A Prospective Multicenter Trial to Evaluate Urinary Metabolomics for Non-invasive Detection of Renal Allograft Rejection (PARASOL): Study Protocol and Patient Recruitment

Background: In an earlier monocentric study, we have developed a novel non-invasive test system for the prediction of renal allograft rejection, based on the detection of a specific urine metabolite constellation. To further validate our results in a large real-world patient cohort, we designed a multicentric observational prospective study (PARASOL) including six independent European transplant centers. This article describes the study protocol and characteristics of recruited better patients as subjects.Methods: Within the PARASOL study, urine samples were taken from renal transplant recipients when kidney biopsies were performed. According to the Banff classification, urine samples were assigned to a case group (renal allograft rejection), a control group (normal renal histology), or an additional group (kidney damage other than rejection).Results: Between June 2017 and March 2020, 972 transplant recipients were included in the trial (1,230 urine samples and matched biopsies, respectively). Overall, 237 samples (19.3%) were assigned to the case group, 541 (44.0%) to the control group, and 452 (36.7%) samples to the additional group. About 65.9% were obtained from male patients, the mean age of transplant recipients participating in the study was 53.7 ± 13.8 years. The most frequently used immunosuppressive drugs were tacrolimus (92.8%), mycophenolate mofetil (88.0%), and steroids (79.3%). Antihypertensives and antidiabetics were used in 88.0 and 27.4% of the patients, respectively. Approximately 20.9% of patients showed the presence of circulating donor-specific anti-HLA IgG antibodies at time of biopsy. Most of the samples (51.1%) were collected within the first 6 months after transplantation, 48.0% were protocol biopsies, followed by event-driven (43.6%), and follow-up biopsies (8.5%). Over time the proportion of biopsies classified into the categories Banff 4 (T-cell-mediated rejection [TCMR]) and Banff 1 (normal tissue) decreased whereas Banff 2 (antibody-mediated rejection [ABMR]) and Banff 5I (mild interstitial fibrosis and tubular atrophy) increased to 84.2 and 74.5%, respectively, after 4 years post transplantation. Patients with rejection showed worse kidney function than patients without rejection.Conclusion: The clinical characteristics of subjects recruited indicate a patient cohort typical for routine renal transplantation all over Europe. A typical shift from T-cellular early rejections episodes to later antibody mediated allograft damage over time after renal transplantation further strengthens the usefulness of our cohort for the evaluation of novel biomarkers for allograft damage.

The Effectiveness of the Sexual Reproduction in Selected Clonal and Nonclonal Species of the Genus Ranunculus

Generative processes have been evaluated in six European buttercup species in order to verify the hypothesis that the reproduction efficiency of clonal species is lower than that of nonclonal ones. The study covered common species (Ficaria verna, Ranunculus auricomus, R. bulbosus, R. cassubicus, R. lanuginosus) and the endangered R. illyricus. The following properties have been assessed: pollen viability (staining method), pollen grain germination and the pollen-tube elongation in pistil tissues (fluorescence microscopy), seed formation efficiency, seed viability (tetrazolium test) and germination ability by introducing factors interrupting dormancy (low temperature and gibberellin application). Additionally, the pistil morphology was documented for R. bulbosus, R. illyricus and R. cassubicus using SEM techniques. It was demonstrated that the reproductive efficiency, expressed as the production of viable seeds able to germinate, was significantly higher in the species reproducing sexually (especially in R. lanuginosus) compared to the clonal ones. However, the complexity observed leads to separation of an additional group (cluster) of apomictic species: R. auricomus and R. cassubicus, distinguished by the lowest pollen viability and a low ability of the seeds to germinate. In the vegetatively reproducing R. illyricus, the seed formation efficiency was just 13.2% despite the having highest number of pistils in its flowers. The developed seeds of this species observed in our experiment were viable, but in general effective methods to stimulate their germination have not been proposed yet. Here, the first comparative study concerning the biology of sexual reproduction of R. illyricus is presented in the context of its decreasing distribution in natural habitats.

Blatant Dehumanization is Not Influenced by Dual Identity Labels: Evidence from the Canadian Context

Blatant dehumanization has been shown to be prevalent in modern society. However, little work has explored the possible ways in which blatant dehumanization may be attenuated. The current study addresses this gap in the literature by exploring if activating a dual identity attenuates (or even erases) blatant dehumanization. To investigate these issues, Canadian participants completed the “Ascent of Man” scale, rating various groups in terms of their perceived evolutionary qualities. Half of our participants saw labels with the qualifier “-Canadians” attached, while the other half saw no such qualifier. Results showed that, regardless of whether the “-Canadians” label was provided, participants rated Filipinos, Christians, Arabs, Muslims, and Indigenous groups as significantly lower than Whites on the evolution scale. As such, provision of the additional group label “-Canadians” did not influence the manifestation of blatant dehumanization. We also found that ratings on the evolution scale significantly correlated with both Social Dominance Orientation and Empathic Concern levels, such that stronger adherence to current power structures and social hierarchies showed stronger blatant dehumanization, while those with a high pre-disposition for altruistic behaviours and emotions showed weaker blatant dehumanization. We discuss our results in the light of other research on blatant dehumanization and intergroup processes.  

Comparative effect of dense-and-disperse versus non-repetitive and non-sequential frequencies in electroacupuncture-induced analgesia in a rodent model of peripheral neuropathic pain

Background: Neuropathic pain (NP) is a complex disease that remains challenging to treat. Low-frequency dense-and-disperse (DD) electroacupuncture (EA) has been used as adjuvant therapy for neuropathic pain; however, its analgesic effect decreases as stimulation time increases, or when it is repeatedly used. We hypothesized that a new frequency parameter could improve the effectiveness of EA, and aimed to compare the efficacy and duration of the analgesic effect between classic DD-EA and non-repetitive and non-sequential frequency (random frequency (RF)-EA) in neuropathic rats. Furthermore, the effect of RF-EA at local traditional acupuncture point locations versus auricular vagus nerve stimulation (aVNS) was evaluated. Methods: Male Wistar rats with peripheral neuropathy were subjected to a single session of DD-EA or RF-EA for 20 or 40 min at ST36 + GB34. An additional group of rats was treated with RF-EA for 20 min using aVNS at the appropriate ear point locations. Paw pressure test, von Frey filaments and spontaneous pain scores were evaluated. Sham-operated rats were used as controls. Results: In all, 20 min of RF-EA reversed hyperalgesia (for 24 h) and allodynia (for 8 h), showing a longer analgesic effect than DD-EA. Both RF-EA and DD-EA induced partial inhibition of spontaneous pain for 8 h. Forty minutes of DD-EA did not interfere with the NP phenomena; however, RF-EA induced significant long-term analgesia. aVNS induced an analgesic effect similar to local stimulation. Conclusion: This pilot study shows that RF-EA at both local traditional acupuncture point and auriculotherapy point locations induces long-lasting analgesia in neuropathic rats, and more effectively so than classical DD-EA.

USPNet: unbiased organism-agnostic signal peptide predictor with deep protein language model

Signal peptide is a short peptide located in the N-terminus of proteins. It plays an important role in targeting and transferring transmembrane proteins and secreted proteins to correct positions. Compared with traditional experimental methods to identify and discover signal peptides,the computational methods are faster and more efficient, which are more practical for the analysis of thousands or even millions of protein sequences in reality, especially for the metagenomic data. Therefore, computational tools are recently proposed to classify signal peptides and predict cleavage site positions, but most of them disregard the extreme data imbalance problem in these tasks. In addition, almost all these methods rely on additional group information of proteins to boost their performances, which, however, may not always be available. To deal with these issues, in this paper, we present Unbiased Organism-agnostic Signal Peptide Network(USPNet), a signal peptide prediction and cleavage site prediction model based on deep protein language model. We propose to use label distribution-aware margin (LDAM) loss and evolutionary scale modeling (ESM) embedding to handle data imbalance and object-dependence problems. Extensive experimental results demonstrate that the proposed method significantly outperforms all the previous methods on the classification performance. Additional study on the simulated metagenomic data further indicates that our model is a more universal and robust tool without dependency on additional group information of proteins, with the Matthews correlation coefficient improved by up to 17.5‰. The proposed method will be potentially useful to discover new signal peptides from the abundant metagenomic data.

Comprehensive Assessment of Smoking and Sex Related Effects in Publicly Available Gene Expression Data

ABSTRACTSmoking greatly reduces life expectancy in both men and women, but with different patterns of morbidity. After adjusting for smoking history, women have higher risk of respiratory effects and diabetes from smoking, while men show greater mortality from smoking-related cancers. While many smoking-related sex differences have been documented, the underlying molecular mechanisms are not well understood. To date, identification of sex differences in response to smoking has been limited to a small number of studies and the resulting smoking-related effects require further validation. Publicly available gene expression data present a unique opportunity to examine molecular-level sex and smoking effects across many tissues and studies. We performed a systematic search to identify smoking-related studies from healthy tissue samples and found 31 separate studies as well as an additional group of overlapping studies that in total span 2,177 samples and 12 tissues. These samples and studies were overall male-biased. In smoking, while effects appeared to be somewhat tissue-specific and largely autosomal, we identified a small number of genes that were consistently differentially expressed across tissues, including AHRR and GZMH. We also identified one gene, AKR1C3, encoding an aldo-keto reductase, which showed strong opposite direction, smoking-related effects in blood and airway epithelium, with higher expression in airway epithelium and lower expression in blood of smokers versus non-smokers. By contrast, at similar significance thresholds, sex-related effects were entirely sex chromosomal and consistent across tissues, providing evidence of stronger effects of smoking than sex on autosomal expression. Due to sample size limitations, we only examined interaction effects in the largest study, where we identified 30 genes with sex differential effects in response to smoking, only one of which, CAPN9, replicated in a held-out analysis. Overall these results present a comprehensive analysis of smoking-related effects across tissues and an initial examination of sex differential smoking effects in public gene expression data.

First Evaluation of Temporal and Spatial Fractionation in Proton Minibeam Radiation Therapy of Glioma-Bearing Rats

(1) Background: Proton minibeam radiation therapy (pMBRT) is a new radiotherapy technique using spatially modulated narrow proton beams. pMBRT results in a significantly reduced local tissue toxicity while maintaining or even increasing the tumor control efficacy as compared to conventional radiotherapy in small animal experiments. In all the experiments performed up to date in tumor bearing animals, the dose was delivered in one single fraction. This is the first assessment on the impact of a temporal fractionation scheme on the response of glioma-bearing animals to pMBRT. (2) Methods: glioma-bearing rats were irradiated with pMBRT using a crossfire geometry. The response of the irradiated animals in one and two fractions was compared. An additional group of animals was also treated with conventional broad beam irradiations. (3) Results: pMBRT delivered in two fractions at the biological equivalent dose corresponding to one fraction resulted in the highest median survival time, with 80% long-term survivors free of tumors. No increase in local toxicity was noted in this group with respect to the other pMBRT irradiated groups. Conventional broad beam irradiations resulted in the most severe local toxicity. (4) Conclusion: Temporal fractionation increases the therapeutic index in pMBRT and could ease the path towards clinical trials.

Daily activity in minimal footwear increases foot strength

The human foot is uniquely adapted to bipedal locomotion and has a deformable arch of variable stiffness. Intrinsic foot muscles regulate arch deformation, making them important for foot function. In this study we explore the hypothesis that normal daily activity in minimal footwear, which provides little or no support, increases foot muscle strength. Western adults wore minimal footwear for a six-month period (the “intervention” group). Foot strength, i.e., maximum isometric plantarflexion strength at the metatarsophalangeal joints, and foot biometrics were measured before and after the intervention. An additional group was investigated to add further insight on the long-term effects of footwear, consisting of Western adults with an average 2.5 years of experience in minimal footwear (the “experienced” group). This study shows that foot strength increases by, on average, 57.4% (p < 0.001) after six months of daily activity in minimal footwear. The experienced group had similar foot strength as the post intervention group, suggesting that six months of regular minimal footwear use is sufficient to gain full strength, which may aid healthy balance and gait.

Advanced Driver Assistance Systems (ADAS): Who’s Driving What and What’s Driving Use?

The emergence of vehicle technologies that promote driver safety and convenience calls for investigation of the prevalence of driver assistance systems as well as of their use rates. A consumer driven understanding as to why certain vehicle technology is used remains largely unexplored. We examined drivers’ experience using 13 different advanced driver assistance systems (ADAS) and several reasons that may explain rates of use through a nationally-distributed survey. Our analysis focused on drivers’ levels of understanding and trust with their vehicle’s ADAS as well as drivers’ perceived ease, or difficulty, in using the systems. Respondents’ age and experience with Level 0 or Level 1 technologies revealed additional group differences, suggesting older drivers (55+), and those with only Level 0 systems as using ADAS more often. These data are interpreted using the Driver Behavior Questionnaire framework and offer a snapshot of the pervasiveness of certain driver safety systems.

Unraveling City-Specific Microbial Signatures and Identifying Sample Origins for the Data From CAMDA 2020 Metagenomic Geolocation Challenge

The composition of microbial communities has been known to be location-specific. Investigating the microbial composition across different cities enables us to unravel city-specific microbial signatures and further predict the origin of unknown samples. As part of the CAMDA 2020 Metagenomic Geolocation Challenge, MetaSUB provided the whole genome shotgun (WGS) metagenomics data from samples across 28 cities along with non-microbial city data for 23 of these cities. In our solution to this challenge, we implemented feature selection, normalization, clustering and three methods of machine learning to classify the cities based on their microbial compositions. Of the three methods, multilayer perceptron obtained the best performance with an error rate of 19.60% based on whether the correct city received the highest or second highest number of votes for the test data contained in the main dataset. We then trained the model to predict the origins of samples from the mystery dataset by including these samples with the additional group label of “mystery.” The mystery dataset compromised of samples collected from a subset of the cities in the main dataset as well as samples collected from new cities. For samples from cities that belonged to the main dataset, error rates ranged from 18.18 to 72.7%. For samples from new cities that did not belong to the main dataset, 57.7% of the test samples could be correctly labeled as “mystery” samples. Furthermore, we also predicted some of the non-microbial features for the mystery samples from the cities that did not belong to main dataset to draw inferences and narrow the range of the possible sample origins using a multi-output multilayer perceptron algorithm.