of TA with a sub-therapeutic treatment of CZ determined in a study of BALB/c mice. Results revealed an increase in cell viability in vitro with TA and were able to reduce both COX-2 expression and PGE2 production while also decreasing NF-ĸB activation during infection. Co-treatment of orally administered TA and a sub-therapeutic treatment of CZ significantly increased survival outcome and cleared the bacterial load within organ tissue. Additionally, we demonstrated that post-exposure TA treatment with sub-therapeutic CZ is effective to treat melioidosis in BALB/c mice.

DNA Damage Response Proteins and Oxygen Modulate Prostaglandin E2 Growth Factor Release in Response to Low and High LET Ionizing Radiation.

Common cancer therapies employ chemicals or radiation that damage DNA. Cancer and normal cells respond to DNA damage by activating complex networks of DNA damage sensor, signal transducer, and effector proteins that arrest cell cycle progression, and repair damaged DNA. If damage is severe enough, the DNA damage response (DDR) triggers programed cell death by apoptosis or other pathways. Caspase 3 is a protease that is activated upon damage and triggers apoptosis, and production of prostaglandin E2 (PGE2), a potent growth factor that can enhance growth of surviving cancer cells leading to accelerated tumor repopulation. Thus, dying tumor cells can promote growth of surviving tumor cells, a pathway aptly named Phoenix Rising. In the present study, we surveyed Phoenix Rising responses in a variety of normal and established cancer cell lines, and in cancer cell lines freshly derived from patients. We demonstrate that IR induces a Phoenix Rising response in many, but not all cell lines, and that PGE2 production generally correlates with enhanced growth of cells that survive irradiation, and of unirradiated cells co-cultured with irradiated cells. We show that PGE2 production is stimulated by low and high LET ionizing radiation, and can be enhanced or suppressed by inhibitors of key DDR proteins. PGE2 is produced downstream of caspase 3 and the cyclooxygenases COX1 and COX2, and we show that the pan COX1-2 inhibitor indomethacin blocks IR-induced PGE2 production in the presence or absence of DDR inhibitors. COX1-2 require oxygen for catalytic activity, and we further show that PGE2 production is markedly suppressed in cells cultured under low (1%) oxygen concentration. Thus, Phoenix Rising is most likely to cause repopulation of tumors with relatively high oxygen, but not in hypoxic tumors. This survey lays a foundation for future studies to further define tumor responses to radiation and inhibitors of the DDR and Phoenix Rising to enhance the efficacy of radiotherapy with the ultimate goal of precision medicine informed by deep understanding of specific tumor responses to radiation and adjunct chemotherapy targeting key factors in the DDR and Phoenix Rising pathways.

An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins.

Although three major classes of systemic antifungal agents are clinically available, each is characterized by important limitations. Thus, there has been considerable ongoing effort to develop novel and repurposed agents for the therapy of invasive fungal infections. In an effort to address these needs, we developed a novel high-throughput, multiplexed screening method that utilizes small molecules to probe candidate drug targets in the opportunistic fungal pathogen Candida albicans. This method is amenable to high-throughput automated screening and is based upon detection of changes in GFP levels of individually tagged target proteins. We first selected four GFP-tagged membrane-bound proteins associated with virulence or antifungal drug resistance in C. albicans. We demonstrated proof-of-principle that modulation of fluorescence intensity can be used to assay the expression of specific GFP-tagged target proteins to inhibitors (and inducers), and this change is measurable within the HyperCyt automated flow cytometry sampling system. Next, we generated a multiplex of differentially color-coded C. albicans strains bearing C-terminal GFP-tags of each gene encoding candidate drug targets incubated in the presence of small molecules from the Prestwick Chemical Library in 384-well microtiter plate format. Following incubation, cells were sampled through the HyperCyt system and modulation of protein levels, as indicated by changes in GFP-levels of each strain, was used to identify compounds of interest. The hit rate for both inducers and inhibitors identified in the primary screen did not exceed 1% of the total number of compounds in the small-molecule library that was probed, as would be expected from a robust target-specific, high-throughput screening campaign. Secondary assays for virulence characteristics based on null mutant strains were then used to further validate specificity. In all, this study presents a method for the identification and verification of new antifungal drugs targeted to fungal virulence proteins using C. albicans as a model fungal pathogen.

Enhanced awareness followed reversible inhibition of human visual cortex: a combined TMS, MRS and MEG study.

This series of experiments investigated the neural basis of conscious vision in humans using a form of transcranial magnetic stimulation (TMS) known as continuous theta burst stimulation (cTBS). Previous studies have shown that occipital TMS, when time-locked to the onset of visual stimuli, can induce a phenomenon analogous to blindsight in which conscious detection is impaired while the ability to discriminate 'unseen' stimuli is preserved above chance. Here we sought to reproduce this phenomenon using offline occipital cTBS, which has been shown to induce an inhibitory cortical aftereffect lasting 45-60 minutes. Contrary to expectations, our first experiment revealed the opposite effect: cTBS enhanced conscious vision relative to a sham control. We then sought to replicate this cTBS-induced potentiation of consciousness in conjunction with magnetoencephalography (MEG) and undertook additional experiments to assess its relationship to visual cortical excitability and levels of the inhibitory neurotransmitter γ-aminobutyric acid (GABA; via magnetic resonance spectroscopy, MRS). Occipital cTBS decreased cortical excitability and increased regional GABA concentration. No significant effects of cTBS on MEG measures were observed, although the results provided weak evidence for potentiation of event related desynchronisation in the ß band. Collectively these experiments suggest that, through the suppression of noise, cTBS can increase the signal-to-noise ratio of neural activity underlying conscious vision. We speculate that gating-by-inhibition in the visual cortex may provide a key foundation of consciousness.

The timing and neuroanatomy of conscious vision as revealed by TMS-induced blindsight.

Following damage to the primary visual cortex, some patients exhibit "blindsight," where they report a loss of awareness while retaining the ability to discriminate visual stimuli above chance. Transient disruption of occipital regions with TMS can produce a similar dissociation, known as TMS-induced blindsight. The neural basis of this residual vision is controversial, with some studies attributing it to the retinotectal pathway via the superior colliculus whereas others implicate spared projections that originate predominantly from the LGN. Here we contrasted these accounts by combining TMS with visual stimuli that either activate or bypass the retinotectal and magnocellular (R/M) pathways. We found that the residual capacity of TMS-induced blindsight occurs for stimuli that bypass the R/M pathways, indicating that such pathways, which include those to the superior colliculus, are not critical. We also found that the modulation of conscious vision was time and pathway dependent. TMS applied either early (0-40 msec) or late (280-320 msec) after stimulus onset modulated detection of stimuli that did not bypass R/M pathways, whereas during an intermediate period (90-130 msec) the effect was pathway independent. Our findings thus suggest a prominent role for the R/M pathways in supporting both the preparatory and later stages of conscious vision. This may help resolve apparent conflict in previous literature by demonstrating that the roles of the retinotectal and geniculate pathways are likely to be more nuanced than simply corresponding to the unconscious/conscious dichotomy.

Comparative incidence rates of mild adverse effects to transcranial magnetic stimulation.

OBJECTIVES: Past research has largely neglected to investigate mild adverse effects (MAEs) to transcranial magnetic stimulation (TMS), including headache and nausea. Here we explored the relationship between MAEs, participant characteristics (age and gender) and protocol parameters, including mode of application, coil geometry, stimulated brain region, TMS frequency, TMS intensity, and active vs. sham stimulation. METHODS: Data from 1270 standard post-monitoring forms was obtained from 113 healthy participants. Analyses aimed to identify the risk factors associated with MAE reports and specific symptoms. RESULTS: The overall rate of MAEs across TMS sessions was ∼5%, with ∼78% of symptoms occurring post-session. Initial TMS sessions were followed by a higher MAE incidence rate relative to later testing sessions. No associations between participant characteristics, TMS frequency, or intensity were observed. CONCLUSIONS: TMS-related MAEs are relatively common and may be exacerbated by initial expectations or anxieties of participants. A significant proportion of MAEs may reflect reporting of coincidental phenomena that are unrelated to TMS. Recommendations for future safety studies are proposed and monitoring documentation is provided. SIGNIFICANCE: Our findings illustrate the importance of standardized monitoring of MAEs. Such research aids our understanding of how MAEs arise and may lead to interventions for reducing their incidence.

Is delayed foveal feedback critical for extra-foveal perception?

Recent neuroimaging evidence suggests that visual inputs arising beyond the fovea can be 'fed back' to foveal visual cortex to construct a new retinotopic representation. However, whether these representations are critical for extra-foveal perception remains unclear. Using transcranial magnetic stimulation we found that relatively late (350-400 msec) disruption of foveal retinotopic cortex impaired perceptual discrimination of objects in the periphery. These results are consistent with the hypothesis that feedback to the foveal retinotopic cortex is crucial for extra-foveal perception, and provide additional evidence for 'constructive' feedback in human vision.

Multivariate curve resolution of time course microarray data.

BACKGROUND: Modeling of gene expression data from time course experiments often involves the use of linear models such as those obtained from principal component analysis (PCA), independent component analysis (ICA), or other methods. Such methods do not generally yield factors with a clear biological interpretation. Moreover, implicit assumptions about the measurement errors often limit the application of these methods to log-transformed data, destroying linear structure in the untransformed expression data. RESULTS: In this work, a method for the linear decomposition of gene expression data by multivariate curve resolution (MCR) is introduced. The MCR method is based on an alternating least-squares (ALS) algorithm implemented with a weighted least squares approach. The new method, MCR-WALS, extracts a small number of basis functions from untransformed microarray data using only non-negativity constraints. Measurement error information can be incorporated into the modeling process and missing data can be imputed. The utility of the method is demonstrated through its application to yeast cell cycle data. CONCLUSION: Profiles extracted by MCR-WALS exhibit a strong correlation with cell cycle-associated genes, but also suggest new insights into the regulation of those genes. The unique features of the MCR-WALS algorithm are its freedom from assumptions about the underlying linear model other than the non-negativity of gene expression, its ability to analyze non-log-transformed data, and its use of measurement error information to obtain a weighted model and accommodate missing measurements.