Probe Size Research Articles

Controlled Assembly of Lipid Molecules via Regulating Transient Spatial Confinement

The constructs of lipid molecules follow self-assembly, driven by intermolecular interactions, forming stacking of lipid bilayer films. Achieving designed geometry at nano- to micro-levels with packing deviating from the near-equilibrium structure is difficult to achieve due to the strong tendency of lipid molecules to self-assemble. Using ultrasmall (<fL) droplets containing designed molecules, our prior work has demonstrated that molecular assembly, in principle, is governed mainly by transient inter-molecular interactions under their dynamic spatial confinement, i.e., tri-phase boundaries during drying. As a result, the assemblies can deviate, sometimes significantly, from the near-equilibrium structures of self-assembly. The present work applies the approach and concept to lipid molecules using 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Taking advantage of the high spatial precision and the minute size of the delivery probe in our combined atomic force microscopy and microfluidic delivery, the transient shape of each liquid droplet is regulated. In doing so, the final geometry of the POPC assemblies has been regulated to the designed geometry with nanometer precision. The results extend the concept of controlled assembly of molecules to amphiphilic systems. The outcomes exhibit high potential in lipid-based biomaterial science and biodevice engineering.

Multivalent supramolecular fluorescent probes for accurate disease imaging.

Optical imaging is a powerful tool for early disease detection and effective treatment planning, but its accuracy is often compromised by the uptake of imaging materials by the mononuclear phagocyte system (MPS). Herein, we leverage multivalent host-guest interactions between cyanine dyes and β-cyclodextrin polymers to develop supramolecular probes with enhanced stability, optical, and transport profiles for accurate in vivo imaging. These multivalent interactions not only ensure the stability of the probes but also enhance fluorescence efficiency by minimizing nonradiative decay. Our self-assembly approach effectively modulates probe size and surface properties, enabling evasion of MPS clearance and promoting prolonged bloodstream circulation, thereby improving the signal-to-background ratio for imaging. The effectiveness of our design is demonstrated by substantial advancements in the early diagnosis of acute kidney injury and by providing high-contrast imaging and precise surgical navigation across various tumor models. Our strategy not only advances optical imaging materials toward clinical translation but also establishes a versatile platform applicable to multiple imaging modalities.

Hand’s Vibration Perception Thresholds—A Systematic Review

The term vibration perception threshold (VPT) refers to the minimum amplitude required for a vibration to be consciously perceived. Knowledge of VPTs can be used to aid in the diagnosis of various pathologies, or to support design decisions during human-machine interface development. However, several factors affect VPT measurements (e.g., contactor size and pressure), thus, comparing VPT results from multiple studies should not be done without considering both the similarities and differences between said studies. This paper presents a systematic review on VPT results obtained across multiple studies, taking into consideration the different factors affecting the values reported in the literature. We intended to answer the following question: “What are the Vibration Perception Thresholds assessed on the glabrous skin of the hands and fingers of healthy humans?” To the best of our knowledge, this is the first attempt at conducting a systematic review focused specifically on numerical VPT results. Starting from 936 records, VPT results from 37 studies were organized according to various factors (gender, age, probe size, contact pressure, psychophysical method, room temperature, skin temperature, and hand location). This data was organized into a table, the Organization Table that is available for readers. This review can help future researchers and developers working on or working with the topic of human perception of vibrations by examining the factors that affect VPTs and discussing strategies to address them. We offer recommendations for future research and insights on how design engineers can utilize VPTs in the development of new haptic devices.

Dynamic Light Scattering Microrheology of Phase-Separated Poly(vinyl) Alcohol–Phytagel Blends

In this investigation, we explored the microrheological characteristics of dilute hydrogels composed exclusively of Poly(vinyl) alcohol (PVA), Phytagel (PHY), and a blend of the two in varying concentrations. Each of these polymers has established applications in the biomedical field, such as drug delivery and lens drops. This study involved varying the sample concentrations from 0.15% to 0.3% (w/w) to assess how the concentration influenced the observed rheological response. Two probe sizes were employed to examine the impact of the size and verify the continuity hypothesis. The use of two polymer blends revealed their immiscibility and tendency to undergo phase separation, as supported by the existing literature. Exploring the microrheological structure is essential for a comprehensive understanding of the molecular scale. Dynamic light scattering (DLS) was chosen due to its wide frequency range and widespread availability. The selected dilute concentration range was hypothesized to fall within the transition from an ergodic to a non-ergodic medium. Properly identifying the sample’s nature during an analysis—whether it is ergodic or not—is critical, as highlighted in the literature. The obtained results clearly demonstrate an overlap in the results for the storage (G’) and loss moduli (G″) for the different probe particle sizes, confirming the fulfillment of the continuum hypothesis.

Unsupervised Learning for the Automatic Counting of Grains in Nanocrystals and Image Segmentation at the Atomic Resolution.

Identifying the grain distribution and grain boundaries of nanoparticles is important for predicting their properties. Experimental methods for identifying the crystallographic distribution, such as precession electron diffraction, are limited by their probe size. In this study, we developed an unsupervised learning method by applying a Gabor filter to HAADF-STEM images at the atomic level for image segmentation and automatic counting of grains in polycrystalline nanoparticles. The methodology comprises a Gabor filter for feature extraction, non-negative matrix factorization for dimension reduction, and K-means clustering. We set the threshold distance and angle between the clusters required for the number of clusters to converge so as to automatically determine the optimal number of grains. This approach can shed new light on the nature of polycrystalline nanoparticles and their structure-property relationships.

Comparison of 6 handheld ultrasound devices by point-of-care ultrasound experts: a cross-sectional study

BackgroundPoint-of-care ultrasound (POCUS) has emerged as an essential bedside tool for clinicians, but lack of access to ultrasound equipment has been a top barrier to POCUS use. Recently, several handheld ultrasound devices (“handhelds”) have become available, and clinicians are seeking data to guide purchasing decisions. Few comparative studies of different handhelds have been done. We conducted a cross-sectional study comparing 6 handhelds readily available in the United States (Butterfly iQ + ™ by Butterfly Network Inc.; Clarius™ by Clarius Mobile Health; Kosmos™ by EchoNous; TE Air™ by Mindray; Vscan Air™ SL and CL by General Electric; and Lumify™ by Philips Healthcare). A multi-specialty group of physician POCUS experts (n = 35) acquired three standard ultrasound views (abdominal right upper quadrant, cardiac apical 4-chamber, and superficial neck and lung views) in random order on the same standardized patients and rated the image quality. Afterward, a final survey of the overall ease of use, image quality, and satisfaction of each handheld was completed.ResultsThirty-five POCUS experts specializing in internal medicine/hospital medicine, critical care, emergency medicine, and nephrology acquired and rated right upper quadrant, apical 4-chamber, and superficial neck and lung views with 6 different handhelds. For image quality, the highest-rated handhelds were Vscan Air™ for the right upper quadrant view, Mindray TE Air™ for the cardiac apical 4-chamber view, and Lumify™ for superficial views of the neck and lung. Overall satisfaction with image quality was highest with Vscan Air™, Lumify™, and Mindray, while overall satisfaction with ease of use was highest with Vscan Air™. The 5 most desirable characteristics of handhelds were image quality, ease of use, portability, probe size, and battery life. Ultimately, all 6 handhelds had notable advantages and disadvantages, with no single device having all desired qualities or features.ConclusionsThe overall satisfaction with image quality was rated highest with Vscan Air™, Lumify™, and Mindray TE Air™when acquiring right upper quadrant, apical 4-chamber, and superficial neck and lung views. No single handheld was perceived to be superior in image quality for all views. Vscan Air™ was rated highest for overall ease of use and was the most preferred handheld for purchase by POCUS experts.

Single-Plane Versus Synchronous Biplane Ultrasound Imaging During Vascular Access Procedures: Which Is Better and How Can We Improve?

Highlights Biplane ultrasound imaging reduces need for probe manipulation during procedure. Providers note clinical benefit of biplane ultrasound imaging for vascular access. Biplane disadvantages include probe size, imaging quality, size of the screen. Thorough didactic and practical education is essential for biplane success. Abstract Background: Use of ultrasound guidance for vascular access procedures is commonplace in inpatient and outpatient care settings. Standard ultrasound probes offer the operator a single-plane view, necessitating rotation of probe to attain dual complimentary views. This mechanical probe rotation increases technical difficulty of ultrasound use. The purpose of this study is to evaluate the rate of cannulation success and efficiency of a synchronous biplane ultrasound mode in ultrasound-guided arterial line placement as compared with a standard single-view ultrasound mode in the operating room setting. Methods: Patients scheduled for elective surgery in which a radial arterial catheter would be used for hemodynamic monitoring were approached for consent to this study. Patients were randomized to either undergo placement with single-plane view versus synchronous biplane view; outcomes were recorded. Providers were provided preprocedural ultrasound education as well as the option of a short hands-on experience; their level of experience was noted. Results: Placement time of a peripheral arterial catheter was longer and required more attempts to be successful using synchronous biplane imaging as compared with single-plane imaging across providers of all skill/experience levels. Subjectively, providers noted the benefit of synchronous biplane imaging in vascular access; however, disadvantages including probe size, quality of imaging, and size of the screen were noted. Discussion: Thorough education regarding the use and functionality of biplane synchronous imaging in vascular access is essential. Additional guided-practice time with experienced operators could also be helpful to overcome the challenges observed in this study.

Value of elastography in characterization of solid renal masses

BackgroundSolid renal masses often come to light as incidental findings during abdominal ultrasound examinations. Once detected, determining whether a renal mass is benign or malignant becomes imperative for informed decision-making regarding management and treatment strategies. In this investigation, the aim was to explore the diagnostic efficacy of real-time strain sonoelastography in assessing solid renal masses.MethodsThis prospective research was steered on 26 individuals diagnosed with a solid renal mass, as endorsed by pathological analysis after surgical removal or biopsy. Elastography was performed on all patients. The measurement of strain index values for tissues was achieved by placing regions of interest of equal or near-equal size on both the tumor (A) and the adjacent normal renal cortex (B).ResultsStrain elastography showed no correlation with patient’s age, size of mass and probe to mass distance with p > 0.05 all. Sensitivity analysis showed that strain index can significantly predict malignant renal masses (P = 0.003) using a cut-off point 2, with 92.9% area under curve, 95.2% sensitivity, 80% specificity, 80% negative predictive value, 95.2% positive predictive value, and overall diagnostic accuracy 92.3%. Strain index > 2 was an independent predictor for malignant renal masses (P = 0.025), odds ratio 7.29 when adjusting for other risk factors. Malignant renal masses were significantly higher strain index compared to benign lesions with (P = 0.001).ConclusionsStrain elastography is a valuable technique for distinguishing between malignant and benign solid renal tumors. Benign lesions have lower strain index values compared to malignant ones, making the strain index a useful screening tool for distinguishing between benign and malignant renal masses using cut-off point 2.

Reliability of Ultrasound Assessment of Hamstring Morphology, Quality, and Stiffness Among Healthy Adults and Athletes: A Systematic Review.

The incidence and recurrence rate of hamstring strain injuries remain persistently high, with recurrent injuries leading to increased time lost during play and extended recovery periods compared with initial injury. Ultrasound imaging assesses important factors such as hamstring fascicle length (FL), pennation angle (PA), cross-sectional area (CSA), muscle thickness (MT), echo intensity (EI), and shear wave elastography (SWE), all impacting athletic performance. However, its reliability must be established before employing any measurement tool in research or clinical settings. To determine the reliability and measurement error of ultrasound for assessing hamstring FL, PA, CSA, MT, EI, and SWE among healthy adults and athletes; to synthesize the information regarding the operationalization of ultrasound. A systematic literature search was done from January 1990 to February 5, 2023, to identify reliability and validity studies of hamstring ultrasound assessment published in peer-reviewed journals with identifiable methodology of outcome measures. Intraclass correlation coefficient measurement of 14 included studies reported moderate to excellent intrarater, interrater, and test-retest reliabilities of FL, PA, and MT regardless of the site of muscle testing, probe size, and setting, state of muscle, and use of different techniques in the extrapolation of FL. Good to excellent test-retest reliability rates for all hamstring anatomic CSA along midmuscle and different percentages of thigh length using panoramic imaging. Good intrarater reliability of EI regardless of gender and orientation of the probe but with excellent intrarater reliability in transverse scan using maximum region of interest. Good intrarater, interrater, and interday repeatability on SWE with the muscle in a stretched position. Evidence from studies with a predominantly low risk of bias shows that ultrasound is a reliable tool to measure hamstring FL, PA, CSA, MT, EI, and SWE in healthy adults and athletes under various experimental conditions.

Wehnelt photoemission in an ultrafast electron microscope: Stability and usability

We tested and compared the stability and usability of three different cathode materials and configurations in a thermionic-based ultrafast electron microscope: (1) on-axis thermionic and photoemission from a custom 100 μm diameter LaB6 source with a graphite guard ring, (2) off-axis photoemission from the Ni aperture surface of the Wehnelt electrode, and (3) on-axis thermionic and photoemission from a custom 200 μm diameter polycrystalline Ta source. For each cathode type and configuration, including the Ni Wehnelt aperture, we illustrate how the photoelectron beam-current stability is deleteriously impacted by simultaneous cooling of the source following thermionic heating. Furthermore, we demonstrate usability via collection of parallel- and convergent-beam electron diffraction patterns and by formation of the optimum probe size. We find that usability of the off-axis Ni Wehnelt-aperture photoemission is at least comparable to on-axis LaB6 thermionic emission, as well as to on-axis photoemission [the heretofore conventional approach to ultrafast electron microscopy (UEM) in thermionic-based instruments]. However, the stability and achievable beam currents for off-axis photoemission from the Wehnelt aperture were superior to that of the other cathode types and configurations, regardless of the electron-emission mechanism. Beam-current stability for this configuration was found to be ±1% (one standard deviation from the mean) for 70 min (longest duration tested), and steady-state beam current was reached within the sampling-time resolution used here (∼1 s) for 15 pA beam currents (i.e., 460 electrons per packet for a 200 kHz repetition rate). Repeatability and robustness of the steady-state condition were also found to be within ±1% of the mean. We discuss the implications of these findings for UEM imaging and diffraction experiments, for pulsed-beam damage measurements, and for practical switching between optimum conventional TEM and UEM operation within the same instrument.

Enhancing higher-order modal response in multifrequency atomic force microscopy with a coupled cantilever system.

Multifrequency atomic force microscopy (AFM) utilizes the multimode operation of cantilevers to achieve rapid high-resolution imaging and extract multiple properties. However, the higher-order modal response of traditional rectangular cantilever is weaker in air, which affects the sensitivity of multifrequency AFM detection. To address this issue, we previously proposed a bridge/cantilever coupled system model to enhance the higher-order modal response of the cantilever. This model is simpler and less costly than other enhancement methods, making it easier to be widely used. However, previous studies were limited to theoretical analysis and preliminary simulations regarding ideal conditions. In this paper, we undertake a more comprehensive investigation of the coupled system, taking into account the influence of probe and excitation surface sizes on the modal response. To facilitate the exploration of the effectiveness and optimal conditions for the coupled system in practical applications, a macroscale experimental platform is established. By conducting finite element analysis and experiments, we compare the performance of the coupled system with that of traditional cantilevers and quantify the enhancement in higher-order modal response. Also, the optimal conditions for the enhancement of macroscale cantilever modal response are explored. Additionally, we also supplement the characteristics of this model, including increasing the modal frequency of the original cantilever and generating additional resonance peaks, demonstrating the significant potential of the coupled system in various fields of AFM.

Research on water equivalence and angle dependence of medical POF scintillation dosimeters

In radiation dosimetry and medical dosimetry, optical fiber dosimeters have great advantages in application due to their small size and long transmission distance. However, in some low-dose radiation environments, the water inequivalence error and angle error of optical fiber dosimeters can have significant impacts that cannot be ignored. In this paper, the effects of ray energy, ray solid angle and optical fiber probe size on water inequivalence error and angle error are analyzed by using Monte Carlo simulation. Due to the complexity of the influencing factors of the angle error, which is difficult to be analyzed precisely and quantitatively, a correction method based on BP neural network is proposed. The final validation results demonstrate that the correction scheme can reduce the total angle error of the optical fiber dosimeter to 2.72%.

Helium expansion revisited: Effects of accessible volume on excess adsorption in kerogen matrices

Enhancing our understanding of the excess adsorption capacity in shale gas reservoirs is paramount for accurately predicting production capabilities and refining extraction processes. A significant factor in this calculation is the accessible volume, which can only be measured indirectly using helium as a proxy. In this study, hybrid grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations were employed to scrutinize the accessible volume and quantify the excess adsorption capacities of various gases in kerogen matrices, characterized by diverse micropore distributions at 363.15 K (90 °C) and pressures up to 50 MPa. We evaluated multiple approaches to determine accessible volume in simulations, emphasizing the importance of selecting a probe size that reflects the actual size of the adsorbate. The simulation outcomes reveal that accessible volumes derived from the helium expansion method, mimicking the traditional experimental techniques, tend to be overestimated by around a factor of two. This finding challenges the reliability of such measurements and suggests a need for their recalibration based on computer simulation models. Furthermore, when our simulations were compared with various theoretical adsorption isotherm models, the more advanced Supercritical Dubinin-Radushkevich and Supercritical Brunauer-Emmett-Teller models demonstrated better accuracy in predicting absolute adsorption values compared to the more conventional Langmuir model. However, neither model accurately predicted the absolute adsorption quantities, indicating room for improvement. Finally, the simulations underscore the significant adsorption capacity of CO2 compared to other gases, highlighting its promising role in facilitating enhanced gas recovery and geological sequestration within shale formations.

Wearing an ultrasound probe during walking does not influence lower limb joint kinematics in adolescents with cerebral palsy and typically developing peers

BackgroundEnhancing traditional three-dimensional gait analysis with a portable ultrasound device at the lower-limb muscle-tendon level enables direct measurement of muscle and tendon lengths during walking. However, it is important to consider that the size of the ultrasound probe and its attachment on the lower limb may potentially influence gait pattern. Research questionWhat is the effect of wearing an ultrasound probe at the lower limb in adolescents with cerebral palsy and typically developing peers? MethodsEleven individuals with cerebral palsy and nine age-matched typically developing peers walking barefoot at their self-selected speed were analyzed. Data collection occurred under three conditions: the reference condition (GAIT), and two conditions involving placement of the ultrasound probe over the distal medial gastrocnemius-Achilles tendon junction (MTJ) and over the medial gastrocnemius mid-belly to capture fascicles (FAS). Data processing included calculating differences between conditions using root mean square error (RMSE) for joint kinematics and comparing them to the overall mean difference. Additionally, Spearman correlations were calculated to examine the relationship between kinematic RMSEs and walking speed. ResultsNo significant differences in stance phase duration or walking speed were observed among the three conditions. Average RMSEs were below 5° for all parameters and condition comparisons in both groups. In both the TD and CP groups, RMSE values during the swing phase were higher than those during the stance phase for all joints. No significant correlations were found between height or body mass and swing phase RMSEs. In the CP group, there was a significant correlation between joint kinematics RMSEs and differences in walking speed at the hip, knee and ankle joints when comparing the MTJ condition with the GAIT condition. SignificanceThis study confirms joint kinematics alterations are smaller than 5° due to wearing to the leg an ultrasound probe during walking.

The activation thresholds and inactivation kinetics of poking-evoked PIEZO1 and PIEZO2 currents are sensitive to subtle variations in mechanical stimulation parameters

ABSTRACT PIEZO1 and PIEZO2 are mechanically activated ion channels that confer mechanosensitivity to various cell types. PIEZO channels are commonly examined using the so-called poking technique, where currents are recorded in the whole-cell configuration of the patch-clamp technique, while the cell surface is mechanically stimulated with a small fire-polished patch pipette. Currently, there is no gold standard for mechanical stimulation, and therefore, stimulation protocols differ significantly between laboratories with regard to stimulation velocity, angle, and size of the stimulation probe. Here, we systematically examined the impact of variations in these three stimulation parameters on the outcomes of patch-clamp recordings of PIEZO1 and PIEZO2. We show that the inactivation kinetics of PIEZO1 and, to a lesser extent, of PIEZO2 change with the angle at which the probe that is used for mechanical stimulation is positioned and, even more prominently, with the size of its tip. Moreover, we found that the mechanical activation threshold of PIEZO2, but not PIEZO1, decreased with increasing stimulation speeds. Thus, our data show that two key outcome parameters of PIEZO-related patch-clamp studies are significantly affected by common variations in the mechanical stimulation protocols, which calls for caution when comparing data from different laboratories and highlights the need to establish a gold standard for mechanical stimulation to improve comparability and reproducibility of data obtained with the poking technique.

A novel method for holdup measurement of three phases by an ultrasonic device with the flexible substrate

The precise measurement of multiphase flow holds significant importance across diverse industrial contexts. However, rigid probes struggle with the variable dimensions of curved surfaces, while flexible probes are hindered by fragility, susceptibility, and challenges in large-scale production. Herein, we propose an ultrasonic device featuring a flexible substrate that seamlessly amalgamates flexibility and rigidity to enable precise measurement of three-phase flow. Through simulation, we determine the optimal ultrasonic frequency (1 MHz) and flexible substrate thickness (3 mm) for a specified probe and pipe size (20 mm). A novel concept, the specific attenuation coefficient (SAC), derived from the voltage-amplitude of transmitted and received signals and propagation distance, is introduced to differentiate between oil and water. The discrepancy between measured and actual three-phase holdups are 0.55 %, 0.36 %, and 0.59 % for water, gas and oil, respectively, with a variance of measurement results 0.027.

Effect of ultrasound geometry on the production efficiency of damaged starch: Determining rheology parameters, and non-isothermal reaction kinetics

Present study investigates the effects of probe size geometry on thermodynamic kinetics, rheology, and microstructure of wheat and tapioca starch. Ultrasound treatment using different probe diameters (20 mm and 100 mm) significantly influenced the gelatinization process. Results showed reduced enthalpy (ΔH) and Gibbs energy (ΔG), indicating enhanced gelatinization efficiency. According to the results, using a 20 mm and 100 mm probe leads to a reduction of 52.7 % and 68.6 % in reaction enthalpy for wheat starch compared to native starch, respectively. Microstructure analysis revealed structural changes, with ultrasound treatment leading to granular fractures and a sheet-like structure with air bubbles. The rheological behavior of the starches is found to exhibit shear thinning behavior, with the Casson model providing the best fit for the experimental data. Moreover, rheology modeling using Herschel-Bulkley and power law models showed increased viscosity and shear stress in larger probes. Numerical simulation data demonstrated that probe size influenced ultrasonic pressure, sound pressure level, and thermal power dissipation density, affecting fluid motion and velocity field components. Moreover, the maximum dissipated power decreases from 8.43 to 0.655 mW/m3 with an increase in probe diameter from 20 to 100 mm. The average yield shear stress values are calculated as 3.36 and 3.14 for wheat and tapioca starches, respectively. The larger probe diameter leads to greater entropy increases, with tapioca starch showing a 4.72 % increase and wheat starch a 4.97 % increase, compared to 2.56 % and 3.11 %, respectively, with the smaller probe. Additionally, the Keller-Miksis model provided insights into bubble dynamics, revealing increased pressure and temperature with higher pressure amplitudes.

Assessing the role of surface layer and molecular probe size in diffusion within meniscus tissue.

Diffusion within extracellular matrix is essential to deliver nutrients and larger metabolites to the avascular region of the meniscus. It is well known that both structure and composition of the meniscus vary across its regions; therefore, it is crucial to fully understand how the heterogenous meniscal architecture affects its diffusive properties. The objective of this study was to investigate the effect of meniscal region (core tissue, femoral, and tibial surface layers) and molecular weight on the diffusivity of several molecules in porcine meniscus. Tissue samples were harvested from the central area of porcine lateral menisci. Diffusivity of fluorescein (MW 332 Da) and three fluorescence-labeled dextrans (MW 3k, 40k, and 150k Da) was measured via fluorescence recovery after photobleaching. Diffusivity was affected by molecular size, decreasing as the Stokes' radius of the solute increased. There was no significant effect of meniscal region on diffusivity for fluorescein, 3k and 40k dextrans (p>0.05). However, region did significantly affect the diffusivity of 150k Dextran, with that in the tibial surface layer being larger than in the core region (p = 0.001). Our findings contribute novel knowledge concerning the transport properties of the meniscus fibrocartilage. This data can be used to advance the understanding of tissue pathophysiology and explore effective approaches for tissue restoration.

Improved LINE-1 Detection through Pattern Matching by Increasing Probe Length.

Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element that accounts for 17% of the human genome. Strong correlations between abnormal L1 expression and diseases, particularly cancer, have been documented by numerous studies. L1PD (LINE-1 Pattern Detection) had been previously created to detect L1s by using a fixed pre-determined set of 50-mer probes and a pattern-matching algorithm. L1PD uses a novel seed-and-pattern-match strategy as opposed to the well-known seed-and-extend strategy employed by other tools. This study discusses an improved version of L1PD that shows how increasing the size of the k-mer probes from 50 to 75 or to 100 yields better results, as evidenced by experiments showing higher precision and recall when compared to the 50-mers. The probe-generation process was updated and the corresponding software is now shared so that users may generate probes for other reference genomes (with certain limitations). Additionally, L1PD was applied to other non-human genomes, such as dogs, horses, and cows, to further validate the pattern-matching strategy. The improved version of L1PD proves to be an efficient and promising approach for L1 detection.

Defining Optimal Settings for Lung Cryobiopsy in End-Stage Pulmonary Disease. A Human, Ex Vivo, Diseased Lung Clinical Trial.

To evaluate optimal settings of probe size, freezing time, and distance to the pleura that influence the size and quality of biopsy specimens during transbronchial lung cryobiopsies in ESPD. We prospectively recruited 17 patients undergoing lung transplantation. We created a nonperfused ex vivo bronchoscopy setting to perform multiple cryobiopsies with different probe sizes (1.7, 1.9, and 2.4mm), freezing times (3, 5, 7, 10, 20, 30 seconds), and probe distance from pleura (5, 10, and 20mm). Alveolated pulmonary parenchyma area≥50% in histology was considered a good quality biopsy, with a minimum procedural artifact. We used logistic regression to identify independent parameters as risk factors for histologic adequacy. A total of 545 cryobiopsies were obtained from 34 explanted lungs after pneumonectomy for lung transplantation. The mean maximum diameter of the specimen achieved with the 1.7 probe was larger (13.5mm) than those obtained with 1.9 and 2.4mm probes (11.3 and 10.7mm, P= 0.07). More pleural macroscopic damage and pleural tissue in histology occurred with the 2.4mm probe ( P <0.001). There was no difference in the quality of specimens between the different freezing times and the distance from the pleura. Freezing time and distance from the pleura did not affect the histologic quality for diagnosing ESPD in severely damaged lungs. Smaller cryoprobe size did not negatively affect sample adequacy.