Structure of a backtracked hexasomal intermediate of nucleosome transcription.

During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS are present. The cryo-EM structure of an intermediate of the nucleosome passage shows a partially unraveled hexasome that lacks the proximal H2A-H2B dimer and interacts with the RNA Pol II jaw, DSIF, and the CTR9trestle helix. RNA Pol II adopts a backtracked state with the RNA 3' end dislodged from the active site and bound in the RNA Pol II pore. Additional structures and biochemical data show that human TFIIS enters the RNA Pol II pore and stimulates the cleavage of the backtracked RNA and nucleosome passage.

Estimates of differential toxin expression governing heterogeneous intracellular lifespans of Streptococcus pneumoniae.

Following invasion of the host cell, pore-forming toxins secreted by pathogens compromise vacuole integrity and expose the microbe to diverse intracellular defence mechanisms. However, the quantitative correlation between toxin expression levels and consequent pore dynamics, fostering the intracellular life of pathogens, remains largely unexplored. In this study, using Streptococcus pneumoniae and its secreted pore-forming toxin pneumolysin (Ply) as a model system, we explored various facets of host-pathogen interactions in the host cytosol. Using time-lapse fluorescence imaging, we monitored pore formation dynamics and lifespans of different pneumococcal subpopulations inside host cells. Based on experimental histograms of various event timescales such as pore formation time, vacuolar death or cytosolic escape time and total degradation time, we developed a mathematical model based on first-passage processes that could correlate the event timescales to intravacuolar toxin accumulation. This allowed us to estimate Ply production rate, burst size and threshold Ply quantities that trigger these outcomes. Collectively, we present a general method that illustrates a correlation between toxin expression levels and pore dynamics, dictating intracellular lifespans of pathogens.

B cell receptors and free antibodies have different antigen-binding kinetics.

Since the pioneering works of Berg and Purcell, discriminating between diffusion followed by binding has played a central role in understanding cell signaling. B cell receptors (BCR) and antibodies (Ab) challenge that simplified view as binding to the antigen follows after a chain of diffusion and rotations, including whole molecule rotation and independent tilts and twists of their Fab arms due to their Y-shaped structure and flexibility. In this paper, we combine analytical calculations with Brownian simulations to derive the first-passage times due to these three rotations positioning the Fab paratopes at a proper distance and orientation required for antigen binding. Our results indicate that when measuring Ab-Ag effective kinetic binding rates, using experimental methods in which the analyte is in solution only gives values proportional to the intrinsic binding rates, [Formula: see text], and [Formula: see text], for values of [Formula: see text] up to [Formula: see text]. Beyond that, a plateau of the effective 3D on rate between [Formula: see text] and [Formula: see text] is attained. Additionally, for BCR-Ag interactions, the effective 2D on and off binding rates can only be inferred from the corresponding effective 3D on and off rates for values of effective 3D on rates lower than [Formula: see text]. This is highly relevant when trying to relate BCR-antigen-binding strength and B cell response, especially during germinal center reactions. Therefore, there is a pressing need to reexamine our current understanding of the BCR-antigen kinetic rates in germinal centers using the latest experimental assays for BCR-Ag interactions.

Serial cell culture passaging in vitro led to complete attenuation and changes in the characteristic features of a virulent porcine deltacoronavirus strain.

Porcine deltacoronavirus (PDCoV) is an important enteric coronavirus that has caused enormous economic losses in the pig industry worldwide. However, no commercial vaccine is currently available. Therefore, developing a safe and efficacious live-attenuated vaccine candidate is urgently needed. In this study, the PDCoV strain CH/XJYN/2016 was continuously passaged in LLC-PK cells until passage 240, and the virus growth kinetics in cell culture, pathogenicity in neonatal piglets, transcriptome differences after LLC-PK infection, changes in the functional characteristics of the spike (S) protein in the high- and low-passage strains, genetic variation of the virus genome, resistance to pepsin and acid, and protective effects of this strain when used as a live-attenuated vaccine were examined. The results of animal experiments demonstrated that the virulent PDCoV strain CH/XJYN/2016 was completely attenuated and not pathogenic in piglets following serial cell passage. Genome sequence analysis showed that amino acid mutations in nonstructural proteins were mainly concentrated in Nsp3, structural protein mutations were mainly concentrated in the S protein, and the N, M, and E genes were conserved. Transcriptome comparison revealed that compared with negative control cells, P10-infected LLC-PK cells had the most differentially expressed genes (DEGs), while P0 and P240 had the least number of DEGs. Analysis of trypsin dependence and related structural differences revealed that the P10 S protein interacted more strongly with trypsin and that the P120 S protein interacted more strongly with the APN receptor. Moreover, the infectivity of P240 was not affected by pepsin but was significantly decreased after exposure to low pH. Furthermore, the P240-based live-attenuated vaccine provided complete protection to piglets against the challenge of virulent PDCoV. In conclusion, we showed that a PDCoV strain was completely attenuated through serial passaging in vitro. These results provide insights into the potential molecular mechanisms of PDCoV attenuation and the development of a promising live-attenuated PDCoV vaccine.IMPORTANCEPorcine deltacoronavirus (PDCoV) is one of the most important enteropathogenic pathogens that cause diarrhea in pigs of various ages, especially in suckling piglets, and causes enormous economic losses in the global commercial pork industry. There are currently no effective measures to prevent and control PDCoV. As reported in previous porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus studies, inactivated vaccines usually elicit less robust protective immune responses than live-attenuated vaccines in native sows. Therefore, identifying potential attenuation mechanisms, gene evolution, pathogenicity differences during PDCoV passaging, and immunogenicity as live-attenuated vaccines is important for elucidating the mechanism of attenuation and developing safe and effective vaccines for virulent PDCoV strains. In this study, we demonstrated that the virulence of the PDCoV strain CH/XJYN/2016 was completely attenuated following serial cell passaging in vitro, and changes in the biological characteristics and protection efficacy of the strain were evaluated. Our results help elucidate the mechanism of PDCoV attenuation and support the development of appropriate designs for the study of live PDCoV vaccines.

Propagating and banking genetically diverse human sapovirus strains using a human duodenal cell line: investigating antigenic differences between strains.

There are four genogroups and 18 genotypes of human sapoviruses (HuSaVs) responsible for acute gastroenteritis. To comprehend their antigenic and virological differences, it is crucial to obtain viral stocks of the different strains. Previously, we utilized the human duodenum-derived cell line HuTu80, and glycocholate, a conjugated bile acid, to replicate and propagate GI.1, GI.2, and GII.3 HuSaVs (H. Takagi et al., Proc Natl Acad Sci U S A 117:32078-32085, 2020, https://10.1073/pnas.2007310117). First, we investigated the impact of HuTu80 passage number on HuSaV propagation. Second, we demonstrated that taurocholate improved the initial replication success rate and viral RNA levels in fecal specimens relative to glycocholate. By propagating 15 HuSaV genotypes (GI.1-7, GII.1-5, -8, and GV.1-2) and accomplishing preparation of viral stocks containing 1.0 × 109 to 3.4 × 1011 viral genomic copies/mL, we found that all strains required bile acids for replication, with GII.4 showing strict requirements for taurocholate. The deduced VP1 sequences of the viruses during the scale-up of serial passaged virus cultures were either identical or differed by only two amino acids from the original sequences in feces. In addition, we purified virions from nine strains of different genotypes and used them as immunogens for antiserum production. Enzyme-linked immunosorbent assays (ELISAs) using rabbit and guinea pig antisera for each of the 15 strains of different genotypes revealed distinct antigenicity among the propagating viruses across genogroups and differences between genotypes. Acquisition of biobanked viral resources and determination of key culture conditions will be valuable to gain insights into the common mechanisms of HuSaV infection. IMPORTANCE: The control of human sapovirus, which causes acute gastroenteritis in individuals of all ages, is challenging because of its association with outbreaks similar to those caused by human norovirus. The establishment of conditions for efficient viral propagation of various viral strains is essential for understanding the infection mechanism and identifying potential control methods. In this study, two critical factors for human sapovirus propagation in a conventional human duodenal cell line were identified, and 15 strains of different genotypes that differed at the genetic and antigenic levels were isolated and used to prepare virus stocks. The preparation of virus stocks has not been successful for noroviruses, which belong to the same family as sapoviruses. Securing virus stocks of multiple human sapovirus strains represents a significant advance toward establishing a reliable experimental system that does not depend on limited virus-positive fecal material.

Spontaneous α Brain Dynamics Track the Episodic "When".

Across species, neurons track time over the course of seconds to minutes, which may feed the sense of time passing. Here, we asked whether neural signatures of time-tracking could be found in humans. Participants stayed quietly awake for a few minutes while being recorded with magnetoencephalography (MEG). They were unaware they would be asked how long the recording lasted (retrospective time) or instructed beforehand to estimate how long it will last (prospective timing). At rest, rhythmic brain activity is nonstationary and displays bursts of activity in the alpha range (α: 7-14 Hz). When participants were not instructed to attend to time, the relative duration of α bursts linearly predicted individuals' retrospective estimates of how long their quiet wakefulness lasted. The relative duration of α bursts was a better predictor than α power or burst amplitude. No other rhythmic or arrhythmic activity predicted retrospective duration. However, when participants timed prospectively, the relative duration of α bursts failed to predict their duration estimates. Consistent with this, the amount of α bursts was discriminant between prospective and retrospective timing. Last, with a control experiment, we demonstrate that the relation between α bursts and retrospective time is preserved even when participants are engaged in a visual counting task. Thus, at the time scale of minutes, we report that the relative time of spontaneous α burstiness predicts conscious retrospective time. We conclude that in the absence of overt attention to time, α bursts embody discrete states of awareness constitutive of episodic timing.SIGNIFICANCE STATEMENT The feeling that time passes is a core component of consciousness and episodic memory. A century ago, brain rhythms called "α" were hypothesized to embody an internal clock. However, rhythmic brain activity is nonstationary and displays on-and-off oscillatory bursts, which would serve irregular ticks to the hypothetical clock. Here, we discovered that in a given lapse of time, the relative bursting time of α rhythms is a good indicator of how much time an individual will report to have elapsed. Remarkably, this relation only holds true when the individual does not attend to time and vanishes when attending to it. Our observations suggest that at the scale of minutes, α brain activity tracks episodic time.

Augmented mitochondrial apoptotic signaling impairs C2C12 myoblast differentiation following cellular aging through sequential passaging.

Aging is associated with the steady decline of several cellular processes. The loss of skeletal muscle mass, termed sarcopenia, is one of the major hallmarks of aging. Aged skeletal muscle exhibits a robust reduction in its regenerative capacity due to dysfunction (i.e., senescence, lack of self-renewal, and impaired differentiation) of resident muscle stem cells, called satellite cells. To replicate aging in vitro, immortalized skeletal muscle cells (myoblasts) can be treated with various agents to mimic age-related dysfunction; however, these come with their own set of limitations. In the present study, we used sequential passaging of mouse myoblasts to mimic impaired differentiation that is observed in aged skeletal muscle. Further, we investigated mitochondrial apoptotic mechanisms to better understand the impaired differentiation in these "aged" cells. Our data shows that sequential passaging (>20 passages) of myoblasts is accompanied with significant reductions in differentiation and elevated cell death. Furthermore, high-passage (HP) myoblasts exhibit greater mitochondrial-mediated apoptotic signaling through mitochondrial BAX translocation, CYCS and AIFM1 release, and caspase-9 activation. Finally, we show that inhibition of mitochondrial outer membrane permeability partly recovered differentiation in HP myoblasts. Together, our findings suggests that mitochondrial apoptotic signaling is a contributing factor to the diminished differentiation that is observed in aged myoblasts.

Continuous gated first-passage processes.

Gated first-passage processes, where completion depends on both hitting a target and satisfying additional constraints, are prevalent across various fields. Despite their significance, analytical solutions to basic problems remain unknown, e.g. the detection time of a diffusing particle by a gated interval, disk, or sphere. In this paper, we elucidate the challenges posed by continuous gated first-passage processes and present a renewal framework to overcome them. This framework offers a unified approach for a wide range of problems, including those with single-point, half-line, and interval targets. The latter have so far evaded exact solutions. Our analysis reveals that solutions to gated problems can be obtained directly from the ungated dynamics. This, in turn, reveals universal properties and asymptotic behaviors, shedding light on cryptic intermediate-time regimes and refining the notion of high-crypticity for continuous-space gated processes. Moreover, we extend our formalism to higher dimensions, showcasing its versatility and applicability. Overall, this work provides valuable insights into the dynamics of continuous gated first-passage processes and offers analytical tools for studying them across diverse domains.

Deciphering adiabatic rotating frame relaxometry in biological tissues.

PURPOSE: This work aims to unravel the intricacies of adiabatic rotating frame relaxometry in biological tissues. THEORY AND METHODS: The classical formalisms of dipolar relaxation R 1 ρ $$ {R}_{1\rho } $$ and R 2 ρ $$ {R}_{2\rho } $$ were systematically analyzed for water molecules reorienting on "fast" and "slow" timescales. These two timescales are, respectively, responsible for the absence and presence of R 1 ρ $$ {R}_{1\rho } $$ dispersion. A time-averaged R 1 ρ $$ {R}_{1\rho } $$ or R 2 ρ $$ {R}_{2\rho } $$ over an adiabatic pulse duration was recast into a sum of R 1 $$ {R}_1 $$ and R 2 $$ {R}_2 $$ , but with different weightings. These weightings depend on the specific modulations of adiabatic pulse waveforms. In this context, stretched hyperbolic secant ( HSn $$ HSn $$ ) pulses were characterized. Previously published H S 1 $$ HS1 $$ R 1 ρ $$ {R}_{1\rho } $$ , continuous-wave (CW) R 1 ρ $$ {R}_{1\rho } $$ , and R 1 $$ {R}_1 $$ measures from 12 agarose phantoms were used to validate the theoretical predictions. A similar validation was also performed on previously published HSn $$ HSn $$ R 1 ρ $$ {R}_{1\rho } $$ ( n $$ n $$ =1, 4, 8) and HS 1 $$ HS1 $$ R 2 ρ $$ {R}_{2\rho } $$ from bovine cartilage specimens. RESULTS: Longitudinal relaxation weighting decreases for HSn $$ HSn $$ pulses as n $$ n $$ increases. Predicted CW R 1 ρ cal $$ {R}_{1\rho}^{cal} $$ values from agarose phantoms align well with the measured CW R 1 ρ exp $$ {R}_{1\rho}^{exp} $$ values, as indicated by a linear regression function: R 1 ρ cal = 1.04 * R 1 ρ exp - 1.96 $$ {R}_{1\rho}^{cal}={1.04}^{\ast }{R}_{1\rho}^{exp}-1.96 $$ . The predicted adiabatic R 1 ρ $$ {R}_{1\rho } $$ and R 2 ρ $$ {R}_{2\rho } $$ from cartilage specimens are consistent with those previously measured, as quantified by: R 1 ρ , 2 ρ cal = 1.10 * R 1 ρ , 2 ρ exp - 0.41 $$ {R}_{1\rho, 2\rho}^{cal}={1.10}^{\ast }{R}_{1\rho, 2\rho}^{exp}-0.41 $$ . CONCLUSION: This work has theoretically and experimentally demonstrated that adiabatic R 1 ρ $$ {R}_{1\rho } $$ and R 2 ρ $$ {R}_{2\rho } $$ can be recast into a sum of R 1 $$ {R}_1 $$ and R 2 $$ {R}_2 $$ , with varying weightings. Therefore, any suggestions that adiabatic rotating frame relaxometry in biological tissues could provide more information than the standard R 1 $$ {R}_1 $$ and R 2 $$ {R}_2 $$ warrant closer scrutiny.

Among-species variation in six decades of changing migration timings explained through ecology, life-history and local migratory abundance.

Species exploiting seasonal environments must alter timings of key life-history events in response to large-scale climatic changes in order to maintain trophic synchrony with required resources. Yet, substantial among-species variation in long-term phenological changes has been observed. Advancing from simply describing such variation towards predicting future phenological responses requires studies that rigorously quantify and explain variation in the direction and magnitude of changing timings across diverse species in relation to key ecological and life-history variables. Accordingly, we fitted multi-quantile regressions to 59 years of multi-species data on spring and autumn bird migration timings through northern Scotland. We demonstrate substantial variation in changes in timings among 72 species, and tested whether such variation can be explained by species ecology, life-history and changes in local abundance. Consistent with predictions, species that advanced their migration timing in one or both seasons had more seasonally restricted diet types, fewer suitable breeding habitat types, shorter generation lengths and capability to produce multiple offspring broods per year. In contrast, species with less seasonally restricted diet types and that produce single annual offspring broods, showed no change. Meanwhile, contrary to prediction, long-distance and short-distance migrants advanced migration timings similarly. Changes in migration timing also varied with changes in local migratory abundance, such that species with increasing seasonal abundance apparently altered their migration timing, whilst species with decreasing abundance did not. Such patterns broadly concur with expectation given adaptive changes in migration timing. However, we demonstrate that similar patterns can be generated by numerical sampling given changing local abundances. Any apparent phenology-abundance relationships should, therefore, be carefully validated and interpreted. Overall, our results show that migrant bird species with differing ecologies and life-histories showed systematically differing phenological changes over six decades contextualised by large-scale environmental changes, potentially facilitating future predictions and altering temporal dynamics of seasonal species co-occurrences.

Cycling temperature treatments affect estimates of digestive performance in prairie lizards (Sceloporus consobrinus).

In nature, many organisms experience a daily range of body temperatures. Thermal performance at stable temperatures is often extrapolated to predict function in cyclical environments. However, temperature order and cyclicity may influence physiological processes. The current study compared energy intake, digestive passage time and energy budgets at a stable temperature (33°C) and two temperature cycles in lizards (Sceloporus consobrinus), to determine (1) whether stable treatments adequately project performance in a cycling environment and (2) whether temperature order influences performance. Cycles had a mean temperature of 33°C, and rotated through 30°C, 33°C and 36°C daily, with equal durations of time at each temperature but differing temperature order, with warm days and cool nights in cycle 1 and cool days and warm nights in cycle 2. For analyses, performance in the stable treatment was compared with that during cycles. If temperature is the primary factor regulating performance, then performance from the stable treatment and cycles should compare favorably. However, physiological performance varied based on temperature treatment. Energy intake and budgets were similar between the stable trial and cycle 1 but not cycle 2. However, passage time did not differ. Notably, the two cycling regimes consistently varied in performance, indicating that temperature order plays a primary role in regulating performance. Physiological data collection requires careful consideration of effects of cycling versus stable temperature treatments. Stable temperatures do not consistently represent performance in cycling regimes and consideration should be paid not only to which temperatures animals experience but also to how temperature is experienced in nature.

Prevalence and predictors of stone passage after double J stenting for symptomatic ureteral stones: a cross-sectional, real-life study.

PURPOSE: To evaluate the rate of and predictors of stone passage (SP) after urgent retrograde stenting for symptomatic ureteral stones. METHODS: We retrospectively analysed data from 249 consecutive patients presenting to the emergency department for symptomatic ureteral stones and treated with retrograde stenting. Demographic, clinical and laboratory characteristics were collected. Stones parameters were collected before stenting and SP was evaluated at 1 month with computerized tomography. Descriptive statistics and logistic regression models tested the association between predictors and SP. RESULTS: Overall, median (IQR) age and stone diameter were 56 (45-68) years and 7.1 (4.4-9.8) mm, respectively. Stones were located in the proximal, mid and distal ureter in 102 (41.0%), 48 (19.3%) and 99 (39.8%) cases. SP was observed in 65 (26.2%) individuals. Stone diameter (3.2 vs. 7.7 mm, p < 0.001) and stone density (416 vs. 741, p < 0.001) were lower and a higher rate of distal stones (76.9% vs. 26.7%, p < 0.001) was found in the SP group compared to that with persistent stones. Multivariable logistic regression analysis showed that distal ureteral stone location (OR 7.9, p < 0.01) and lower HU (OR 0.9, p < 0.01) were associated with SP, after accounting for stone volume. Patients with a distal stone of 500 HU had a 75% probability of SP. CONCLUSION: Stone passage occurred in 26% of patients with indwelling stent due to symptomatic ureteral stones. Lower stone density and distal stone location were independent predictors of stone passage. Patients with these criteria should be managed with follow-up imaging and stent removal instead of ureteroscopy.

Novel Near-Infrared-II In Vivo Visualization Revealed Rapid Calcium Intestine Turnover in Daphnia magna with Delayed Impact by Cadmium and Acidification.

Calcium is a highly demanded metal, and its transport across the intestine of Daphnia magna remains a significant unresolved question. Due to technical constraints, the visualization of the kinetic process of Ca passage through D. magna has been challenging. Here, we developed the second near-infrared Ca sensor (NIR-II Ca) and conducted real-time in vivo imaging of Ca in daphnids with a high signal-to-noise ratio, deep tissue penetration, and minimal damage. Through the utilization of the NIR-II Ca sensor, we for the first time visualized and quantified the kinetic process of Ca passage in the intestine in real time. The results revealed that trophically available Ca passed through the intestines in 24 h, whereas waterborne Ca required only 35 min. This rapid "flushing through" mechanism established waterborne Ca as the primary source of Ca absorption. However, environmental stressors such as water acidification and cadmium significantly delayed the Ca passage and absorption. The development of NIR imaging and sensors allows for real-time dynamic visualization of contaminants/nutrients in organisms and holds great potential as a powerful tool for future studies into material kinetic processes in living animals.

Pluronic F127-Complexed PEGylated Poly(glutamic acid)-Cisplatin Nanomedicine for Enhanced Glioblastoma Therapy.

Glioblastoma is one of the most aggressive and treatment-resistant forms of primary brain cancer, posing significant challenges in effective therapy. This study aimed to enhance the effectiveness of glioblastoma therapy by developing a unique nanomedicine composed of Pluronic F127-complexed PEGylated poly(glutamic acid)-cisplatin (PLG-PEG/PF127-CDDP). PLG-PEG/PF127-CDDP demonstrated an optimal size of 133.97 ± 12.60 nm, facilitating efficient cell uptake by GL261 glioma cells. In vitro studies showed significant cytotoxicity against glioma cells with a half-maximal (50%) inhibitory concentration (IC50) of 12.61 µg mL-1 at 48 h and a 72.53% ± 1.89% reduction in cell invasion. Furthermore, PLG-PEG/PF127-CDDP prolonged the circulation half-life of cisplatin to 9.75 h in vivo, leading to a more than 50% reduction in tumor size on day 16 post-treatment initiation in a murine model of glioma. The treatment significantly elevated lactate levels in GL261 cells, indicating enhanced metabolic disruption. Therefore, PLG-PEG/PF127-CDDP offers a promising approach for glioblastoma therapy due to its effects on improving drug delivery efficiency, therapeutic outcomes, and safety while minimizing systemic side effects. This work underscores the potential of polymer-based nanomedicines in overcoming the challenges of treating brain tumors, paving the way for future clinical applications.

Distinctive features of experiential time: Duration, speed and event density.

William James's use of "time in passing" and "stream of thoughts" may be two sides of the same coin that emerge from the brain segmenting the continuous flow of information into discrete events. Herein, we investigated how the density of events affects two temporal experiences: the felt duration and speed of time. Using a temporal bisection task, participants classified seconds-long videos of naturalistic scenes as short or long (duration), or slow or fast (passage of time). Videos contained a varying number and type of events. We found that a large number of events lengthened subjective duration and accelerated the felt passage of time. Surprisingly, participants were also faster at estimating their felt passage of time compared to duration. The perception of duration scaled with duration and event density, whereas the felt passage of time scaled with the rate of change. Altogether, our results suggest that distinct mechanisms underlie these two experiential times.

First Passage Times of Long Transient Dynamics in Ecology.

Long transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attractors or alternative stable states. We propose an intuitive threshold for first passage time analysis applicable to both bistable and ghost attractor regimes. By formulating the first passage time problem as a backward Kolmogorov equation, we examine how the mean first passage time changes as parameters are varied from the ghost attractor regime to the bistable one, through a saddle-node bifurcation. Our results reveal that the mean and variance of first passage times vary smoothly across the bifurcation threshold, eliminating the deterministic distinction between ghost attractors and bistable regimes. This work suggests that first passage time analysis can be an informative way to classify the length of a long transient. A better understanding of the duration of long transients may contribute to greater ecological understanding and more effective environmental management.

Predictors of spontaneous passage of ingested foreign bodies in adults: twelve years of experience.

BACKGROUND: Foreign body ingestion in adults is commonly encountered in clinical practice. The therapeutic approach of whether to follow-up or extract is often controversial. AIM: We aimed to explore predictors for spontaneous passage of ingested foreign bodies by focusing on foreign body type, length, and location of impaction. METHODS: We performed a 12-year retrospective single-center study. Logistic regression analysis was done to identify predictors of spontaneous passage. RESULTS: Overall, 365 patients with foreign body ingestion were included. The rate of spontaneous passage was 53.7% in general, while the spontaneous passage rate was 47.9% in food impaction, 44.3% in sharp objects, 88.7% in blunt objects and only 22.2% in long blunt objects (> 6 cm). On regression analysis, esophageal location was associated with a higher impaction rate and lower spontaneous passage vs. stomach and small and large intestine (OR 0.15, 95% CI 0.07-0.31, OR 0.18, 95% CI 0.09-0.37 and OR 0.02, 95% CI 0.003-0.14), respectively. Performing Receiver operating characteristics (ROC) analysis found that the maximal length above which the foreign body will fail to pass spontaneously was 3.5 cm in the stomach and 3 cm in the small intestine, with area under the curve (AUC) of 0.8509 in stomach and 0.8073 in small intestine. CONCLUSION: Endoscopic removal was needed for all esophageal foreign bodies, and all foreign bodies more than 3.5 cm above the duodenum. Spontaneous passage of ingested foreign body in a selected cohort of patients depends on foreign body type, location, and length.

Intravenous treatment with a molecular chaperone designed against ß-amyloid toxicity improves Alzheimer's disease pathology in mouse models.

Attempts to treat Alzheimer's disease with immunotherapy against the ß-amyloid (Aß) peptide or with enzyme inhibitors to reduce Aß production have not yet resulted in effective treatment, suggesting that alternative strategies may be useful. Here we explore the possibility of targeting the toxicity associated with Aß aggregation by using the recombinant human (rh) Bri2 BRICHOS chaperone domain, mutated to act selectively against Aß42 oligomer generation and neurotoxicity in vitro. We find that treatment of Aß precursor protein (App) knockin mice with repeated intravenous injections of rh Bri2 BRICHOS R221E, from an age close to the start of development of Alzheimer's disease-like pathology, improves recognition and working memory, as assessed using novel object recognition and Y maze tests, and reduces Aß plaque deposition and activation of astrocytes and microglia. When treatment was started about 4 months after Alzheimer's disease-like pathology was already established, memory improvement was not detected, but Aß plaque deposition and gliosis were reduced, and substantially reduced astrocyte accumulation in the vicinity of Aß plaques was observed. The degrees of treatment effects observed in the App knockin mouse models apparently correlate with the amounts of Bri2 BRICHOS detected in brain sections after the end of the treatment period.

Towards characterization of cell culture conditions for reliable proteomic analysis: in vitro studies on A549, differentiated THP-1, and NR8383 cell lines.

Proteomic investigations result in high dimensional datasets, but integration or comparison of different studies is hampered by high variances due to different experimental setups. In addition, cell culture conditions can have a huge impact on the outcome. This study systematically investigates the impact of experimental parameters on the proteomic profiles of commonly used cell lines-A549, differentiated THP-1 macrophage-like cells, and NR8383-for toxicity studies. The work focuses on analyzing the influence at the proteome level of cell culture setup involving different vessels, cell passage numbers, and post-differentiation harvesting time, aiming to improve the reliability of proteomic analyses for hazard assessment. Mass-spectrometry-based proteomics was utilized for accurate protein quantification by means of a label-free approach. Our results showed that significant proteome variations occur when cells are cultivated under different setups. Further analysis of these variations revealed their association to specific cellular pathways related to protein misfolding, oxidative stress, and proteasome activity. Conversely, the influence of cell passage numbers on the proteome is minor, suggesting a reliable range for conducting reproducible biological replicates. Notable, substantial proteome alterations occur over-time post-differentiation of dTHP-1 cells, particularly impacting pathways crucial for macrophage function. This finding is key for the interpretation of experimental results. These results highlight the need for standardized culture conditions in proteomic-based evaluations of treatment effects to ensure reliable results, a prerequisite for achieving regulatory acceptance of proteomics data.

Effect of impeller rotational phase on the FDA blood pump velocity fields.

BACKGROUND: The Food and Drug Administration (FDA) blood pump is an open-source benchmark cardiovascular device introduced for validating computational and experimental performance analysis tools. The time-resolved velocity field for the whole impeller has not been established, as is undertaken in this particle image velocimetry (PIV) study. The level of instantaneous velocity fluctuations is important, to assess the flow-induced rotor vibrations which may contribute to the total blood damage. METHODS: To document these factors, time-resolved two-dimensional PIV experiments were performed that were precisely phase-locked with the impeller rotation angle. The velocity fields in the impeller and in the volute conformed with the previous single blade passage experiments of literature. RESULTS: Depending on the impeller orientation, present experiments showed that volute outlet nozzle flow can fluctuate up to 34% during impeller rotation, with a maximum standard experimental uncertainty of 2.2%. Likewise, the flow fields in each impeller passage also altered in average 33.5%. Considerably different vortex patterns were observed for different blade passages, with the largest vortical structures reaching an average core radii of 7 mm. The constant volute area employed in the FDA pump design contributes to the observed velocity imbalance, as illustrated in our velocity measurements. CONCLUSIONS: By introducing the impeller orientation parameter for the nozzle flow, this study considers the possible uncertainties influencing pump flow. Expanding the available literature data, analysis of inter-blade relative velocity fields is provided here for the first-time to the best of our knowledge. Consequently, our research fills a critical knowledge gap in the understanding of the flow dynamics of an important benchmark cardiovascular device. This study prompts the need for improved hydrodynamic designs and optimized devices to be used as benchmark test devices, to build more confidence and safety in future ventricular assist device performance assessment studies.