Sampling frequency influences sample entropy of kinematics during walking

Sample entropy (SaEn) has been used to assess the regularity of lower limb joint angles during walking. However, changing sampling frequency and the number of included strides can potentially affect the sample entropy. The present study investigated the effect of sample frequency and the number of included strides on the calculations of SaEn in joint angle signals recorded during treadmill walking. Eleven subjects walked at their preferred walking speed for 10 minutes, and SaEn was calculated on sagittal plane hip, knee and ankle angle signals extracted from 50, 100, 200, 300 and 400 strides at sampling frequencies of 60, 120, 240 and 480Hz. Increase in sampling frequency decreased the SaEn significantly for the three joints. The number of included strides had no effect on the SaEn calculated on the hip joint angle and only limited effect on the SaEn calculated on the knee and ankle joint signals. The present study suggests that the number of data points within each stride to a greater extent determines the size of the SaEn compared to the number of strides and emphasizes the use of a fixed number of data points within each stride when applying SaEn to lower limb joint angles during walking

On the Calculation of Sample Entropy Using Continuous and Discrete Human Gait Data

Sample entropy (SE) has relative consistency using biologically-derived, discrete data \u3e500 data points. For certain populations, collecting this quantity is not feasible and continuous data has been used. The effect of using continuous versus discrete data on SE is unknown, nor are the relative effects of sampling rate and input parameters m (comparison vector length) and r(tolerance). Eleven subjects walked for 10-minutes and continuous joint angles (480 Hz) were calculated for each lower-extremity joint. Data were downsampled (240, 120, 60 Hz) and discrete range-of-motion was calculated. SE was quantified for angles and range-of-motion at all sampling rates and multiple combinations of parameters. A differential relationship between joints was observed between range-of-motion and joint angles. Range-of-motion SE showed no difference; whereas, joint angle SE significantly decreased from ankle to knee to hip. To confirm findings from biological data, continuous signals with manipulations to frequency, amplitude, and both were generated and underwent similar analysis to the biological data. In general, changes to m, r, and sampling rate had a greater effect on continuous compared to discrete data. Discrete data was robust to sampling rate and m. It is recommended that different data types not be compared and discrete data be used for SE

How much of protein sequence space has been explored by life on Earth?

We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency

Polygalacturonase from Sitophilus oryzae: Possible horizontal transfer of a pectinase gene from fungi to weevils

Endo-polygalacturonase, one of the group of enzymes known collectively as pectinases, is widely distributed in bacteria, plants and fungi. The enzyme has also been found in several weevil species and a few other insects, such as aphids, but not in Drosophila melanogaster, Anopheles gambiae, or Caenorhabditis elegans or, as far as is known, in any more primitive animal species. What, then, is the genetic origin of the polygalacturonases in weevils? Since some weevil species harbor symbiotic microorganisms, it has been suggested, reasonably, that the symbionts' genomes of both aphids and weevils, rather than the insects' genomes, could encode polygalacturonase. We report here the cloning of a cDNA that encodes endo-polygalacturonase in the rice weevil, Sitophilus oryzae (L.), and investigations based on the cloned cDNA. Our results, which include analysis of genes in antibiotic-treated rice weevils, indicate that the enzyme is, in fact, encoded by the insect genome. Given the apparent absence of the gene in much of the rest of the animal kingdom, it is therefore likely that the rice weevil polygalacturonase gene was incorporated into the weevil's genome by horizontal transfer, possibly from a fungus

Pectinmethylesterase from the rice weevil, Sitophilus oryzae: cDNA isolation and sequencing, genetic origin, and expression of the recombinant enzyme

A cDNA clone encoding pectinmethylesterase of the rice weevil, Sitophilus oryzae (L.) has been isolated and sequenced. The cDNA clone was expressed in cultured insect cells and active pectinmethylesterase was purified from the culture medium, thus confirming that the cDNA encodes pectinmethylesterase. In situ hybridization indicated that the enzyme's transcript was present in the midgut. Weevils treated with tetracycline so that they lack genes of known symbiotic organisms still contained the pectinmethylesterase gene, indicating that the gene is encoded by the rice weevil genome. The rice weevil enzyme is most similar in sequence to bacterial pectinmethylesterases. Given this and the enzyme's apparently rather general absence from animal species, we suggest the possibility that this gene was transferred horizontally to an ancient weevil, possibly from a bacterial symbiont, and exists in Sitophilus species now as a result of that ancestral horizontal transfer

Characterization of Intact Proviruses in Blood and Lymph Node from HIV-Infected Individuals Undergoing Analytical Treatment Interruption.

The role of lymphoid tissue as a potential source of HIV-1 rebound following interruption of antiretroviral therapy (ART) is uncertain. To address this issue, we compared the latent viruses obtained from CD4+ T cells in peripheral blood and lymph nodes to viruses emerging during treatment interruption. Latent viruses were characterized by sequencing near-full-length (NFL) proviral DNA and env from viral outgrowth assays (VOAs). Five HIV-1-infected individuals on ART were studied, four of whom participated in a clinical trial of a TLR9 agonist that included an analytical treatment interruption. We found that 98% of intact or replication-competent clonal sequences overlapped between blood and lymph node. In contrast, there was no overlap between 205 latent reservoir and 125 rebound sequences in the four individuals who underwent treatment interruption. However, rebound viruses could be accounted for by recombination. The data suggest that CD4+ T cells carrying latent viruses circulate between blood and lymphoid tissues in individuals on ART and support the idea that recombination may play a role in the emergence of rebound viremia.IMPORTANCE HIV-1 persists as a latent infection in CD4+ T cells that can be found in lymphoid tissues in infected individuals during ART. However, the importance of this tissue reservoir and its contribution to viral rebound upon ART interruption are not clear. In this study, we sought to compare latent HIV-1 from blood and lymph node CD4+ T cells from five HIV-1-infected individuals. Further, we analyzed the contribution of lymph node viruses to viral rebound. We observed that the frequencies of intact proviruses were the same in blood and lymph node. Moreover, expanded clones of T cells bearing identical proviruses were found in blood and lymph node. These latent reservoir sequences did not appear to be the direct origin of rebound virus. Instead, latent proviruses were found to contribute to the rebound compartment by recombination

Optimizing active surveillance strategies to balance the competing goals of early detection of grade progression and minimizing harm from biopsies

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142555/1/cncr31101.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142555/2/cncr31101_am.pd

Roosting Habitat Use by Sandhill Cranes and Waterfowl on the North and South Platte Rivers in Nebraska

Migration ecology and habitat use of spring migrating birds using the Central Platte River is a well-explored topic, yet less is known about use of the North and South Platte rivers (NSPR) in western Nebraska. The efficiency and effectiveness of conservation efforts in the NSPR could be greatly improved with access to information about where and when birds roost and landscape prioritization tools. We used aerial surveys to determine population distribution and migration phenology of sandhill cranes Antigone canadensis, Canada geese Branta canadensis, and ducks using the NSPR for roosting during the mid-February to mid-April spring migration. We used these data and geospatial information to identify important river reaches for these species and habitat covariates that discriminate between those used at lower and higher densities. We found that sandhill cranes and waterfowl generally roosted in different segments of the NSPR and, subsequently, different factors were associated with high densities. Sandhill crane density was positively correlated with distance from obstructions greater than 1 m high and negatively correlated with area of unvegetated sandbar within 1 km. Density of Canada geese and ducks was high in segments positively associated with wetland and sand pit habitats. Human disturbance variables such as roads and bridges in this rural region had little effect on identification of roosting areas used by high densities of all groups. On the basis of our results, habitat conservation efforts that specifically target sandhill cranes will not have similar positive effects on waterfowl use and distribution in the NSPR. Our identification of the most important river segments should allow managers to better target land acquisition or management resources to areas that will have the greatest effect on either waterfowl or sandhill cranes during spring migration

Human Breast Milk and Antiretrovirals Dramatically Reduce Oral HIV-1 Transmission in BLT Humanized Mice

Currently, over 15% of new HIV infections occur in children. Breastfeeding is a major contributor to HIV infections in infants. This represents a major paradox in the field because in vitro, breast milk has been shown to have a strong inhibitory effect on HIV infectivity. However, this inhibitory effect has never been demonstrated in vivo. Here, we address this important paradox using the first humanized mouse model of oral HIV transmission. We established that reconstitution of the oral cavity and upper gastrointestinal (GI) tract of humanized bone marrow/liver/thymus (BLT) mice with human leukocytes, including the human cell types important for mucosal HIV transmission (i.e. dendritic cells, macrophages and CD4+ T cells), renders them susceptible to oral transmission of cell-free and cell-associated HIV. Oral transmission of HIV resulted in systemic infection of lymphoid and non-lymphoid tissues that is characterized by the presence of HIV RNA in plasma and a gradual decline of CD4+ T cells in peripheral blood. Consistent with infection of the oral cavity, we observed virus shedding into saliva. We then evaluated the role of human breast milk on oral HIV transmission. Our in vivo results demonstrate that breast milk has a strong inhibitory effect on oral transmission of both cell-free and cell-associated HIV. Finally, we evaluated the effect of antiretrovirals on oral transmission of HIV. Our results show that systemic antiretrovirals administered prior to exposure can efficiently prevent oral HIV transmission in BLT mice

Sickle Cell Disease Subjects Have a Distinct Abnormal Autonomic Phenotype Characterized by Peripheral Vasoconstriction With Blunted Cardiac Response to Head-Up Tilt

In sickle cell disease (SCD), prolonged capillary transit times, resulting from reduced peripheral blood flow, increase the likelihood of rigid red cells entrapment in the microvasculature, predisposing to vaso-occlusive crisis. Since changes in peripheral flow are mediated by the autonomic nervous system (ANS), we tested the hypothesis that the cardiac and peripheral vascular responses to head-up tilt (HUT) are abnormal in SCD. Heart rate, respiration, non-invasive continuous blood pressure and finger photoplethysmogram (PPG) were monitored before, during, and after HUT in SCD, anemic controls and healthy subjects. Percent increase in heart rate from baseline was used to quantify cardiac ANS response, while percent decrease in PPG amplitude represented degree of peripheral vasoconstriction. After employing cluster analysis to determine threshold levels, the HUT responses were classified into four phenotypes: (CP) increased heart rate and peripheral vasoconstriction; (C) increased heart rate only; (P) peripheral vasoconstriction only; and (ST) subthreshold cardiac and peripheral vascular responses. Multinomial logistic regression (MLR) was used to relate these phenotypic responses to various parameters representing blood properties and baseline cardiovascular activity. The most common phenotypic response, CP, was found in 82% of non-SCD subjects, including those with chronic anemia. In contrast, 70% of SCD subjects responded abnormally to HUT: C-phenotype = 22%, P-phenotype = 37%, or ST-phenotype = 11%. MLR revealed that the HUT phenotypes were significantly associated with baseline cardiac parasympathetic activity, baseline peripheral vascular variability, hemoglobin level and SCD diagnosis. Low parasympathetic activity at baseline dramatically increased the probability of belonging to the P-phenotype in SCD subjects, even after adjusting for hemoglobin level, suggesting a characteristic autonomic dysfunction that is independent of anemia. Further analysis using a mathematical model of heart rate variability revealed that the low parasympathetic activity in P-phenotype SCD subjects was due to impaired respiratory-cardiac coupling rather than reduced cardiac baroreflex sensitivity. By having strong peripheral vasoconstriction without compensatory cardiac responses, P-phenotype subjects may be at increased risk for vaso-occlusive crisis. The classification of autonomic phenotypes based on HUT response may have potential use for guiding therapeutic interventions to alleviate the risk of adverse outcomes in SCD