Interpreting the retinal neural code for natural scenes: From computations to neurons.

Understanding the circuit mechanisms of the visual code for natural scenes is a central goal of sensory neuroscience. We show that a three-layer network model predicts retinal natural scene responses with an accuracy nearing experimental limits. The model's internal structure is interpretable, as interneurons recorded separately and not modeled directly are highly correlated with model interneurons. Models fitted only to natural scenes reproduce a diverse set of phenomena related to motion encoding, adaptation, and predictive coding, establishing their ethological relevance to natural visual computation. A new approach decomposes the computations of model ganglion cells into the contributions of model interneurons, allowing automatic generation of new hypotheses for how interneurons with different spatiotemporal responses are combined to generate retinal computations, including predictive phenomena currently lacking an explanation. Our results demonstrate a unified and general approach to study the circuit mechanisms of ethological retinal computations under natural visual scenes.

A machine learning photon detection algorithm for coherent x-ray ultrafast fluctuation analysis.

X-ray free electron laser experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring atomic motion. One such area is the ability to use finely spaced sets of coherent x-ray pulses to be compared after scattering from a dynamic system at different times. This enables the study of fluctuations in many-body quantum systems at the level of the ultrafast pulse durations, but this method has been limited to a select number of examples and required complex and advanced analytical tools. By applying a new methodology to this problem, we have made qualitative advances in three separate areas that will likely also find application to new fields. As compared to the "droplet-type" models, which typically are used to estimate the photon distributions on pixelated detectors to obtain the coherent x-ray speckle patterns, our algorithm achieves an order of magnitude speedup on CPU hardware and two orders of magnitude improvement on GPU hardware. We also find that it retains accuracy in low-contrast conditions, which is the typical regime for many experiments in structural dynamics. Finally, it can predict photon distributions in high average-intensity applications, a regime which up until now has not been accessible. Our artificial intelligence-assisted algorithm will enable a wider adoption of x-ray coherence spectroscopies, by both automating previously challenging analyses and enabling new experiments that were not otherwise feasible without the developments described in this work.

Synchronous inhibitory pathways create both efficiency and diversity in the retina.

Sensory receptive fields combine features that originate in different neural pathways. Retinal ganglion cell receptive fields compute intensity changes across space and time using a peripheral region known as the surround, a property that improves information transmission about natural scenes. The visual features that construct this fundamental property have not been quantitatively assigned to specific interneurons. Here, we describe a generalizable approach using simultaneous intracellular and multielectrode recording to directly measure and manipulate the sensory feature conveyed by a neural pathway to a downstream neuron. By directly controlling the gain of individual interneurons in the circuit, we show that rather than transmitting different temporal features, inhibitory horizontal cells and linear amacrine cells synchronously create the linear surround at different spatial scales and that these two components fully account for the surround. By analyzing a large population of ganglion cells, we observe substantial diversity in the relative contribution of amacrine and horizontal cell visual features while still allowing individual cells to increase information transmission under the statistics of natural scenes. Established theories of efficient coding have shown that optimal information transmission under natural scenes allows a diverse set of receptive fields. Our results give a mechanism for this theory, showing how distinct neural pathways synthesize a sensory computation and how this architecture both generates computational diversity and achieves the objective of high information transmission.

Lower extremity arterial interventions in England.

INTRODUCTION: The increasing prevalence of diabetes mellitus and advances in endovascular therapies continue to have an impact on the epidemiology and management of lower extremity arterial disease. This study describes trends in lower extremity revascularisation and major lower limb amputation in NHS England over the past two decades (2000-2019). METHODS: Numbers of lower extremity endovascular interventions, open surgical procedures and major lower limb amputations performed in NHS England between 2000 and 2019 were extracted from publicly available hospital admitted patient care activity reports. Trends in intervention were assessed with linear regression models and chi-square tests for trend. RESULTS: Over this period, 527,131 revascularisations and 92,053 amputations were performed. The mean age of patients was 67.5 years (standard deviation 1.6 years) and 65.3% were male. The number of lower limb revascularisation procedures increased by 402.4 units/year (95% confidence interval, CI, 290.1-514.6, p < 0.001). The number of endovascular interventions rose by 43.5% (10,912 in 2000 vs 15,657 in 2019; ß = 359.5.0, 95% CI 279.3-439.8, p < 0.001) compared with no significant increase in the number of open surgical procedures (8,483 in 2000 vs 7,872 in 2019; ß = 42.8, 95% CI -8.3 to 94.0, p = 0.095). The number of major lower limb amputations has decreased by 9.4% (5,418 in 2000 vs 4,907 in 2019; ß = -31.0; 95% CI -49.6 to -12.5, R2 = 0.42, p = 0.003). CONCLUSIONS: There has been a significant increase in the rate of lower limb revascularisation procedures associated with decreased numbers of major lower limb amputations over the past two decades. These changes in overall trends may affect both service provision and vascular surgery training planning.

Mechanism and dynamics of fatty acid photodecarboxylase.

Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.

Real-time assessment of learning curve for robot-assisted laparoscopic prostatectomy.

INTRODUCTION: The learning curves analysed to date for robot-assisted laparoscopic prostatectomy are based on arbitrary cut-offs of the total cases. METHODS: We analysed a large dataset of robot-assisted laparoscopic prostatectomies from a single centre between 2008 and 2019 for assessment of the learning curve for perioperative outcomes with respect to time and individual cases. RESULTS: A total of 1,406 patients were evaluated, with mean operative time 198.08 minutes and mean console time 161.05 minutes. A plot of operative time and console time showed an initial decline followed by a near-constant phase. The inflection points were detected at 1,398 days (308th case) for operative time and 1,470 days (324th case) for console time, with a declining trend of 8.83 minutes and 7.07 minutes, respectively, per quarter-year (p<0.001). Mean estimated blood loss showed a 70.04% reduction between the start (214.76ml) and end (64.35ml) (p<0.001). The complication rate did not vary with respect to time (p=0.188) or the number of procedures (p=0.354). There was insufficient evidence to claim that the number of operations (p=0.326), D'Amico classification (p=0.114 for intermediate versus low; p=0.158 for high versus low) or time (p=0.114) was associated with the odds of positive surgical margins. CONCLUSIONS: It takes about 300 cases and nearly 4 years to standardise operative and console times, with a requirement of around 80 cases per annum for a single surgical team in the initial years to optimise the outcomes of robot-assisted laparoscopic prostatectomy.

Effect of footplate neuromuscular electrical stimulation on functional and quality-of-life parameters in patients with peripheral artery disease: pilot, and subsequent randomized clinical trial.

BACKGROUND: Supervised exercise programmes for intermittent claudication have poor access and limited compliance. Neuromuscular electrical stimulation (NMES) may be an effective alternative. A proof-of-concept study and RCT were conducted. METHODS: In study 1, eligible patients underwent baseline assessment; treadmill testing for initial (ICD) and maximum (MCD) claudication distance; EuroQoL Five Dimensions five-level instrument (EQ-5D-5L™) and Intermittent Claudication Questionnaire (ICQ) assessment; and measurement of ultrasound haemodynamics of the superficial femoral artery. After familiarization with the NMES device, participants underwent a 30-min session of stimulation with concomitant recording of haemodynamic measures at 15 min, and after device cessation. Measurements were repeated after 6 weeks of daily use of NMES. In study 2, consecutive patients underwent baseline assessment before online randomization to a supervised exercise programme only, or adjunctive NMES treatment for 6 weeks, followed by repeat measurements. RESULTS: Study 1 (20 patients) showed a significant improvement in MCD (46 per cent; P < 0·001) and ICD (71 per cent; P < 0·001). The RCT (42 patients) showed a significant adjunctive benefit of NMES in ICD (46 per cent; P = 0·014). Improvements were seen in the ICQ (9 points; P = 0·009) and EQ-5D-5L™ (P = 0·007) in study 1, and there was a significant adjunctive benefit of NMES on the ICQ score in patients who did supervised exercise (11·2 points; P = 0·031). Blood volume flow and time-adjusted mean velocity increased significantly with the device on (P < 0·050). Overall, NMES compliance exceeded 95 per cent. CONCLUSION: Footplate NMES significantly improved walking distance in patients with intermittent claudication when used independently and also as an adjunct to supervised exercise. Registration number: trial 1, NCT02436200; trial 2, NCT02429310 (http://www.clinicaltrials.gov).

ANTECEDENTES: Los programas de ejercicio supervisado (supervised exercise programmes, SEP) para la claudicación intermitente (intermittent claudication, IC) tienen un acceso y un cumplimiento deficientes. La estimulación eléctrica neuromuscular (neuromuscular electrical stimulation, NMES) puede ser una alternativa clínicamente efectiva. Se realizó un estudio de prueba de concepto y un ensayo controlado aleatorizado. MÉTODOS: Estudio 1: Veinte pacientes elegibles se sometieron a una evaluación inicial que incluía una prueba en la cinta de correr para la distancia inicial de claudicación (initial claudication distance, ICD) y la distancia máxima de claudicación (maximum claudication distance, MCD), EuroQoL-5D (EQ-5D), valoración mediante el cuestionario de claudicación intermitente (intermittent claudication questionnaire, ICQ), y hemodinámica por ecografía de la arteria femoral superficial. Después de familiarizarse con el dispositivo NMES, los participantes se sometieron a una sesión de estimulación de 30 minutos con el registro concomitante de medidas hemodinámicas a los 15 minutos y después del cese del dispositivo. Se realizaron mediciones repetidas después de 6 semanas de uso diario de NMES. Estudio 2: Se reclutaron 42 pacientes que tras una evaluación inicial y posterior aleatorización al azar en línea, se asignaron al Grupo A, utilizando SEP solamente; o al el Grupo B, con tratamiento NMES complementario durante 6 semanas seguido de medidas repetidas. RESULTADOS: El estudio 1 mostró una mejoría significativa de la MCD (46%, P < 0,0001) y de la ICD (71%, P < 0.004). El ensayo clínico mostró un beneficio coadyuvante significativo de NMES en la ICD (46%, P = 0,014). Se observaron mejorías en la puntuación del ICQ (9 puntos, P < 0,01) y del EQ-5D (P < 0,05) en el estudio 1, con un beneficio coadyuvante significativo de NMES en la puntuación del ICQ (11 puntos, P < 0,05). El flujo de volumen de sangre (CC/min) y TAMV (cm/s) aumentaron significativamente con el dispositivo en funcionamiento (P < 0,05). El cumplimiento global de la NMES superó el 95%. CONCLUSIÓN: La plataforma de NMES para el pie mejora significativamente las distancias de caminar en la claudicación intermitente cuando se usa de forma independiente y también proporciona un beneficio complementario al ejercicio supervisado en la distancia caminada sin dolor. La mejora del flujo sanguíneo puede ser un mecanismo para explicar estos resultados.

A mobile telehealth program for behavioral treatment of urinary incontinence in women veterans: Development and pilot evaluation of MyHealtheBladder.

AIM: To develop and pilot test an interactive mobile telehealth program (mHealth) for behavioral treatment of women veterans with urinary incontinence (UI). METHODS: We developed an evidence-based 8-week behavioral mHealth program, MyHealtheBladder, with input from women veterans, behavioral medicine and health education experts, and clinical providers treating UI in the VA system. The program was story-based and included pelvic floor muscle exercises, bladder control strategies, fluid management, risk factor reduction, and self-monitoring. Participants were women veterans seeking outpatient treatment for UI occurring at least twice weekly. The primary efficacy estimate was the change in UI frequency, volume and impact on the quality of life as measured by the validated International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF; range: 0-21, 2.5 points for minimal clinically important difference [MCID]). RESULTS: We enrolled 29 women veterans (ages 29-77 years; mean = 54.4 ± 10.4), including 15 (52%) African-American women, 13 (45%) women with high school education, and 16 (55%) with a college degree. Twenty of 29 women (69%) completed all 8 weeks of the intervention with a 97% adherence rate to the daily sessions among completers. We found reductions in ICIQ-SF scores from a mean 12.6 ± 3.9 at baseline to 10.4 ± 4.11 at 5 weeks, to 8.7 ± 4.0 at the end of the 8-week intervention. CONCLUSIONS: Women veterans using an 8-week behavioral mHealth program for the treatment of UI had symptom improvements that exceeded the MCID for the ICIQ-SF. Our next step involves comparing the effectiveness of MyHealtheBladder to usual care in a larger clinical trial.

The Lister AirSeal® port closure technique - Initial patient outcomes.

INTRODUCTION: The 12-mm AirSeal® port is widely used in robotically assisted laparoscopic prostatectomy due to its ability to maintain stable pneumoperitoneal pressures and smoke evacuation. However, it creates a potential risk of port site hernia. We have traditionally used EndoClose™ to perform full thickness closure of this port, but noted that patients experienced increased pain related to this procedure, which sometimes persisted for several months. Using the Da Vinci Si we performed peritoneal closure with 2-0 vicryl by switching the fourth arm to the right master controller. The external oblique sheath was closed outside with 1 Ethibond. MATERIALS AND METHODS: We performed this closure in 20 consecutive patients (group 1). Postoperative day 1, 2 and post-discharge telephone consultation pain scores (1-10) were recorded and compared with the previous 20 consecutive patients who had the EndoClose closure (group 2). RESULTS: We recorded an instructional video to enable reproduction of the new technique. The mean length of stay was 1.5 days for patients in group 1 and 1.9 days for those in group 2 (P = 0.04). There was no difference in operating time or average day 1 pain scores. Post-discharge follow-up call revealed 1 of 20 patients who had AirSeal port site pain in group 1 and 5 of 17 in group 2 (P = 0.04). Pain scores also tended to be higher for group 2. CONCLUSIONS: Our preliminary analysis of this novel technique to close the AirSeal port in two separate layers improves postoperative pain related to this port site.

Observational study of the medical management of patients with peripheral artery disease.

BACKGROUND: Previous research has suggested that patients with peripheral artery disease (PAD) are not offered adequate risk factor modification, despite their high cardiovascular risk. The aim of this study was to assess the cardiovascular profiles of patients with PAD and quantify the survival benefits of target-based risk factor modification. METHODS: The Vascular and Endovascular Research Network (VERN) prospectively collected cardiovascular profiles of patients with PAD from ten UK vascular centres (April to June 2018) to assess practice against UK and European goal-directed best medical therapy guidelines. Risk and benefits of risk factor control were estimated using the SMART-REACH model, a validated cardiovascular prediction tool for patients with PAD. RESULTS: Some 440 patients (mean(s.d.) age 70(11) years, 24·8 per cent women) were included in the study. Mean(s.d.) cholesterol (4·3(1·2) mmol/l) and LDL-cholesterol (2·7(1·1) mmol/l) levels were above recommended targets; 319 patients (72·5 per cent) were hypertensive and 343 (78·0 per cent) were active smokers. Only 11·1 per cent of patients were prescribed high-dose statin therapy and 39·1 per cent an antithrombotic agent. The median calculated risk of a major cardiovascular event over 10 years was 53 (i.q.r. 44-62) per cent. Controlling all modifiable cardiovascular risk factors based on UK and European guidance targets (LDL-cholesterol less than 2 mmol/l, systolic BP under 140 mmHg, smoking cessation, antiplatelet therapy) would lead to an absolute risk reduction of the median 10-year cardiovascular risk by 29 (20-38) per cent with 6·3 (4·0-9·3) cardiovascular disease-free years gained. CONCLUSION: The medical management of patients with PAD in this secondary care cohort was suboptimal. Controlling modifiable risk factors to guideline-based targets would confer significant patient benefit.

HIV self-screening distribution preferences and experiences among men who have sex with men in Mpumalanga Province: Informing policy for South Africa.

Current research suggests that HIV self-screening (HIVSS) is a feasible and acceptable approach to increase HIV testing among men who have sex with men (MSM). However, few data are available to shape policy around dissemination and implementation. Gaps in knowledge include preferences for distribution of HIVSS kits, potential social harms and benefits of their use, and how much test users would be willing to pay for the kits. The aim was to inform policy recommendations to optimise distribution of HIVSS kits to MSM in South Africa (SA), where there is a high HIV incidence and unmet testing needs. MSM in the high-HIV-prevalence Gert Sibande and Ehlanzeni districts of Mpumalanga Province, SA, were enrolled between October 2015 and May 2017. Participants were provided with their choice of blood or oral fluid HIVSS test kits, receiving 5 kits at enrolment and 4 additional kits at the 3-month follow-up visit. Questionnaires were administered at enrolment, 3 months and 6 months. We analysed participants' reported social benefits and harms, and their preferences for kit distribution and pricing. Among 127 MSM screened and enrolled, 114 responded to follow-up questionnaires regarding distribution preferences, 49.3% preferred to acquire HIVSS kits at a community-based organisation (CBO) and 42.7% at a clinic, with 8% preferring a pharmacy. Participants with higher education preferred CBO sites for distribution; in other respects preferences were similar by demographic characteristics. Reported social benefits were common, including knowing one's status, prevention knowledge gained and improved communication with partners. Despite ubiquitous interest in using the kits, the majority of MSM could not afford to purchase test kits. SA guidelines have integrated HIVSS into HIV and testing policy, but little has been published regarding distribution channels of the kits for MSM and other key populations. There is a partnership between the National Department of Health and CBOs that specialise in key population programming to ensure MSM and other populations with unmet testing needs can access affordable test kits. We observed no social harms, and there were multiple social benefits. Consequently, we recommend immediate free or low-cost distribution of HIVSS kits to MSM through community-based initiatives. Future research should continue to assess optimised linkage to care.

Correlation Judgment and Visualization Features: A Comparative Study.

Recent visualization research efforts have incorporated experimental techniques and perceptual models from the vision science community. Perceptual laws such as Weber's law, for example, have been used to model the perception of correlation in scatterplots. While this thread of research has progressively refined the modeling of the perception of correlation in scatterplots, it remains unclear as to why such perception can be modeled using relatively simple functions, e.g., linear and log-linear. In this paper, we investigate a longstanding hypothesis that people use visual features in a chart as a proxy for statistical measures like correlation. For a given scatterplot, we extract 49 candidate visual features and evaluate which best align with existing models and participant judgments. The results support the hypothesis that people attend to a small number of visual features when discriminating correlation in scatterplots. We discuss how this result may account for prior conflicting findings, and how visual features provide a baseline for future model-based approaches in visualization evaluation and design.

Electron Ghost Imaging.

In this Letter we report a demonstration of electron ghost imaging. A digital micromirror device directly modulates the photocathode drive laser to control the transverse distribution of a relativistic electron beam incident on a sample. Correlating the structured illumination pattern to the total sample transmission then retrieves the target image, avoiding the need for a pixelated detector. In our example, we use a compressed sensing framework to improve the reconstruction quality and reduce the number of shots compared to raster scanning a small beam across the target. Compressed electron ghost imaging can reduce both acquisition time and sample damage in experiments for which spatially resolved detectors are unavailable (e.g., spectroscopy) or in which the experimental architecture precludes full frame direct imaging.

Age bias in survey sampling and implications for estimating HIV prevalence in men who have sex with men: insights from mathematical modelling.

Respondent-driven sampling (RDS) is widely used to estimate HIV prevalence in men who have sex with men (MSM). Mathematical models that are calibrated to these data may be compromised if they fail to account for selection biases in RDS surveys. To quantify the potential extent of this bias, an agent-based model of HIV in South Africa was calibrated to HIV prevalence and sexual behaviour data from South African studies of MSM, first reweighting the modelled MSM population to match the younger age profile of the RDS surveys (age-adjusted analysis) and then without reweighting (unadjusted analysis). The model estimated a median HIV prevalence in South African MSM in 2015 of 34.6% (inter-quartile range (IQR): 31.4-37.2%) in the age-adjusted analysis, compared with 26.1% (IQR: 24.1-28.4%) in the unadjusted analysis. The median lifetime risk of acquiring HIV in exclusively homosexual men was 88% (IQR: 82-92%) in the age-adjusted analysis, compared with 76% (IQR: 64-85%) in the unadjusted analysis. These results suggest that RDS studies may under-estimate the exceptionally high HIV prevalence rates in South African MSM because of over-sampling of younger MSM. Mathematical models that are calibrated to these data need to control for likely over-sampling of younger MSM.

Detecting Intestinal Malrotation on Hepatobiliary Scintigraphy: Making a Case for a Better Standardized Reporting Template.

Intestinal malrotation displays classic pattern of the small bowel activity on hepatobiliary scintigraphy that could lead to the diagnosis, but only if an interpreting physician looks for it. Presented are 2 cases, one demonstrates diagnostic findings during the first 60-minute phase, whereas the other reveals the diagnosis only on the later sincalide stimulation phase. The currently recommended structured reporting for hepatobiliary scintigraphy does not include examination of bowel activity pattern, which could result in a missed diagnosis. Including interrogation of the small bowel pattern into the structured reporting checklist would ensure consistent detection of this rare but most consequential diagnosis.

Femtosecond mega-electron-volt electron microdiffraction.

To understand and control the basic functions of physical, chemical and biological processes from micron to nano-meter scale, an instrument capable of visualizing transient structural changes of inhomogeneous materials with atomic spatial and temporal resolutions, is required. One such technique is femtosecond electron microdiffraction, in which a short electron pulse with femtosecond-scale duration is focused into a micron-scale spot and used to obtain diffraction images to resolve ultrafast structural dynamics over a localized crystalline domain. In this letter, we report the experimental demonstration of time-resolved mega-electron-volt electron microdiffraction which achieves a 5 µm root-mean-square (rms) beam size on the sample and a 110 fs rms temporal resolution. Using pulses of 10k electrons at 4.2 MeV energy with a normalized emittance 3 nm-rad, we obtained high quality diffraction from a single 10 µm paraffin (C44H90) crystal. The phonon softening mode in optical-pumped polycrystalline Bi was also time-resolved, demonstrating the temporal resolution limits of the instrument. This new characterization capability will open many research opportunities in material and biological sciences.

Truncal varicose vein diameter and patient-reported outcome measures.

BACKGROUND: Varicose veins and chronic venous disease are common, and some funding bodies ration treatment based on a minimum diameter of the incompetent truncal vein. This study assessed the effect of maximum vein diameter on clinical status and patient symptoms. METHODS: A prospective observational cohort study of patients presenting with symptomatic varicose veins to a tertiary referral public hospital vascular clinic between January 2011 and July 2012. Patients underwent standardized assessment with venous duplex ultrasonography, and completed questionnaires assessing quality of life (QoL) and symptoms (Aberdeen Varicose Vein Questionnaire, EuroQol Five Domain QoL assessment and EuroQol visual analogue scale). Clinical scores (Venous Clinical Severity Score (VCSS) and Clinical Etiologic Anatomic Pathophysiologic (CEAP) class) were also calculated. Regression analysis was used to investigate the relationship between QoL, symptoms and vein diameter. RESULTS: Some 330 patients were assessed before surgery. The median maximum vein diameter was 7·0 (i.q.r. 5·3-9·2) mm overall, 7·9 (6·0-9·8) mm for great saphenous vein and 6·0 (5·2-8·9) mm for small saphenous vein. In linear regression analysis, vein diameter was shown to have a significant association with VCSS (P = 0·041). For every 1-mm increase in vein diameter, there was a 2·75-fold increase in risk of being in CEAP class C4 compared with C2. No other QoL or symptom measures were related to vein diameter. CONCLUSION: Incompetent truncal vein diameter was associated with increasing VCSS, but not a variety of other varicose vein disease-specific and generic patient-reported outcome measures.

Perineal body length and perineal lacerations during delivery in primigravid patients.

This study assessed the relation between perineal body length and the risk of perineal laceration extending into the anal sphincter during vaginal delivery in primigravid patients at an institution with a low utilization of episiotomy. This was a prospective study of primigravid patients in active labor. Primigravid women with singleton pregnancies who were in the first stage of labor at 37 weeks gestation or greater were recruited, and the admitting physician measured the length of the perineal body. The degree of perineal laceration and other delivery characteristics were recorded. Data were analyzed using univariate analyses, receiver-operator curve analyses, and multiple logistic regression for factors associated with increased severity of vaginal lacerations. The perineal body length, duration of second stage of labor, type of delivery, and patient age were associated (P < 0.1) with third- and fourth-degree (severe) perineal lacerations in primigravid women using receiver-operator curve analysis. Using logistic regression, only the duration of second stage of labor and length of the perineal body were significant (P < 0.04) predictors of third- and fourth-degree lacerations, with odds ratios of 32 (1.3 to 807 as 95% CI) and 24 (1.3 to 456), respectively. Both a perineal body length of ≤3.5 cm and a duration of second stage of labor >99 minutes were associated with an increased risk of third- and fourth-degree lacerations in primigravid patients.

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY.

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.