Miracle-dz/UniFAR-FTUs huggingface dataset:
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. Results In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. Availability and implementation UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot. org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi. ac.uk/uniprot-public/unifire.
A Conceptual Framework for Modelling Safe Walking and Cycling Routes to High Schools

Active transport to or from school presents an opportunity for adolescents to engage in daily physical activity. Multiple factors influence whether adolescents actively travel to/from school. Creating safe walking and cycling routes to school is a promising strategy to increase rates of active transport. This article presents a comprehensive conceptual framework for modelling safe walking and cycling routes to high schools. The framework has been developed based on several existing relevant frameworks including (a) ecological models, (b) the “Five Es” (engineering, education, enforcement, encouragement, and evaluation) framework of transport planning, and (c) a travel mode choice framework for school travel. The framework identifies built environment features (land use mix, pedestrian/cycling infrastructure, neighbourhood aesthetics, and accessibility to local facilities) and traffic safety factors (traffic volume and speed, safe road crossings, and quality of path surface) to be considered when modelling safe walking/cycling routes to high schools. Future research should test this framework using real-world data in different geographical settings and with a combination of tools for the assessment of both macro-scale and micro-scale built environment features. To be effective, the modelling and creation of safe routes to high schools should be complemented by other interventions, including education, enforcement, and encouragement in order to minimise safety concerns and promote active transport.
RETRACTED ARTICLE: Long noncoding RNA RHPN1-AS1 exerts pro-oncogenic actions in osteosarcoma by functioning as a molecular sponge of miR-506 to positively regulate SNAI2 expression

Statement of Retraction We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Limin Wang and Yanbing Liu. Long noncoding RNA RHPN1-AS1 exerts pro-oncogenic actions in osteosarcoma by functioning as a molecular sponge of miR-506 to positively regulate SNAI2 expression. Cell Cycle. 2020;19(12):1517-1529. doi: 10.1080/15384101.2020. 1762039 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors have been unable to fully address the concerns raised and have not been able to provide their original data in the appropriate format. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
Lateralization of epilepsy using intra‐hemispheric brain networks based on resting‐state MEG data

Focal epilepsy originates within networks in one hemisphere. However, previous studies have investigated network topologies for the entire brain. In this study, magnetoencephalography (MEG) was used to investigate functional intra‐hemispheric networks of healthy controls (HCs) and patients with left‐ or right‐hemispheric temporal lobe or temporal plus extra‐temporal lobe epilepsy. 22 HCs, 25 left patients (LPs), and 16 right patients (RPs) were enrolled. The debiased weighted phase lag index was used to calculate functional connectivity between 246 brain regions in six frequency bands. Global efficiency, characteristic path length, and transitivity were computed for left and right intra‐hemispheric networks. The right global graph measures (GGMs) in the theta band were significantly different (p < .005) between RPs and both LPs and HCs. Right and left GGMs in higher frequency bands were significantly different (p < .05) between HCs and the patients. Right GGMs were used as input features of a Naïve‐Bayes classifier to classify LPs and RPs (78.0% accuracy) and all three groups (75.5% accuracy). The complete theta band brain networks were compared between LPs and RPs with network‐based statistics (NBS) and with the clustering coefficient (CC), nodal efficiency (NE), betweenness centrality (BC), and eigenvector centrality (EVC). NBS identified a subnetwork primarily composed of right intra‐hemispheric connections. Significantly different (p < .05) nodes were primarily in the right hemisphere for the CC and NE and primarily in the left hemisphere for the BC and EVC. These results indicate that intra‐hemispheric MEG networks may be incorporated in the diagnosis and lateralization of focal epilepsy.
Resilience Mediates the Relationship Between PTSD Symptoms and Disordered Eating in College Women Who Have Experienced Sexual Victimization

It is widely known that sexual assault disproportionately affects women, and college-aged women are particularly at risk. Sexual assault can occur at any age and may have a varying range of emotional consequences for survivors, including pathological coping mechanisms such as disordered eating behaviors. This study examined the mediating effect of resilience on the relationship between posttraumatic stress disorder (PTSD) symptoms and disordered eating behavior in a sample of women who reported experiencing sexual assault in adulthood. The sample included 312 undergraduate women who identified as majority White (81.4%) and heterosexual (77.9%). Participants completed measures assessing history of sexual experiences, PTSD symptoms, disordered eating behavior, and resilience. Only those who reported experiences of sexual victimization since age 14+ were included in analyses. Results confirmed the hypothesis, as resilience significantly mediated the relationship between PTSD symptoms and disordered eating behavior in a sample of women with a history of sexual victimization. These results highlight the importance of resilience as a mitigating factor in recovery from sexual trauma. Other research indicates that resilience may have emotion-regulatory benefits that mitigate the development of disordered eating behavior. However, the specific functionality of resilience as a protective factor after sexual victimization is unclear. Further research should focus on ways to foster resilience in a clinical setting for those with a history of sexual victimization. Limitations of this study include underrepresentation of racial and ethnic minorities, as well as use of entirely self-report measures.
Laser-Induced Periodic Surface Structuring of Poly(trimethylene terephthalate) Films Containing Tungsten Disulfide Nanotubes

We report the study of the formation of Laser Induced Periodic Surface Structures (LIPSS), with UV femtosecond laser pulses (λ = 265 nm), in free-standing films of both Poly(trimethylene terephthalate) (PTT) and the composite PTT/tungsten disulfide inorganic nanotubes (PTT-WS2). We characterized the range of fluences and number of pulses necessary to induce LIPSS formation and measured the topography of the samples by Atomic Force Microscopy, the change in surface energy and contact angle using the sessile drop technique, and the modification in both Young’s modulus and adhesion force values with Peak Force-Quantitative Nanomechanical Mapping. LIPSS appeared parallel to the laser polarization with a period close to its wavelength in a narrow fluence and number of pulses regime, with PTT-WS2 needing slightly larger fluence than raw PTT due to its higher crystallinity and heat diffusion. Little change was found in the total surface energy of the samples, but there was a radical increase in the negative polar component (γ−). Besides, we measured small variations in the samples Young’s modulus after LIPSS formation whereas adhesion is reduced by a factor of four. This reduction, as well as the increase in γ−, is a result of the modification of the surface chemistry, in particular a slight oxidation, during irradiation.
Statistical aspects in adjuvant and neoadjuvant trials for gastrointestinal cancer in 2020: focus on time-to-event endpoints.

PURPOSE OF REVIEW Clinical-trial design, analysis, and interpretation entails the use of efficient and reliable endpoints. Statistical issues related to endpoints warrant continued attention, as they may have a substantial impact on the conduct of clinical trials and on interpretation of their results. RECENT FINDINGS We review concepts and discuss recent developments related to the use of time-to-event endpoints in studies on adjuvant and neoadjuvant therapy for colon, pancreatic, and gastric adenocarcinomas. The definition of endpoints has varied to a considerable in these settings. Although these variations are relevant in interpreting results from individual trials, they probably have a small impact when considered in aggregate. In terms of surrogacy, most published reports so far have used aggregated data. A few studies based on the preferred method of a metaanalysis of individual-patient data have shown that disease-free survival (DFS) is a surrogate for overall survival in the adjuvant therapy of stage III colon cancer and in gastric cancer, whereas DFS with a landmark of six months is a surrogate for overall survival in the neoadjuvant therapy of adenocarcinoma of the esophagus, gastroesophageal junction, or stomach. SUMMARY Testing novel agents in gastrointestinal cancer requires continued attention to statistical issues related to endpoints.
Surface Comparison of Three Different Commercial Custom-Made Titanium Meshes Produced by SLM for Dental Applications

The use of individualized titanium meshes has been referred to in scientific literature since 2011. There are many advantages to its use, however, the main complications are related to early or late exposures. As some aspects such as its surface properties have been pointed out to influence the soft tissue response, this study was designed to compare the surface characteristics of three commercially available individualized titanium meshes between them and according to the manufacturer’s specifications. The results from the scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction and the contact profilometry measurements were analyzed and cross-checked. It was discovered that, the BoneEasy’s post-processing superficial treatment was more refined, as it delivers the mesh with the lowest Ra value, 0.61 ± 0.14 µm, due to the applied electropolishing. On the other hand, the Yxoss CBR® mesh from ReOss® was sandblasted, presenting an extremely rough surface with a Ra of 6.59 ± 0.76 µm.
Enhanced Oocyte Activation by Intracytoplasmic Injection of Porcine Spermatozoa Pre-treated with Dithiothreitol

Abstract: The aim of this study was to confirm the effect of dithiothreitol (DTT)-treated spermatozoa on oocyte activation following intracytoplasmic sperm injection (ICSI). Boar spermatozoa with or without DTT treatment (5 mM, 30 min) were injected into in vitro matured porcine oocytes, and the nuclear phase in presumptive zygotes was observed at 3 h intervals up to 12 h after ICSI. Furthermore, developmental competence of embryos produced by DTT-treated or non-treated spermatozoa was monitored after cultivation in vitro for 144 h. Male and female pronuclear formation rates in the oocytes injected with DTT-treated spermatozoa were significantly (P < 0.05) higher than those in the oocytes injected with non-treated spermatozoa. Additionally, we observed that female pronuclear formation was linked to male pronuclear formation. Sperm treatment with DTT improved (P < 0.05) subsequent development up to the blastocyst stage. These findings confirm the efficiency of DTT in in vitro porcine embryo production mediated by ICSI. We conclude that DTT treatment improves the formation of not only male pronuclei but also female pronuclei in porcine ICSI.
Toxicity of Carbon, Silicon, and Metal-Based Nanoparticles to the Hemocytes of Three Marine Bivalves

Simple Summary The growing nanotechnology industry disposes of a variety of nanoparticles with different physiochemical properties in everyday life. However, the dependence of the safety and toxicity of nanoparticles on their physicochemical properties remains unclear. Bivalve molluscs represent an efficient model for the investigation of nanoparticle toxicity owing to their filtrating ability and feeding on particles suspended in the water. Moreover, the blood cells of bivalve molluscs, the hemocytes, have been suggested as a good analog test-object to mammalian immune cells, phagocytes. In this study, we used hemocytes of three marine bivalve species, namely, Crenomytilus grayanus, Modiolus modiolus, and Arca boucardi, to evaluate and compare the toxic effects of 10 different types of nanoparticles. We gave short-term exposure of the nanoparticles to the hemocytes and registered viability and changes in their cell membrane polarization by employing flow cytometry. Metal-based nanoparticles were the most toxic to the cells of all three tested bivalve mollusc species. However, the sensitivity to different nanoparticle types varied between species. Moreover, the registered cell membrane depolarization indicated an early toxic response and raised concern that chronic long-term exposure of nanoparticles (even if they were previously declared as safe) is a serious threat for aquatic organisms. Abstract Nanoparticles (NPs) have broad applications in medicine, cosmetics, optics, catalysis, environmental purification, and other areas nowadays. With increasing annual production of NPs, the risks of their harmful influence on the environment and human health are also increasing. Currently, our knowledge about the mechanisms of the interaction between NPs and living organisms is limited. The marine species and their habitat environment are under continuous stress owing to the anthropogenic activities, which result in the release of NPs in the aquatic environment. We used a bioassay model with hemocytes of three bivalve mollusc species, namely, Crenomytilus grayanus, Modiolus modiolus, and Arca boucardi, to evaluate the toxicity of 10 different types of NPs. Specifically, we compared the cytotoxic effects and cell-membrane polarization changes in the hemocytes exposed to carbon nanotubes, carbon nanofibers, silicon nanotubes, cadmium and zinc sulfides, Au-NPs, and TiO2 NPs. Viability and the changes in hemocyte membrane polarization were measured by the flow cytometry method. The highest aquatic toxicity was registered for metal-based NPs, which caused cytotoxicity to the hemocytes of all the studied bivalve species. Our results also highlighted different sensitivities of the used tested mollusc species to specific NPs.
Liver-specific ceramide reduction alleviates steatosis and insulin resistance in alcohol-fed mice[S]

Alcohol’s impairment of both hepatic lipid metabolism and insulin resistance (IR) are key drivers of alcoholic steatosis, the initial stage of alcoholic liver disease (ALD). Pharmacologic reduction of lipotoxic ceramide prevents alcoholic steatosis and glucose intolerance in mice, but potential off-target effects limit its strategic utility. Here, we employed a hepatic-specific acid ceramidase (ASAH) overexpression model to reduce hepatic ceramides in a Lieber-DeCarli model of experimental alcoholic steatosis. We examined effects of alcohol on hepatic lipid metabolism, body composition, energy homeostasis, and insulin sensitivity as measured by hyperinsulinemic-euglycemic clamp. Our results demonstrate that hepatic ceramide reduction ameliorates the effects of alcohol on hepatic lipid droplet (LD) accumulation by promoting VLDL secretion and lipophagy, the latter of which involves ceramide cross-talk between the lysosomal and LD compartments. We additionally demonstrate that hepatic ceramide reduction prevents alcohol’s inhibition of hepatic insulin signaling. These effects on the liver are associated with a reduction in oxidative stress markers and are relevant to humans, as we observe peri- LD ASAH expression in human ALD. Together, our results suggest a potential role for hepatic ceramide inhibition in preventing ALD.
Improvement in Purity of Healthy Tomato Seeds Using an Image-Based One-Class Classification Method

The feasibility of a color machine vision technique with the one-class classification method was investigated for the quality assessment of tomato seeds. The health of seeds is an important quality factor that affects their germination rate, which may be affected by seed contamination. Hence, segregation of healthy seeds from diseased and infected seeds, along with foreign materials and broken seeds, is important to improve the final yield. In this study, a custom-built machine vision system containing a color camera with a white light emitting diode (LED) light source was adopted for image acquisition. The one-class classification method was used to identify healthy seeds after extracting the features of the samples. A significant difference was observed between the features of healthy and infected seeds, and foreign materials, implying a certain threshold. The results indicated that tomato seeds can be classified with an accuracy exceeding 97%. The infected tomato seeds indicated a lower germination rate (<10%) compared to healthy seeds, as confirmed by the organic growing media germination test. Thus, identification through image analysis and rapid measurement were observed as useful in discriminating between the quality of tomato seeds in real time.
Lack of mate-guarding in a territorial passerine bird with a low intensity of sperm competition, the pied flycatcher (Ficedula hypoleuca)

We examined a Norwegian population of pied flycatchers (Ficedula hypoleuca) for behaviour associated with the paternity-protection tactic of mate-guarding and found that this tactic was absent. The absence of mate-guarding and the fact that pied flycatchers do not have a high rate of copulation make this population unusual to the extent that the current literature implies that, in birds, one or other paternity guard should be present. Comparison of our population with a Swedish population that does exhibit mate-guarding lends some support to the notion that differences in nesting density may drive the relative risk of extra-pair copulation, leading to the need for paternity guards such as mate-guarding. However, we conclude that, whilst the results of both our study and the Swedish study are consistent with the nesting-density hypothesis, there is at least one other plausible hypothesis that fits the available data. Specifically, we direct attention to the role of the female in determining overall patterns of pair behaviour and, potentially, the rate of extra-pair paternity, challenging the primacy of male-male competition as the driving force behind the sperm-competition dynamics of this species.
Lower functioning patients demonstrate atypical hip joint loading before and following total hip arthroplasty for osteoarthritis

Previous studies have established that up to 1 year post total hip arthroplasty (THA), patients do not recover normal function and the magnitude of hip joint loading remains reduced compared to healthy individuals. However, the temporal nature of the loading profile has not been considered to identify individuals who are at a greater risk of poor functional outcomes following THA. This study aimed to determine changes to the profile and magnitude of the resultant hip joint reaction force before and up to 6 months post‐primary THA, and factors associated with atypical loading profiles. Hip joint loading was computed using a personalized lower‐limb musculoskeletal model in 43 participants awaiting primary THA for osteoarthritis (mean age: SD = 65, 14 years; body mass index: SD = 30, 5 kg/m2) before and up to 6 months after THA. Atypical, single‐peak loading profiles were observed for 11 patients before surgery, where four showed a single peak at 6 months. Patients displaying a single‐peak profile walked slower (mean difference: −0.4 m/s) compared to individuals displaying double‐peak profile (P = <.001) and had significantly reduced sagittal plane hip range of motion during gait (mean difference −9.6°, P = <.001). Self‐reported pain, function, and stiffness did not differentiate between patients with a single or double‐peak loading profile. Individuals with a single‐peak force profile did not meet the minimal clinically important hip range of motion during gait and would be classified as low‐functioning THA patients. Clinical Relevance: The temporal nature of the force profile may help to identify individuals who are at the greatest risk of poor functional outcomes after THA.
Design, synthesis, chemical characterization, biological evaluation, and docking study of new 1,3,4-oxadiazole homonucleoside analogs

Abstract Herein, we report the synthetic strategies and characterization of some novel 1,3,4-oxadiazole homonucleoside analogs that are relevant to potential antitumor and cytotoxic activities. The structure of all compounds is confirmed using various spectroscopic methods such as 1H-NMR, 13C-NMR, HRMS, and FTIR. These compounds were evaluated against three human cancer cell lines (MCF-7, SKBR3, and HL60 Cell Line). Preliminary investigations showed that the cytotoxic activity was markedly dependent on the nucleobase. Introduction of 5-Iodouracil 4g and theobromine 6b proved to be extremely beneficial even they were more potent than the reference drug (DOX). Also, the synthesized compounds were tested for their antiviral activities against the human varicella-zoster virus (VZV). The product 4h was (6-azauracil derivative) more potent to the reference (acyclovir) against the deficient TK − VZV strain by about 2-fold. Finally, molecular docking suggested that the anticancer activities of compounds 6b and 4g mediated by inhibiting dual proteins EGFR/HER2 with low micromolar inhibition constant Ki range. The 1,3,4-oxadiazole homonucleosides showed a strong affinity to binding sites of target proteins by forming H-bond, carbon–hydrogen bond, Pi-anion, Pi-sulfur, Pi-sigma, alkyl, and Pi-alkyl interactions.