Breakdown of disordered media by surface loads

We model an interface layer connecting two parts of a solid body by N parallel elastic springs connecting two rigid blocks. We load the system by a shear force acting on the top side. The springs have equal stiffness but are ruptured randomly when the load reaches a critical value. For the considered system, we calculate the shear modulus, G, as a function of the order parameter, \phi, describing the state of damage, and also the ``spalled'' material (burst) size distribution. In particular, we evaluate the relation between the damage parameter and the applied force and explore the behaviour in the vicinity of material breakdown. Using this simple model for material breakdown, we show that damage, caused by applied shear forces, is analogous to a first-order phase transition. The scaling behaviour of G with \phi is explored analytically and numerically, close to \phi=0 and \phi=1 and in the vicinity of \phi_c, when the shear load is close but below the threshold force that causes material breakdown. Our model calculation represents a first approximation of a system subject to wear induced loads.Comment: 15 pages, 7 figure

Topoisomerase 1 inhibits MYC promoter activity by inducing G-quadruplex formation

We have investigated the function of human topoisomerase 1 (TOP1) in regulation of G-quadruplex (G4) formation in the Pu27 region of the MYC P1 promoter. Pu27 is among the best characterized G4 forming sequences in the human genome and it is well known that promoter activity is inhibited upon G4 formation in this region. We found that TOP1 downregulation stimulated transcription from a promoter with wildtype Pu27 but not if the G4 motif in Pu27 was interrupted by mutation(s). The effect was not specific to the MYC promoter and similar results were obtained for the G4 forming promoter element WT21. The other major DNA topoisomerases with relaxation activity, topoisomerases 2α and β, on the other hand, did not affect G4 dependent promoter activity. The cellular studies were supported by in vitro investigations demonstrating a high affinity of TOP1 for wildtype Pu27 but not for mutant sequences unable to form G4. Moreover, TOP1 was able to induce G4 formation in Pu27 inserted in double stranded plasmid DNA in vitro. This is the first time TOP1 has been demonstrated capable of inducing G4 formation in double stranded DNA and of influencing G4 formation in cells

Involuntary Monitoring of Sound Signals in Noise Is Reflected in the Human Auditory Evoked N1m Response

Constant sound sequencing as operationalized by repeated stimulation with tones of the same frequency has multiple effects. On the one hand, it activates mechanisms of habituation and refractoriness, which are reflected in the decrease of response amplitude of evoked responses. On the other hand, the constant sequencing acts as spectral cueing, resulting in tones being detected faster and more accurately. With the present study, by means of magnetoencephalography, we investigated the impact of repeated tone stimulation on the N1m auditory evoked fields, while listeners were distracted from the test sounds. We stimulated subjects with trains of either four tones of the same frequency, or with trains of randomly assigned frequencies. The trains were presented either in a silent or in a noisy background. In silence, the patterns of source strength decline originating from repeated stimulation suggested both, refractoriness as well as habituation as underlying mechanisms. In noise, in contrast, there was no indication of source strength decline. Furthermore, we found facilitating effects of constant sequencing regarding the detection of the single tones as indexed by a shortening of N1m latency. We interpret our findings as a correlate of a bottom-up mechanism that is constantly monitoring the incoming auditory information, even when voluntary attention is directed to a different modality

Simulation of a suite of generic long-pulse neutron instruments to optimize the time structure of the European Spallation Source

We here describe the result of simulations of 15 generic neutron instruments for the long pulsed European Spallation Source. All instruments have been simulated for 20 different settings of the source time structure, corresponding to pulse lengths between 1 ms and 2 ms; and repetition frequencies between 10 Hz and 25 Hz. The relative change in performance with time structure is given for each instrument, and an unweighted average is calculated. The performance of the instrument suite is proportional to a the peak flux and b the duty cycle to a power of approximately 0.3. This information is an important input to determining the best accelerator parameters. In addition, we find that in our simple guide systems, most neutrons reaching the sample originate from the central 3 5 cm of the moderator. This result can be used as an input in later optimization of the moderator design. We discuss the relevance and validity of defining a single figure of merit for a full facility and compare with evaluations of the individual instrument classes

Risk Factors for Being Seronegative following SARS-CoV-2 Infection in a Large Cohort of Health Care Workers in Denmark

Most individuals seroconvert after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but being seronegative is observed in 1 to 9%. We aimed to investigate the risk factors associated with being seronegative following PCR-confirmed SARS-CoV-2 infection. In a prospective cohort study, we screened health care workers (HCW) in the Capital Region of Denmark for SARS-CoV-2 antibodies. We performed three rounds of screening from April to October 2020 using an enzyme-linked immunosorbent assay (ELISA) method targeting SARS-CoV-2 total antibodies. Data on all participants’ PCR for SARS-CoV-2 RNA were captured from national registries. The Kaplan-Meier method and Cox proportional hazards models were applied to investigate the probability of being seronegative and the related risk factors, respectively. Of 36,583 HCW, 866 (2.4%) had a positive PCR before or during the study period. The median (interquartile range [IQR]) age of 866 HCW was 42 (31 to 53) years, and 666 (77%) were female. After a median of 132 (range, 35 to 180) days, 21 (2.4%) of 866 were seronegative. In a multivariable model, independent risk factors for being seronegative were self-reported asymptomatic or mild infection hazard ratio (HR) of 6.6 (95% confidence interval [CI], 2.6 to 17; P < 0.001) and body mass index (BMI) of ≥30, HR 3.1 (95% CI, 1.1 to 8.8; P = 0.039). Only a few (2.4%) HCW were not seropositive. Asymptomatic or mild infection as well as a BMI above 30 were associated with being seronegative. Since the presence of antibodies against SARS-CoV-2 reduces the risk of reinfection, efforts to protect HCW with risk factors for being seronegative may be needed in future COVID-19 surges. IMPORTANCE Most individuals seroconvert after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but negative serology is observed in 1 to 9%. We found that asymptomatic or mild infection as well as a BMI above 30 were associated with being seronegative. Since the presence of antibodies against SARS-CoV-2 reduces the risk of reinfection, efforts to protect HCW with risk factors for being seronegative may be needed in future COVID-19 surges

Improving model construction of profile HMMs for remote homology detection through structural alignment

<p>Abstract</p> <p>Background</p> <p>Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the <it>Twilight Zone</it>, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.</p> <p>Results</p> <p>We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test.</p> <p>Conclusion</p> <p>We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.</p

Danish study of Non-Invasive testing in Coronary Artery Disease 2 (Dan-NICAD 2): study design for a controlled study of diagnostic accuracy

Background: Coronary computed tomography angiography (CTA) is the preferred primary diagnostic modality when examining patients with low to intermediate pre-test probability of coronary artery disease (CAD). Only 20-30% of these have potentially obstructive CAD. Because of the relatively poor positive predictive value of coronary CTA, unnecessary invasive coronary angiographies (ICA) are conducted with the costs and risks associated with the procedure. Hence, an optimized diagnostic CAD algorithm may reduce the numbers of ICAs not followed by revascularization. The Dan-NICAD 2 study has three equivalent main aims: 1) to examine the diagnostic precision of a sound based diagnostic algorithm, The CADScor®System (Acarix A/S, Denmark), in patients with a low to intermediate pre-test risk of CAD referred to a primary examination by coronary CTA. We hypothesize that the CADScor®System provides better stratification prior to coronary CTA than clinical risk stratification scores alone. 2) to compare the diagnostic accuracy of 3 Tesla cardiac magnetic resonance imaging (3T CMRI), 82Rubidium positron emission tomography (82Rb-PET) and CT-derived fractional flow reserve (FFRCT) in patients where obstructive CAD cannot be ruled out by coronary CTA using ICA fractional flow reserve (FFR) as reference standard. 3) to compare the diagnostic performance of quantitative flow ratio (QFR) and ICA-FFR in patients with low to intermediate pre-test probability of CAD using 82Rb-PET as reference standard. Methods/design: Dan-NICAD 2 is a prospective, multicenter, cross-sectional study including approximately 2,000 patients with low to intermediate pre-test probability of CAD and without previous history of CAD. Patients are referred to CTA because of symptoms suggestive of CAD, as evaluated by a cardiologist. Patient interviews, sound recordings, and blood samples are obtained in connection with the coronary CTA. If coronary CTA does not rule-out obstructive CAD, patients will be examined by both 3T CMRI, 82Rb-PET, FFRCT, ICA and FFR. Reference standard is ICA-FFR. Obstructive CAD is defined as an FFR ≤0.80 or as high-grade stenosis (>90 % diameter stenosis) by visual assessment. Diagnostic performance will be evaluated as sensitivity, specificity, predictive values, likelihood ratios, calibration, and discrimination. Enrolment started January 2018 and is expected to be completed by June 2020. Patients are followed for 10 years after inclusion. Discussion: The results of the Dan-NICAD 2 study are expected to contribute to the improvement of diagnostic strategies for patients suspected of CAD in three different steps; risk-stratification prior to coronary CTA, diagnostic strategy after coronary CTA and invasive wireless QFR analysis as an alternative to ICA-FFR. Study registration: Clinicaltrials.gov identifier, NCT03481712. Registered on January 25th 2018.Aarhus UniversityHealth Research Fund of Central Denmark RegionAcarix A/

Molecular networks of human muscle adaptation to exercise and age

Physical activity and molecular ageing presumably interact to precipitate musculoskeletal decline in humans with age. Herein, we have delineated molecular networks for these two major components of sarcopenic risk using multiple independent clinical cohorts. We generated genome-wide transcript profiles from individuals (n = 44) who then undertook 20 weeks of supervised resistance-exercise training (RET). Expectedly, our subjects exhibited a marked range of hypertrophic responses (3% to +28%), and when applying Ingenuity Pathway Analysis (IPA) up-stream analysis to ~580 genes that co-varied with gain in lean mass, we identified rapamycin (mTOR) signaling associating with growth (P = 1.4×10−30). Paradoxically, those displaying most hypertrophy exhibited an inhibited mTOR activation signature, including the striking down-regulation of 70 rRNAs. Differential analysis found networks mimicking developmental processes (activated all-trans-retinoic acid (ATRA, Z-score = 4.5; P = 6×10−13) and inhibited aryl-hydrocarbon receptor signaling (AhR, Z-score = −2.3; P = 3×10−7)) with RET. Intriguingly, as ATRA and AhR gene-sets were also a feature of endurance exercise training (EET), they appear to represent “generic” physical activity responsive gene-networks. For age, we found that differential gene-expression methods do not produce consistent molecular differences between young versus old individuals. Instead, utilizing two independent cohorts (n = 45 and n = 52), with a continuum of subject ages (18–78 y), the first reproducible set of age-related transcripts in human muscle was identified. This analysis identified ~500 genes highly enriched in post-transcriptional processes (P = 1×10−6) and with negligible links to the aforementioned generic exercise regulated gene-sets and some overlap with ribosomal genes. The RNA signatures from multiple compounds all targeting serotonin, DNA topoisomerase antagonism, and RXR activation were significantly related to the muscle age-related genes. Finally, a number of specific chromosomal loci, including 1q12 and 13q21, contributed by more than chance to the age-related gene list (P = 0.01–0.005), implying possible epigenetic events. We conclude that human muscle age-related molecular processes appear distinct from the processes regulated by those of physical activity