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The nuclear ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions are commonly used to identify fungi and other eukaryotic taxa in amplicon sequencing. The highly conserved rRNA regions flanking the ITS are often trimmed before being used for taxonomic assignment. The Python software package ITSxpress rapidly trims single-end or paired-end sequences in FASTQ format for use in amplicon sequence variant clustering methods like DADA2. This new major release of ITSxpress improves the paired-end merging method, simplifies installation of the QIIME 2 ITSxpress plugin, removes major dependencies, adds use cases, and is compatible with newer compression formats. This article discusses the modifications to ITSxpress that improve the output and user experience, leading to a major version increase.IMPORTANCEITSxpress is a sequence trimming method applied to internal transcribed spacer (ITS) amplicon sequences before calling amplicon sequence variants (ASVs). The ITS region is used to understand the composition of eukaryotic microbial communities. ITS sequences provide good taxonomic resolution due to their hypervariability, but are flanked by conserved regions that allow their primers to be more universal. Amplicons generated with such primers contain regions with different evolutionary rates, and trimming these conserved regions results in better taxonomic classification and a more valid set of ASVs. This package can be used for most amplicon sequencing methods including for newer long-read sequencing formats, such as PacBio. ITSxpress can be installed from Bioconda, used as a Docker image, or installed from source code. The package works well with high-performance computing clusters or laptops due to its low-resource requirements.

While inverse probability of treatment weighting (IPTW) is a commonly used approach for treatment comparisons in observational data, the resulting estimates may be subject to bias and excessively large variance under lack of overlap. By smoothly down-weighting units with extreme propensity scores, i.e., those that are close (or equal) to zero or one, overlap weighting (OW) can help mitigate the bias and variance issues associated with IPTW. Although theoretical and simulation results have supported the use of OW with continuous and binary outcomes, its performance with survival outcomes remains to be further investigated, especially when the target estimand is defined based on the restricted mean survival time (RMST). We combine propensity score weighting and inverse probability of censoring weighting to estimate the restricted mean counterfactual survival times, and provide computationally-efficient variance estimators when the propensity scores are estimated by logistic regression and the censoring process is estimated by Cox regression. We conduct simulations to compare the performance of weighting methods in terms of bias, variance, and 95% interval coverage, under various degrees of overlap. Under moderate and weak overlap, we demonstrate the advantage of OW over IPTW, trimming and truncation, with respect to bias, variance, and coverage when estimating RMST., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The use of propensity score methods has become ubiquitous in causal inference. At the heart of these methods is the positivity assumption. Violation of the positivity assumption leads to the presence of extreme propensity score weights when estimating average causal effects, which affects statistical inference. To circumvent this issue, trimming or truncating methods have been widely used. Unfortunately, these methods require that we pre-specify a threshold. There are a number of alternative methods to deal with the lack of positivity when we estimate the average treatment effect (ATE). However, no other methods exist beyond trimming and truncation to deal with the same issue when the goal is to estimate the average treatment effect on the treated (ATT). In this article, we propose a propensity score weight-based alternative for the ATT, called overlap weighted average treatment effect on the treated. The appeal of our proposed method lies in its ability to obtain similar or even better results than trimming and truncation while relaxing the constraint to choose an a priori threshold (or related measures). The performance of the proposed method is illustrated via a series of Monte Carlo simulations and a data analysis on racial disparities in health care expenditures., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

The abrasive waterjet machining process was introduced in the 1980s as a new cutting tool; the process has the ability to cut almost any material. Currently, the AWJ process is used in many world-class factories, producing parts for use in daily life. A description of this process and its influencing parameters are first presented in this paper, along with process models for the AWJ tool itself and also for the jet-material interaction. The AWJ material removal process occurs through the high-velocity impact of abrasive particles, whose tips micromachine the material at the microscopic scale, with no thermal or mechanical adverse effects. The macro-characteristics of the cut surface, such as its taper, trailback, and waviness, are discussed, along with methods of improving the geometrical accuracy of the cut parts using these attributes. For example, dynamic angular compensation is used to correct for the taper and undercut in shape cutting. The surface finish is controlled by the cutting speed, hydraulic, and abrasive parameters using software and process models built into the controllers of CNC machines. In addition to shape cutting, edge trimming is presented, with a focus on the carbon fiber composites used in aircraft and automotive structures, where special AWJ tools and manipulators are used. Examples of the precision cutting of microelectronic and solar cell parts are discussed to describe the special techniques that are used, such as machine vision and vacuum-assist, which have been found to be essential to the integrity and accuracy of cut parts. The use of the AWJ machining process was extended to other applications, such as drilling, boring, milling, turning, and surface modification, which are presented in this paper as actual industrial applications. To demonstrate the versatility of the AWJ machining process, the data in this paper were selected to cover a wide range of materials, such as metal, glass, composites, and ceramics, and also a wide range of thicknesses, from 1 mm to 600 mm. The trends of Industry 4.0 and 5.0, AI, and IoT are also presented.

Introduction: Cannabis sativa L. inflorescences are widely used in the medicinal field as treatments for a variety of symptoms and illnesses due to their unique phytochemicals such as cannabinoids and terpenes. Common postharvest procedures for cannabis inflorescence include trimming, followed by drying, curing, and subsequent storage. The postharvest trimming step, particularly its timing (pre- or post-drying) and the extent of trimming, is not optimally refined in terms of its impact on the cannabinoid and terpene content. In this study, our objective was to identify the optimal trimming conditions for a commercially available medicinal cannabis hybrid chemovar, with the goal of maximizing its cannabinoid and terpene content., Methods: To achieve this, we investigated the effects of pre- versus post-drying trimming and evaluated the impact of mild versus aggressive trimming prior to drying on the cannabinoid and terpene profiles using liquid and gas chromatography., Results: Our results indicated that pre-drying mild trimming yielded the highest cannabinoid concentration, possibly due to optimal balance between stress signals and precursor influx from the sugar leaves to the inflorescence. On the other, post-drying trimming yielded the highest terpene content., Conclusion: Identifying the optimal trimming conditions that maximize both cannabinoid and terpene levels in cannabis is challenging. Therefore, growers face a decision in their trimming practices: to prioritize either enhanced cannabinoid content or increased aromatic terpene concentrations, as optimizing for both simultaneously appears to be difficult., Competing Interests: The authors have no conflicts of interest to declare., (© 2024 The Author(s). Published by S. Karger AG, Basel.)

Introduction: Stainless steel crowns (SSCs) are the most durable and effective restorations for primary teeth. Titanium-coated SSCs are newer on the market, and this study was conducted to assess the amount of nickel (Ni) and titanium ions released from titanium-coated SSCs, with and without trim, in artificial saliva., Materials and Methods: A total of 60 titanium-coated SSCs were divided into two groups-group I ( n = 30, without trim) and group II ( n = 30, with trim) and were immersed in 5 mL artificial saliva. The amount of Ni and titanium released in each group was measured by inductively coupled plasma-mass spectrometry on days 1, 7, and 21., Results: The amount of Ni ion released in group I on day 1 was 0.0096 ppm and reduced on day 7 (0.0091 ppm) and day 21 (0.0088 ppm). Whereas the amount of Ni ion released in group II was the same for all 3 days (0.0096 ppm). The amount of titanium ion released in both groups was the same on all 3 days (0.00108 ppm)., Conclusion: There was no significant difference seen in the mean Ni and titanium ion release between the two groups on all 3 days. The cumulative release of metals from titanium-coated SSCs in each of the groups was significantly lower than the level required to produce any harmful effects. Any of the groups of commercially available SSCs can be used in pediatric dentistry., How to Cite This Article: Biradar R, Siaddaiah SB, Bhat PK. Evaluation of Nickel and Titanium Releasing from Titanium-coated Stainless Steel Crowns Regarding Trimming: An In Vitro Study. Int J Clin Pediatr Dent 2024;17(5):524-527., Competing Interests: Source of support: Nil Conflict of interest: NoneConflict of interest: None, (Copyright © 2024; The Author(s).)

Tillering/branching pattern plays a significant role in determining the structure and diversity of grass, and trimming has been found to induce tillering in turfgrass. Recently, it has been reported that hydrogen peroxide (H 2 O 2 ) regulates axillary bud development. However, the role of H 2 O 2 in trimming-induced tillering in bermudagrass, a kind of turfgrass, remains unclear. Our study unveils the significant impact of trimming on promoting the sprouting and growth of tiller buds in stolon nodes, along with an increase in the number of tillers in the main stem. This effect is accompanied by spatial-temporal changes in cytokinin and sucrose content, as well as relevant gene expression in axillary buds. In addition, the partial trimming of new-born tillers results in an increase in sucrose and starch reserves in their leaves, which can be attributed to the enhanced photosynthesis capacity. Importantly, trimming promotes a rapid H 2 O 2 burst in the leaves of new-born tillers and axillary stolon buds. Furthermore, exogenous application of H 2 O 2 significantly increases the number of tillers after trimming by affecting the expression of cytokinin-related genes, bolstering photosynthesis potential, energy reserves and antioxidant enzyme activity. Taken together, these results indicate that both endogenous production and exogenous addition of H 2 O 2 enhance the inductive effects of trimming on the tillering process in bermudagrass, thus helping boost energy supply and maintain the redox state in newly formed tillers., Competing Interests: The authors declare there are no competing interests., (©2024 Li et al.)

Background: Lameness has been associated with compromised animal welfare and reduced productivity in dairy cattle herds worldwide. However, little is known about the prevalence of claw lesions in the dairy buffalo population in Egypt. Furthermore, the optimum measurements for claw trimming in buffalo are unknown. A cross-sectional cadaver study was conducted where 135 pair buffalo hind feet were collected from 4 slaughterhouses and examined for the presence of claw lesions. The proportion and associated 95% confidence interval (CI) of each type of lesion were calculated. A separate set of healthy claws (n = 26) underwent ultrasonography (US) and computed tomography (CT). The agreement between US and CT measurements was assessed using Passing-Bablok regression and intraclass correlation coefficient. The CT measurements were used to calculate trimming recommendations., Results: At least one lesion was identified in 242 claws (89.6%, 95% CI = 85.4-93.0). In healthy claws, poor to moderate agreement was identified between US and CT measurements which could be due a sample size of the study. The average ± standard deviation (SD) minimum recommended external wall length of the lateral and medial claws in heifers was 7.1 ± 0.36 cm and 7.5 ± 0.35 cm, respectively. The average ± SD minimum recommended external wall length in buffaloes over five years of age was 8.2 ± 0.27 cm and 8.4 ± 0.39 cm for the lateral and medial claws, respectively., Conclusions: The study found a high prevalence of claw lesions in buffalo in Egypt, the clinical significance of which requires further elucidation. Recommended measurements will help guide claw trimming in buffalo to minimise lesions., (© 2024. The Author(s).)

The first aim of this study was to calculate the prevalence of painful lesions of the digits ("alarm" lesions; ALs) in Swiss dairy herds and cow-calf operations over a three-year study period. The following ALs were included in the calculation: the M2 stage of digital dermatitis (DD M2), ulcers (U), white line fissures (WLF) of moderate and high severity, white line abscesses (WLA), interdigital phlegmon (IP) and swelling of the coronet and/or bulb (SW). Between February 2020 and February 2023, digit disorders were electronically recorded during routine trimmings by 40 specially trained hoof trimmers on Swiss cattle farms participating in the national claw health programme. The data set used consisted of over 35,000 observations from almost 25,000 cows from 702 herds. While at the herd-level, the predominant AL documented in 2022 was U with 50.3% followed by WLF with 38.1%, at the cow-level, in 2022, it was DD M2 with 5.4% followed by U with 3.7%. During the study period, within-herd prevalences of ALs ranged from 0.0% to a maximum of 66.1% in 2020. The second aim of this study was to determine herd- and cow-level risk factors associated with digital dermatitis (DD), U and white line disease (WL) in dairy cows using data from 2022. While for DD, analysed herd-level factors appeared to have a greater effect on the probability of its occurrence, the presence of U and WL was mainly associated with the analysed cow-level factors. The risk for DD increased with a higher herd trimming frequency. Herds kept in tie stalls had a lower risk for DD and WL and a higher risk for U compared to herds kept in loose housing systems. Herds with predominantly Holstein Friesian cows as well as Holstein Friesian cows had a higher risk for the occurrence of DD compared to herds and cows of other breeds. With increasing parity, cows had a higher risk of developing U and WL, whereas for DD, parity was negatively associated with prevalence. Cows trimmed during the grazing period had a higher risk of U and WL than cows trimmed during the housing period. These findings may contribute to improve management measures affecting the health of the digits in farms with structures similar to those evaluated in the current study, such as small herds with frequent access to pasture. Further research is warranted to demonstrate how measures addressing the current results combined with those of individual herd risk assessments might contribute to an improvement in the health of the digits in the respective dairy herds.

This contribution presents a model order reduction framework for real-time efficient solution of trimmed, multi-patch isogeometric Kirchhoff-Love shells. In several scenarios, such as design and shape optimization, multiple simulations need to be performed for a given set of physical or geometrical parameters. This step can be computationally expensive in particular for real world, practical applications. We are interested in geometrical parameters and take advantage of the flexibility of splines in representing complex geometries. In this case, the operators are geometry-dependent and generally depend on the parameters in a non-affine way. Moreover, the solutions obtained from trimmed domains may vary highly with respect to different values of the parameters. Therefore, we employ a local reduced basis method based on clustering techniques and the Discrete Empirical Interpolation Method to construct affine approximations and efficient reduced order models. In addition, we discuss the application of the reduction strategy to parametric shape optimization. Finally, we demonstrate the performance of the proposed framework to parameterized Kirchhoff-Love shells through benchmark tests on trimmed, multi-patch meshes including a complex geometry. The proposed approach is accurate and achieves a significant reduction of the online computational cost in comparison to the standard reduced basis method., Competing Interests: Conflict of interestThe authors have no Conflict of interest to declare that are relevant to the content of this article., (© The Author(s) 2024.)

This work focuses on the coupling of trimmed shell patches using Isogeometric Analysis, based on higher continuity splines that seamlessly meet the C 1 requirement of Kirchhoff-Love-based discretizations. Weak enforcement of coupling conditions is achieved through the symmetric interior penalty method, where the fluxes are computed using their correct variationally consistent expression that was only recently proposed and is unprecedentedly adopted herein in the context of coupling conditions. The constitutive relationship accounts for generically laminated materials, although the proposed tests are conducted under the assumption of uniform thickness and lamination sequence. Numerical experiments assess the method for an isotropic and a laminated plate, as well as an isotropic hyperbolic paraboloid shell from the new shell obstacle course. The boundary conditions and domain force are chosen to reproduce manufactured analytical solutions, which are taken as reference to compute rigorous convergence curves in the L 2 , H 1 , and H 2 norms, that closely approach optimal ones predicted by theory. Additionally, we conduct a final test on a complex structure comprising five intersecting laminated cylindrical shells, whose geometry is directly imported from a STEP file. The results exhibit excellent agreement with those obtained through commercial software, showcasing the method's potential for real-world industrial applications., Competing Interests: Conflict of interestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© The Author(s) 2024.)

Correlative Light Electron Microscopy (CLEM) encompasses a wide range of experimental approaches with different degrees of complexity and technical challenges where the attributes of both light and electron microscopy are combined in a single experiment. Although the biological question always determines what technology is the most appropriate, we generally set out to apply the simplest workflow possible. For 2D cell cultures expressing fluorescently tagged molecules, we report on a simple and very powerful CLEM approach by using gridded finder imaging dishes. We first determine the gross localization of the fluorescence using light microscopy and subsequently we retrace the origin/localization of the fluorescence by projecting it onto the ultrastructural reference space obtained by transmission electron microscopy (TEM). Here we describe this workflow and highlight some basic principles of the sample preparation for such a simple CLEM experiment. We will specifically focus on the steps following the resin embedding for TEM and the introduction of the sample in the electron microscope., (Copyright © 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.)

Background: Hyperuricemia can lead to synovial hyperplasia in the wrist. In severe cases, it can lead to the deposition of gouty stone in the carpal tunnel, resulting in increased pressure in the carpal tunnel and compression of the median nerve to cause carpal tunnel syndrome (CTS), which is called gouty carpal tunnel syndrome (GCTS). As for the surgical treatment of gouty carpal tunnel syndrome, scholars have different opinions on whether it is necessary to remove the superficial flexor tendon. The purpose of this study was to compare the clinical efficacy of trimming and resection of the diseased superficial flexor tendon in the treatment of gouty carpal tunnel syndrome., Methods: Clinical data were collected from May 2016 to July 2021 from 10 patients (13 affected wrists) diagnosed with gouty carpal tunnel syndrome and classified into two groups according to the surgical modality: the diseased portion of the gout-eroded superficial finger tendon was trimmed in 9 wrists, and the diseased superficial finger flexor tendon was excised in 4 wrists. Values related to flexion and extension functions, 2-PD, DASH, BCTQ, VAS and recurrence in the affected fingers were compared between the two groups as well as before and after surgery in each group., Results: All affected limbs used were cleared of gouty stones, finger numbness improved, no skin necrosis occurred, and all incisions healed at stage I. At follow-up (13.58 ± 5.53 months), there was no significant difference between groups in flexion and extension function, 2-PD, DASH, BCTQ, and VAS with respect to the affected fingers, and patients in both groups improved significantly before and after surgery. Treatment of only one wrist involved trimming to remove lesion-affected portions of tendon, which reappeared 1 year after surgery, and there was one case of poor recovery from greater piriformis muscle atrophy in both procedures., Conclusion: Regarding surgical treatment of patients with gouty carpal tunnel syndrome in which the gouty stone has invaded the superficial flexor tendons of the fingers, the diseased superficial flexor tendons can be selectively excised, and the postoperative mobility of the affected fingers may not be impaired., (© 2023. The Author(s).)

Objectives: Propensity score (PS) weighting methods are commonly used to adjust for confounding in observational treatment comparisons. However, in the setting of substantial covariate imbalance, PS values may approach 0 and 1, yielding extreme weights and inflated variance of the estimated treatment effect. Adaptations of the standard inverse probability of treatment weights (IPTW) can reduce the influence of extremes, including trimming methods that exclude people with PS values near 0 or 1. Alternatively, overlap weighting (OW) optimizes criteria related to bias and variance, and performs well compared to other PS weighting and matching methods. However, it has not been compared to propensity score stratification (PSS). PSS has some of the same potential advantages; being insensitive extreme values. We sought to compare these methods in the setting of substantial covariate imbalance to generate practical recommendations., Methods: Analytical derivations were used to establish connections between methods, and simulation studies were conducted to assess bias and variance of alternative methods., Results: We find that OW is generally superior, particularly as covariate imbalance increases. In addition, a common method for implementing PSS based on Mantel-Haenszel weights (PSS-MH) is equivalent to a coarsened version of OW and can perform nearly as well. Finally, trimming methods increase bias across methods (IPTW, PSS and PSS-MH) unless the PS model is re-fit to the trimmed sample and weights or strata are re-derived. After trimming with re-fitting, all methods perform similarly to OW., Conclusions: These results may guide the selection, implementation and reporting of PS methods for observational studies with substantial covariate imbalance., Competing Interests: Competing interests: Authors state no conflict of interest., (© 2023 Walter de Gruyter GmbH, Berlin/Boston.)

The aim of the current in vivo, observational study was to investigate the effects of different hoof manipulations on landing duration (LandD), location (IC loc ) and angle of initial contact (IC angle ) in the front feet of horses. A novel, hoof-mounted, inertial measurement unit sensor system (IMU) was used. Ten sound, crossbred horses were fitted with an IMU sensor at the dorsal hoof wall and examined barefoot and after trimming. Additionally, the application of 120 g lateral weights and 5° medial side wedges as well as steel, aluminium, egg bar, and lateral extension shoes were tested. Horses were guided in a straight line on firm ground. The use of steel shoes increased LandD compared to barefoot and enhanced the individual IC loc in trot. Application of rolled toe shoes caused a longer LandD than use of plain shoes. None of the other modifications significantly influenced the timing or spatial variables of hoof landing. Trimming and shoeing have less impact on the landing pattern of horses than assumed in practice. Still, the use of steel shoes changes sliding properties of the hooves on firm ground and increases weight causing a longer LandD and reinforcement of the individual IC loc ., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: The author does not get a fee or any other support by the Werkman Factory. She is an associated professor at the Leipzig University and self-employed. But Werkman provided help for data export and preparation of the raw data for statistical analysis by the work of Joris Bouwker. The statistical analysis themselves were done by independent biostatistical experts. But because the custom system does not allow data export, the help of the Werkman engineer Joris Bouwer was necessary. In the past the authors gave short seminars for the company. But at the time of submission no financial or personal relationships between Werkman and Dr. Hagen existed. At no time, Werkman tried to influence the study design, statistical analysis or the outcome of the study, which was part of the doctoral thesis of Franziska Jung. Joris Brouwer has received personal fees from WerkmanEquilytics and HoofBeat BV outside the submitted work; In addition Joris Brouwer has two patents pending, both licensed to WerkmanHoofcare BV., (Copyright © 2023. Published by Elsevier Inc.)

It is important to understand the effects of hoof trimming on hoof and limb conformation to maximize its benefits on the health of the appendicular skeleton of horses, thus promoting improvements in athletic performance and sporting longevity with regard to athletic horses. There is little information on possible changes in the angulation of the thoracic limb joints after hoof trimming and correlations between the angulation of the thoracic limb joints with hoof measurements. To that purpose, nineteen Mangalarga mares received routine hoof trimming. Visual recordings (photographs) were taken before and after the procedure. Differences ( p < 0.05) were found in hoof length, toe angle, heel angle, medial heel height, and metacarpophalangeal angle. Before trimming, correlations were found between frog length and scapulohumeral angle (SH) ( r = -0.457; p = 0.049), and between toe length and shoulder-ground angle (SG) ( r = -0.553; p = 0.049). A correlation was also seen between the distance from the frog to the lateral wall and the SH angle ( r = 0.690; p = 0.001). After trimming, there was a correlation between humeroradial (HR) and SH joint angles ( r = 0.669; p = 0.002), and the SG and SH angles ( r = 0.488; p = 0.034). This study showed an immediate effect of trimming on the toe angle and heel angle and on the metacarpophalangeal joint angle, in addition to correlations between the hoof and proximal joint angles, following trimming, thus evidencing the relevance of trimming not only in hoof morphology, but also in the conformation of the appendicular skeleton of horses.

The yeast Sup35 protein misfolds into the infectious [ PSI + ] prion, which is then propagated by the severing activity of the molecular chaperone, Hsp104. Unlike other yeast prions, this prion is unique in that it is efficiently cured by the overexpression as well as the inactivation of Hsp104. However, it is controversial whether curing by overexpression is due to the dissolution of the prion seeds by the trimming activity of Hsp104 or the asymmetric segregation of the prion seeds between mother and daughter cells which requires cell division. To answer this question, we conducted experiments and found no difference in the extent of curing between mother and daughter cells when half of the cells were cured by Hsp104 overexpression in one generation. Furthermore, curing was not affected by the lack of Sir2 expression, which was reported to be required for asymmetric segregation of the [ PSI + ] seeds. More importantly, when either hydroxyurea or ethanol were used to inhibit cell division, the extent of curing by Hsp104 overexpression was not significantly reduced. Therefore, the curing of [ PSI + ] by Hsp104 overexpression is not due to asymmetric segregation of the prion seeds, but rather their dissolution by Hsp104.

Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree-based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree-based analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, and etc. The step-by-step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick-start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle-based analyses., Competing Interests: The authors declare no conflicts of interest., (© 2023 The Authors. iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.)

Human epidermal growth factor receptor (EGFR) is involved in strong association with malignant proliferation, which has been shown to play a central role in the development and progression of non-small cell lung cancer and other solid tumors. The tumor-suppressor protein MIG6 is a negative regulator of EGFR kinase activity by binding at the activation interface of asymmetric dimer of EGFR kinase domain to disrupt EGFR dimerization and then inactivate the kinase. The protein adopts two discrete fragments 1 and 2 to directly interact with EGFR. It is revealed that the MIG6 fragment 2 is intrinsically disordered in free unbound state, but would fold into a well-structured β-hairpin when binding to EGFR, thus characterized by a so-called coupled folding-upon-binding process, which can be regarded as a compromise between favorable direct readout and unfavorable indirect readout. Here, a 23-mer F2P peptide was derived from MIG6 fragment 2, trimmed into a 17-mer tF2P peptide that contains the binding hotspot region of the fragment 2, and then constrained with an ordered hairpin conformation in free unbound state by disulfide stapling, finally resulting in a rationally stapled/trimmed stF2P peptide that largely minimizes the unfavorable indirect readout effect upon its binding to EGFR kinase domain, with affinity improved considerably upon the trimming and stapling/trimming. These rationally designed β-hairpin peptides may be further exploited as potent anti-lung cancer agents to target the activation event of EGFR dimerization., (© 2022. European Biophysical Societies' Association.)

Penalized Cox regression can efficiently be used for the determination of biomarkers in high-dimensional genomic data related to disease prognosis. However, results of Penalized Cox regression is influenced by the heterogeneity of the samples who have different dependent structure between survival time and covariates from most individuals. These observations are called influential observations or outliers. A robust penalized Cox model (Reweighted Elastic Net-type maximum trimmed partial likelihood estimator, Rwt MTPL-EN) is proposed to improve the prediction accuracy and identify influential observations. A new algorithm AR-Cstep to solve Rwt MTPL-EN model is also proposed. This method has been validated by simulation study and application to glioma microarray expression data. When there were no outliers, the results of Rwt MTPL-EN were close to the Elastic Net (EN). When outliers existed, the results of EN were impacted by outliers. And whenever the censored rate was large or low, the robust Rwt MTPL-EN performed better than EN. and could resist the outliers in both predictors and response. In terms of outliers detection accuracy, Rwt MTPL-EN was much higher than EN. The outliers who "lived too long" made EN perform worse, but were accurately detected by Rwt MTPL-EN. Through the analysis of glioma gene expression data, most of the outliers identified by EN were those "failed too early", but most of them were not obvious outliers according to risk estimated from omics data or clinical variables. Most of the outliers identified by Rwt MTPL-EN were those who "lived too long", and most of them were obvious outliers according to risk estimated from omics data or clinical variables. Rwt MTPL-EN can be adopted to detect influential observations in high-dimensional survival data.

Many membrane-resident and secreted proteins, including growth factors and their receptors are N-glycosylated. The initial N-glycan structure is synthesized in the endoplasmic reticulum (ER) as a branched structure on a lipid anchor (dolicholpyrophosphate) and then co-translationally, "en bloc" transferred and linked via N-acetylglucosamine to asparagine within a specific N-glycosylation acceptor sequence of the nascent recipient protein. In the ER and then the Golgi apparatus, the N-linked glycan structure is modified by hydrolytic removal of sugar residues ("trimming") followed by re-glycosylation with additional sugar residues ("processing") such as galactose, fucose or sialic acid to form complex N-glycoproteins. While the sequence of the reactions leading to biosynthesis, "en bloc" transfer and processing of N-glycans is well investigated, it is still not completely understood how N-glycans affect the biological fate and function of N-glycoproteins. This review will discuss the biology of N-glycoprotein synthesis, processing and function with specific reference to the physiology and pathophysiology of the immune and nervous system, as well as infectious diseases such as Covid-19., (© 2023. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

Data on the foot lesions of housed dairy goats, especially those that are not lame, is sparse. In this study, visits were made to four farms for whole herd locomotion scoring after milking and to observe routine foot trimming. During trimming, the amount of trimming required for each hoof was recorded, alongside the presence of lesions. The process was repeated at the next routine foot trim on three of the four farms (on Farm 1 whole herd locomotion scoring after milking was not feasible). Across both visits, 3445 locomotion scores were recorded, alongside 3850 trimming and lesion records. There were large differences between farms and visits in the proportion of lame goats (6.7 to 25.5%) and in the proportion of goats which needed a substantial trim of all four feet (15.1-33.1%). Hoof lesions were observed in 65.5% of trimmed goats. We defined lesions by their site and presence of separation and/or granuloma, with white line separation being the most commonly recorded lesion (41.5% of goats). On all visits on the three farms which were locomotion scored, the number of goats recorded as lame was lower than the number observed with white line lesions, but the relative proportion ranged from 17% to 95.4%. Separations were much more common than granulomas, as granulomas were usually accompanied by separation. Toe lesions were much more likely to be associated with granulomas than white line lesions, with 91.5% of toe separations having granulomas but only 10.6% of white line separations. This study provides useful baseline data for comparing lesions and locomotion scoring between goat herds but also identifies areas where we need more data and more consensus., Competing Interests: Conflict of interest statement None of the authors has any financial or personal relationships that could inappropriately influence or bias the content of the paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

The process of brain cutting followed by trimming is quite important to make adequate specimens for sufficient neuropathological observations. The protocol described herein is recommended as an optimized implementation for suitable preparation, which inevitably leads to an accurate neuropathological diagnosis. To obtain neuropathological cues, macroscopic observation of the brain before cutting presents an important opportunity. Gross examination provides a clue to the neuropathological diagnosis and shows clinicopathological correlations. Brain cutting should be preceded by a careful review of the clinical notes and consideration of the possible pathological diagnosis. Therefore, the medical staff associated with the patient should attend the procedure to provide clinical information. The process involves removing the brainstem and cerebellum from the cerebrum, sectioning the cerebrum, removing the cerebellum from the brainstem, and sectioning the cerebellum, brainstem and spinal cord followed by trimming. Trimming should be performed in accordance with the internationally accepted guidelines for the pathological diagnosis of different types of neurodegenerative diseases. In each stage acquiring clear photographs is significant, the observations must be concisely recorded, and which side of the specimen is to be sliced and stained has to be indicated. Additionally, it is necessary to photograph all trimmed tissues to assist with orientation of the brain in later assessments. The three-dimensional structure and individual differences have to be considered. These skills are essential, and knowledge of neuropathology, neurology and neuroanatomy is required for appropriately cutting and trimming of the brain., (© 2022 Japanese Society of Neuropathology.)

The inverse probability of treatment weighting (IPTW) approach is popular for evaluating causal effects in observational studies, but extreme propensity scores could bias the estimator and induce excessive variance. Recently, the overlap weighting approach has been proposed to alleviate this problem, which smoothly down-weights the subjects with extreme propensity scores. Although advantages of overlap weighting have been extensively demonstrated in literature with continuous and binary outcomes, research on its performance with time-to-event or survival outcomes is limited. In this article, we propose estimators that combine propensity score weighting and inverse probability of censoring weighting to estimate the counterfactual survival functions. These estimators are applicable to the general class of balancing weights, which includes IPTW, trimming, and overlap weighting as special cases. We conduct simulations to examine the empirical performance of these estimators with different propensity score weighting schemes in terms of bias, variance, and 95% confidence interval coverage, under various degrees of covariate overlap between treatment groups and censoring rates. We demonstrate that overlap weighting consistently outperforms IPTW and associated trimming methods in bias, variance, and coverage for time-to-event outcomes, and the advantages increase as the degree of covariate overlap between the treatment groups decreases., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

A compact and efficient IC architecture is presented as an alternative to laser-trimmed precision thin-film resistors or look-up tables. The objective is to keep the device, such as a four-terminal Wheatstone bridge, but to compensate for post-manufacturing offset and to avoid the so-induced degradation of performances in terms of full-scale, non-linearity, power supply noise rejection and scale factor. Expected advantages are a reduced cost due to the electrical-only implementation and a possible on-field calibration of high-end sensors. Application of the proposed solution is illustrated on an example to demonstrate improvement factors on offset and sensitivity accuracy of 32 and 10, respectively. Additionally, the power supply rejection ratio is improved by 30 dB. The experimental results finally demonstrate both efficiency and versatility of the proposed solution thanks to a first silicon prototype, fabricated in a 0.35 μm Technology from AMS, connected to an off-the-shelf pressure sensor.

Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

With third generation DNA sequencing and a general reduction of sequencing costs, the production of bioinformatic data has become easier than ever. Several pipeline automation tools have emerged to ease data processing through a multitude of steps. Here, we describe the setup and use of Snakemake, a pipeline automation tool derived from GNU MAKE., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

In the causal analysis of observational data, the positivity assumption requires that all treatments of interest be observed in every patient subgroup. Violations of this assumption are indicated by nonoverlap in the data in the sense that patients with certain covariate combinations are not observed to receive a treatment of interest, which may arise from contraindications to treatment or small sample size. In this paper, we emphasize the importance and implications of this often-overlooked assumption. Further, we elaborate on the challenges nonoverlap poses to estimation and inference and discuss previously proposed methods. We distinguish between structural and practical violations and provide insight into which methods are appropriate for each. To demonstrate alternative approaches and relevant considerations (including how overlap is defined and the target population to which results may be generalized) when addressing positivity violations, we employ an electronic health record-derived data set to assess the effects of metformin on colon cancer recurrence among diabetic patients., (© 2021 John Wiley & Sons Ltd.)

Population genetic variability in immune system genes can often underlie variability in immune responses to pathogens. Cytotoxic T-lymphocytes are emerging as critical determinants of both severe acute respiratory syndrome coronavirus 2 infection severity and long-term immunity, after either recovery or vaccination. A hallmark of coronavirus disease 2019 is its highly variable severity and breadth of immune responses between individuals. To address the underlying mechanisms behind this phenomenon, we analyzed the proteolytic processing of S1 spike glycoprotein precursor antigenic peptides across ten common allotypes of endoplasmic reticulum aminopeptidase 1 (ERAP1), a polymorphic intracellular enzyme that can regulate cytotoxic T-lymphocyte responses by generating or destroying antigenic peptides. We utilized a systematic proteomic approach that allows the concurrent analysis of hundreds of trimming reactions in parallel, thus better emulating antigen processing in the cell. While all ERAP1 allotypes were capable of producing optimal ligands for major histocompatibility complex class I molecules, including known severe acute respiratory syndrome coronavirus 2 epitopes, they presented significant differences in peptide sequences produced, suggesting allotype-dependent sequence biases. Allotype 10, previously suggested to be enzymatically deficient, was rather found to be functionally distinct from other allotypes. Our findings suggest that common ERAP1 allotypes can be a major source of heterogeneity in antigen processing and through this mechanism contribute to variable immune responses in coronavirus disease 2019., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

In this audio/video authenticity research project, 44 original MOV files were produced on an Apple iPhone 12 Pro Max mobile device, running the iOS 14.2.1 operating system, in all available video formats and at four different nominal recording lengths. Each of the original files was then trimmed, using the Apple Photos app, in three different ways: deleting a portion of the beginning, a portion of the end, and portions of both the beginning and end. These 176 original and trimmed files were transferred to a laboratory computer and the footer and other metadata were analyzed with a hex editor. This analysis revealed that the trimmed recordings could be differentiated from the originals; that the iPhone model and the iOS operating system version could be identified; that important recording dates and times can be determined; and that the type of trimming, in some cases, could be determined., (© 2021 American Academy of Forensic Sciences.)

To extend previous simulations on the performance of propensity score (PS) weighting and trimming methods to settings without and with unmeasured confounding, Poisson outcomes, and various strengths of treatment prediction (PS c statistic), we simulated studies with a binary intended treatment T as a function of 4 measured covariates. We mimicked treatment withheld and last-resort treatment by adding 2 "unmeasured" dichotomous factors that directed treatment to change for some patients in both tails of the PS distribution. The number of outcomes Y was simulated as a Poisson function of T and confounders. We estimated the PS as a function of measured covariates and trimmed the tails of the PS distribution using 3 strategies ("Crump," "Stürmer," and "Walker"). After trimming and reestimation, we used alternative PS weights to estimate the treatment effect (rate ratio): inverse probability of treatment weighting, standardized mortality ratio (SMR)-treated, SMR-untreated, the average treatment effect in the overlap population (ATO), matching, and entropy. With no unmeasured confounding, the ATO (123%) and "Crump" trimming (112%) improved relative efficiency compared with untrimmed inverse probability of treatment weighting. With unmeasured confounding, untrimmed estimates were biased irrespective of weighting method, and only Stürmer and Walker trimming consistently reduced bias. In settings where unmeasured confounding (e.g., frailty) may lead physicians to withhold treatment, Stürmer and Walker trimming should be considered before primary analysis., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objective: Aim of the current in vivo, observational study was to investigate the effect of trimming, heel elevation and different types of shoeing on breakover duration (BreakD) with a novel, hoof-mounted inertial measurement unit (IMU) sensor system., Methods: Ten sound, crossbred horses were examined barefoot before and after trimming fitted with an IMU sensor at the dorsal hoof wall. Additionally, application of 5° heel wedges, plain steel shoes, rolled-toe shoes and palmarly-placed quarter-clip shoes was tested. Horses were guided in a straight line on firm ground. Obtained data were speed corrected prior to calculations testing the influence of different manipulations for their significance on BreakD., Results: Trimming had no significant influence on BreakD. Heel elevation caused a significant decrease of BreakD in walk and trot. Shoeing with a plain steel shoe resulted in a significant increase in BreakD in walk. This could be rescinded by creating a rolled toe or placing the shoe palmarly., Conclusion: Obtained results emphasize the use of heel wedges or rolled-toe and palmarly-placed shoes to ease breakover in the context of therapeutic shoeing. Hoof-mounted IMU sensors with high resolution seem to be a practical and valuable approach to accurately examine BreakD and factors influencing this parameter., (© 2021 The Authors. Veterinary Record published by John Wiley & Sons Ltd on behalf of British Veterinary Association.)

Purpose: The aim of this work was to develop and experimentally validate a Dynamic Collimation Monte Carlo (DCMC) simulation package specifically designed for the simulation of collimators in pencil beam scanning proton therapy (PBS-PT). The DCMC package was developed using the TOPAS Monte Carlo platform and consists of a generalized PBS source model and collimator component extensions., Methods: A divergent point-source model of the IBA dedicated nozzle (DN) at the Miami Cancer Institute (MCI) was created and validated against on-axis commissioning measurements taken at MCI. The beamline optics were mathematically incorporated into the source to model beamlet deflections in the X and Y directions at the respective magnet planes. Off-axis measurements taken at multiple planes in air were used to validate both the off-axis spot size and divergence of the source model. The DCS trimmers were modeled and incorporated as TOPAS geometry extensions that linearly translate and rotate about the bending magnets. To validate the collimator model, a series of integral depth dose (IDD) and lateral profile measurements were acquired at MCI and used to benchmark the DCMC performance for modeling both pristine and range shifted beamlets. The water equivalent thickness (WET) of the range shifter was determined by quantifying the shift in the depth of the 80% dose point distal to the Bragg peak between the range shifted and pristine uncollimated beams., Results: A source model of the IBA DN system was successfully commissioned against on- and off-axis IDD and lateral profile measurements performed at MCI. The divergence of the source model was matched through an optimization of the source-to-axis distance and comparison against in-air spot profiles. The DCS model was then benchmarked against collimated IDD and in-air and in-phantom lateral profile measurements. Gamma analysis was used to evaluate the agreement between measured and simulated lateral profiles and IDDs with 1%/1 mm criteria and a 1% dose threshold. For the pristine collimated beams, the average 1%/1 mm gamma pass rates across all collimator configurations investigated were 99.8% for IDDs and 97.6% and 95.2% for in-air and in-phantom lateral profiles. All range shifted collimated IDDs passed at 100% while in-air and in-phantom lateral profiles had average pass rates of 99.1% and 99.8%, respectively. The measured and simulated WET of the polyethylene range shifter was determined to be 40.9 and 41.0 mm, respectively., Conclusions: We have developed a TOPAS-based Monte Carlo package for modeling collimators in PBS-PT. This package was then commissioned to model the IBA DN system and DCS located at MCI using both uncollimated and collimated measurements. Validation results demonstrate that the DCMC package can be used to accurately model other aspects of a DCS implementation via simulation., (© 2021 American Association of Physicists in Medicine.)

The purpose of this paper is to show in regression clustering how to choose the most relevant solutions, analyze their stability, and provide information about best combinations of optimal number of groups, restriction factor among the error variance across groups and level of trimming. The procedure is based on two steps. First we generalize the information criteria of constrained robust multivariate clustering to the case of clustering weighted models. Differently from the traditional approaches which are based on the choice of the best solution found minimizing an information criterion (i.e. BIC), we concentrate our attention on the so called optimal stable solutions. In the second step, using the monitoring approach, we select the best value of the trimming factor. Finally, we validate the solution using a confirmatory forward search approach. A motivating example based on a novel dataset concerning the European Union trade of face masks shows the limitations of the current existing procedures. The suggested approach is initially applied to a set of well known datasets in the literature of robust regression clustering. Then, we focus our attention on a set of international trade datasets and we provide a novel informative way of updating the subset in the random start approach. The Supplementary material, in the spirit of the Special Issue, deepens the analysis of trade data and compares the suggested approach with the existing ones available in the literature., (© The Author(s) 2021.)

Propensity score weighting methods are often used in non-randomized studies to adjust for confounding and assess treatment effects. The most popular among them, the inverse probability weighting, assigns weights that are proportional to the inverse of the conditional probability of a specific treatment assignment, given observed covariates. A key requirement for inverse probability weighting estimation is the positivity assumption, i.e. the propensity score must be bounded away from 0 and 1. In practice, violations of the positivity assumption often manifest by the presence of limited overlap in the propensity score distributions between treatment groups. When these practical violations occur, a small number of highly influential inverse probability weights may lead to unstable inverse probability weighting estimators, with biased estimates and large variances. To mitigate these issues, a number of alternative methods have been proposed, including inverse probability weighting trimming, overlap weights, matching weights, and entropy weights. Because overlap weights, matching weights, and entropy weights target the population for whom there is equipoise (and with adequate overlap) and their estimands depend on the true propensity score, a common criticism is that these estimators may be more sensitive to misspecifications of the propensity score model. In this paper, we conduct extensive simulation studies to compare the performances of inverse probability weighting and inverse probability weighting trimming against those of overlap weights, matching weights, and entropy weights under limited overlap and misspecified propensity score models. Across the wide range of scenarios we considered, overlap weights, matching weights, and entropy weights consistently outperform inverse probability weighting in terms of bias, root mean squared error, and coverage probability.

Purpose: When designing a collimation system for pencil beam spot scanning proton therapy, a decision must be made whether or not to rotate, or focus, the collimator to match beamlet deflection as a function of off-axis distance. If the collimator is not focused, the beamlet shape and fluence will vary as a function of off-axis distance due to partial transmission through the collimator. In this work, we quantify the magnitude of these effects and propose a focused dynamic collimation system (DCS) for use in proton therapy spot scanning., Methods: This study was done in silico using a model of the Miami Cancer Institute's (MCI) IBA Proteus Plus system created in Geant4-based TOPAS. The DCS utilizes rectangular nickel trimmers mounted on rotating sliders that move in synchrony with the pencil beam to provide focused collimation at the edge of the target. Using a simplified setup of the DCS, simulations were performed at various off-axis locations corresponding to beam deflection angles ranging from 0° to 2.5°. At each off-axis location, focused (trimmer rotated) and unfocused (trimmer not rotated) simulations were performed. In all simulations, a 4 cm water equivalent thickness range shifter was placed upstream of the collimator, and a voxelized water phantom that scored dose was placed downstream, each with 4 cm airgaps., Results: Increasing the beam deflection angle for an unfocused trimmer caused the collimated edge of the beamlet profile to shift 0.08-0.61 mm from the baseline 0° simulation. There was also an increase in low-dose regions on the collimated edge ranging from 14.6% to 192.4%. Lastly, the maximum dose, D max , was 0-5% higher for the unfocused simulations. With a focused trimmer design, the profile shift and dose increases were all eliminated., Conclusions: We have shown that focusing a collimator in spot scanning proton therapy reduces dose at the collimated edge compared to conventional, unfocused collimation devices and presented a simple, mechanical design for achieving focusing for a range of source-to-collimator distances., (© 2020 American Association of Physicists in Medicine.)

New sensor and sensor manufacturing technologies are identified as a key factor for a successful digitalisation and are therefore economically important for manufacturers and industry. To address various requirements, a new sputter coating system has been invented at the Institute of Micro Production Technology. It enables the deposition of sensor systems directly onto technical surfaces. Compared to commercially available systems, it has no spatial limitations concerning the maximum coatable component size. Moreover, it enables a simultaneous structuring of deposited layers. Within this paper, characterisation techniques, results and challenges concerning directly deposited thin film strain gauges with the new sputter coating system are presented. Constantan (CuNiMn 54/45/1) and NiCr 80/20 are used as sensor materials. The initial resistance, temperature coefficient of resistance and gauge factor/k-factor of quarter-bridge strain gauges are characterised. The influence of a protective layer on sensor behaviour and layer adhesion is investigated as well. Moreover, the temperature compensation quality of directly deposited half-bridge strain gauges is evaluated, optimised with an external trimming technology and benchmarked against commercial strain gauges. Finally, the suitability for high-temperature strain measurement is investigated. Results show a maximum operation temperature of at least 400 °C, which is above the current state-of-the-art of commercial foil-based metal strain gauges.

We consider removing lower order statistics from the classical Hill estimator in extreme value statistics, and compensating for it by rescaling the remaining terms. Trajectories of these trimmed statistics as a function of the extent of trimming turn out to be quite flat near the optimal threshold value. For the regularly varying case, the classical threshold selection problem in tail estimation is then revisited, both visually via trimmed Hill plots and, for the Hall class, also mathematically via minimizing the expected empirical variance. This leads to a simple threshold selection procedure for the classical Hill estimator which circumvents the estimation of some of the tail characteristics, a problem which is usually the bottleneck in threshold selection. As a by-product, we derive an alternative estimator of the tail index, which assigns more weight to large observations, and works particularly well for relatively lighter tails. A simple ratio statistic routine is suggested to evaluate the goodness of the implied selection of the threshold. We illustrate the favourable performance and the potential of the proposed method with simulation studies and real insurance data., (© The Author(s) 2020.)

MicroRNAs (miRNAs) broadly regulate gene expression through association with Argonaute (Ago), which also protects miRNAs from degradation. However, miRNA stability is known to vary and is regulated by poorly understood mechanisms. A major emerging process, termed target-directed miRNA degradation (TDMD), employs specialized target RNAs to selectively bind to miRNAs and induce their decay. Here, we report structures of human Ago2 (hAgo2) bound to miRNAs and TDMD-inducing targets. miRNA and target form a bipartite duplex with an unpaired flexible linker. hAgo2 cannot physically accommodate the RNA, causing the duplex to bend at the linker and display the miRNA 3' end for enzymatic attack. Altering 3' end display by changing linker flexibility, changing 3' end complementarity, or mutationally inducing 3' end release impacts TDMD efficiency, leading to production of distinct 3'-miRNA isoforms in cells. Our results uncover the mechanism driving TDMD and reveal 3' end display as a key determinant regulating miRNA activity via 3' remodeling and/or degradation., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Laminitis is associated with failure of the suspensory apparatus of the distal phalanx (SADP) connecting the distal phalanx to the hoof wall. The specific aim of this study was to examine in vitro whether thinning of the hoof wall leading to increased deformability influences the damage of the laminar tissue created by loading of the hoof. Paired cadaver forelimbs from twelve horses were used. For each pair, the hoof wall from one hoof was thinned by 25%; this was ascertained by radiography. The contralateral hooves were used as controls. In a material testing machine, hooves were loaded in a proximodistal direction at 0.5mm/s until a cut-off value of 8kN or 14mm was reached. Afterwards, samples of the SADP were taken for histology. Image-based evaluation of the destruction of the SADP was performed using quantitative histogram analysis. Additionally, three examiners masked to treatment (trimmed/untrimmed) qualitatively evaluated SADP destruction. During hoof loading with forces from 0.5 to 1.8 times the body mass of the donor horses, hooves with thinned hoof wall underwent significantly more deformation (P<0.05). Quantitative histogram analysis detected a shift to higher brightness values and a higher pixel intensity in control hooves, representing disruption in the histologic analysis. Qualitative evaluation of histology sections showed significantly more disruption of the SADP in untrimmed hooves (P=0.03). These results confirm the hypothesis that reduced hoof wall thickness can decrease disruption of laminar tissue in vitro, thus supporting the evaluation of hoof wall reduction as a prophylactic measure in horses at imminent risk of SADP failure., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Presentation of short peptides, produced through intracellular proteolysis, by MHC class I molecules (MHC-I) is the basis of adaptive immune surveillance and responses by cytolytic CD8 + T lymphocytes. In the principal pathway of peptide processing for MHC-I that operates in all nucleated cells, MHC-I-binding peptides are produced through stepwise proteolysis starting with source protein degradation by cytosolic proteasome complexes. Among the fraction of proteasome products reaching the lumen of the endoplasmic reticulum, a significant proportion is thought to have a length exceeding that adapted to MHC class I binding and requires N-terminal trimming. This is carried out by one murine and two human endoplasmic reticulum aminopeptidases, the ERAP enzymes. While the critical role of ERAP for producing a ligandome optimized for MHC-I is well documented, it remains unclear how this is mechanistically achieved. In this review, we will discuss the evidence supporting the alternative "MHC template" and "molecular ruler" models that have been proposed to explain how ERAP activity adapts to the ligand requirements of MHC-I. We will also review evidence for dimerization of the two human ERAP enzymes and its potential functional relevance., (Copyright © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.)

The 3' ends of metazoan microRNAs (miRNAs) are initially defined by the RNase III enzymes during maturation, but subsequently experience extensive modifications by several enzymatic activities. For example, terminal nucleotidyltransferases (TENTs) elongate miRNAs by adding one or a few nucleotides to their 3' ends, which occasionally leads to differential regulation of miRNA stability or function. However, the catalytic entities that shorten miRNAs and the molecular consequences of such shortening are less well understood, especially in vertebrates. Here, we report that poly(A)-specific ribonuclease (PARN) sculpts the 3' ends of miRNAs in human cells. By generating PARN knockout cells and characterizing their miRNAome, we demonstrate that PARN digests the 3' extensions of miRNAs that are derived from the genome or attached by TENTs, thereby effectively reducing the length of miRNAs. Surprisingly, PARN-mediated shortening has little impact on miRNA stability, suggesting that this process likely operates to finalize miRNA maturation, rather than to initiate miRNA decay. PARN-mediated shortening is pervasive across most miRNAs and appears to be a conserved mechanism contributing to the 3' end formation of vertebrate miRNAs. Our findings add miRNAs to the expanding list of noncoding RNAs whose 3' end formation depends on PARN., (© 2019 Lee et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU's) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github., Competing Interests: No competing interests were disclosed.

Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms have resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented preprocessing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open-source Java toolkit designed to standardize and preprocess read data from different platforms. It manages FASTQ- and SAM-formatted inputs while dealing with platform-specific peculiarities and provides a standard SAM compliant output. The code and executable are available at https://github.com/magicDGS/ReadTools., (© 2017 John Wiley & Sons Ltd.)

Context: Stainless steel crowns (SSCs) are the most durable and effective restorations for the primary teeth. Allergy to nickel as major components is common., Aims: The purpose of this study is to evaluate the effect of pH, time, oral temperature, and SSCs trimming on the nickel releasing., Settings and Design: This in vitro study was done on 18 same size crowns., Subjects and Methods: Group A (without trim 0 and Group B (with trim) were immersed in 5 ml artificial saliva. The amount of nickel releasing in each 18 subgroup composed from 3 pH (3.5, 5, and 6.75) and 3 temperatures (27°C, 37°C, and 47°C) in 3 times (1, 7, and 21 days), was measured by Atomic Absorption Spectrophotometer., Statistical Analysis: Data were analyzed by SPSS software (SPSS 20, IBM, Armonk, NY, USA) and use of t-test, Duncan, and Tukey's test for analysis of variances. Results were reported with 95% confidence., Results: The amount of nickel releasing reduced with crown trimming, significantly (P = 0.0001). A significant difference was observed in the amount of released nickel in temperature 47°C in comparison with 37°C (P = 0.0001); this measurement was not significant between 47°C and 27°C (P = 0.442). There was no significant difference between concentration of released nickel in 3 pH conditions and also in 3-time situations. The concentration of nickel was lower in trimmed group in comparison to intact group (P = 0.0001)., Conclusions: The concentration of released nickel decreased with trimming of margins and increased when temperature increased. Time and pH had no significant effect on released nickel., Competing Interests: There are no conflicts of interest

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos., Competing Interests: The authors declare that they have no competing interests.

Objectives: To increase transparency in studies reporting propensity scores by using graphical methods that clearly illustrate (1) the number of participant exclusions that occur as a consequence of the analytic strategy and (2) whether treatment effects are constant or heterogeneous across propensity scores., Study Design and Setting: We applied graphical methods to a real-world pharmacoepidemiologic study that evaluated the effect of initiating statin medication on the 1-year all-cause mortality post-myocardial infarction. We propose graphical methods to show the consequences of trimming and matching on the exclusion of participants from the analysis. We also propose the use of meta-analytical forest plots to show the magnitude of effect heterogeneity., Results: A density plot with vertical lines demonstrated the proportion of subjects excluded because of trimming. A frequency plot with horizontal lines demonstrated the proportion of subjects excluded because of matching. An augmented forest plot illustrates the amount of effect heterogeneity present in the data., Conclusion: Our proposed techniques present additional and useful information that helps readers understand the sample that is analyzed with propensity score methods and whether effect heterogeneity is present., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Experience-dependent plasticity induces lasting changes in the structure of synapses, dendrites, and axons at both molecular and anatomical levels. Whilst relatively well studied in the cortex, little is known about the molecular changes underlying experience-dependent plasticity at peripheral levels of the sensory pathways. Given the importance of glutamatergic neurotransmission in the somatosensory system and its involvement in plasticity, in the present study, we investigated gene and protein expression of glutamate receptor subunits and associated molecules in the trigeminal ganglion (TG) of young adult rats. Microarray analysis of naïve rat TG revealed significant differences in the expression of genes, coding for various glutamate receptor subunits and proteins involved in clustering and stabilization of AMPA receptors, between left and right ganglion. Long-term exposure to sensory-enriched environment increased this left-right asymmetry in gene expression. Conversely, unilateral whisker trimming on the right side almost eliminated the mentioned asymmetries. The above manipulations also induced side-specific changes in the protein levels of glutamate receptor subunits. Our results show that sustained changes in sensory input induce modifications in glutamatergic transmission-related gene expression in the TG, thus supporting a role for this early sensory-processing node in experience-dependent plasticity.