Tag: pubmed

Proc Natl Acad Sci U S A. 2023 Nov 21;120(47):e2307935120. doi: 10.1073/pnas.2307935120. Epub 2023 Nov 14.

ABSTRACT

Stochastic processes on graphs can describe a great variety of phenomena ranging from neural activity to epidemic spreading. While many existing methods can accurately describe typical realizations of such processes, computing properties of extremely rare events is a hard task, particularly so in the case of recurrent models, in which variables may return to a previously visited state. Here, we build on the matrix product cavity method, extending it fundamentally in two directions: First, we show how it can be applied to Markov processes biased by arbitrary reweighting factors that concentrate most of the probability mass on rare events. Second, we introduce an efficient scheme to reduce the computational cost of a single node update from exponential to polynomial in the node degree. Two applications are considered: inference of infection probabilities from sparse observations within the SIRS epidemic model and the computation of both typical observables and large deviations of several kinetic Ising models.

PMID:37963253 | DOI:10.1073/pnas.2307935120

Anal Chem. 2023 Nov 14. doi: 10.1021/acs.analchem.3c03887. Online ahead of print.

ABSTRACT

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging is used across many fields for the atomic and molecular characterization of surfaces, with both high sensitivity and high spatial resolution. When large analysis areas are required, standard ToF-SIMS instruments allow for the acquisition of adjoining tiles, which are acquired by rastering the primary ion beam. For such large area scans, tiling artifacts are a ubiquitous challenge, manifesting as intensity gradients across each tile and/or sudden changes in intensity between tiles. Such artifacts are thought to be related to a combination of sample charging, local detector sensitivity issues, and misalignment of the primary ion gun, among other instrumental factors. In this work, we investigated six different computational tiling artifact removal methods: tensor decomposition, multiplicative linear correction, linear discriminant analysis, seamless stitching, simple averaging, and simple interpolating. To ensure robustness in the study, we applied these methods to three hyperspectral ToF-SIMS data sets and one OrbiTrapSIMS data set. Our study includes a carefully designed statistical analysis and a quantitative survey that subjectively assessed the quality of the various methods employed. Our results demonstrate that while certain methods are useful and preferred more often, no one particular approach can be considered universally acceptable and that the effectiveness of the artifact removal method is strongly dependent on the particulars of the data set analyzed. As examples, the multiplicative linear correction and seamless stitching methods tended to score more highly on the subjective survey; however, for some data sets, this led to the introduction of new artifacts. In contrast, simple averaging and interpolation methods scored subjectively poorly on the biological data set, but more highly on the microarray data sets. We discuss and explore these findings in depth and present general recommendations given our findings to conclude the work.

PMID:37963228 | DOI:10.1021/acs.analchem.3c03887

PLoS One. 2023 Nov 14;18(11):e0289622. doi: 10.1371/journal.pone.0289622. eCollection 2023.

ABSTRACT

BACKGROUND: Infective endocarditis (IE) has increased in rural states such as West Virginia (WV) with high injection drug use. IE is medically managed with antimicrobial treatment alone or combined with surgical treatment. This study aimed to characterize the predictors associated with surgical treatment and rates of inpatient mortality and readmission among IE patients in WV’s rural centers.

METHODS: This retrospective review of electronic health records includes all adults hospitalized for IE at major rural tertiary cardiovascular centers in WV during 2014-2018. Descriptive statistics were presented on demographics, history of injection drug use, clinical characteristics, and hospital utilization by surgery status, and multivariable logistic regression examined the association of surgery with key predictor variables, generating odds ratios (OR).

RESULTS: Of the 780 patients with IE, 38% had surgery, with a 26-fold increase in patients undergoing surgery between 2014-2018. Comparing surgery and non-surgery patients revealed significant differences. Surgery patients were significantly younger (median age 35.6 vs. 40.5 years; p<0.001); had higher rates of drug use history (80% vs. 65%; p<0.001), psychiatric disorders (57% vs. 31%; p<0.001), and readmissions (18% vs.12%; p = 0.015). Surgery patients had lower rates of discharge against medical advice (11% vs.17%; p = 0.028) and in-hospital mortality (5% vs.12%; p<0.001). In the multivariable logistic regression, surgery was associated with injection drug use (OR: 1.9; 95% CI:1.09-3. 3), indications for surgery (OR: 1.68; 95% CI:1.48-1.91), left-sided IE (OR: 2.14; 95%CI:1.43-3.19) and later years (OR:3.75; 95%CI:2.5-5.72).

CONCLUSION: This study characterizes the predictors associated with surgical treatment and rates of inpatient mortality and readmission among IE patients across rural WV. The decision to perform cardiac surgery on IE patients is complex. Results with increased injection drug use-associated IE emphasize the importance of comprehensive care by a multidisciplinary team for optimal management of patients with IE.

PMID:37963173 | DOI:10.1371/journal.pone.0289622

PLoS One. 2023 Nov 14;18(11):e0285992. doi: 10.1371/journal.pone.0285992. eCollection 2023.

ABSTRACT

Gul and Mohsin 2021 developed a new modified form of renowned “Half logistic” distribution introduced by Balakrishnan (1991) and named it half logistic-truncated exponential distribution (HL-TEXPD). Some mathematical characteristics are studied, including hazard function, Pth percentile, moment generating function and Shannon entropy. Simulation study is performed to examine the behaviour of parameter estimates. The proposed model is fitted on three real data sets to check its efficacy. Additionally, TTT (total time on test) plot is drawn to study the failure rate of the three data sets. The results verdict that HL-TEXPD can be efficiently utilized in the field of engineering and medical sciences based on the data sets under study contrary to the classical and baseline models.

PMID:37963157 | DOI:10.1371/journal.pone.0285992

PLoS One. 2023 Nov 14;18(11):e0289183. doi: 10.1371/journal.pone.0289183. eCollection 2023.

ABSTRACT

Clostridium novyi has demonstrated selective efficacy against solid tumors largely due to the microenvironment contained within dense tumor cores. The core of a solid tumor is typically hypoxic, acidic, and necrotic-impeding the penetration of current therapeutics. C. novyi is attracted to the tumor microenvironment and once there, can both lyse and proliferate while simultaneously re-activating the suppressed immune system. C. novyi systemic toxicity is easily mitigated by knocking out the phage DNA plasmid encoded alpha toxin resulting in C. novyi-NT; but, after intravenous injection spores are quickly cleared by phagocytosis before accomplishing significant tumor localization. C. novyi-NT could be designed to accomplish intravenous delivery with the potential to target all solid tumors and their metastases in a single dose. This study characterizes CRISPR/Cas9 modified C. novyi-NT to insert the gene for RGD, a tumor targeting peptide, expressed within the promoter region of a spore coat protein. Expression of the RGD peptide on the outer spore coat of C. novyi-NT indicates an increased capacity for tumor localization of C. novyi upon intravenous introduction based on the natural binding of RGD with the αvβ3 integrin commonly overexpressed on the epithelial tissue surrounding a tumor, and lead to immune stimulation.

PMID:37963142 | DOI:10.1371/journal.pone.0289183

PLoS One. 2023 Nov 14;18(11):e0293287. doi: 10.1371/journal.pone.0293287. eCollection 2023.

ABSTRACT

In laparoscopic surgery, one of the main byproducts is the gaseous particles, called surgical smoke, which is found hazardous for both the patient and the operating room staff due to their chemical composition, and this implies a need for its effective elimination. The dynamics of surgical smoke are monitored by the underlying flow inside the abdomen and the hidden Lagrangian Coherent Structures (LCSs) present therein. In this article, for an insufflated abdomen domain, we analyse the velocity field, obtained from a computational fluid dynamics model, first, by calculating the flow rates for the outlets and then by identifying the patterns which are responsible for the transportation, mixing and accumulation of the material particles in the flow. From the finite time Lyapunov exponent (FTLE) field calculated for different cross-sections of the domain, we show that these material curves are dependent on the angle, positions and number of the outlets, and the inlet. The ridges of the backward FTLE field reveal the regions of vortex formation, and the maximum accumulation, details which can inform the effective placement of the instruments for efficient removal of the surgical smoke.

PMID:37963139 | DOI:10.1371/journal.pone.0293287

Am Nat. 2023 Nov;202(5):699-720. doi: 10.1086/726036. Epub 2023 Oct 18.

ABSTRACT

AbstractDifferences among hummingbird species in bill length and shape have rightly been viewed as adaptive in relation to the morphology of the flowers they visit for nectar. In this study we examine functional variation in a behaviorally related but neglected feature: hummingbird feet. We gathered records of hummingbirds clinging by their feet to feed legitimately as pollinators or illegitimately as nectar robbers-“unorthodox” feeding behaviors. We measured key features of bills and feet for 220 species of hummingbirds and compared the 66 known “clinger” species (covering virtually the entire scope of hummingbird body size) with the 144 presumed “non-clinger” species. Once the effects of phylogenetic signal, body size, and elevation above sea level are accounted for statistically, hummingbirds display a surprising but functionally interpretable negative correlation. Clingers with short bills and long hallux (hind-toe) claws have evolved-independently-more than 20 times and in every major clade. Their biomechanically enhanced feet allow them to save energy by clinging to feed legitimately on short-corolla flowers and by stealing nectar from long-corolla flowers. In contrast, long-billed species have shorter hallux claws, as plant species with long-corolla flowers enforce hovering to feed, simply by the way they present their flowers.

PMID:37963119 | DOI:10.1086/726036

Am Nat. 2023 Nov;202(5):616-629. doi: 10.1086/726220. Epub 2023 Oct 19.

ABSTRACT

AbstractMortality is considered one of the main costs of dispersal. A reliable evaluation of mortality, however, is often hindered by a lack of information about the fate of individuals that disappear under unexplained circumstances (i.e., missing individuals). Here, we addressed this uncertainty by applying a Bayesian mortality analysis that inferred the fate of missing individuals according to information from individuals with known fate. Specifically, we tested the hypothesis that mortality during dispersal is higher than mortality among nondispersers using 32 years of mark-resighting data from a free-ranging population of the endangered African wild dog (Lycaon pictus) in northern Botswana. Contrary to expectations, we found that mortality during dispersal was lower than mortality among nondispersers, indicating that higher mortality is not a universal cost of dispersal. Our findings suggest that group living can incur costs for certain age classes, such as limited access to resources as group density increases, that exceed the mortality costs associated with dispersal. By challenging the accepted expectation of higher mortality during dispersal, we urge for further investigations of this key life history trait and propose a robust statistical approach to reduce bias in mortality estimates.

PMID:37963118 | DOI:10.1086/726220

JMIR Form Res. 2023 Nov 14;7:e48637. doi: 10.2196/48637.

ABSTRACT

BACKGROUND: Working pregnant women often need to adjust their physically demanding jobs for a healthy pregnancy. However, uncertainty about the extent of these adjustments can hinder their effectiveness. To address this, we developed the Job Adjustment mobile app, which allows users to input job and health details to generate a variety of personalized action plans. As this is the first version of the app, assessing its feasibility and usability is crucial.

OBJECTIVE: This study aims to verify the feasibility and usability of the Job Adjustment mobile app.

METHODS: A longitudinal observational study was conducted on pregnant Japanese women who were allowed to use the app anytime from 12 to 34 weeks of gestation; they received reminder emails every 2 weeks encouraging app use. A questionnaire was administered before app use and at 20 and 32 weeks of gestation. Feasibility was evaluated across 4 domains: implementation, demand, acceptability, and adverse events. Implementation was evaluated based on 3 parameters: dropout rate, initial reminder email receipt rate, and adherence rate (measured as pregnant women who used the app at intervals of 2.5 weeks or less). Demand was measured by intervals between use and intervals between log-in, and participants answered 15 questions to assess acceptability. Adverse events were assessed by analyzing the degree of anxiety related to work. Demographic data were analyzed to determine any statistically significant differences in intervals between uses. Usability was evaluated using the System Usability Scale.

RESULTS: The analysis included 66 pregnant women, and 61% (n=40) of them were multipara. The dropout rate, adherence rate, and initial reminder email receipt rate were 18% (13/71), 44% (29/66), and 79% (52/66) respectively. The median intervals between use and intervals between log-in were 2.94 (IQR 2.00-5.13) weeks and 2.28 (IQR 1.81-4.00) weeks, respectively. Overall, 60% (35/58) to 90% (52/58) of the participants responded positively to all 15 questions assessing acceptability, and no anxiety regarding work was recorded. The mean System Usability Scale score was 66.1 points. Multipara women had significantly longer intervals between app use compared to primipara women (P=.01).

CONCLUSIONS: The results demonstrated acceptable levels of feasibility and usability of the app. However, the low adherence rates, especially among multipara women, suggest the need for modifications to reduce the time burden of the app. Further research should explore more effective and acceptable intervals between use and timing, involving a larger sample and accounting for diverse characteristics of pregnant women.

TRIAL REGISTRATION: UMIN Clinical Trials Registry UMIN000042943; https://tinyurl.com/ydrchfas.

PMID:37962945 | DOI:10.2196/48637

JMIR Res Protoc. 2023 Nov 14;12:e52565. doi: 10.2196/52565.

ABSTRACT

BACKGROUND: Mycoplasma genitalium is an emerging sexually transmitted pathogen associated with increasing antibiotic resistance. The current treatment guidelines recommend moxifloxacin-sequential therapy for macrolide-resistant Mgenitalium or strains with unknown resistance profiles. However, it is unclear whether sitafloxacin, a 4th-generation fluoroquinolone antibiotic, is effective against resistant strains.

OBJECTIVE: This study aims to assess and compare the efficacy and safety of sitafloxacin- and moxifloxacin-based treatment regimens for managing Mgenitalium infections.

METHODS: We will conduct this randomized controlled trial at multiple centers in Japan. Eligible participants include adults aged 18 years or older with a confirmed Mgenitalium infection, as determined through the nucleic acid amplification test. Patients will be randomly assigned using a stratified approach based on the treatment facility and infection site. The interventions comprise oral sitafloxacin (200 mg) daily for 7 days (with optional pretreatment of oral doxycycline, 200 mg, daily for up to 7 days), with a control group receiving oral doxycycline (200 mg) daily for 7 days followed by moxifloxacin (400 mg) daily for another 7 days. The primary outcome is the treatment success rate with a superiority margin of 10%, as confirmed through the nucleic acid amplification test. Secondary outcomes encompass changes in the bacterial load at the urogenital or rectal sites and the emergence of posttreatment-resistant mutant strains.

RESULTS: Enrollment commenced in June 2023 and will conclude in December 2024, with findings anticipated by 2025. The expected success rates fall within the range of 80% for sitafloxacin and 42% for moxifloxacin against Mgenitalium carrying the G248T (S83I) mutation, based on previous studies. Accordingly, with a 5% significance level (2-sided) and 80% statistical power, we aim to recruit 50 participants per group, factoring in a 10% expected dropout rate.

CONCLUSIONS: This study will provide valuable insights into the efficacy and safety of sitafloxacin- versus moxifloxacin-based sequential therapy in treating Mgenitalium infections. These findings have the potential to influence clinical guidelines, favoring more effective therapeutic choices. The multicenter approach enhances the robustness of this study. However, a limitation is the potential insufficiency of statistical power to detect posttreatment-resistant mutant strains in each group, rendering posttreatment-resistance mutations a notable concern. In the future, we may need to increase the sample size to enhance power.

TRIAL REGISTRATION: Japan Registry of Clinical Trials (jRCTs031230111); https://jrct.niph.go.jp/en-latest-detail/jRCTs031230111.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/52565.

PMID:37962941 | DOI:10.2196/52565