Search

Organ segmentation has become a preliminary task for computer-aided intervention, diagnosis, radiation therapy, and critical robotic surgery. Automatic organ segmentation from medical images is a challenging task due to the inconsistent shape and size of different organs. Besides this, low contrast at the edges of organs due to similar types of tissue confuses the network's ability to segment the contour of organs properly. In this paper, we propose a novel convolution neural network based uncertainty-driven boundary-refined segmentation network (UDBRNet) that segments the organs from CT images. The CT images are segmented first and produce multiple segmentation masks from multi-line segmentation decoder. Uncertain regions are identified from multiple masks and the boundaries of the organs are refined based on uncertainty data. Our method achieves remarkable performance, boasting dice accuracies of 0.80, 0.95, 0.92, and 0.94 for Esophagus, Heart, Trachea, and Aorta respectively on the SegThor dataset, and 0.71, 0.89, 0.85, 0.97, and 0.97 for Esophagus, Spinal Cord, Heart, Left-Lung, and Right-Lung respectively on the LCTSC dataset. These results demonstrate the superiority of our uncertainty-driven boundary refinement technique over state-of-the-art segmentation networks such as UNet, Attention UNet, FC-denseNet, BASNet, UNet++, R2UNet, TransUNet, and DS-TransUNet. UDBRNet presents a promising network for more precise organ segmentation, particularly in challenging, uncertain conditions. The source code of our proposed method will be available at https://github.com/riadhassan/UDBRNet., Competing Interests: NO authors have competing interests., (Copyright: © 2024 Hassan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The purpose of this study was to characterize changes in cortical activity and connectivity in stroke survivors when vibration is applied to the wrist flexor tendons during a visuomotor tracking task. Data were collected from 10 chronic stroke participants and 10 neurologically-intact controls while tracking a target through a figure-8 pattern in the horizontal plane. Electroencephalography (EEG) was used to measure cortical activity (beta band desynchronization) and connectivity (beta band task-based coherence) with movement kinematics and performance error also being recorded during the task. All participants came into our lab on two separate days and performed three blocks (16 trials each, 48 total trials) of tracking, with the middle block including vibration or sham applied at the wrist flexor tendons. The order of the sessions (Vibe vs. Sham) was counterbalanced across participants to prevent ordering effects. During the Sham session, cortical activity increased as the tracking task progressed (over blocks). This effect was reduced when vibration was applied to controls. In contrast, vibration increased cortical activity during the vibration period in participants with stroke. Cortical connectivity increased during vibration, with larger effect sizes in participants with stroke. Changes in tracking performance, standard deviation of hand speed, were observed in both control and stroke groups. Overall, EEG measures of brain activity and connectivity provided insight into effects of vibration on brain control of a visuomotor task. The increases in cortical activity and connectivity with vibration improved patterns of activity in people with stroke. These findings suggest that reactivation of normal cortical networks via tendon vibration may be useful during physical rehabilitation of stroke patients., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Snyder et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The eggshell of the fruit fly Drosophila melanogaster is a useful model for understanding the synthesis of a complex extracellular matrix. The eggshell is synthesized during mid-to-late oogenesis by the somatic follicle cells that surround the developing oocyte. We previously reported that female flies mutant for the gene drop-dead (drd) are sterile, but the underlying cause of the sterility remained unknown. In this study, we examined the role of drd in eggshell synthesis. We show that eggs laid by drd mutant females are fertilized but arrest early in embryogenesis, and that the innermost layer of the eggshell, the vitelline membrane, is abnormally permeable to dye in these eggs. In addition, the major vitelline membrane proteins fail to become crosslinked by nonreducible bonds, a process that normally occurs during egg activation following ovulation, as evidenced by their solubility and detection by Western blot in laid eggs. In contrast, the Cp36 protein, which is found in the outer chorion layers of the eggshell, becomes crosslinked normally. To link the drd expression pattern with these phenotypes, we show that drd is expressed in the ovarian follicle cells beginning in mid-oogenesis, and, importantly, that all drd mutant eggshell phenotypes could be recapitulated by selective knockdown of drd expression in the follicle cells. To determine whether drd expression was required for the crosslinking itself, we performed in vitro activation and crosslinking experiments. The vitelline membranes of control egg chambers could become crosslinked either by incubation in hyperosmotic medium, which activates the egg chambers, or by exogenous peroxidase and hydrogen peroxide. In contrast, neither treatment resulted in the crosslinking of the vitelline membrane in drd mutant egg chambers. These results indicate that drd expression in the follicle cells is necessary for vitelline membrane proteins to serve as substrates for peroxidase-mediated cross-linking at the end of oogenesis., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Sheahan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Maintenance of germline function under stress conditions is crucial for species survival. The germ line in many species is especially sensitive to elevated temperature. We have investigated the role of the pocket protein LIN-35 in preserving fertility in Caenorhabditis elegans under moderate temperature stress. We show that lin-35 mutants display several temperature sensitive germline defects, and more severe reductions in brood size at elevated temperatures compared to wild type. This loss of fertility under temperature stress is primarily due to loss of zygotic, but not maternal, LIN-35. Additionally, we have found that expression of LIN-35 is necessary in both the germ line and soma for the preserving fertility under moderate temperature stress. Specifically, while LIN-35 function in the germ line is required for maintaining fertility in hermaphrodites, broad somatic expression of LIN-35 is also necessary for oocyte formation and/or function under moderate temperature stress. Together, our data add to the emerging understanding of the critical role that LIN-35 plays in preserving tissues against stress., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Mikeworth et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Awake craniotomies provide unique and invaluable scientific opportunities for neurophysiological experimentation in consenting human subjects. While such experimentation carries a long history, rigorous reporting of methodologies focusing on synchronizing data across multiple platforms is not universally reported and often not translatable to across operating rooms, facilities, or behavioral tasks. Therefore, here we detail an intraoperative data synchronization methodology designed to work across multiple commercially available platforms to collect behavioral and surgical field videos, electrocorticography, brain stimulation timing, continuous finger joint angles, and continuous finger force production. Our technique was developed to be nonobstructive to operating room (OR) staff and generalizable to a variety of hand-based tasks. We hope that the detailed reporting of our methods will support the scientific rigor and reproducibility of future studies, as well as aid other groups interested in performing related experiments., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Taquet et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: To investigate changes in sociocultural stressors and protective factors, and mental health in Latina mothers before and after the 2016 Republican presidential nomination., Methods: We examined changes in sociocultural stressors, protective factors, and mental health from two prospective cohorts of Latina mothers from interior and border US cities (Nashville, TN, n = 39 and San Diego, CA, ns range = 78-83; 2013-2020)., Results: We identified significant longitudinal increases in depression, anxiety, and perceived stress in the border city, and reductions in protective factors (e.g., optimism, social support, and familism) across sites. Discrimination varied by location, and was associated with higher stress only at baseline in the border city, and with higher anxiety in the interior city at follow-up. Acculturative stress was consistently associated with worse mental health across time points in the border city. Various protective factors were associated with reduced stress and anxiety across time points in both cities., Discussion: We identified decreased mental health at the border city, and reduced protective factors in Latina mothers across both study sites in the years following the 2016 presidential nomination, during a time of shifting sociopolitical climate. We also identify increased acculturative stress and discrimination over time, particularly at the border city. Interventions to maintain and enhance psychosocial protective factors amongst Latina mothers are warranted., Competing Interests: The authors have declared that no competing interests exist.

In the context of economic games, adults sacrifice money to avoid unequal outcomes, showing so-called inequity aversion. Child-friendly adaptations of these games have shown that children, too, show inequity aversion. Moreover, inequity aversion shows a clear developmental trajectory, with young children rejecting only disadvantageously unequal distributions and older children rejecting both disadvantageously and advantageously unequal distributions. However, based on existing work, it is difficult to compare adult and child responses to inequity because (1) adapting economic games to make them child-friendly may importantly alter the dynamics of the fairness interaction and (2) adult work typically uses abstract rewards such as money while work with children typically uses more concrete rewards like candy, stickers or toys. Here we adapted the Inequity Game-a paradigm designed to study children's responses to inequality in isolation from other concerns-to test inequity aversion in adults (N = 104 pairs). We manipulated whether participants made decisions about concrete rewards (candy) or abstract rewards (tokens that could be traded in for money). We found that, like children, adults rejected unequal payoffs in this task. Additionally, we found that reward type mattered: adults rejected disadvantageous-but not advantageous-monetary distributions, yet rejected both disadvantageous and advantageous candy distributions. These findings allow us to draw clearer comparisons across child and adult responses to unfairness and help paint a fuller picture of inequity aversion in humans., Competing Interests: The authors have declared that no competing interests exist.

Introduction: The single-leg heel raise test (SLHR) is commonly used in clinical settings to approximate plantar flexor strength, yet this is neither validated nor supported physiologically. The purposes of this study were to: determine (1) associations between SLHR repetitions, maximal plantar flexor strength, and reductions in strength; and (2) whether sex differences exist in performance of the SLHR., Methods: Twenty-eight young, healthy participants (14 males,14 females, 19-30 years) performed repeated single-leg heel raises to task failure. Pre- and post-task measures included maximal voluntary isometric contractions (MVIC), and voluntary activation and contractile properties of the plantar flexor muscles, assessed using peripheral electrical stimulation of the tibial nerve. Surface electromyography was recorded for the medial and lateral gastrocnemius, soleus, and anterior tibialis muscles., Results: The SLHR resulted in 20.5% reductions in MVIC torque (p<0.001). However, the number of SLHR repetitions was not correlated with either the baseline MVIC (maximal strength; p = 0.979) or the reduction in MVIC following the SLHR (p = 0.23). There were no sex differences in either the number of SLHR repetitions (p = 0.14), baseline MVIC torque (p = 0.198), or the reduction of MVIC (p = 0.14). MVIC decline was positively associated with the reduction in voluntary activation (r = 0.841, p<0.001), but was not associated with the change in twitch amplitude (p = 0.597)., Conclusions: The SLHR was similar in young males and females yet was a poor predictor of maximal plantar flexor strength but evaluates performance fatigability of the lower extremity specific to dynamic contractions. The reduction in maximal strength at task failure was explained by reduced neural drive to the plantar flexor muscles in both males and females., Impact Statement: SLHR performance is not a clinical assessment of plantar flexor strength but assesses dynamic lower extremity fatigability that is similar in males and females. Alternate clinical measures for maximal plantar flexion strength need to be developed., Competing Interests: The authors have declared that no competing interests exist.

Background: Many college students register each semester for courses, leading to productive careers and fulfilled lives. During this time, the students have to manage many stressors stemming from academic, personal, and, sometimes, work lives. Students, who lack appropriate stress management skills, may find it difficult to balance these responsibilities., Objectives: This study examined stress, coping mechanisms, and gender differences in undergraduate students towards the end of the semester., Design and Method: University students (n = 448) enrolled in three different undergraduate exercise science courses were assessed. Two instruments, the Perceived Stress Scale and Brief Cope, were administered during the twelfth week of the semester, four weeks prior to final exams. T-tests were used to detect gender differences for the stress levels and coping strategies., Results: Overall, females indicated higher levels of stress than their male counterparts. Gender differences were evident in both coping dimensions and individual coping strategies used. Females were found to utilize the emotion-focused coping dimension and endorsed the use of four coping strategies more often than males. These included self-distraction, emotional support, instrumental support, and venting., Conclusions: This research adds to the existing literature by illuminating the level of perceived stress and different coping strategies used by undergraduate female and male students. In turn, students may need educational interventions to develop effective and healthy coping strategies to last a lifetime. Faculty and other university officials may want to highlight and understand these various factors to protect the students' wellbeing in their classes., Competing Interests: The authors have declared that no competing interests exist.

One of the central goals of ecology is to determine the mechanisms that enable coexistence among species. Evidence is accruing that conspecific negative density dependence (CNDD), the process by which plant seedlings are unable to survive in the area surrounding adults of their same species, is a major contributor to tree species coexistence. However, for CNDD to maintain community-level diversity, three conditions must be met. First, CNDD must maintain diversity for the majority of the woody plant community (rather than merely specific groups). Second, the pattern of repelled recruitment must increase in with plant size. Third, CNDD should extend to the majority of plant life history strategies. These three conditions are rarely tested simultaneously. In this study, we simultaneously test all three conditions in a woody plant community in a North American temperate forest. We examined whether understory and canopy woody species across height categories and dispersal syndromes were overdispersed-a spatial pattern indicative of CNDD-using spatial point pattern analysis across life history stages and strategies. We found that there was a strong signal of overdispersal at the community level. Across the whole community, larger individuals were more overdispersed than smaller individuals. The overdispersion of large individuals, however, was driven by canopy trees. By contrast, understory woody species were not overdispersed as adults. This finding indicates that the focus on trees for the vast majority of CNDD studies may have biased the perception of the prevalence of CNDD as a dominant mechanism that maintains community-level diversity when, according to our data, CNDD may be restricted largely to trees., Competing Interests: The authors have declared that no competing interests exist.

To understand driving biological factors for complex diseases like cancer, regulatory circuity of genes needs to be discovered. Recently, a new gene regulation mechanism called competing endogenous RNA (ceRNA) interactions has been discovered. Certain genes targeted by common microRNAs (miRNAs) "compete" for these miRNAs, thereby regulate each other by making others free from miRNA regulation. Several computational tools have been published to infer ceRNA networks. In most existing tools, however, expression abundance sufficiency, collective regulation, and groupwise effect of ceRNAs are not considered. In this study, we developed a computational tool named Crinet to infer genome-wide ceRNA networks addressing critical drawbacks. Crinet considers all mRNAs, lncRNAs, and pseudogenes as potential ceRNAs and incorporates a network deconvolution method to exclude the spurious ceRNA pairs. We tested Crinet on breast cancer data in TCGA. Crinet inferred reproducible ceRNA interactions and groups, which were significantly enriched in the cancer-related genes and processes. We validated the selected miRNA-target interactions with the protein expression-based benchmarks and also evaluated the inferred ceRNA interactions predicting gene expression change in knockdown assays. The hub genes in the inferred ceRNA network included known suppressor/oncogene lncRNAs in breast cancer showing the importance of non-coding RNA's inclusion for ceRNA inference. Crinet-inferred ceRNA groups that were consistently involved in the immune system related processes could be important assets in the light of the studies confirming the relation between immunotherapy and cancer. The source code of Crinet is in R and available at https://github.com/bozdaglab/crinet., Competing Interests: The authors have declared that no competing interests exist.

In this study, a new flexible lifetime model called Burr XII moment exponential (BXII-ME) distribution is introduced. We derive some of its mathematical properties including the ordinary moments, conditional moments, reliability measures and characterizations. We employ different estimation methods such as the maximum likelihood, maximum product spacings, least squares, weighted least squares, Cramer-von Mises and Anderson-Darling methods for estimating the model parameters. We perform simulation studies on the basis of the graphical results to see the performance of the above estimators of the BXII-ME distribution. We verify the potentiality of the BXII-ME model via monthly actual taxes revenue and fatigue life applications., Competing Interests: The authors have declared that no competing interests exist.

Masks are an effective tool in combatting the spread of COVID-19, but some people still resist wearing them and mask-wearing behavior has not been experimentally studied in the United States. To understand the demographics of mask wearers and resistors, and the impact of mandates on mask-wearing behavior, we observed shoppers (n = 9935) entering retail stores during periods of June, July, and August 2020. Approximately 41% of the June sample wore a mask. At that time, the odds of an individual wearing a mask increased significantly with age and was also 1.5x greater for females than males. Additionally, the odds of observing a mask on an urban or suburban shopper were ~4x that for rural areas. Mask mandates enacted in late July and August increased mask-wearing compliance to over 90% in all groups, but a small percentage of resistors remained. Thus, gender, age, and location factor into whether shoppers in the United States wear a mask or face covering voluntarily. Additionally, mask mandates are necessary to increase mask wearing among the public to a level required to mitigate the spread of COVID-19., Competing Interests: The authors have declared that no competing interests exist.

The SIR ('susceptible-infectious-recovered') formulation is used to uncover the generic spread mechanisms observed by COVID-19 dynamics globally, especially in the early phases of infectious spread. During this early period, potential controls were not effectively put in place or enforced in many countries. Hence, the early phases of COVID-19 spread in countries where controls were weak offer a unique perspective on the ensemble-behavior of COVID-19 basic reproduction number Ro inferred from SIR formulation. The work here shows that there is global convergence (i.e., across many nations) to an uncontrolled Ro = 4.5 that describes the early time spread of COVID-19. This value is in agreement with independent estimates from other sources reviewed here and adds to the growing consensus that the early estimate of Ro = 2.2 adopted by the World Health Organization is low. A reconciliation between power-law and exponential growth predictions is also featured within the confines of the SIR formulation. The effects of testing ramp-up and the role of 'super-spreaders' on the inference of Ro are analyzed using idealized scenarios. Implications for evaluating potential control strategies from this uncontrolled Ro are briefly discussed in the context of the maximum possible infected fraction of the population (needed to assess health care capacity) and mortality (especially in the USA given diverging projections). Model results indicate that if intervention measures still result in Ro > 2.7 within 44 days after first infection, intervention is unlikely to be effective in general for COVID-19., Competing Interests: The authors have declared that no competing interests exist.

Background: Severe acute malnutrition (SAM) affects about 13 million under-five children (U5), with an estimated one million dying every year. In this study we aimed at determining the in hospital mortality and its associated factors among U5s admitted with SAM., Methods: This was a prospective cohort study of children 6 months to 5 years with SAM admitted at Mbarara Regional Referral Hospital (MRRH) between June and August 2015. Care-takers were interviewed to collect socio-demographic and clinical information. Children under-went physical examination and had blood drawn for HIV, serum glucose, malaria, full blood count, culture and serum electrolytes investigation. Children were managed according to WHO treatment guidelines for SAM. All participants were followed up for a maximum period of 30 days. The proportion of U5 deaths within the first 48 hours and during the entire admission period was calculated. Using Poisson regression analysis, predictors of in-hospital mortality were analyzed with STATA/IC 11.0., Results: We enrolled 122 children, median age of 15 months [IQR:11-24], 58.2% males, 90% immunized, 81% ill for more than 2 weeks before admission, 71% from lower health facilities and majority with unknown HIV status(76%). Overall, 13 (10.7%) children died in hospital. Seven (5.7%) died within the first 48 hours. Intravenous (IV) fluid administration significantly predicted in-hospital mortality (adjusted IRR: 7.2, 95%CI: 2.14-24.08, p = 0.001)., Conclusion: The in-hospital mortality in U5s with SAM was lower than that previously reported in central Uganda. Intravenous fluid administration significantly predicted overall in-hospital mortality. While Administration of intravenous fluids is still the main stay of managing severely malnourished children with shock, more research needs to be conducted in order to review the parameters presently used to assess children for shock with a view of diagnosing and managing shock in these children when it is still early. Adequate guidance on use of IV fluids in management of severely malnourished children should be prioritized during continuous medical education for healthcare workers and in the treatment guidelines., Competing Interests: The authors have declared that no competing interests exist.

After mating, female mosquitoes need animal blood to develop their eggs. In the process of acquiring blood, they may acquire pathogens, which may cause different diseases in humans such as malaria, zika, dengue, and chikungunya. Therefore, knowing the parity status of mosquitoes is useful in control and evaluation of infectious diseases transmitted by mosquitoes, where parous mosquitoes are assumed to be potentially infectious. Ovary dissections, which are currently used to determine the parity status of mosquitoes, are very tedious and limited to few experts. An alternative to ovary dissections is near-infrared spectroscopy (NIRS), which can estimate the age in days and the infectious state of laboratory and semi-field reared mosquitoes with accuracies between 80 and 99%. No study has tested the accuracy of NIRS for estimating the parity status of wild mosquitoes. In this study, we train an artificial neural network (ANN) models on NIR spectra to estimate the parity status of wild mosquitoes. We use four different datasets: An. arabiensis collected from Minepa, Tanzania (Minepa-ARA); An. gambiae s.s collected from Muleba, Tanzania (Muleba-GA); An. gambiae s.s collected from Burkina Faso (Burkina-GA); and An.gambiae s.s from Muleba and Burkina Faso combined (Muleba-Burkina-GA). We train ANN models on datasets with spectra preprocessed according to previous protocols. We then use autoencoders to reduce the spectra feature dimensions from 1851 to 10 and re-train the ANN models. Before the autoencoder was applied, ANN models estimated parity status of mosquitoes in Minepa-ARA, Muleba-GA, Burkina-GA and Muleba-Burkina-GA with out-of-sample accuracies of 81.9±2.8 (N = 274), 68.7±4.8 (N = 43), 80.3±2.0 (N = 48), and 75.7±2.5 (N = 91), respectively. With the autoencoder, ANN models tested on out-of-sample data achieved 97.1±2.2% (N = 274), 89.8 ± 1.7% (N = 43), 93.3±1.2% (N = 48), and 92.7±1.8% (N = 91) accuracies for Minepa-ARA, Muleba-GA, Burkina-GA, and Muleba-Burkina-GA, respectively. These results show that a combination of an autoencoder and an ANN trained on NIR spectra to estimate the parity status of wild mosquitoes yields models that can be used as an alternative tool to estimate parity status of wild mosquitoes, especially since NIRS is a high-throughput, reagent-free, and simple-to-use technique compared to ovary dissections., Competing Interests: The authors have declared that no competing interests exist.

The heptapeptide angiotensin-(1-7) (Ang-(1-7)) is protective in the cardiovascular system through its induction of vasodilator production and angiogenesis. Despite acting antagonistically to the effects of elevated, pathophysiological levels of angiotensin II (AngII), recent evidence has identified convergent and beneficial effects of low levels of both Ang-(1-7) and AngII. Previous work identified the AngII receptor type I (AT1R) as a component of the protein complex formed when Ang-(1-7) binds its receptor, Mas1. Importantly, pharmacological blockade of AT1R did not alter the effects of Ang-(1-7). Here, we use a novel mutation of AT1RA in the Dahl salt-sensitive (SS) rat to test the hypothesis that interaction between Mas1 and AT1R contributes to proangiogenic Ang-(1-7) signaling. In a model of hind limb angiogenesis induced by electrical stimulation, we find that the restoration of skeletal muscle angiogenesis in SS rats by Ang-(1-7) infusion is impaired in AT1RA knockout rats. Enhancement of endothelial cell (EC) tube formation capacity by Ang-(1-7) is similarly blunted in AT1RA mutant ECs. Transcriptional changes elicited by Ang-(1-7) in SS rat ECs are altered in AT1RA mutant ECs, and tandem mass spectrometry-based proteomics demonstrate that the protein complex formed upon binding of Ang-(1-7) to Mas1 is altered in AT1RA mutant ECs. Together, these data support the hypothesis that interaction between AT1R and Mas1 contributes to proangiogenic Ang-(1-7) signaling., Competing Interests: The authors have declared that no competing interests exist.

Chaperones and autophagy are components of the protein quality control system that contribute to the management of proteins that are misfolded and aggregated. Here, we use yeast prions, which are self-perpetuating aggregating proteins, as a means to understand how these protein quality control systems influence aggregate loss. Chaperones, such as Hsp104, fragment prion aggregates to generate more prion seeds for propagation. While much is known about the role of chaperones, little is known about how other quality control systems contribute to prion propagation. We show that the aprotic solvent dimethyl sulfoxide (DMSO) cures a range of [PSI+] prion variants, which are related to several misfolded aggregated conformations of the Sup35 protein. Our studies show that DMSO-mediated curing is quicker and more efficient than guanidine hydrochloride, a prion curing agent that inactivates the Hsp104 chaperone. Instead, DMSO appears to induce Hsp104 expression. Using the yTRAP system, a recently developed transcriptional reporting system for tracking protein solubility, we found that DMSO also rapidly induces the accumulation of soluble Sup35 protein, suggesting a potential link between Hsp104 expression and disassembly of Sup35 from the prion aggregate. However, DMSO-mediated curing appears to also be associated with other quality control systems. While the induction of autophagy alone does not lead to curing, we found that DMSO-mediated curing is dramatically impaired in autophagy related (atg) gene mutants, suggesting that other factors influence this DMSO mechanism of curing. Our data suggest that DMSO-mediated curing is not simply dependent upon Hsp104 overexpression alone, but may further depend upon other aspects of proteostasis., Competing Interests: The authors have declared that no competing interests exist.

The curved planes of the human dentition seen in the sagittal view, the mandibular curve of Spee and the maxillary compensating curve, have clinical importance to modern dentistry and potential relevance to the craniofacial evolution of hominins. However, the mechanism providing the formation of these curved planes is poorly understood. To explore this further, we use a simplified finite element model, consisting of maxillary and mandibular "blocks", developed to simulate tooth eruption, and forces opposing eruption, during simplified masticatory function. We test our hypothesis that curved occlusal planes develop from interplay between tooth eruption, occlusal load, and mandibular movement. Our results indicate that our simulation of rhythmic chewing movement, tooth eruption, and tooth eruption inhibition, applied concurrently, results in a transformation of the contacting maxillary and mandibular block surfaces from flat to curved. The depth of the curvature appears to be dependent on the radius length of the rotating (chewing) movement of the mandibular block. Our results suggest mandibular function and maxillo-mandibular spatial relationship may contribute to the development of human occlusal curvature., Competing Interests: The authors have declared that no competing interests exist.

Background: Near infrared spectroscopy (NIRS) is currently complementing techniques to age-grade mosquitoes. NIRS classifies lab-reared and semi-field raised mosquitoes into < or ≥ 7 days old with an average accuracy of 80%, achieved by training a regression model using partial least squares (PLS) and interpreted as a binary classifier., Methods and Findings: We explore whether using an artificial neural network (ANN) analysis instead of PLS regression improves the current accuracy of NIRS models for age-grading malaria transmitting mosquitoes. We also explore if directly training a binary classifier instead of training a regression model and interpreting it as a binary classifier improves the accuracy. A total of 786 and 870 NIR spectra collected from laboratory reared An. gambiae and An. arabiensis, respectively, were used and pre-processed according to previously published protocols. The ANN regression model scored root mean squared error (RMSE) of 1.6 ± 0.2 for An. gambiae and 2.8 ± 0.2 for An. arabiensis; whereas the PLS regression model scored RMSE of 3.7 ± 0.2 for An. gambiae, and 4.5 ± 0.1 for An. arabiensis. When we interpreted regression models as binary classifiers, the accuracy of the ANN regression model was 93.7 ± 1.0% for An. gambiae, and 90.2 ± 1.7% for An. arabiensis; while PLS regression model scored the accuracy of 83.9 ± 2.3% for An. gambiae, and 80.3 ± 2.1% for An. arabiensis. We also find that a directly trained binary classifier yields higher age estimation accuracy than a regression model interpreted as a binary classifier. A directly trained ANN binary classifier scored an accuracy of 99.4 ± 1.0 for An. gambiae and 99.0 ± 0.6% for An. arabiensis; while a directly trained PLS binary classifier scored 93.6 ± 1.2% for An. gambiae and 88.7 ± 1.1% for An. arabiensis. We further tested the reproducibility of these results on different independent mosquito datasets. ANNs scored higher estimation accuracies than when the same age models are trained using PLS. Regardless of the model architecture, directly trained binary classifiers scored higher accuracies on classifying age of mosquitoes than regression models translated as binary classifiers., Conclusion: We recommend training models to estimate age of An. arabiensis and An. gambiae using ANN model architectures (especially for datasets with at least 70 mosquitoes per age group) and direct training of binary classifier instead of training a regression model and interpreting it as a binary classifier., Competing Interests: The authors have declared that no competing interests exist.

Understanding how people modify their stepping to maintain gait stability may provide information on fall risk and help to understand strategies used to reduce loss of balance. The purpose of this study was to identify the stepping strategies healthy young individuals select to maintain balance while walking on a destabilizing surface in various directions. A treadmill mounted on top of a 6 degree-of-freedom motion base was used to generate support surface oscillations in different degrees of freedom and amplitudes. Fifteen healthy young adults (21.3 ± 1.4 years) walked at self-selected speeds while continuous sinusoidal oscillations were imposed to the support surface in a one degree of freedom: rotation or translation in the mediolateral (ML) direction and rotation or translation in the anteroposterior (AP) direction, with each condition repeated at three different amplitudes. We compared step width, length, and frequency and the mean and variability of margin of stability (MoS) during each experimental walking condition with a control condition, in which the support surface was stationary. Subjects chose a common strategy of increasing step width (p < 0.001) and decreasing step length (p = 0.008) while increasing mediolateral MoS (p < 0.001), particularly during oscillations that challenged frontal plane control, with rotations of the walking surface producing the greatest changes to stepping., Competing Interests: The authors have declared that no competing interests exist.

The purpose of this study was to quantify the magnitude and time course of dynamic balance control adaptations to prolonged step-by-step frontal plane forces applied to the trunk during walking. Healthy young participants (n = 10, 5 female) walked on an instrumented split-belt treadmill while an external cable-driven device applied frontal plane forces to the trunk. Two types of forces were applied: 1) forces which accentuated COM movement in the frontal plane (destabilizing) and 2) forces which resisted COM movement in the frontal plane (stabilizing). We quantified dynamic balance control using frontal plane measures of (1) the extent of center of mass (COM) movement over a gait cycle (COM sway), (2) the magnitude of base of support (step width), and (3) cadence. During destabilizing force conditions, COM sway, step width, and cadence increased. In response to stabilizing force conditions, COM sway decreased. In addition, during destabilizing balance conditions participants made quicker adaptations to their step width compared to the time to adapt to stabilizing forces. Taken together, these results provide important insight into differences in dynamic balance control strategies in response to stabilizing and destabilizing force fields., Competing Interests: The authors have declared that no competing interests exist.

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria., Competing Interests: The authors have declared that no competing interests exist.

A new enzymatic assay for the bacterial enzyme succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) is described. This assay employs N6-methyl-N2-succinyl-L,L-diaminopimelic acid (N6-methyl-L,L-SDAP) as the substrate with ninhydrin used to detect cleavage of the amide bond of the modified substrate, wherein N6-methylation enables selective detection of the primary amine enzymatic product. Molecular modeling supported preparation of the mono-N6-methylated-L,L-SDAP as an alternate substrate for the assay, given binding in the active site of DapE predicted to be comparable to the endogenous substrate. The alternate substrate for the assay, N6-methyl-L,L-SDAP, was synthesized from the tert-butyl ester of Boc-L-glutamic acid employing a Horner-Wadsworth-Emmons olefination followed by an enantioselective reduction employing Rh(I)(COD)(S,S)-Et-DuPHOS as the chiral catalyst. Validation of the new ninhydrin assay was demonstrated with known inhibitors of DapE from Haemophilus influenza (HiDapE) including captopril (IC50 = 3.4 [± 0.2] μM, 3-mercaptobenzoic acid (IC50 = 21.8 [±2.2] μM, phenylboronic acid (IC50 = 316 [± 23.6] μM, and 2-thiopheneboronic acid (IC50 = 111 [± 16] μM. Based on these data, this assay is simple and robust, and should be amenable to high-throughput screening, which is an important step forward as it opens the door to medicinal chemistry efforts toward the discovery of DapE inhibitors that can function as a new class of antibiotics.

Men outperform women in many athletic endeavors due to physiological and anatomical differences (e.g. larger and faster muscle); however, the observed sex differences in elite athletic performance are typically larger than expected, and may reflect sex-related differences in opportunity or incentives. As collegiate rowing in the United States has been largely incentivized for women over the last 20 years, but not men, the purpose of this study was to examine sex differences in elite rowing performance over that timeframe. Finishing times from grand finale races for collegiate championship on-water performances (n = 480) and junior indoor performances (n = 1,280) were compared between men and women across 20 years (1997-2016), weight classes (heavy vs. lightweight) and finishing place. Participation of the numbers of men and women rowers were also quantified across years. Men were faster than women across all finishing places, weight classes and years of competition and performance declined across finishing place for both men and women (P<0.001). Interestingly, the reduction in performance time across finishing place was greater (P<0.001) for collegiate men compared to women in the heavyweight division. This result is opposite to other sports (e.g. running and swimming), and to lightweight rowing in this study, which provides women fewer incentives than in heavyweight rowing. Correspondingly, participation in collegiate rowing has increased by ~113 women per year (P<0.001), with no change (P = 0.899) for collegiate men. These results indicate that increased participation and incentives within collegiate rowing for women vs. men contribute to sex differences in athletic performance.

Schistosomiasis is one of the major Neglected Tropical Diseases (NTDs) in sub-Saharan Africa. In sub-Saharan Africa, two major human schistosome species namely Schistosoma mansoni and S. haematobium often occur sympatrically largely affecting children. Recognizing the public health impact of Schistosomiasis, the World Health Organization (WHO) is urging member states to regularly treat at least 75% and up to 100%, of all school-aged children at risk of morbidity. For control strategies based on targeted mass drug administration (MDA) to succeed it is essential to have a simple and sensitive test for monitoring the success of these interventions. Current available diagnostic tests, such as egg detection in stool by Kato-Katz (KK) for S. mansoni and detection of eggs or blood (hematuria) in urine for S. haematobium have reduced sensitivity in low intensity settings. The objective of the study was to evaluate active single or duo schistosome infections in school children following MDA using molecular diagnostics (PCR) on filtered urine samples and comparing that against traditional diagnostic tests. This cross-sectional study was conducted among 111 school children aged 7-15 years in Chongwe and Siavonga Districts in Zambia. Species-specific cell-free repeat DNA fragment were amplified from 111 filtered urine samples. Our approach detected eight times more positive cases (total 77) than by KK (9) for S. mansoni and six times more (total 72) than by hematuria (11) for S. haematobium and even more against urine filtration (77 compared to only 6). The same pattern was observed when stratified for age group and sex specific analysis with 100% sensitivity and specificity devoid of any cross amplification. In addition, 69 individuals (62%) were co-infected by both parasites. We have demonstrated a significantly higher prevalence of both species than indicated by the traditional tests and the persistent maintenance of reservoir of infection after MDA. Our approach is an effective means of detecting low intensity infection, which will enhance the effectiveness of surveillance and assess the impact of MDA control programs against schistosomiasis.

Background: Despite great achievements by insecticide-treated nets (ITNs) and indoor residual spraying (IRS) in reducing malaria transmission, it is unlikely these tools will be sufficient to eliminate malaria transmission on their own in many settings today. Fortunately, field experiments indicate that there are many promising vector control interventions that can be used to complement ITNs and/or IRS by targeting a wide range of biological and environmental mosquito resources. The majority of these experiments were performed to test a single vector control intervention in isolation; however, there is growing evidence and consensus that effective vector control with the goal of malaria elimination will require a combination of interventions., Method and Findings: We have developed a model of mosquito population dynamic to describe the mosquito life and feeding cycles and to optimize the impact of vector control intervention combinations at suppressing mosquito populations. The model simulations were performed for the main three malaria vectors in sub-Saharan Africa, Anopheles gambiae s.s, An. arabiensis and An. funestus. We considered areas having low, moderate and high malaria transmission, corresponding to entomological inoculation rates of 10, 50 and 100 infective bites per person per year, respectively. In all settings, we considered baseline ITN coverage of 50% or 80% in addition to a range of other vector control tools to interrupt malaria transmission. The model was used to sweep through parameters space to select the best optimal intervention packages. Sample model simulations indicate that, starting with ITNs at a coverage of 50% (An. gambiae s.s. and An. funestus) or 80% (An. arabiensis) and adding interventions that do not require human participation (e.g. larviciding at 80% coverage, endectocide treated cattle at 50% coverage and attractive toxic sugar baits at 50% coverage) may be sufficient to suppress all the three species to an extent required to achieve local malaria elimination., Conclusion: The Vector Control Optimization Model (VCOM) is a computational tool to predict the impact of combined vector control interventions at the mosquito population level in a range of eco-epidemiological settings. The model predicts specific combinations of vector control tools to achieve local malaria elimination in a range of eco-epidemiological settings and can assist researchers and program decision-makers on the design of experimental or operational research to test vector control interventions. A corresponding graphical user interface is available for national malaria control programs and other end users.

Dysregulation of MST1/STK4, a key kinase component of the Hippo-YAP pathway, is linked to the etiology of many cancers with poor prognosis. However, how STK4 restricts the emergence of aggressive cancer remains elusive. Here, we investigated the effects of STK4, primarily localized in the cytoplasm, lipid raft, and nucleus, on cell growth and gene expression in aggressive prostate cancer. We demonstrated that lipid raft and nuclear STK4 had superior suppressive effects on cell growth in vitro and in vivo compared with cytoplasmic STK4. Using RNA sequencing and bioinformatics analysis, we identified several differentially expressed (DE) genes that responded to ectopic STK4 in all three subcellular compartments. We noted that the number of DE genes observed in lipid raft and nuclear STK4 cells were much greater than cytoplasmic STK4. Our functional annotation clustering showed that these DE genes were commonly associated with oncogenic pathways such as AR, PI3K/AKT, BMP/SMAD, GPCR, WNT, and RAS as well as unique pathways such as JAK/STAT, which emerged only in nuclear STK4 cells. These findings indicate that MST1/STK4/Hippo signaling restricts aggressive tumor cell growth by intersecting with multiple molecular pathways, suggesting that targeting of the STK4/Hippo pathway may have important therapeutic implications for cancer.

We present a new thermomechanical method and a platform to measure the phase transition temperature at microscale. A thin film metal sensor on a membrane simultaneously measures both temperature and mechanical strain of the sample during heating and cooling cycles. This thermomechanical principle of operation is described in detail. Physical hydrogel samples are prepared as a disc-shaped gels (200 μm thick and 1 mm diameter) and placed between an on-chip heater and sensor devices. The sol-gel transition temperature of gelatin solution at various concentrations, used as a model physical hydrogel, shows less than 3% deviation from in-depth rheological results. The developed thermomechanical methodology is promising for precise characterization of phase transition temperature of thermogels at microscale.

Purpose: Choroideremia is a progressive X-linked recessive dystrophy, characterized by degeneration of the retinal pigment epithelium (RPE), choroid, choriocapillaris, and photoreceptors. We examined photoreceptor structure in a series of subjects with choroideremia with particular attention to areas bordering atrophic lesions., Methods: Twelve males with clinically-diagnosed choroideremia and confirmed hemizygous mutations in the CHM gene were examined. High-resolution images of the retina were obtained using spectral domain optical coherence tomography (SD-OCT) and both confocal and non-confocal split-detector adaptive optics scanning light ophthalmoscope (AOSLO) techniques., Results: Eleven CHM gene mutations (3 novel) were identified; three subjects had the same mutation and one subject had two mutations. SD-OCT findings included interdigitation zone (IZ) attenuation or loss in 10/12 subjects, often in areas with intact ellipsoid zones; RPE thinning in all subjects; interlaminar bridges in the imaged areas of 10/12 subjects; and outer retinal tubulations (ORTs) in 10/12 subjects. Only split-detector AOSLO could reliably resolve cones near lesion borders, and such cones were abnormally heterogeneous in morphology, diameter and density. On split-detector imaging, the cone mosaic terminated sharply at lesion borders in 5/5 cases examined. Split-detector imaging detected remnant cone inner segments within ORTs, which were generally contiguous with a central patch of preserved retina., Conclusions: Early IZ dropout and RPE thinning on SD-OCT are consistent with previously published results. Evidence of remnant cone inner segments within ORTs and the continuity of the ORTs with preserved retina suggests that these may represent an intermediate state of retinal degeneration prior to complete atrophy. Taken together, these results supports a model of choroideremia in which the RPE degenerates before photoreceptors., Competing Interests: The authors have declared that no competing interests exist.

Engineered nanoparticles are becoming increasingly incorporated into technology and consumer products. In 2014, over 300 tons of copper oxide nanoparticles were manufactured in the United States. The increased production of nanoparticles raises concerns regarding the potential introduction into the environment or human exposure. Copper oxide nanoparticles commonly release copper ions into solutions, which contribute to their toxicity. We quantified the inhibitory effects of both copper oxide nanoparticles and copper sulfate on C. elegans toxicological endpoints to elucidate their biological effects. Several toxicological endpoints were analyzed in C. elegans, including nematode reproduction, feeding behavior, and average body length. We examined three wild C. elegans isolates together with the Bristol N2 laboratory strain to explore the influence of different genotypic backgrounds on the physiological response to copper challenge. All strains exhibited greater sensitivity to copper oxide nanoparticles compared to copper sulfate, as indicated by reduction of average body length and feeding behavior. Reproduction was significantly reduced only at the highest copper dose, though still more pronounced with copper oxide nanoparticles compared to copper sulfate treatment. Furthermore, we investigated the effects of copper oxide nanoparticles and copper sulfate on neurons, cells with known vulnerability to heavy metal toxicity. Degeneration of dopaminergic neurons was observed in up to 10% of the population after copper oxide nanoparticle exposure. Additionally, mutants in the divalent-metal transporters, smf-1 or smf-2, showed increased tolerance to copper exposure, implicating both transporters in copper-induced neurodegeneration. These results highlight the complex nature of CuO nanoparticle toxicity, in which a nanoparticle-specific effect was observed in some traits (average body length, feeding behavior) and a copper ion specific effect was observed for other traits (neurodegeneration, response to stress)., Competing Interests: The authors have declared that no competing interests exist.

Single-stranded DNA binding (SSB) proteins coordinate DNA replication, repair, and recombination and are critical for maintaining genomic integrity. SSB binds to single-stranded DNA (ssDNA) rapidly and with very high affinity making it a useful molecular tool to detect free ssDNA in solution. We have labeled SSB from Plasmodium falciparum (Pf-SSB) with the MDCC (7-diethylamino-3-((((2-maleimidyl)ethyl)amino)-carbonyl)coumarin) fluorophore which yields a four-fold increase in fluorescence upon binding to ssDNA. Pf-SSBMDCC binding to DNA is unaffected by NaCl or Mg2+ concentration and does not display salt-dependent changes in DNA binding modes or cooperative binding on long DNA substrates. These features are unique to Pf-SSB, making it an ideal tool to probe the presence of free ssDNA in any biochemical reaction. Using this Pf-SSBMDCC probe as a sensor for free ssDNA, we have investigated the clearing of preformed yeast Rad51 nucleoprotein filaments by the Srs2 helicase during HR. Our studies provide a rate for the disassembly of the Rad51 filament by full length Srs2 on long ssDNA substrates. Mutations in the conserved 2B domain in the homologous bacterial UvrD, Rep and PcrA helicases show an enhancement of DNA unwinding activity, but similar mutations in Srs2 do not affect its DNA unwinding or Rad51 clearing properties. These studies showcase the utility of the Pf-SSB probe in mechanistic investigation of enzymes that function in DNA metabolism.

Functional magnetic resonance imaging (fMRI) studies have demonstrated alterations during task-induced brain activation in spinal cord injury (SCI) patients. The interruption to structural integrity of the spinal cord and the resultant disrupted flow of bidirectional communication between the brain and the spinal cord might contribute to the observed dynamic reorganization (neural plasticity). However, the effect of SCI on brain resting-state connectivity patterns remains unclear. We undertook a prospective resting-state fMRI (rs-fMRI) study to explore changes to cortical activation patterns following SCI. With institutional review board approval, rs-fMRI data was obtained in eleven patients with complete cervical SCI (>2 years post injury) and nine age-matched controls. The data was processed using the Analysis of Functional Neuroimages software. Region of interest (ROI) based analysis was performed to study changes in the sensorimotor network using pre- and post-central gyri as seed regions. Two-sampled t-test was carried out to check for significant differences between the two groups. SCI patients showed decreased functional connectivity in motor and sensory cortical regions when compared to controls. The decrease was noted in ipsilateral, contralateral, and interhemispheric regions for left and right precentral ROIs. Additionally, the left postcentral ROI demonstrated increased connectivity with the thalamus bilaterally in SCI patients. Our results suggest that cortical activation patterns in the sensorimotor network undergo dynamic reorganization following SCI. The presence of these changes in chronic spinal cord injury patients is suggestive of the inherent neural plasticity within the central nervous system.

DNA methylation is an important epigenetic event that effects gene expression during development and various diseases such as cancer. Understanding the mechanism of action of DNA methylation is important for downstream analysis. In the Illumina Infinium HumanMethylation 450K array, there are tens of probes associated with each gene. Given methylation intensities of all these probes, it is necessary to compute which of these probes are most representative of the gene centric methylation level. In this study, we developed a feature selection algorithm based on sequential forward selection that utilized different classification methods to compute gene centric DNA methylation using probe level DNA methylation data. We compared our algorithm to other feature selection algorithms such as support vector machines with recursive feature elimination, genetic algorithms and ReliefF. We evaluated all methods based on the predictive power of selected probes on their mRNA expression levels and found that a K-Nearest Neighbors classification using the sequential forward selection algorithm performed better than other algorithms based on all metrics. We also observed that transcriptional activities of certain genes were more sensitive to DNA methylation changes than transcriptional activities of other genes. Our algorithm was able to predict the expression of those genes with high accuracy using only DNA methylation data. Our results also showed that those DNA methylation-sensitive genes were enriched in Gene Ontology terms related to the regulation of various biological processes.

RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH and ratchet domain) coordinate with the helicase domains and what roles they are playing in regulating Mtr4p helicase activity are unknown. We created a library of Mtr4p structural domain mutants for the first time and screened for those defective in the turnover of TRAMP and exosome substrate, hypomodified tRNAiMet. We found these domains regulate Mtr4p enzymatic activities differently through characterizing the arch domain mutants K700N and P731S, WH mutant K904N, and ratchet domain mutant R1030G. Arch domain mutants greatly reduced Mtr4p RNA binding, which surprisingly did not lead to significant defects on either in vivo tRNAiMet turnover, or in vitro unwinding activities. WH mutant K904N and Ratchet domain mutant R1030G showed decreased tRNAiMet turnover in vivo, as well as reduced RNA binding, ATPase and unwinding activities of Mtr4p in vitro. Particularly, K904 was found to be very important for steady protein levels in vivo. Overall, we conclude that arch domain plays a role in RNA binding but is largely dispensable for Mtr4p enzymatic activities, however the structural domains in the helicase core significantly contribute to Mtr4p ATPase and unwinding activities.

Sensory stimulation of wrist musculature can enhance stability in the proximal arm and may be a useful therapy aimed at improving arm control post-stroke. Specifically, our prior research indicates tendon vibration can enhance stability during point-to-point arm movements and in tracking tasks. The goal of the present study was to investigate the influence of forearm tendon vibration on endpoint stability, measured at the hand, immediately following forward arm movements in an unstable environment. Both proximal and distal workspaces were tested. Ten hemiparetic stroke subjects and 5 healthy controls made forward arm movements while grasping the handle of a two-joint robotic arm. At the end of each movement, the robot applied destabilizing forces. During some trials, 70 Hz vibration was applied to the forearm flexor muscle tendons. 70 Hz was used as the stimulus frequency as it lies within the range of optimal frequencies that activate the muscle spindles at the highest response rate. Endpoint position, velocity, muscle activity and grip force data were compared before, during and after vibration. Stability at the endpoint was quantified as the magnitude of oscillation about the target position, calculated from the power of the tangential velocity data. Prior to vibration, subjects produced unstable, oscillating hand movements about the target location due to the applied force field. Stability increased during vibration, as evidenced by decreased oscillation in hand tangential velocity.

Individuals with chronic stroke have reduced perfusion of the paretic lower limb at rest; however, the hyperemic response to graded muscle contractions in this patient population has not been examined. This study quantified blood flow to the paretic and non-paretic lower limbs of subjects with chronic stroke after submaximal contractions of the knee extensor muscles and correlated those measures with limb function and activity. Ten subjects with chronic stroke and ten controls had blood flow through the superficial femoral artery quantified with ultrasonography before and immediately after 10 second contractions of the knee extensor muscles at 20, 40, 60, and 80% of the maximal voluntary contraction (MVC) of the test limb. Blood flow to the paretic and non-paretic limb of stroke subjects was significantly reduced at all load levels compared to control subjects even after normalization to lean muscle mass. Of variables measured, increased blood flow after an 80% MVC was the single best predictor of paretic limb strength, the symmetry of strength between the paretic and non-paretic limbs, coordination of the paretic limb, and physical activity. The impaired hemodynamic response to high intensity contractions was a better predictor of lower limb function than resting perfusion measures. Stroke-dependent weakness and atrophy of the paretic limb do not explain the reduced hyperemic response to muscle contraction alone as the response is similarly reduced in the non-paretic limb when compared to controls. These data may suggest a role for perfusion therapies to optimize rehabilitation post stroke.

Lianas (woody vines) are particularly abundant in tropical forests, and their abundance is increasing in the neotropics. Lianas can compete intensely with trees for above- and belowground resources, including water. As tropical forests experience longer and more intense dry seasons, competition for water is likely to intensify. However, we lack an understanding of how liana abundance affects soil moisture and hence competition with trees for water in tropical forests. To address this critical knowledge gap, we conducted a large-scale liana removal experiment in a seasonal tropical moist forest in central Panama. We monitored shallow and deep soil moisture over the course of three years to assess the effects of lianas in eight 0.64 ha removal plots and eight control plots. Liana removal caused short-term effects in surface soils. Surface soils (10 cm depth) in removal plots dried more slowly during dry periods and accumulated water more slowly after rainfall events. These effects disappeared within four months of the removal treatment. In deeper soils (40 cm depth), liana removal resulted in a multi-year trend towards 5-25% higher soil moisture during the dry seasons with the largest significant effects occurring in the dry season of the third year following treatment. Liana removal did not affect surface soil temperature. Multiple and mutually occurring mechanisms may be responsible for the effects of liana removal on soil moisture, including competition with trees, and altered microclimate, and soil structure. These results indicate that lianas influence hydrologic processes, which may affect tree community dynamics and forest carbon cycling.

The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3' end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3'splice site of TRα2 mRNA and antisense to the 3'UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing.

Coarctation of the aorta (CoA) is a constriction of the proximal descending thoracic aorta and is one of the most common congenital cardiovascular defects. Treatments for CoA improve life expectancy, but morbidity persists, particularly due to the development of chronic hypertension (HTN). Identifying the mechanisms of morbidity is difficult in humans due to confounding variables such as age at repair, follow-up duration, coarctation severity and concurrent anomalies. We previously developed an experimental model that replicates aortic pathology in humans with CoA without these confounding variables, and mimics correction at various times using dissolvable suture. Here we present the most comprehensive description of differentially expressed genes (DEGs) to date from the pathology of CoA, which were obtained using this model. Aortic samples (n=4/group) from the ascending aorta that experiences elevated blood pressure (BP) from induction of CoA, and restoration of normal BP after its correction, were analyzed by gene expression microarray, and enriched genes were converted to human orthologues. 51 DEGs with >6 fold-change (FC) were used to determine enriched Gene Ontology terms, altered pathways, and association with National Library of Medicine Medical Subject Headers (MeSH) IDs for HTN, cardiovascular disease (CVD) and CoA. The results generated 18 pathways, 4 of which (cell cycle, immune system, hemostasis and metabolism) were shared with MeSH ID's for HTN and CVD, and individual genes were associated with the CoA MeSH ID. A thorough literature search further uncovered association with contractile, cytoskeletal and regulatory proteins related to excitation-contraction coupling and metabolism that may explain the structural and functional changes observed in our experimental model, and ultimately help to unravel the mechanisms responsible for persistent morbidity after treatment for CoA.

The purpose of this study was to understand how stretch-related sensory feedback from an antagonist muscle affects agonist muscle output at different contraction levels in healthy adults. Ten young (25.3 ± 2.4 years), healthy subjects performed constant isometric knee flexion contractions (agonist) at 6 torque levels: 5%, 10%, 15%, 20%, 30%, and 40% of their maximal voluntary contraction. For half of the trials, subjects received patellar tendon taps (antagonist sensory feedback) during the contraction. We compared error in targeted knee flexion torque and hamstring muscle activity, with and without patellar tendon tapping, across the 6 torque levels. At lower torque levels (5%, 10%, and 15%), subjects produced greater knee torque error following tendon tapping compared with the same torque levels without tendon tapping. In contrast, we did not find any difference in torque output at higher target levels (20%, 30%, and 40%) between trials with and without tendon tapping. We also observed a load-dependent increase in the magnitude of agonist muscle activity after tendon taps, with no associated load-dependent increase in agonist and antagonist co-activation, or reflex inhibition from the antagonist tapping. The findings suggest that at relatively low muscle activity there is a deficiency in the ability to correct motor output after sensory disturbances, and cortical centers (versus sub-cortical) are likely involved.

Background: Large-cage experiments indicate pyriproxifen (PPF) can be transferred from resting sites to aquatic habitats by Anopheles arabiensis--malaria vector mosquitoes to inhibit emergence of their own offspring. PPF coverage is amplified twice: (1) partial coverage of resting sites with PPF contamination results in far higher contamination coverage of adult mosquitoes because they are mobile and use numerous resting sites per gonotrophic cycle, and (2) even greater contamination coverage of aquatic habitats results from accumulation of PPF from multiple oviposition events., Methods and Findings: Deterministic mathematical models are described that use only field-measurable input parameters and capture the biological processes that mediate PPF autodissemination. Recent successes in large cages can be rationalized, and the plausibility of success under full field conditions can be evaluated a priori. The model also defines measurable properties of PPF delivery prototypes that may be optimized under controlled experimental conditions to maximize chances of success in full field trials. The most obvious flaw in this model is the endogenous relationship that inevitably occurs between the larval habitat coverage and the measured rate of oviposition into those habitats if the target mosquito species is used to mediate PPF transfer. However, this inconsistency also illustrates the potential advantages of using a different, non-target mosquito species for contamination at selected resting sites that shares the same aquatic habitats as the primary target. For autodissemination interventions to eliminate malaria transmission or vector populations during the dry season window of opportunity will require comprehensive contamination of the most challenging subset of aquatic habitats [Formula: see text] that persist or retain PPF activity (Ux) for only one week [Formula: see text], where Ux = 7 days). To achieve >99% contamination coverage of these habitats will necessitate values for the product of the proportional coverage of the ovipositing mosquito population with PPF contamination (CM) by the ovitrap-detectable rates of oviposition by wild mosquitoes into this subset of habitats [Formula: see text], divided by the titre of contaminated mosquitoes required to render them unproductive [Formula: see text], that approximately approach unity [Formula: see text]., Conclusions: The simple multiplicative relationship between CM and [Formula: see text], and the simple exponential decay effect they have upon uncontaminated aquatic habitats, allows application of this model by theoreticians and field biologists alike.

Introduction: Current research suggests that the neuropathology of dementia-including brain changes leading to memory impairment and cognitive decline-is evident years before the onset of this disease. Older adults with cognitive decline have reduced functional independence and quality of life, and are at greater risk for developing dementia. Therefore, identifying biomarkers that can be easily assessed within the clinical setting and predict cognitive decline is important. Early recognition of cognitive decline could promote timely implementation of preventive strategies., Methods: We included 89 community-dwelling adults aged 70 years and older in our study, and collected 32 measures of physical function, health status and cognitive function at baseline. We utilized an L1-L2 regularized regression model (elastic net) to identify which of the 32 baseline measures were strongly predictive of cognitive function after one year. We built three linear regression models: 1) based on baseline cognitive function, 2) based on variables consistently selected in every cross-validation loop, and 3) a full model based on all the 32 variables. Each of these models was carefully tested with nested cross-validation., Results: Our model with the six variables consistently selected in every cross-validation loop had a mean squared prediction error of 7.47. This number was smaller than that of the full model (115.33) and the model with baseline cognitive function (7.98). Our model explained 47% of the variance in cognitive function after one year., Discussion: We built a parsimonious model based on a selected set of six physical function and health status measures strongly predictive of cognitive function after one year. In addition to reducing the complexity of the model without changing the model significantly, our model with the top variables improved the mean prediction error and R-squared. These six physical function and health status measures can be easily implemented in a clinical setting.

Aim: Excess mitochondrial reactive oxygen species (mROS) play a vital role in cardiac ischemia reperfusion (IR) injury. P66Shc, a splice variant of the ShcA adaptor protein family, enhances mROS production by oxidizing reduced cytochrome c to yield H2O2. Ablation of p66Shc protects against IR injury, but it is unknown if and when p66Shc is activated during cardiac ischemia and/or reperfusion and if attenuating complex I electron transfer or deactivating PKCβ alters p66Shc activation during IR is associated with cardioprotection., Methods: Isolated guinea pig hearts were perfused and subjected to increasing periods of ischemia and reperfusion with or without amobarbital, a complex I blocker, or hispidin, a PKCβ inhibitor. Phosphorylation of p66Shc at serine 36 and levels of p66Shc in mitochondria and cytosol were measured. Cardiac functional variables and redox states were monitored online before, during and after ischemia. Infarct size was assessed in some hearts after 120 min reperfusion., Results: Phosphorylation of p66Shc and its translocation into mitochondria increased during reperfusion after 20 and 30 min ischemia, but not during ischemia only, or during 5 or 10 min ischemia followed by 20 min reperfusion. Correspondingly, cytosolic p66Shc levels decreased during these ischemia and reperfusion periods. Amobarbital or hispidin reduced phosphorylation of p66Shc and its mitochondrial translocation induced by 30 min ischemia and 20 min reperfusion. Decreased phosphorylation of p66Shc by amobarbital or hispidin led to better functional recovery and less infarction during reperfusion., Conclusion: Our results show that IR activates p66Shc and that reversible blockade of electron transfer from complex I, or inhibition of PKCβ activation, decreases p66Shc activation and translocation and reduces IR damage. These observations support a novel potential therapeutic intervention against cardiac IR injury.

The temperature sensitivity of the germ line is conserved from nematodes to mammals. Previous studies in C. briggsae and Drosophila showed that isolates originating from temperate latitudes lose fertility at a lower temperature than strains originating from tropical latitudes. In order to investigate these relationships in C. elegans, analysis of the fertility of 22 different wild-type isolates of C. elegans isolated from equatorial, tropical and temperate regions was undertaken. It was found that there are significant temperature, genotype and temperature × genotype effects on fertility but region of isolation showed no significant effect on differences in fertility. For most isolates 100% of the population maintained fertility from 20°C to 26°C, but there was a precipitous drop in the percentage of fertile hermaphrodites at 27°C. In contrast, all isolates show a progressive decrease in brood size as temperature increases from 20°C to 26°C, followed by a brood size near zero at 27°C. Temperature shift experiments were performed to better understand the causes of high temperature loss of fertility. Males up-shifted to high temperature maintained fertility, while males raised at high temperature lost fertility. Down-shifting males raised at high temperature generally did not restore fertility. This result differs from that observed in Drosophila and suggested that in C. elegans spermatogenesis or sperm function is irreversibly impaired in males that develop at high temperature. Mating and down-shifting experiments with hermaphrodites were performed to investigate the relative contributions of spermatogenic and oogenic defects to high temperature loss of fertility. It was found that the hermaphrodites of all isolates demonstrated loss in both spermatogenic and oogenic germ lines that differed in their relative contribution by isolate. These studies uncovered unexpectedly high variation in both the loss of fertility and problems with oocyte function in natural variants of C. elegans at high temperature.

The Fluorescence2D is free software that allows analysis of two-dimensional fluorescence spectra obtained using the accelerated "triangular" acquisition schemes. The software is a combination of Python and MATLAB-based programs that perform conversion of the triangular data, display of the two-dimensional spectra, extraction of 1D slices at different wavelengths, and output in various graphic formats.

RNA surveillance plays an important role in posttranscriptional regulation. Seminal work in this field has largely focused on yeast as a model system, whereas exploration of RNA surveillance in mammals is only recently begun. The increased transcriptional complexity of mammalian systems provides a wider array of targets for RNA surveillance, and, while many questions remain unanswered, emerging data suggest the nuclear RNA surveillance machinery exhibits increased complexity as well. We have used a small interfering RNA in mouse N2A cells to target the homolog of a yeast protein that functions in RNA surveillance (Mtr4p). We used high-throughput sequencing of polyadenylated RNAs (PA-seq) to quantify the effects of the mMtr4 knockdown (KD) on RNA surveillance. We demonstrate that overall abundance of polyadenylated protein coding mRNAs is not affected, but several targets of RNA surveillance predicted from work in yeast accumulate as adenylated RNAs in the mMtr4KD. microRNAs are an added layer of transcriptional complexity not found in yeast. After Drosha cleavage separates the pre-miRNA from the microRNA's primary transcript, the byproducts of that transcript are generally thought to be degraded. We have identified the 5' leading segments of pri-miRNAs as novel targets of mMtr4 dependent RNA surveillance.

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role of each domain of the enzyme we engineered dimerization domain deletion mutants of DapEs from Haemophilus influenzae and Vibrio cholerae, and characterized these proteins structurally and biochemically. No activity was observed for all deletion mutants. Structural comparisons of wild-type, inactive monomeric DapE enzymes with other M20 peptidases suggest that the dimerization domain is essential for DapE enzymatic activity. Structural analysis and molecular dynamics simulations indicate that removal of the dimerization domain increased the flexibility of a conserved active site loop that may provide critical interactions with the substrate.

In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient's tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing.

Regulation of myosin light chain phosphatase (MLCP) via protein kinase C (PKC) and the 17 kDa PKC-potentiated inhibitor of myosin light chain phosphatase (CPI-17) has been reported as a Ca(2+) sensitization signaling pathway in smooth muscle (SM), and thus may be involved in tonic vs. phasic contractions. This study examined the protein expression and spatial-temporal distribution of PKCα and CPI-17 in intact SM tissues. KCl or carbachol (CCh) stimulation of tonic stomach fundus SM generates a sustained contraction while the phasic stomach antrum generates a transient contraction. In addition, the tonic fundus generates greater relative force than phasic antrum with 1 µM phorbol 12, 13-dibutyrate (PDBu) stimulation which is reported to activate the PKCα - CPI-17 pathway. Western blot analyses demonstrated that this contractile difference was not caused by a difference in the protein expression of PKCα or CPI-17 between these two tissues. Immunohistochemical results show that the distribution of PKCα in the longitudinal and circular layers of the fundus and antrum do not differ, being predominantly localized near the SM cell plasma membrane. Stimulation of either tissue with 1 µM PDBu or 1 µM CCh does not alter this peripheral PKCα distribution. There are no differences between these two tissues for the CPI-17 distribution, but unlike the PKCα distribution, CPI-17 appears to be diffusely distributed throughout the cytoplasm under relaxed tissue conditions but shifts to a primarily peripheral distribution at the plasma membrane with stimulation of the tissues with 1 µM PDBu or 1 µM CCh. Results from double labeling show that neither PKCα nor CPI-17 co-localize at the adherens junction (vinculin/talin) at the membrane but they do co-localize with each other and with caveoli (caveolin) at the membrane. This lack of difference suggests that the PKCα - CPI-17 pathway is not responsible for the tonic vs. phasic contractions observed in stomach fundus and antrum.