Pan-cancer analysis of genomic scar patterns caused by homologous repair deficiency (HRD)

Homologous repair deficiency (HRD) is present in many cancer types at variable prevalence and can indicate response to platinum-based chemotherapy and PARP inhibition. We developed a tumor classification system based on the loss of function of genes in the homologous recombination repair (HRR) pathway. To this end, somatic and germline alterations in BRCA1/2 and 140 other HRR genes were included and assessed for the impact on gene function. Additionally, information on the allelic hit type and on BRCA1 promoter hypermethylation was included. The HRDsum score including LOH, LST, and TAI was calculated for 8847 tumors of the TCGA cohort starting from genotyping data and for the subcohort of ovarian cancer also starting from WES data. Pan-cancer, deleterious BRCA1/2 alterations were detected in 4% of the tumors, while 18% of the tumors were HRD-positive (HRDsum ≥ 42). Across 33 cancer types, both BRCA1/2 alterations and HRD-positivity were most prevalent in ovarian cancer (20% and 69%). Pan-cancer, tumors with biallelic deleterious alterations in BRCA1/2 were separated strongly from tumors without relevant alterations (AUC = 0.89), while separation for tumors with monoallelic deleterious BRCA1/2 alterations was weak (AUC = 0.53). Tumors with biallelic deleterious alterations in other HHR genes were separated moderately from tumors without relevant alterations (AUC = 0.63), while separation for tumors with such monoallelic alterations was weaker (AUC = 0.57). In ovarian cancer, HRDsum scores calculated from WES data correlated strongly with HRDsum scores calculated from genotyping data (R = 0.87) and were slightly (4%) higher. We comprehensively analyzed HRD scores and their association with mutations in HRR genes in common cancer types. Our study identifies important parameters influencing HRD measurement and argues for an integration of HRDsum score with specific mutational profiles.

[From panel diagnostics to comprehensive genomic analysis : Infobesity or empowerment?]

Precision oncology is obtaining a central role in the therapy of malignant diseases. The indication for targeted therapy is based on the identification of molecular targets for which next-generation sequencing (NGS) is commonly used nowadays. All approved predictive biomarkers and molecular targets, including gene fusions and copy number alterations, can be identified depending on panel design and method applied. Some clinical scenarios, however, may require more holistic genomic approaches, such as whole-genome/whole-exome and transcriptome analysis, which must be embedded in a clinical trial. Here, key aspects and applications of each method are summarized and discussed.

Temporal, but not spatial, context modulates a masked prime's effect on temporal order judgment, but not on response latency

Three experiments investigated a dissociation originally described by Neumann, Esselmann, and Klotz. Stimuli were geometric shapes, preceded by similar shapes that were masked by metacontrast. Each experiment consisted of three parts. In the reaction time (RT) part, participants saw an array of geometric shapes, one of which was marked by bars, and had to respond to the marked shape's position by pressing an appropriate button. A prime (a similar, but smaller stimulus) preceded either the marked or an unmarked stimulus. In the temporal order judgment (TOJ) part, the task was to judge the temporal order of the marked and the unmarked stimulus. In the detection part, detectability of the prime was tested. Although its detectability was zero or close to zero, the prime affected both RT and the apparent onset as measured by TOJ. The effect on RT was significantly larger than the effect on TOJ (Exp. 1). Increasing the spatial context (number of non-target stimuli in the display) did not affect this pattern (Exp. 2). By contrast, reducing the temporal context (range of stimulus onset asynchronies) abolished the prime's effect in the TOJ task, although the prime affected RT under identical conditions. It is concluded that partially different mechanisms mediate the prime's effect in the two tasks and that the effect of stimulus context on TOJ found in the Neumann et al. study was due to temporal, not spatial context.

Manual and verbal responses to completely masked (unreportable) stimuli: exploring some conditions for the metacontrast dissociation

As reported by Neumann and Klotz [1994, in Attention and Performance XV: Conscious and Nonconscious Information Processing Eds C Umiltà, M Moscovitch (Cambridge, MA: MIT Press) pp 123-150], a geometric shape masked by metacontrast can affect response latency (RT) even if it is not visible, i.e. if it yields a d' value of zero in a signal-detection (SD) task (metacontrast dissociation). In the initial study as well as in most subsequent experiments, the RT task was manual and the SD task was verbal. Hence tasks and output modes were confounded. In the present study, two experiments were conducted to find out which of these factors is responsible for the metacontrast dissociation. In experiment 1, participants performed an RT task in either a manual or a verbal output mode. In experiment 2, these output modes were compared in an SD task. Independently of output modes, the masked primes affected RT but could not be detected in the SD task. It is concluded that tasks, but not output modes, are crucial for the metacontrast dissociation. Implications for the mechanisms underlying the metacontrast dissociation and for the functional difference between judgments and responses are discussed.

Energy requirement for eating in cattle

We determined the energy requirement for the activity associated with eating in an experiment with four adult Hinterwälder steers weighing 640+/-25 kg BW (mean+/-SD), using indirect calorimetry in respiration chambers. Heat production was measured during 3 h with and 3 h without ad libitum access to wheat straw, and the energy cost of eating was calculated as the difference, which was on average 27+/-13 J/(min x kg BW) (mean+/-SD). Straw intake, the time spent for eating, and the number of jaw movements were recorded. Values for the energy cost of eating reported in the literature are similar to those in this study, and values for ruminating amount to approximately 27% of those for eating. The energy cost of eating (literature values) varies greatly between feeds and feed treatments, when related to the amount of feed ingested, but it was relatively constant when related to time spent eating and was similar for cattle, sheep, and horses, when related to BW or metabolic BW (35 J/[min x kg BW] or 124 J/ [min x kg BW.75]). Calculations indicated that in high-quality roughage 10% of the ME and in untreated straw approximately 30% of the ME provided by the feed are used for eating and ruminating. This might be the main reason for the lower efficiency of ME utilization in roughages. The energy requirement for eating and ruminating should therefore be considered as a distinct proportion of the total ME requirement.

Effects of a two-week physiological dehydroepiandrosterone substitution on cognitive performance and well-being in healthy elderly women and men

The levels of dehydroepiandrosterone (DHEA) and its sulfate ester DHEAS decrease with age after a peak around 25 yr. Animal studies as well as the first studies in humans have generated the idea that DHEA replacement in elderly subjects may have beneficial effects on well-being and cognitive functions. In the present experiment 40 healthy elderly men and women (mean age, 69 yr) participated in a double blind, placebo-controlled DHEA substitution study. For 2 weeks subjects took 50 mg DHEA daily, followed by a 2-week wash-out period and a 2-week placebo period. The treatment sequence was randomized in a cross-over design. After 2 weeks of DHEA or placebo, psychological and physical well-being as well as cognitive performance were assessed using several questionnaires and neuropsychological tests. All subjects had low DHEAS baseline levels. DHEA substitution lead to a 5-fold increase in DHEAS levels in women (from 0.67 +/- 0.1 to 4.1 +/- 0.4 micrograms/mL; P < 0.001) and men (from 0.85 +/- 0.1 to 4.5 +/- 0.4 micrograms/mL; P < 0.001). DHEA, androstenedione, and testosterone levels also increased significantly in both sexes (all P < 0.001). No significant changes were observed in insulin-like growth factor I or insulin-like growth factor-binding protein-3 levels. DHEA replacement had no strong beneficial effect on any of the measured psychological or cognitive parameters. Only women tended to report an increase in well-being (P = 0.11) and mood (P = 0.10), as assessed with questionnaires. They also showed better performance in one of six cognitive tests (picture memory) after DHEA. However, after Bonferroni alpha adjustment, this difference was no longer significant. No such trend was observed in men (P > 0.20). Likewise, no beneficial effects of DHEA substitution could be observed in any of the other tests of the neuropsychological test battery in either sex (all P > 0.20). In conclusion, the present data do not support the idea of strong beneficial effects of a physiological DHEA substitution on well-being or cognitive performance in healthy elderly individuals.

Short-term estradiol treatment enhances pituitary-adrenal axis and sympathetic responses to psychosocial stress in healthy young men

Evidence from animal studies and clinical observations suggest that the activity of the pituitary-adrenal axis is under significant influence of sex steroids. The present study investigated how a short term elevation of estradiol levels affects ACTH, cortisol, norepinephrine, and heart rate responses to mental stress in healthy men. In a double blind study, 16 men received a patch delivering 0.1 mg estradiol/day transdermally, and age- and body mass index-matched control subjects received a placebo patch. Twenty-four to 48 h later, they were exposed to a brief psychosocial stressor (free speech and mental arithmetic in front of an audience). In response to the psychosocial stressor, ACTH, cortisol, norepinephrine, and heart rate were increased in both experimental groups (all P < 0.0001). However, the estradiol-treated subjects showed exaggerated peak ACTH (P < 0.001) and cortisol (P < 0.002) responses compared to the placebo group. Also, the norepinephrine area under the response curve was greater in the estradiol group (P < 0.05). Although heart rate responses differences failed to reach statistical significance, they, too, tended to be larger in the estradiol group. Neither mood ratings before or after the stressor, nor ratings of the perception of the stressor could explain the observed endocrine response differences. In conclusion, short term estradiol administration resulted in hyperresponses of the pituitary-adrenal axis and norepinephrine to psychosocial stress in healthy young men independent of psychological effects, as assessed in this study.

A dissociation between reaction time to sinusoidal gratings and temporal-order judgment

The effect of the spatial frequency (SF) of visual gratings on reaction time (RT) and temporal-order judgment (TOJ) was examined in three experiments. In experiment 1 the visual stimuli were vertical sinusoidal gratings with SFs between 2 and 8 cycles deg-1 and the comparison stimulus in the TOJ task was a 2300 Hz tone. Whereas SF had a highly significant effect on RT, it left TOJ completely unaffected. To test whether this dissociation was due to the sharp (high SF) horizontal edges of the gratings, a second experiment was carried out with circular stimuli with no sharp edges. These stimuli did produce an effect of SF on TOJ, but it was significantly smaller than was the effect on RT. In experiment 3 we confirmed that this difference was not due to differences in grating orientation between the first two experiments. These findings (a) solve discrepancies between findings reported in the literature and (b) strongly suggest that RT and TOJ cannot be regarded as converging operations for determining 'visual latency'. This dissociation can best be accounted for by assuming that the output of early stimulus analysis can feed directly into the motor system (direct parameter specification), whereas the conscious representation that is used for TOJ is based on later integrative processes.

Differential effects of visual-spatial attention on response latency and temporal-order judgment

Theorists from both classical structuralism and modern attention research have claimed that attention to a sensory stimulus enhances processing speed. However, they have used different operations to measure this effect, viz., temporal-order judgment (TOJ) and reaction-time (RT) measurement. We report two experiments that compared the effect of a spatial cue on RT and TOJ. Experiment 1 demonstrated that a nonmasked, peripheral cue (the brief brightening of a box) affected both RT and TOJ. However, the former effect was significantly larger than the latter. A masked cue had a smaller, but reliable, effect on TOJ. In Experiment 2, the effects of a masked cue on RT and TOJ were compared under identical stimulus conditions. While the cue had a strong effect on RT, it left TOJ unaffected. These results suggest that a spatial cue may have dissociable effects on response processes and the processes that lead to a conscious percept. Implications for the concept of direct parameter specification and for theories of visual attention are discussed.

Apparent distance reduction with moving stimuli (Tandem Effect): evidence for an attention-shifting model

When two vertical rods move through a horizontal window in close succession, the Tandem Effect can be observed. It consists of a spatial illusion (distance between the rods looking smaller than it actually is) and a temporal illusion (under certain conditions both rods are seen simultaneously in the window, though the first rod has left the window before the second rod enters it). We report six experiments that explored the distance-reduction illusion and tested an attentional model of the effect. It assumes that attention is initially focused on the first rod and then shifted to the second, when it enters the window. The percept of the pair of rods is integrated from the first rod's position at the beginning, and the second rod's position at the end, of the focus shift. Consequently their subjective distance will be smaller than their physical distance by the distance that they travel during the focus shift. Experiments 1 and 2 established the Tandem Effect as an empirical phenomenon and showed that its size depends on stimulus parameters such as window size and movement speed. Experiments 3-5 tested specific predictions from the attentional model. Experiment 6 examined a further illusion, the Fröhlich Effect, and showed that it can be subsumed under the model. The experiments produced some unexpected effects and some predictions from the model were only partly confirmed. It is shown that the main findings can be combined into two quantitative functions that describe the course of focusing. One implication is that visual attention does not "move" from one object to another; rather all attention shifts originate in the fovea. We discuss several alternative interpretations of our data and show that they are less satisfactory than the attentional model.

Direct parameter specification and the concept of perception

Stimuli that reach the sensory surface may result in perception, or serve to guide action. How are these two potential consequences of sensory stimulation related? I discuss three aspects of this problem. The conceptual aspect concerns the status of the concept of perception in an objective psychology. The methodological aspect pertains to the problem of how psychophysics is related to the assessment of performance measures. The functional aspect relates to the function(s) of perception for action control. I argue that (a) conceptually, the term perception belongs to a different level of description than the constructs of information-processing models: (b) methodologically, psychophysical judgements and performance measures are not necessarily converging operations: (c) functionally, sensory information can be used for the control of action without perception as a mediating stage (direct parameter specification). Taken together, this suggests that perception should be conceptualized not as a processing stage, but as a class of actions that serve to establish and update an internal representation of the environment.