Nevin Manimala

Sci Rep. 2022 Jan 7;12(1):98. doi: 10.1038/s41598-021-04037-6.

ABSTRACT

In this paper, we analyze a massive dataset with registers of the movement of vehicles in the bus rapid transit system Metrobús in Mexico City from February 2020 to April 2021. With these records and a division of the system into 214 geographical regions (segments), we characterize the vehicles’ activity through the statistical analysis of speeds in each zone. We use the Kullback-Leibler distance to compare the movement of vehicles in each segment and its evolution. The results for the dynamics in different zones are represented as a network where nodes define segments of the system Metrobús and edges describe similarity in the activity of vehicles. Community detection algorithms in this network allow the identification of patterns considering different levels of similarity in the distribution of speeds providing a framework for unsupervised classification of the movement of vehicles. The methods developed in this research are general and can be implemented to describe the activity of different transportation systems with detailed records of the movement of users or vehicles.

PMID:34997045 | DOI:10.1038/s41598-021-04037-6

Sci Rep. 2022 Jan 7;12(1):171. doi: 10.1038/s41598-021-04034-9.

ABSTRACT

The configuration of proteins is critical for their biochemical behavior. Mechanical stresses that act on them can affect their behavior leading to the development of decease. The von Willebrand factor (vWF) protein circulating with the blood loses its efficacy when it undergoes non-physiological hemodynamic stresses. While often overlooked, extensional stresses can affect the structure of vWF at much lower stress levels than shear stresses. The statistical distribution of extensional stress as it applies on models of the vWF molecule within turbulent flow was examined here. The stress on the molecules of the protein was calculated with computations that utilized a Lagrangian approach for the determination of the molecule trajectories in the flow filed. The history of the stresses on the proteins was also calculated. Two different flow fields were considered as models of typical flows in cardiovascular mechanical devises, one was a Poiseuille flow and the other was a Poiseuille-Couette flow field. The data showed that the distribution of stresses is important for the design of blood flow devices because the average stress can be below the critical value for protein damage, but tails of the distribution can be outside the critical stress regime.

PMID:34997036 | DOI:10.1038/s41598-021-04034-9

Sci Rep. 2022 Jan 7;12(1):200. doi: 10.1038/s41598-021-04011-2.

ABSTRACT

Isotopic techniques have been used to study phenomena in the geological, environmental, and ecological sciences. For example, isotopic values of multiple elements elucidate the pathways energy and nutrients take in the environment. Isoscapes interpolate isotopic values across a geographical surface and are used to study environmental processes in space and time. Thus, isoscapes can reveal ecological shifts at local scales, and show distribution thresholds in the wider environment at the macro-scale. This study demonstrates a further application of isoscapes, using soil isoscapes of ¹³C/¹²C and ¹⁵N/¹⁴N as an environmental baseline, to understand variation in trophic ecology across a population of Eurasian badgers (Meles meles) at a regional scale. The use of soil isoscapes reduced error, and elevated the statistical signal, where aggregated badger hairs were used, and where individuals were identified using genetic microarray analysis. Stable isotope values were affected by land-use type, elevation, and meteorology. Badgers in lowland habitats had diets richer in protein and were adversely affected by poor weather conditions in all land classes. It is concluded that soil isoscapes are an effective way of reducing confounding biases in macroscale, isotopic studies. The method elucidated variation in the trophic and spatial ecology of economically important taxa at a landscape level. These results have implications for the management of badgers and other carnivores with omnivorous tendencies in heterogeneous landscapes.

PMID:34997035 | DOI:10.1038/s41598-021-04011-2

Sci Rep. 2022 Jan 7;12(1):78. doi: 10.1038/s41598-021-03902-8.

ABSTRACT

Optical imaging is paramount for disease diagnosis and to access its progression over time. The proposed optical flow imaging (VFC/iLIFE) is a powerful technique that adds new capabilities (3D volume visualization, organelle-level resolution, and multi-organelle screening) to the existing system. Unlike state-of-the-art point-illumination-based biomedical imaging techniques, the sheet-based VFC technique is capable of single-shot sectional visualization, high throughput interrogation, real-time parameter estimation, and instant volume reconstruction with organelle-level resolution of live specimens. The specimen flow system was realized on a multichannel (Y-type) microfluidic chip that enables visualization of organelle distribution in several cells in-parallel at a relatively high flow-rate (2000 nl/min). The calibration of VFC system requires the study of point emitters (fluorescent beads) at physiologically relevant flow-rates (500-2000 nl/min) for determining flow-induced optical aberration in the system point spread function (PSF). Subsequently, the recorded raw images and volumes were computationally deconvolved with flow-variant PSF to reconstruct the cell volume. High throughput investigation of the mitochondrial network in HeLa cancer cell was carried out at sub-cellular resolution in real-time and critical parameters (mitochondria count and size distribution, morphology, entropy, and cell strain statistics) were determined on-the-go. These parameters determine the physiological state of cells, and the changes over-time, revealing the metastatic progression of diseases. Overall, the developed VFC system enables real-time monitoring of sub-cellular organelle organization at a high-throughput with high-content capacity.

PMID:34997009 | DOI:10.1038/s41598-021-03902-8

Sci Rep. 2022 Jan 7;12(1):127. doi: 10.1038/s41598-021-03945-x.

ABSTRACT

Identification of new genetic markers may improve the prediction of colorectal cancer prognosis. Our objective was to examine genome-wide associations of germline genetic variants with disease-specific survival in an analysis of 16,964 cases of colorectal cancer. We analyzed genotype and colorectal cancer-specific survival data from a consortium of 15 studies. Approximately 7.5 million SNPs were examined under the log-additive model using Cox proportional hazards models, adjusting for clinical factors and principal components. Additionally, we ran secondary analyses stratifying by tumor site and disease stage. We used a genome-wide p-value threshold of 5 × 10^-8 to assess statistical significance. No variants were statistically significantly associated with disease-specific survival in the full case analysis or in the stage-stratified analyses. Three SNPs were statistically significantly associated with disease-specific survival for cases with tumors located in the distal colon (rs698022, HR = 1.48, CI 1.30-1.69, p = 8.47 × 10^-9) and the proximal colon (rs189655236, HR = 2.14, 95% CI 1.65-2.77, p = 9.19 × 10^-9 and rs144717887, HR = 2.01, 95% CI 1.57-2.58, p = 3.14 × 10^-8), whereas no associations were detected for rectal tumors. Findings from this large genome-wide association study highlight the potential for anatomical-site-stratified genome-wide studies to identify germline genetic risk variants associated with colorectal cancer-specific survival. Larger sample sizes and further replication efforts are needed to more fully interpret these findings.

PMID:34996992 | DOI:10.1038/s41598-021-03945-x

Sci Rep. 2022 Jan 7;12(1):70. doi: 10.1038/s41598-021-03878-5.

ABSTRACT

Peritoneal dialysis (PD) catheter exit-site care is critically important for the prevention of catheter-related infections (CRIs) and subsequent peritonitis. The postoperative management of the site is particularly essential because it has an open wound that is always adjacent to a PD catheter tube. This study aimed to examine the effectiveness of negative-pressure wound therapy (NPWT) for postoperative PD catheter exit sites. Thirty patients with end-stage renal disease who underwent simultaneous PD catheter insertion and exit-site formation were randomly assigned to receive NPWT (NPWT group) or conventional dressing (non-NPWT group) for the first seven postoperative days. The exit-site scores on the seventh postoperative day was lower in the NPWT group than in the non-NPWT group (p = 0.0049). Analysis of variance F statistic for the effect of NPWT over 180 days was highly significant (11.482595, p = 0.007). There were no statistically significant differences between the time to first CRI and PD-related peritonitis between the two groups. There was one case of CRI with relapsing peritonitis and catheter loss in the non-NPWT group. These findings demonstrate the association between NPWT and low exit-site score. NPWT can be recommended for the management of PD catheter exit sites in the early postoperative period.

PMID:34996968 | DOI:10.1038/s41598-021-03878-5

Sci Rep. 2022 Jan 7;12(1):250. doi: 10.1038/s41598-021-03755-1.

ABSTRACT

The verification of trace explosives detection systems is often constrained to small sample sets, so it is important to support the significance of the results with statistical analysis. As binary measurements, the trials are assessed using binomial statistics. A method is described based on the probability confidence interval and expressed in terms of the upper confidence interval bound that reports the probability of successful detection and its level of statistical confidence. These parameters provide useful measures of the system’s performance. The propriety of combining statistics for similar tests-for example in trace detection trials of an explosive on multiple surfaces-is examined by statistical tests. The use of normal statistics is commonly applied to binary testing, but the confidence intervals are known to behave poorly in many circumstances, including small sample numbers. The improvement of the normal approximation with increasing sample number is shown not to be substantial for the typical numbers used in this type of explosives detection system testing, and binary statistics are preferred. The methods and techniques described here for testing trace detection can be applied as well to performance testing of explosives detection systems in general.

PMID:34996947 | DOI:10.1038/s41598-021-03755-1

Sci Rep. 2022 Jan 7;12(1):195. doi: 10.1038/s41598-021-03071-8.

ABSTRACT

Workplace settings-both internal and external-can influence how workers are physically active or sedentary. Although research has identified some indoor environmental attributes associated with sitting at work, few studies have examined associations of workplace neighbourhood built-environment attributes with workplace sitting time. We examined the cross-sectional associations of perceived and objective workplace neighbourhood built-environment attributes with sitting time at work and for transport among desk-based workers in Japan. Data were collected from a nationwide online survey. The Abbreviated Neighborhood Environment Walkability Scale (n = 2137) and Walk Score® (for a subsample of participants; n = 1163) were used to assess perceived and objective built-environment attributes of workplace neighbourhoods. Self-reported daily average sitting time at work, in cars and in public transport was measured using a Japanese validated questionnaire. Linear regression models estimated the associations of workplace neighbourhood built-environment attributes with sitting time. All perceived workplace neighbourhood built-environment attributes were positively correlated with Walk Score®. However, statistically significant associations with Walk Score® were found for sitting for transport but not for sitting at work. Workers who perceived their workplace neighbourhoods to be more walkable reported a longer time sitting at work and in public transport but a shorter sitting time in cars. Our findings suggest that walkable workplace neighbourhoods may discourage longer car use but have workplaces where workers spend a long time sitting at work. The latter finding further suggests that there may be missed opportunities for desk-based workers to reduce sitting time. Future workplace interventions to reduce sitting time may be developed, taking advantage of the opportunities to take time away from work in workplace neighbourhoods.

PMID:34996917 | DOI:10.1038/s41598-021-03071-8

Sci Rep. 2022 Jan 7;12(1):77. doi: 10.1038/s41598-021-03471-w.

ABSTRACT

Although the function of the BRCA1 gene has been extensively studied, the relationship between BRCA1 gene expression and tumor aggressiveness remains controversial in sporadic breast cancers. Because the BRCA1 protein is known to regulate estrogen signaling, we selected microarray data of ER⁺ breast cancers from the GEO public repository to resolve previous conflicting findings. The BRCA1 gene expression level in highly proliferative luminal B tumors was shown to be higher than that in luminal A tumors. Survival analysis using a cure model indicated that patients of early ER⁺ breast cancers with high BRCA1 expression developed rapid distant metastasis. In addition, the proliferation marker genes MKI67 and PCNA, which are characteristic of aggressive tumors, were also highly expressed in patients with high BRCA1 expression. The associations among high BRCA1 expression, high proliferation marker expression, and high risk of distant metastasis emerged in independent datasets, regardless of tamoxifen treatment. Tamoxifen therapy could improve the metastasis-free fraction of high BRCA1 expression patients. Our findings link BRCA1 expression with proliferation and possibly distant metastasis via the ER signaling pathway. We propose a testable hypothesis based on these consistent results and offer an interpretation for our reported associations.

PMID:34996912 | DOI:10.1038/s41598-021-03471-w

Sci Rep. 2022 Jan 7;12(1):118. doi: 10.1038/s41598-021-02808-9.

ABSTRACT

Integrating the spatiotemporal information acquired from the highly dynamic world around us is essential to navigate, reason, and decide properly. Although this is particularly important in a face-to-face conversation, very little research to date has specifically examined the neural correlates of temporal integration in dynamic face perception. Here we present statistically robust observations regarding the brain activations measured via electroencephalography (EEG) that are specific to the temporal integration. To that end, we generate videos of neutral faces of individuals and non-face objects, modulate the contrast of the even and odd frames at two specific frequencies ([Formula: see text] and [Formula: see text]) in an interlaced manner, and measure the steady-state visual evoked potential as participants view the videos. Then, we analyze the intermodulation components (IMs: ([Formula: see text]), a linear combination of the fundamentals with integer multipliers) that consequently reflect the nonlinear processing and indicate temporal integration by design. We show that electrodes around the medial temporal, inferior, and medial frontal areas respond strongly and selectively when viewing dynamic faces, which manifests the essential processes underlying our ability to perceive and understand our social world. The generation of IMs is only possible if even and odd frames are processed in succession and integrated temporally, therefore, the strong IMs in our frequency spectrum analysis show that the time between frames (1/60 s) is sufficient for temporal integration.

PMID:34996892 | DOI:10.1038/s41598-021-02808-9