Prevalence of Painful Lesions of the Digits and Risk Factors Associated with Digital Dermatitis, Ulcers and White Line Disease on Swiss Cattle Farms

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.

Immediate Effect of Hoof Trimming on Hoof and Thoracic Joint Angles in Mangalarga Mares

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.

Overexpression of Hsp104 by Causing Dissolution of the Prion Seeds Cures the Yeast [PSI+] Prion

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.

Addressing substantial covariate imbalance with propensity score stratification and balancing weights: connections and recommendations

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.

Addressing Extreme Propensity Scores in Estimating Counterfactual Survival Functions via the Overlap Weights

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.

Brain cutting and trimming

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.

Fully Electrical Post-Fabrication Trimming of Resistive Sensors

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.

Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 spike glycoprotein

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.

Effects of content trimming iPhone 12 Pro Max video files in iOS 14

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.

Core concepts in pharmacoepidemiology: Violations of the positivity assumption in the causal analysis of observational data: Consequences and statistical approaches

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.

Propensity Score Weighting and Trimming Strategies for Reducing Variance and Bias of Treatment Effect Estimates: A Simulation Study

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.

Influence of trimming, hoof angle and shoeing on breakover duration in sound horses examined with hoof-mounted inertial sensors

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.

Development and validation of the Dynamic Collimation Monte Carlo simulation package for pencil beam scanning proton therapy

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.

Propensity score weighting under limited overlap and model misspecification

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.

Development, Characterisation and High-Temperature Suitability of Thin-Film Strain Gauges Directly Deposited with a New Sputter Coating System

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.

Design of a focused collimator for proton therapy spot scanning using Monte Carlo methods

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.

Structural Basis for Target-Directed MicroRNA Degradation

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.

Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs

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.

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

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.

Evaluation of nickel releasing from stainless steel crowns regarding to "trimming": An in vitro study

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.

ReadTools: A universal toolkit for handling sequence data from different sequencing platforms

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.

Sensory Input-Dependent Changes in Glutamatergic Neurotransmission- Related Genes and Proteins in the Adult Rat Trigeminal Ganglion

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.

High-Speed Edge Trimming of CFRP and Online Monitoring of Performance of Router Tools Using Acoustic Emission

Carbon fiber reinforced polymers (CFRPs) have found wide-ranging applications in numerous industrial fields such as aerospace, automotive, and shipping industries due to their excellent mechanical properties that lead to enhanced functional performance. In this paper, an experimental study on edge trimming of CFRP was done with various cutting conditions and different geometry of tools such as helical-, fluted-, and burr-type tools. The investigation involves the measurement of cutting forces for the different machining conditions and its effect on the surface quality of the trimmed edges. The modern cutting tools (router tools or burr tools) selected for machining CFRPs, have complex geometries in cutting edges and surfaces, and therefore a traditional method of direct tool wear evaluation is not applicable. An acoustic emission (AE) sensing was employed for on-line monitoring of the performance of router tools to determine the relationship between AE signal and length of machining for different kinds of geometry of tools. The investigation showed that the router tool with a flat cutting edge has better performance by generating lower cutting force and better surface finish with no delamination on trimmed edges. The mathematical modeling for the prediction of cutting forces was also done using Artificial Neural Network and Regression Analysis.

High pressure spray with water shows similar efficiency to trimming in controlling microorganisms on poultry carcasses

A study was conducted to evaluate a high pressure spray (HPS) with water as an alternative to trimming to remove gastrointestinal contamination on poultry carcasses and improve microbiological quality. The study was conducted under commercial conditions in 5 slaughter plants with one plant presenting approximately 5% of carcasses with visible gastrointestinal contamination (VGC), and the others showing approximately 12% of VGC. In all 5 plants, carcasses were sampled from the slaughter line and separated into 6 groups corresponding to 3 different treatments: A) carcasses with VGC before and after trimming; B) carcasses with VGC before and after HPS; and C) carcasses with no VGC before and after HPS. At the end of Trial A and prior to Trials B and C, an HPS equipment was installed before the end of the slaughter line. The HPS equipment was operated with 10 kgf/cm² of pressure and 1.5 L of potable water per carcass. Carcasses were analyzed using a rinsing procedure, and the following microbiological parameters were evaluated: the prevalence of Salmonella and Campylobacter, the abundance of Escherichia coli (EC), Enterobacteriaceae (EB), and the Total Viable Count (TVC). Salmonella was found in all plants at a prevalence ranging from 0.8% (plant 1) to 17.3% (plant 5), and the difference between plants was significant (P < 0.05%). The prevalence of Campylobacter ranged from 2.1 (plant 1) to 18.6% (plant 4) (P < 0.05%). The prevalence of Campylobacter was similar in plants 2, 3, and 5, and a significant difference (P < 0.05%) was observed compared to plants 1 and 4. In all plants, the EC, EB, and TVC counts did not show a significant difference (P > 0.05%) in any treatments. These results demonstrate that HPS with water is an alternative method for removing VGC and improving or maintaining the microbiological quality and safety of broiler carcasses.

Effect of triggering and entrapment on tendon gliding properties following digital flexor tendon laceration: in vitro study on turkey tendon

The optimal management of partial flexor tendon laceration is controversial and remains a clinical challenge. Abnormal tendon gliding (triggering and entrapment) was assessed at the A2 pulley in 40 turkey tendons in three groups: intact, partially divided (palmar or lateral), and trimmed. Testing was of gliding resistance and friction coefficient at 30° and 70° of flexion, loaded with 2 and 4 N. We observed for triggering and entrapment. The changes in gliding properties were compared and analysed using Wilcoxon matched pair testing. A significant difference was found in the change in gliding properties of intact to lacerated and lacerated to trimmed tendons and between tendons that glided normally compared with those exhibiting triggering or entrapment. This suggests that palmar and lateral lacerations which, through clinical examination and visualization, are found to glide normally should be treated with early mobilization. However, partial lacerations that exhibit triggering or entrapment should be trimmed.

Diagnosing and responding to violations in the positivity assumption

The assumption of positivity or experimental treatment assignment requires that observed treatment levels vary within confounder strata. This article discusses the positivity assumption in the context of assessing model and parameter-specific identifiability of causal effects. Positivity violations occur when certain subgroups in a sample rarely or never receive some treatments of interest. The resulting sparsity in the data may increase bias with or without an increase in variance and can threaten valid inference. The parametric bootstrap is presented as a tool to assess the severity of such threats and its utility as a diagnostic is explored using simulated and real data. Several approaches for improving the identifiability of parameters in the presence of positivity violations are reviewed. Potential responses to data sparsity include restriction of the covariate adjustment set, use of an alternative projection function to define the target parameter within a marginal structural working model, restriction of the sample, and modification of the target intervention. All of these approaches can be understood as trading off proximity to the initial target of inference for identifiability; we advocate approaching this tradeoff systematically.

Effectiveness of Trimming and/or Washing on Microbiological Quality of Beef Carcasses

Beef carcass sides (n = 48) were selected randomly on three different days in a commercial processing facility and microbiologically analyzed before being moved to the cooler. Four types of samples were obtained per side from the inside round area: no trim and no wash (NTNW); trim, but no wash (TNW); trim and wash (TW), and no trim but wash (NTW). A flame-sterilized knife, forceps, and scalpel were used for each trimming treatment and sampling. Significant differences (P < 0.05) were observed in mean aerobic plate counts (APCs) between treatments. The greatest reduction in APC (log₁₀ colony forming units [CFU] per cm²) was observed in TNW samples followed by TW and NTW, with the corresponding mean APC reductions relative to NTNW being 3.0, 0.9, and 0.3, respectively, indicating that trimming can be an effective control point in reducing bacterial contamination in the slaughter process. Although TNW samples, had the lowest counts, samples from the same location after wash (TW) had counts 2 log cycles higher than TNW samples. These results indicate that washing spreads contamination to adjacent carcass sites. However, washing of carcasses was effective in lowering microbial populations relative to the NTNW treatment. Escherichia coli and coliform counts in all samples were low (0.03 to 0.4 log₁₀ CFU/cm²); however, the mean E. coli or coliform count in NTNW samples was higher (P < 0.05) than those in the rest of the treatments.

Hot-Fat Trimming Effects on the Microbiological Quality of Beef Carcasses and Subprimals

Subcutaneous and kidney-pelvic-heart fat were trimmed from one side of each beef carcass (n = 9) immediately after cold water washing. Both sides were sampled for aerobic plate counts (APCs) before being moved to the chill room (0 h) and after 72 h of cold storage. The mean APCs (log₁₀ colony-forming units (CFU)/cm²) of trimmed (HFT) sides at 0 or 72 h were not different (P > 0.05) from those of the nontrimmed (NFT) sides. All sides at 72 h had reduced microbial counts compared to 0 h. By 72 h, HFT sides had numerically lower counts than NFT sides, indicating that the microbial reduction effect of the chill temperature may have been greater on fat-trimmed carcasses than on nontrimmed carcasses. Subprimals from HFT and NFT sides that were trimmed to 0.64-cm fat thickness were microbiologically analyzed before (0 days) and after (14 days) vacuum storage. APCs of all subprimals were slightly reduced after 14 d; however, no difference (P > 0.05) occurred in treatment effect. The mean APC was higher for HFT-side subprimals than for NFT-side subprimals at both 0 and 14 days. This difference probably was due to the fat trimming required for NFT-side subprimals at day 0 as compared to minimal or no trimming of HFT-side subprimals. Those HFT subprimals which were not subsequently trimmed may have picked up additional microorganisms from contact surfaces during fabrication. Based on our trimming protocol, although HFT did not show any negative impact on the microbial quality of carcasses, the higher APC of HFT-side subprimals indicated that extensive trimming may not be effective in improving the microbial quality of meat.

Microbiological and Visual Effects of Trimming and/or Spray Washing for Removal of Fecal Material from Beef

Microbiological and visual evaluations were performed to compare the efficacy of hand trimming, spray washing, or a combination of treatments, in the removal of bacteria and fecal material from beef adipose tissue. Subcutaneous adipose samples with intact fascia from the surfaces of briskets (obtained within 15 min postmortem) were inoculated on different sizes of surface areas (0, 0.3125, 0,625, 1.25, 1.875, or 2.50 cm²) with a bovine fecal paste containing a culture of streptomycin-resistant Escherichia coli ATCC 11370. The samples were then spray washed with water at 35°C in a specially designed automated spray washing cabinet at pressures of 2.76, 13.79, 20.68, or 27.58 bar and at chain speeds equivalent to 100, 200, or 300 carcasses per hour (exposure times of 36, 18, or 12 s). Total aerobic mesophilic plate counts, streptomycin-resistant bacterial plate counts and visual scores for fecal contamination were obtained. There was a reduction (P < 0.05) in microbiological counts on the treated samples compared with those on the unwashed and/or untrimmed inoculated (control) samples. The variation in removal of fecal material from, and in reduction of microbiological contamination on, different sizes of surface areas of fecal material contamination and with different chain-speeds was minor under the conditions of the study. Hand trimming followed by spray washing compared to spray washing alone were similiar in their effectiveness for reduction of microbiological contamination and slightly different in the extent of fecal material removal. Overall, however, higher spray washing pressures (20.68 or 27.58 bar) were more effective (P < 0.05) than the lower spray washing pressures (2.76 or 13.79 bar) in removing fecal material from and reducing bacterial numbers on adipose tissue samples.