Nevin Manimala

J Math Biol. 2021 Aug 21;83(3):28. doi: 10.1007/s00285-021-01654-7.

ABSTRACT

Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if [Formula: see text] and [Formula: see text] are rooted binary phylogenetic X-trees that infer the same set of rooted triples, then [Formula: see text] and [Formula: see text] are isomorphic. However, in general, this sufficiency does not extend to rooted binary phylogenetic networks. In this paper, we show that trinets, phylogenetic network analogues of rooted triples, are sufficient to encode rooted binary orchard networks. Rooted binary orchard networks naturally generalise rooted binary tree-child networks. Moreover, we present a polynomial-time algorithm for building a rooted binary orchard network from its set of trinets. As a consequence, this algorithm affirmatively answers a previously-posed question of whether there is a polynomial-time algorithm for building a rooted binary tree-child network from the set of trinets it infers.

PMID:34420100 | DOI:10.1007/s00285-021-01654-7

Insights Imaging. 2021 Aug 21;12(1):120. doi: 10.1186/s13244-021-01063-w.

ABSTRACT

PURPOSE: To compare the imaging quality, T stage and extramural venous invasion (EMVI) evaluation between the conventional and synthetic T2-weighted imaging (T2WI), and to investigate the role of quantitative values obtained from synthetic magnetic resonance imaging (MRI) for assessing nodal staging in rectal cancer (RC).

METHODS: Ninety-four patients with pathologically proven RC who underwent rectal MRI examinations including synthetic MRI were retrospectively recruited. The image quality of conventional and synthetic T2WI was compared regarding signal-to-noise ratio (SNR), contrast-to-noise (CNR), sharpness of the lesion edge, lesion conspicuity, absence of motion artifacts, and overall image quality. The accuracy of T stage and EMVI evaluation on conventional and synthetic T2WI were compared using the Mc-Nemar test. The quantitative T1, T2, and PD values were used to predict the nodal staging of MRI-evaluated node-negative RC.

RESULTS: There were no statistically significant differences between conventional and synthetic T2WI in SNR, CNR, overall image quality, lesion conspicuity, and absence of motion artifacts (p = 0.058-0.978). There were no significant differences in the diagnostic accuracy of T stage and EMVI between conventional and synthetic T2WI from two observers (p = 0.375 and 0.625 for T stage; p = 0.625 and 0.219 for EMVI). The T2 value showed good diagnostic performance for predicting the nodal staging of RC with the area under the receiver operating characteristic, sensitivity, specificity, and accuracy of 0.854, 90.0%, 71.4%, and 80.3%, respectively.

CONCLUSIONS: Synthetic MRI may facilitate preoperative staging and EMVI evaluation of RC by providing synthetic T2WI and quantitative maps in one acquisition.

PMID:34420097 | DOI:10.1186/s13244-021-01063-w

Heart Vessels. 2021 Aug 22. doi: 10.1007/s00380-021-01924-w. Online ahead of print.

ABSTRACT

Pulmonary embolism (PE) patients with right ventricular (RV) involvement are a heterogenous group who mandate further risk stratification. Our objective was to evaluate the efficacy of the PE severity index (PESI) for predicting adverse clinical outcomes among PE patients with RV involvement. Consecutive normotensive PE patients with RV involvement were allocated according to admission PESI score (PESI ≤ III vs. PESI ≥ IV). The primary outcome included hemodynamic instability and in-hospital mortality. Secondary outcomes included each component of the primary outcome as well as mechanical ventilation, thrombolytic therapy, acute kidney injury, and major bleeding. Multivariable logistic regression model was performed to assess the independent association between the PESI score and primary outcome. C-Statistic was used to compare the PESI with the BOVA score. A total of 253 patients were evaluated: 95 (38%) with a PESI ≥ IV. Of them, 82 (32%) patients were classified as intermediate-low risk and 171 (68%) as intermediate-high risk. Fifty (20%) patients had at least 1 adverse event. Multivariate analysis demonstrated the PESI to be an independent predictor for the primary outcome (HR 4.81, CI 95%, 1.15-20.09, p = 0.031), which was increased with a concomitant increase of the PESI score (PESI I 4.2%, PESI II 3.4%, PESI III 12%, PESI IV 16.3%, PESI V 23.1%, p for trend < 0.001). C-Statistic analysis for the PESI score yielded an AUC-0.746 (0.637-0.854), p = 0.001, compared to the BOVA score: AUC-0.679 (0.584-0.775), p = 0.011. PESI score was found to predict adverse outcomes among normotensive PE patients with RV involvement.

PMID:34420078 | DOI:10.1007/s00380-021-01924-w

Geriatr Nurs. 2021 Aug 18;42(5):1084-1092. doi: 10.1016/j.gerinurse.2021.06.016. Online ahead of print.

ABSTRACT

A theory-guided non-experimental, descriptive, correlational design was used to evaluate how entry and passage variables were related to nursing home adjustment for individuals with dementia. Older adults with dementia may be unable to speak for themselves, therefore proxy responses of Certified Nursing Assistants (CNAs) provided the data for completion of the Nursing Home Adjustment Scale.¹ Guided by the Meleis’ Theory of Transitions, entry level factors (i.e. age, previous residence, gender, and choice), and passage variables (i.e. length of stay, extent of dementia, functional abilities, and depression) were entered into a regression equation as predictors of nursing home adjustment. Information about extent of dementia, functional abilities and depression was derived from the Minimum Data Set (MDS) maintained for all residents per Medicare and Medicaid guidelines. Descriptive and inferential statistics were calculated using IBM Statistical Package for the Social Sciences (SPSS) 26.0 software. Results indicated an inverse relationship between nursing home adjustment and depression as measured by the PHQ-9. There was no support for relationships among other variables. CNA proxy responses were found to be reliable in that they were significantly correlated with nursing responses on the same measure. This study supports the use of CNA proxy responses as a method to evaluate the experience of individuals with dementia.

PMID:34418841 | DOI:10.1016/j.gerinurse.2021.06.016

J Contam Hydrol. 2021 Aug 14;243:103870. doi: 10.1016/j.jconhyd.2021.103870. Online ahead of print.

ABSTRACT

Subsurface remediation using nanoscale zero valent iron (nZVI) is a promising in-situ technology that can transform certain groundwater contaminants into non-toxic compounds. However, field scale implementation of nZVI technology has faced major challenges due to poor subsurface mobility, limited longevity and well clogging, all leading to a shorter nZVI travel distance. This distance nZVI travels in the subsurface is an important parameter since it influences the amount of contaminants that can be reached and thereby remediated. There are several factors which may affect nZVI travel distance such as groundwater velocity, injection concentration and rate, lag period (duration when nZVI injection is stopped), solution viscosity, and subsurface heterogeneity. Although various studies have been performed to reveal the effect of different factors on nZVI transport in homogeneous domains, few studies have focused on heterogeneous media, which is more representative of field conditions. In this study, a statistical analysis was performed using a two-dimensional numerical model which simulated carboxymethyl cellulose (CMC) stabilized nZVI transport in randomly distributed soil permeability fields of two aquifers to examine the factors that have the greatest impact on nZVI travel distance. Among all possible factors, field scale solution viscosity and injection rate had a statistically significant effect on nZVI travel distance in both the horizontal and vertical directions, as well as, on the attached mass. Additionally, the lag period between injections had a statistically significant effect on the attached mass, but not the travel distance. These results suggest that having a long injection period followed by a short lag phase during field deployment may result in less nZVI attachment. Lastly, aquifer heterogeneity impacted the nZVI spread while the impact of intrinsic groundwater velocity and injection concentration was found not to be statistically significant. Results from this numerical study can aid in field-scale CMC-nZVI injection by identifying key factors for remediation optimization.

PMID:34418819 | DOI:10.1016/j.jconhyd.2021.103870

J Contam Hydrol. 2021 Aug 9;243:103864. doi: 10.1016/j.jconhyd.2021.103864. Online ahead of print.

ABSTRACT

We propose a simulation-optimization (SO) model based on a novel two-step strategy for the optimal design of groundwater remediation systems. The SO models are developed by coupling simulation models directly or through the extreme learning machine (ELM) with evolutionary hunting strategy based metaheuristics (EHSMs). In the first step, EHSMs with a combinatorial optimization technique are used to obtain optimal pumping locations by minimizing the percentage of contaminant mass that remained in the aquifer while keeping the pumping strategy as constant. In the second step, the optimal pumping locations are directly used as input, and a composite function is employed to minimize the sum of the water extraction rates and the percentage of extracted contaminant mass by constraining hydraulic heads and contaminant concentrations. The performance of the two-step strategy is found to be slightly better and computationally more efficient than the alternate approach. Moreover, various statistical measures suggest the superiority of EHSMs over other metaheuristics for groundwater remediation.

PMID:34418818 | DOI:10.1016/j.jconhyd.2021.103864

Int J Surg Case Rep. 2021 Aug 10;86:106298. doi: 10.1016/j.ijscr.2021.106298. Online ahead of print.

ABSTRACT

INTRODUCTION: Spontaneous quadriceps tendon rupture (SQTR) is a rare injury to the knee extensor mechanism that is usually associated with systemic diseases such as end stage renal diseases (ESRD) and it is more prevalent in the elderly. Due to the underlying pathology, quadriceps tendon rupture warrants special considerations and management in its repair.

CASE REPORT: We present two cases of quadriceps tendon rupture in end-stage renal disease (ESRD) patients. The first case; a 57 years old female who had bilateral SQTR and is undergoing hemodialysis. The second patient, a 26 years old male had unilateral quadriceps tendon rupture caused by minimal trauma. The first patient had a trans-osseous repair by direct suturing the quadriceps tendon stump to the proximal pole patella. The second patient was repaired with a modified Bunnel suture and anchor placement on the proximal pole patella. The first case had a re-rupture of the right quadriceps tendon and the second case has recovered with improved outcomes.

DISCUSSION: Spontaneous quadriceps tendon rupture is usually underlined by degenerative changes of the tendons. Special care is needed to address the pathologic tendon underlying SQTR. The current surgical literature still lacks the statistical data that shows which surgical approach is most optimal for SQTR in ESRD patients.

CONCLUSION: SQTR rupture is generally an injury of brittle tendons caused by underlying diseases. A multidisciplinary and comprehensive approach including a proper surgical approach and postoperative managements are crucial for good functional outcomes of the extensor mechanism.

PMID:34418804 | DOI:10.1016/j.ijscr.2021.106298

J Chromatogr B Analyt Technol Biomed Life Sci. 2021 Aug 16;1180:122899. doi: 10.1016/j.jchromb.2021.122899. Online ahead of print.

ABSTRACT

In this study, we used ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to measure the concentration of narciclasine and 7-deoxynarciclasine in mouse blood after intravenous (i.v.) and oral administration (p.o.), and we used this method to investigate their pharmacokinetics profiles in mice. Chromatographic separation of the analytes was achieved using a UPLC HSS T3 column (2.1 mm × 100 mm, 1.8 μm) with a mobile phase consisting of acetonitrile-water (0.1% formic acid) by gradient elution. Electrospray ionization (ESI positive-ion mode)-tandem mass spectrometry in multiple reaction monitoring (MRM) mode was employed for quantitative analysis of the analytes in mouse blood samples. Twelve mice were administered narciclasine and 7-deoxynarciclasine (2 mg/kg) intravenously (iv), while the other twelve mice were administered narciclasine and 7-deoxynarciclasine (10 mg/kg) orally. The mouse blood was withdrawn from the caudal vein to be processed, after which the blood was analyzed by UPLC-MS/MS, and the corresponding data were fitted using the Drug and Statistics (DAS) software. Standard curves of narciclasine and 7-deoxynarciclasine were generated over the concentration range of 5-5000 ng/mL. The intra-day accuracy of narciclasine and 7-deoxynarciclasine was 90-105%, and the corresponding inter-day accuracy was 87-108%. The intra-day precision was less than 13%, while the inter-day precision was less than 14%. Matrix effects were also observed (between 94% and 104%), and the recovery calculated was higher than 70%. The developed and validated UPLC-MS/MS method was then successfully applied in determining the mouse pharmacokinetics of narciclasine and 7-deoxynarciclasine. From this, thebioavailabilityofnarciclasine and 7-deoxynarciclasinewasdetermined to be 10.3%and35.4%, respectively.

PMID:34418798 | DOI:10.1016/j.jchromb.2021.122899

J Mech Behav Biomed Mater. 2021 Aug 5;123:104760. doi: 10.1016/j.jmbbm.2021.104760. Online ahead of print.

ABSTRACT

The fatigue behavior and FEA analysis of different ceramic materials cemented over distinct substrates for implant-supported crowns were evaluated in this study. Discs of 10 mm in diameter of both restorative and substrate materials were made and randomly allocated into pairs (n = 15) considering the two study factors: ‘restorative ceramic material’ (1 mm thickness) – polymer-infiltrated ceramic network (PICN), lithium disilicate (LD), zirconia-reinforced lithium silicate (ZLS), or translucent zirconia (TZ); and ‘foundation substrate’ (2 mm thickness) – polyetheretherketone (Peek) or yttrium-stabilized zirconia (YZ). Adhesive cementation was made with a dual cure resin cement. Fatigue testing was run using the step-stress methodology: initial load of 200 N for 5000 cycles, followed by steps of 10,000 cycles starting at 400 N up to 2800 N or until failure, step size of 200 N, frequency of 20 Hz. Data were analyzed by the Kaplan Meier and log-rank post-hoc tests. Fractography analysis (stereomicroscope and SEM) and FEA were also performed. Both factors under study and their interaction statistically influenced the fatigue failure load (FFL), cycles for failure (CFF) and survival rates (p < 0.001). The restorative materials bonded to YZ had higher FFL and CFF than when adhering to Peek, while restorative materials with more crystalline content (TZ and ZLS) showed higher FFL and CFF than LD and PICN. The fractography analysis showed that all materials bonded to YZ resulted in failures starting at the occlusal surface (Hertzian cone cracks), while materials bonded to Peek had radial cracks from the ceramic-cement intaglio surface. FEA analysis showed that tensile stress concentration decreased in the intaglio surface when testing the restorative material over a stiffer (YZ) foundation substrate. In addition, the higher the restorative material’s crystalline content, the more the stress is concentrated within the material (TZ > ZLS ≥ LD > PICN) when bonded to the same foundation substrate. Thus, it concluded that a stiffer foundation substrate (YZ) enhances the load-bearing capacity under fatigue of the restorative set; that restorative materials with higher crystalline content results in higher fatigue performance of the set, regardless of the foundation used; and that the foundation material influences the failure pattern of the restorative set.

PMID:34418777 | DOI:10.1016/j.jmbbm.2021.104760

Ann Diagn Pathol. 2021 Aug 16;54:151807. doi: 10.1016/j.anndiagpath.2021.151807. Online ahead of print.

ABSTRACT

Digital pathology has become an integral part of pathology education in recent years, particularly during the COVID-19 pandemic, for its potential utility as a teaching tool that augments the traditional 1-to-1 sign-out experience. Herein, we evaluate the utility of whole slide imaging (WSI) in reducing diagnostic errors in pigmented cutaneous lesions by pathology fellows without subspecialty training in dermatopathology. Ten cases of 4 pigmented cutaneous lesions commonly encountered by general pathologists were selected. Corresponding whole slide images were distributed to our fellows, along with two sets of online surveys, each composed of 10 multiple-choice questions with 4 answers. Identical cases were used for both surveys to minimize variability in trainees’ scores depending on the perceived level of difficulty, with the second set being distributed after random shuffling. Brief image-based teaching slides as self-assessment tool were provided to trainees between each survey. Pre- and post-self-assessment scores were analyzed. 61% (17/28) and 39% (11/28) of fellows completed the first and second surveys, respectively. The mean score in the first survey was 5.2/10. The mean score in the second survey following self-assessment increased to 7.2/10. 64% (7/11) of trainees showed an improvement in their scores, with 1 trainee improving his/her score by 8 points. No fellow scored less post-self-assessment than on the initial assessment. The difference in individual scores between two surveys was statistically significant (p = 0.003). Our study demonstrates the utility of WSI-based self-assessment learning as a source of improving diagnostic skills of pathology trainees in a short period of time.

PMID:34418768 | DOI:10.1016/j.anndiagpath.2021.151807