Variability in Manual Segmentation of Temporal Bone Structures in Cone Beam CT Images.

PURPOSE: Manual segmentation of anatomical structures is the accepted "gold standard" for labeling structures in clinical images. However, the variability in manual segmentation of temporal bone structures in CBCT images of the temporal bone has not been systematically evaluated using multiple reviewers. Therefore, we evaluated the intravariability and intervariability of manual segmentation of inner ear structures in CBCT images of the temporal bone. METHODS: Preoperative CBCTs scans of the inner ear were obtained from 10 patients who had undergone cochlear implant surgery. The cochlea, facial nerve, chorda tympani, mid-modiolar (MM) axis, and round window (RW) were manually segmented by five reviewers in two separate sessions that were at least 1 month apart. Interreviewer and intrareviewer variabilities were assessed using the Dice coefficient (DICE), volume similarity, mean Hausdorff Distance metrics, and visual review. RESULTS: Manual segmentation of the cochlea was the most consistent within and across reviewers with a mean DICE of 0.91 (SD = 0.02) and 0.89 (SD = 0.01) respectively, followed by the facial nerve with a mean DICE of 0.83 (SD = 0.02) and 0.80 (SD = 0.03), respectively. The chorda tympani had the greatest amount of reviewer variability due to its thin size, and the location of the centroid of the RW and the MM axis were also quite variable between and within reviewers. CONCLUSIONS: We observed significant variability in manual segmentation of some of the temporal bone structures across reviewers. This variability needs to be considered when interpreting the results in studies using one manual reviewer.

Further Validity Evidence for Patient-Specific Virtual Reality Temporal Bone Surgical Simulation.

OBJECTIVE: Patient-specific virtual reality (VR) simulation of cochlear implant (CI) surgery potentially enables preoperative rehearsal and planning. We aim to gather supporting validity evidence for patient-specific simulation through the analysis of virtual performance and comparison with postoperative imaging. METHODS: Prospective, multi-institutional study. Pre- and postoperative cone-beam CT scans of CI surgical patients were obtained and processed for patient-specific VR simulation. The virtual performances of five trainees and four attendings were recorded and (1) compared with volumes removed during actual surgery as determined in postoperative imaging, and (2) assessed using the Copenhagen Cochlear Implant Surgery Assessment Tool (CISAT) by two blinded raters. The volumes compared were cortical mastoidectomy, facial recess, and round window (RW) cochleostomy as well as violation of the facial nerve and chorda. RESULTS: Trainees drilled more volume in the cortical mastoidectomy and facial recess, whereas attendings drilled more volume for the RW cochleostomy and made more violations. Except for the cochleostomy, attendings removed volumes closer to that determined in postoperative imaging. Trainees achieved a higher CISAT performance score compared with attendings (22.0 vs. 18.4 points) most likely due to lack of certain visual cues. CONCLUSION: We found that there were differences in performance of trainees and attendings in patient-specific VR simulation of CI surgery as assessed by raters and in comparison with actual drilled volumes. The presented approach of volume comparison is novel and might be used for further validation of patient-specific VR simulation before clinical implementation for preoperative rehearsal in temporal bone surgery. LEVEL OF EVIDENCE: n/a Laryngoscope, 134:1403-1409, 2024.

Mental health-related presentations to a tertiary emergency department during the COVID-19 pandemic.

Introduction: The coronavirus disease 2019 (COVID-19) pandemic has caused significant mental distress in populations globally. At the frontline of the pandemic, emergency departments (EDs) are the prime setting to observe the effects of the pandemic on the mental health of the population. We aimed to describe the trend of mental health-related ED attendances at an acute hospital in Singapore before and during the various stages of the COVID-19 pandemic. Methods: This is a retrospective, descriptive study of patients who presented to the ED between 1 January 2019 and 31 December 2020. Patients diagnosed with mental health-related systematised nomenclature of medicine who visited the ED during this period were identified and were placed into mental health diagnosis categories for analysis. A comparison was made between patients who presented before the pandemic (2019) and during the pandemic (2020). Results: During the study periods, we identified 1,421 patients, of whom 27 were excluded due to non-mental health-related diagnoses, leaving 1,394 patients for analysis. There was a 36.7% increase in mental health-related ED presentations from 2019 to 2020. The proportion of higher-acuity mental health-related ED attendances and number of suicide attempts also increased. Conclusion: Our study described an increase in the proportion of high-acuity mental health-related ED attendances during the COVID-19 pandemic. Emergency physicians must be cognisant of the effects of the pandemic on mental health. Further research should be conducted to better equip the healthcare system for handling all aspects of the pandemic.

Few-body hydrodynamic interactions probed by optical trap pulling experiment.

We study the hydrodynamic coupling of neighboring micro-beads placed in a multiple optical trap setup allowing us to precisely control the degree of coupling and directly measure time-dependent trajectories of entrained beads. We performed measurements on configurations with increasing complexity starting with a pair of entrained beads moving in one dimension, then in two dimensions, and finally a triplet of beads moving in two dimensions. The average experimental trajectories of a probe bead compare well with the theoretical computation, illustrating the role of viscous coupling and setting timescales for probe bead relaxation. The findings also provide direct experimental corroborations of hydrodynamic coupling at large, micrometer spatial scales and long, millisecond timescales, of relevance to, e.g., microfluidic device design and hydrodynamic-assisted colloidal assembly, improving the capability of optical tweezers, and understanding the coupling between micrometer-scale objects within a living cell.

Characterization of the common bed bug's eggshell and egg glue proteins.

An insect egg is one of the most vulnerable stages of insect life, and the evolutionary success of a species depends on the eggshell protecting the embryo and the egg glue securing the attachment. The common bed bug (Cimex lectularius), notorious for its painful and itchy bites, infests human dwellings to feed on blood. They are easier to find these days as they adapt to develop resistance against commonly used insecticides. In this study, we identify and characterize the eggshell protein and the probable egg glue protein (i.e. keratin associated protein 5-10 like protein) of the bed bug by using mass spectrometry and bioinformatics analysis. Furthermore, by using transcription profiling and in vivo RNA interference, we show evidences that the keratin associated protein 5-10 like protein functions as the glue protein. Finally, structural characterizations on the two proteins are performed using recombinant proteins. Amino acid sequences of various insect eggshell and egg glue proteins support their independent evolution among different insect groups. Hence, inhibiting the function of these proteins related to the earliest stage of life can achieve species-specific population control. In this respect, our results would be a starting point in developing new ways to control bed bug population.

Development of machine learning models based on molecular fingerprints for selection of small molecule inhibitors against JAK2 protein.

Janus kinase 2 (JAK2) is emerging as a potential therapeutic target for many inflammatory diseases such as myeloproliferative disorders (MPD), cancer and rheumatoid arthritis (RA). In this study, we have collected experimental data of JAK2 protein containing 6021 unique inhibitors. We then characterized them based on Morgan (ECFP6) fingerprints followed by clustering into training and test set based on their molecular scaffolds. These data were used to build the classification models with various supervised machine learning (ML) algorithms that could prioritize novel inhibitors for future drug development against JAK2 protein. The best model built by Random Forest (RF) and Morgan fingerprints achieved the G-mean value of 0.84 on the external test set. As an application of our classification model, virtual screening was performed against Drugbank molecules in order to identify the potential inhibitors based on the confidence score by RF model. Nine potential molecules were identified, which were further subject to molecular docking studies to evaluate the virtual screening results of the best RF model. This proposed method can prove useful for developing novel target-specific JAK2 inhibitors.

A systems biology investigation of curcumin potency against TGF-ß-induced EMT signaling in lung cancer.

Curcumin (diferuloylmethane) is bioactive phenolic compound which exerts diverse antimetastatic effect. Several studies have reported the antimetastatic effect of curcumin by its ability to modulate the epithelial-to-mesenchymal transition (EMT) process in different cancers, but underlying molecular mechanism is poorly understood. EMT is a highly conserved biological process in which epithelial cells acquire mesenchymal-like characteristics by losing their cell-cell junctions and polarity. As a consequence, deviation in cellular mechanism leads to cancer metastasis and thereby death. In this perspective, we explored the antimetastatic potential and mechanism of curcumin on the EMT process by establishing in vitro EMT model in lungs cancer (A549) cells induced by TGF-ß1. Our results showed that curcumin mitigates EMT by regulating the expression of crucial mesenchymal markers such as MMP2, vimentin and N-cadherin. Besides, the transcriptional analysis revealed that the curcumin treatment differentially regulated the expression of 75 genes in NanoString nCounter platform. Further protein-protein interaction network and clusters analysis of differentially expressed genes revealed their involvement in essential biological processes that plays a key role during EMT transition. Altogether, the study provides a comprehensive overview of the antimetastatic potential of curcumin in TGF-ß1-induced EMT in lung cancer cells. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03360-7.

A rare case of catatonia associated with COVID-19 infection.

COVID-19, caused by the SARS-CoV-2 virus, has well-documented common symptoms such as cough and fever. There is also extensive documentation on the more severe outcomes, such as sepsis and death. However, there is minimal literature regarding the neuropsychiatric effects of COVID-19. This case report outlines a patient who presented with apparent psychosis shortly after COVID-19 infection. Shortly after hospitalization, she began to develop symptoms of catatonia. Her catatonia subsequently was recognized and resolved with appropriate treatment with lorazepam. There have been a handful of similar reports regarding patients with COVID-19 developing catatonia and responding well to lorazepam. Therefore, catatonia may be associated with COVID-19. Clinicians should consider catatonia diagnosis in patients with COVID-19 who have changes in behaviour, mental status, or motor function, to prevent deterioration secondary to untreated catatonia. Furthermore, COVID-19 testing should be considered in patients with acute psychiatric presentations.

In Silico Screening of Quorum Sensing Inhibitor Candidates Obtained by Chemical Similarity Search.

Quorum sensing (QS) is a bacterial communication using signal molecules, by which they sense population density of their own species, leading to group behavior such as biofilm formation and virulence. Autoinducer-2 (AI2) is a QS signal molecule universally used by both gram-positive and gram-negative bacteria. Inhibition of QS mediated by AI2 is important for various practical applications, including prevention of gum-disease caused by biofilm formation of oral bacteria. In this research, molecular docking and molecular dynamics (MD) simulations were performed for molecules that are chemically similar to known AI2 inhibitors that might have a potential to be quorum sensing inhibitors. The molecules that form stable complexes with the AI2 receptor protein were found, suggesting that they could be developed as a novel AI2 inhibitors after further in vitro validation. The result suggests that combination of ligand-based drug design and computational methods such as MD simulation, and experimental verification, may lead to development of novel AI inhibitor, with a broad range of practical applications.

Use of d-galactose to regulate biofilm growth of oral streptococci.

In the oral microbial community, commensals can compete with pathogens and reduce their colonization in the oral cavity. A substance that can inhibit harmful bacteria and enrich beneficial bacteria is required to maintain oral health. The purpose of this study was to examine the effect of d-galactose on the biofilm formation of the cariogenic bacteria Streptococcus mutans and oral commensal streptococci and to evaluate their use in solution and in paste form. Biofilms of S. mutans, Streptococcus oralis, and Streptococcus mitis were formed on saliva-coated glass slips in the absence or presence of d-galactose and evaluated by staining with 1 % crystal violet. d-Galactose significantly inhibited the biofilm formation of S. mutans at concentrations ranging from 2 µM to 200 mM but increased the biofilm formation of S. oralis and S. mitis at concentrations of 2-200 mM. d-Galactose significantly inhibited three glucosyltransferase genes, gtfB, gtfC, and gtfD. The effect of d-galactose in the form of solution and paste was evaluated using bovine teeth. Pretreatment with 100 mM d-galactose on bovine teeth resulted in significantly reduced S. mutans biofilm formation. Our results suggest that d-galactose can be a candidate substance for the development of oral hygiene products to prevent caries by inhibiting the biofilm formation of S. mutans and simultaneously increasing the biofilm formation of commensal oral streptococci.

Hydrodynamic interaction facilitates the unsteady transport of two neighboring vesicles.

We obtain a numerical solution of the equation for the synchronous unsteady motion of two spherical vesicles in incompressible viscous fluid in the presence of both Stokes drag and hydrodynamics memory. We find that for a given amount of work performed, the final distance traveled by each vesicle is increased by the presence of the other vesicle moving in the same direction. The result suggests that the unsteady transport of the vesicles by molecular motors in vivo may be facilitated due to an effective hydrodynamic interaction between the neighboring vesicles.

Bifidobacterium pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms.

Starches resistant to mammalian digestion are present in foods and pass to the large bowel, where they may be degraded and fermented by the microbiota. Increases in relative abundances of bifidobacteria (blooms) have been reported in rats whose diet was supplemented with Hi-Maize resistant starch. We determined that the bifidobacterial species present in the rat cecum under these circumstances mostly belonged to Bifidobacterium animalis However, cultures of B. animalis isolated from the rats failed to degrade Hi-Maize starch to any extent. In contrast, Bifidobacterium pseudolongum also detected in the rat microbiota had high starch-degrading ability. Transcriptional comparisons showed increased expression of a type 1 pullulanase, alpha-amylase, and glycogen debranching enzyme by B. pseudolongum when cultured in medium containing Hi-Maize starch. Maltose was released into the culture medium, and B. animalis cultures had shorter doubling times in maltose medium than did B. pseudolongum Thus, B. pseudolongum, which was present at a consistently low abundance in the microbiota, but which has extensive enzymatic capacity to degrade resistant starch, showed the attributes of a keystone species associated with the bifidobacterial bloom.IMPORTANCE This study addresses the microbiology and function of a natural ecosystem (the rat gut) using DNA-based observations and in vitro experimentation. The microbial community of the large bowel of animals, including humans, has been studied extensively through the use of high-throughput DNA sequencing methods and advanced bioinformatics analysis. These studies reveal the compositions and genetic capacities of microbiotas but not the intricacies of how microbial communities function. Our work, combining DNA sequence analysis and laboratory experiments with cultured strains of bacteria, revealed that the increased abundance of bifidobacteria in the rat gut, induced by feeding indigestible starch, involved a species that cannot itself degrade the starch (Bifidobacterium animalis) but cohabits with a species that can (Bifidobacterium pseudolongum). B. pseudolongum has the characteristics of a keystone species in the community because it had low abundance but high ability to perform a critical function, the hydrolysis of resistant starch.

Derivation of Markov processes that violate detailed balance.

Time-reversal symmetry of the microscopic laws dictates that the equilibrium distribution of a stochastic process must obey the condition of detailed balance. However, cyclic Markov processes that do not admit equilibrium distributions with detailed balance are often used to model systems driven out of equilibrium by external agents. I show that for a Markov model without detailed balance, an extended Markov model can be constructed, which explicitly includes the degrees of freedom for the driving agent and satisfies the detailed balance condition. The original cyclic Markov model for the driven system is then recovered as an approximation at early times by summing over the degrees of freedom for the driving agent. I also show that the widely accepted expression for the entropy production in a cyclic Markov model is actually a time derivative of an entropy component in the extended model. Further, I present an analytic expression for the entropy component that is hidden in the cyclic Markov model.

The Effect of Underwater Blast on Aggregating Brain Cell Cultures.

Although the deleterious effects of primary blast on gas-filled organs are well accepted, the effect of blast-induced shock waves on the brain is less clear because of factors that complicate the interpretation of clinical and experimental data. Brain cell aggregate cultures are comprised of multiple differentiated brain cell types and were used to examine the effects of underwater blast. Suspensions of these cultures encased in dialysis tubing were exposed to explosive-generated underwater blasts of low (∼300 kPa), medium (∼2,700 kPa), or high (∼14,000 kPa) intensities and harvested at 1-28 days post-exposure. No changes in gross morphology were noted immediately or weeks after blast wave exposure, and no increases in either apoptotic (caspase-3) or necrotic (lactate dehydrogenase) cell death were observed. Changes in neuronal (neurofilament H, acetylcholinesterase, and choline acetyltransferase) and glial (glial fibrillary acidic protein, glutamine synthetase) endpoints did not occur. However, significant time- and pressure-related increases in Akt (protein kinase B) phosphorylation were noted, as well as declines in vascular endothelial growth factor levels, implicating pathways involved in cellular survival mechanisms. The free-floating nature of the aggregates during blast wave exposure, coupled with their highly hydrolyzed dialysis tubing containment, results in minimized boundary effects, thus enabling accurate assessment of brain cell response to a simplified shock-induced stress wave. This work shows that, at its simplest, blast-induced shock waves produce subtle changes in brain tissue. This study has mechanistic implications for the study of primary blast-induced traumatic brain injury and supports the thesis that underwater blast may cause subtle changes in the brains of submerged individuals.

D-Galactose as an autoinducer 2 inhibitor to control the biofilm formation of periodontopathogens.

Autoinducer 2 (AI-2) is a quorum sensing molecule to which bacteria respond to regulate various phenotypes, including virulence and biofilm formation. AI-2 plays an important role in the formation of a subgingival biofilm composed mostly of Gram-negative anaerobes, by which periodontitis is initiated. The aim of this study was to evaluate D-galactose as an inhibitor of AI-2 activity and thus of the biofilm formation of periodontopathogens. In a search for an AI-2 receptor of Fusobacterium nucleatum, D-galactose binding protein (Gbp, Gene ID FN1165) showed high sequence similarity with the ribose binding protein (RbsB), a known AI-2 receptor of Aggregatibacter actinomycetemcomitans. D-Galactose was evaluated for its inhibitory effect on the AI-2 activity of Vibrio harveyi BB152 and F. nucleatum, the major coaggregation bridge organism, which connects early colonizing commensals and late pathogenic colonizers in dental biofilms. The inhibitory effect of D-galactose on the biofilm formation of periodontopathogens was assessed by crystal violet staining and confocal laser scanning microscopy in the absence or presence of AI-2 and secreted molecules of F. nucleatum. D-Galactose significantly inhibited the AI-2 activity of V. harveyi and F. nucleatum. In addition, D-galactose markedly inhibited the biofilm formation of F. nucleatum, Porphyromonas gingivalis, and Tannerella forsythia induced by the AI-2 of F. nucleatum without affecting bacterial growth. Our results demonstrate that the Gbp may function as an AI-2 receptor and that galactose may be used for prevention of the biofilm formation of periodontopathogens by targeting AI-2 activity.

Microcanonical analysis of a finite-size nonequilibrium system.

Microcanonical analysis is a powerful method that can be used to generalize the concept of phase transitions to finite-size systems. However, microcanonical analysis has only been applied to equilibrium systems. I show that it is possible to conduct the microcanonical analysis of a finite-size nonequilibrium system by generalizing the concept of microcanonical entropy. A one-dimensional asymmetric diffusion process is studied as an example for which such a generalized entropy can be explicitly found, and the microcanonical method is used to define a generalized phase transition for the finite-size nonequilibrium system.

Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.

Many proteins undergo large-scale motions where relatively rigid domains move against each other. The identification of rigid domains, as well as the hinge residues important for their relative movements, is important for various applications including flexible docking simulations. In this work, we develop a method for protein rigid domain identification based on an exhaustive enumeration of maximal rigid domains, the rigid domains not fully contained within other domains. The computation is performed by mapping the problem to that of finding maximal cliques in a graph. A minimal set of rigid domains are then selected, which cover most of the protein with minimal overlap. In contrast to the results of existing methods that partition a protein into non-overlapping domains using approximate algorithms, the rigid domains obtained from exact enumeration naturally contain overlapping regions, which correspond to the hinges of the inter-domain bending motion. The performance of the algorithm is demonstrated on several proteins.

Single molecule conformational memory extraction: p5ab RNA hairpin.

Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others.

RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel.

Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope ((13)C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [(13)C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect (13)C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the (13)C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA-stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.

Nonadditive entropies yield probability distributions with biases not warranted by the data.

Different quantities that go by the name of entropy are used in variational principles to infer probability distributions from limited data. Shore and Johnson showed that maximizing the Boltzmann-Gibbs form of the entropy ensures that probability distributions inferred satisfy the multiplication rule of probability for independent events in the absence of data coupling such events. Other types of entropies that violate the Shore and Johnson axioms, including nonadditive entropies such as the Tsallis entropy, violate this basic consistency requirement. Here we use the axiomatic framework of Shore and Johnson to show how such nonadditive entropy functions generate biases in probability distributions that are not warranted by the underlying data.