Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations of TLR4 and IL-8 genes polymorphisms with age-related macular degeneration (AMD): a systematic review and meta-analysis

ABSTRACT Background The results of different studies have indicated the possible associations of TLR4 and IL-8 genes polymorphisms with Age-related Macular Degeneration (AMD). A meta-analysis study was designed to evaluate the possible associations of TLR4 (rs4986790/c.896A>G and rs4986791/ c.1196 C > T) and IL-8 (rs4073/c.251A>T and rs2227306/c.781 C > T) genes polymorphisms with AMD. Method A systematic literature search was carried out in PubMed, Embase, Web of Science, and Scopus databases to identify relevant publications. Pooled Odds Ratio (OR) with 95% Confidence Interval (CI) was used to evaluate the power of association. Results A total of 12 case-control studies with 4804 AMD patients and 4422 healthy controls were included in this meta-analysis. The analysis of genotypic and allelic models demonstrated significant associations between IL-8 c.781 C > T (CC vs. TT+TC: OR = 0.62 [0.48–0.81], P < .01; CC vs. TC: OR = 0.65 [0.48–0.89], P < .01; TT vs. CC: OR = 1.64 [1.04–2.57], P = .03; and C vs. T: OR = 0.71 [0.65–0.79], P < .01) and risk of AMD, which all of them passed Bonferroni correction for multiple testing (P-value≤0.01), except for TT vs. CC model. In addition, we found associations under the genotypic model of TLR4 c.896A>G (AA vs. AG+GG: OR = 0.73 [0.55–0.97], P = .03; and AA vs. AG: OR = 0.71 [0.53–0.95], P = .02) although after Bonferroni correction (P′-value<0.02) none of these associations remained significant. However, the data from this meta-analysis declined the associations of TLR4 c.1196 C > T and IL-8 c.251A>T polymorphisms with AMD. Conclusion The current meta-analysis study suggested that IL-8 c.781 C > T polymorphism is associated with susceptibility to AMD. Graphical abstract
Late onset neutropenia after rituximab and obinutuzumab treatment – characteristics of a class-effect toxicity

Abstract Late onset neutropenia (LON) after rituximab is a previously described complication. We aimed to assess and characterize LON after obinutuzumab, a novel anti-CD20 antibody, in the real-world setting and compare it to LON after rituximab therapy. We retrospectively analyzed 330 consecutive patients with lymphoproliferative neoplasms (rituximab-treated n = 283; obinutuzumab-treated n = 47). LON occurred in 23% patients with similar incidence in rituximab (n = 66, 23%) or obinutuzumab (n = 10, 21%) groups (p = 0.853). Patients treated for CLL and post-transplantation lymphoproliferative disease (PTLD) were at higher risk to develop LON (multivariate analysis: HR for CLL − 6.62 CI 95% 1.33–32.92; HR for PTLD 15.82 CI 95% 2.04–122.4). Febrile neutropenia was uncommon during LON and occurred in 15 patients (4.5%; rituximab (n = 14) and obinutuzumab (n = 1). These data suggest that LON after obinutuzumab treatment is as common as with rituximab. The similarities in LON after rituximab and obinutuzumab argue for a possible class effect for anti-CD20 monoclonal antibodies.
The effect of body weight-supported overground gait training for patients with Parkinson’s disease: A retrospective case-control observational study

Objective To evaluate the effects of body weight-supported overground gait training (BWSOGT) on motor abilities, such as gait and balance, in patients with Parkinson’s disease (PD). Design Retrospective case-controlled observational study with a 4-week follow-up. Setting Inpatient rehabilitation. Participants We selected 37 of 68 patients with PD. Inclusion criteria were (1) Hoehn & Yahr stage II–IV, (2) no medication adjustment during the study period, (3) at least 1 week since last medication adjustment, and (4) ability to walk more than 10 meters on their own. Exclusion criteria were (1) cerebrovascular disease or other complications affecting movement, (2) difficulty in measurement, (3) early discharge, (4) medication change during the study, and (5) development of complications. Interventions Patients were divided into two groups. Patients in Group I underwent 20 minutes of BWSOGT with a mobile hoist in addition to the standard exercises; Group II performed 20 minutes of gait training in place of BWSOGT. In both groups, training was performed for a total of 15 times/4 weeks. Main outcome measure(s) Participants were evaluated using the Unified Parkinson’s Disease Rating Scale total, part II, and part III; 10-m walk test; velocity; stride length; 6-minute walk test; timed up and go test; Berg Balance Scale; and freezing of gait before and after the intervention. Results There were significant decreases in the Unified Parkinson’s Disease Rating Scale total, part II, and part III in both groups; however, 6-minute walk test, timed up and go test, and freezing of gait results only improved in Group I. Conclusions BWSOGT for patients with PD improves gait ability and dynamic balance more than standard gait training.
Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol‐phosphate dehydratase

Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis (TB), employs ten enzymes including imidazoleglycerol‐phosphate dehydratase (IGPD) for de novo biosynthesis of histidine. The absence of histidine‐biosynthesis in humans combined with its essentiality for Mtb makes the enzymes of this pathway major anti‐TB drug targets. We explored the inhibitory potential of a small molecule β‐(1,2,4‐Triazole‐3‐yl)‐DL‐alanine (DLA) against Mtb IGPD. DLA exhibits an in vitro inhibitory efficacy in the lower micromolar range. Higher‐resolution crystal structures of native and substrate‐bound Mtb IGPD provided additional structural features of this important drug target. Crystal structure of IGPD‐DLA complex at a resolution of 1.75 Å, confirmed that DLA locks down the function of the enzyme by binding in the active site pocket of the IGPD mimicking the substrate‐binding mode to a high degree. In our biochemical study, DLA showed an efficient inhibition of Mtb IGPD. Furthermore, DLA also showed bactericidal activity against Mtb and Mycobacterium smegmatis and inhibited their growth in respective culture medium. Importantly, owing to the favorable ADME and physicochemical properties, it serves as an important lead molecule for further derivatizations.
Sex differences in sensory processing in children with autism spectrum disorder

Despite the high prevalence of sensory processing difficulties in children with autism spectrum disorder (ASD), little research has focused on the sex differences in sensory processing. Furthermore, there is a lack of knowledge on the female‐specific symptoms of ASD, contributing to later referral, diagnosis and intervention. In this study, we examined the sex differences in sensory processing symptoms in large cohorts of ASD children (N = 168; 26 females, 142 males) and typically developing (TD) children (N = 439; 209 females, 230 males). For this, we translated the sensory processing measure (SPM) and SPM – Preschool (SPM‐P) Home Forms to French. The SPM/SPM‐P are parent/caregiver questionnaires that assess typical behavioral responses to sensory stimuli. Overall, our results showed that the magnitude of the differences in sensory processing between males and females is larger in ASD children relative to TD children, with females showing more severe symptoms in Hearing, as well as Balance and Motion subscales. Additionally, linear discriminant analysis showed that the SPM/SPM‐P are good at discriminating TD children from ASD, children with higher accuracy rates for females than for males. These findings are discussed in light of the heterogeneity of sensory processing difficulties present in ASD. Overall, our results suggest that there seem to be female‐specific profiles in sensory processing difficulties in ASD. Implications of findings concerning sex differences in sensory processing and their potential for improving identification and diagnosis of ASD females are discussed.
The impact of the end of COVID confinement on pandemic dreams, as assessed by a weekly sleep diary: a longitudinal investigation in Italy

The Coronavirus 2019 pandemic strongly affected our sleep and dream activity. Many cross‐sectional studies highlighted increased dream recall frequency, and revealed a great presence of pandemic‐related oneiric contents. Here, we present the first prospective study carried out on an Italian sample. One‐hundred subjects were requested to fill out a web‐survey including socio‐demographic information, and questionnaires collecting sleep and clinical measures during lockdown. A final sample of 90 subjects participated in the longitudinal protocol lasting 2 weeks: (a) the first week (April 28–May 4) of full lockdown; and (b) the second week (May 5–May 11) of easing of restrictions. Subjects were asked to record at home their dream experiences, and complete a sleep‐dream diary each morning. Statistical comparisons showed that participants had higher numbers of awakenings, lower ease of falling asleep, higher dream recall and lucid dream frequency during lockdown than post‐lockdown. Further, subjects reported more dreams, including “being in crowded places” during post‐lockdown than lockdown. The poorer sleep quality during lockdown is quite consistent with previous findings. The relationship between traumatic events and dream recall frequency confirmed the idea of pandemic as “collective trauma”. Also, we hypothesized that the greater presence of lucid dreams during confinement could reflect the attempt to cope with the waking pandemic‐experiences. Finally, the presence of crowded places into dream scenarios during the second week of our protocol appears consistent with the continuity‐hypothesis, as the possibility to access places frequented by other people could represent a relevant experience after a long period of confinement.
Clinical and laboratory profile of different dengue sub types in dengue virus infection

Background: Dengue infection, an arthropod-borne viral hemorrhagic fever is caused by Arbovirus of Flavivirus genus and transmitted by Aedes aegypti , Aedes albopictus. Liver involvement in dengue fever is manifested by the elevation of transaminases representing reactive hepatitis, due to direct attack of virus itself or the use of hepatotoxic drugs. The objective of the study was to investigate clinical and laboratory profile of different dengue sub type’s patients admitted for dengue fever. Methods: All the adult patients with clinical features such as fever and later confirmed positive by dengue serology test admitted as inpatients were included in the study. Vitals parameters and systemic examination were performed. Investigation of dengue serotology, liver function test, routine investigations like hemoglobin percentage, total count, ESR, packed cell volume, platelet count, partial thromboplastin and activated partial thromboplastin time, blood urea, serum creatinine, and blood sugar estimation were done. Results: On comparison of clinical signs in different dengue subgroups it was observed that the mean value of pulse, blood pressure and respiratory rate were significantly more deranged in the DSS group as compared to the DF group. Platelet count was significantly lower in all the sub groups whereas PT/aPTT was more dearranged in the DSS and DHF group as compared to the DF group. Comparison between the mean values of liver function test in different dengue sub groups had been shown, elevated transaminases, hypoproteinaemia and hypoalbuminaemia, in higher frequency in dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS) as compared to classical dengue fever (DF) (P values significant). SGOT was significantly higher than the SGPT levels and SGOT was much more elevated in the DSS sub group compared to the DFS and DF group. Conclusions: The liver enzymes serum aminotransferase levels were significantly raised in patients with dengue shock syndrome compared to other two groups. Serum aminotransferases directly correlate with severity of infection in all the sub groups. Patients with secondary dengue infection were more prone for developing bleeding manifestations and shock syndrome.
Ultrastructural heterogeneity of the mitochondrial population in rat embryonic and induced pluripotent stem cells

Even though rats are popular model animals, the ultrastructure of their pluripotent cells, that is, embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), remains unexplored, although fine structure of pluripotent stem cells of mice and humans and its changes during differentiation have been investigated well. In the present study, we carried out ultrastructural and morphometric analyses of three lines of rat ESCs and two lines of rat iPSCs. The rat pluripotent stem cells were found to have the main typical morphological features of pluripotent cells: large nuclei of irregular or nearly round shape, scanty cytoplasm with few membrane organelles, and a poorly developed Golgi apparatus and endoplasmic reticulum. The cytoplasm of the rat pluripotent cells contains clusters of glycogen, previously described in human ESCs. To identify possible differences between rat ESCs and iPSCs, we performed a morphometric analysis of cell parameters. The mean area of cells and nuclei, the nuclear/cytoplasmic ratio, distributions of glycogen and diversity of mitochondria showed marked variations among the lines of rat pluripotent stem cells and were more pronounced than variations between rat ESCs and iPSCs as separate types of pluripotent stem cells. We noted morphological heterogeneity of the mitochondrial population in the rat pluripotent stem cells. The cells contained three types of mitochondria differing in the structure of cristae and in matrix density, and our morphometric analysis revealed differences in cristae structure.
Robust and efficient software for reference‐free genomic diversity analysis of genotyping‐by‐sequencing data on diploid and polyploid species

Genotyping‐by‐sequencing (GBS) is a widely used and cost‐effective technique for obtaining large numbers of genetic markers from populations by sequencing regions adjacent to restriction cut sites. Although a standard reference‐based pipeline can be followed to analyse GBS reads, a reference genome is still not available for a large number of species. Hence, reference‐free approaches are required to generate the genetic variability information that can be obtained from a GBS experiment. Unfortunately, available tools to perform de novo analysis of GBS reads face issues of usability, accuracy and performance. Furthermore, few available tools are suitable for analysing data sets from polyploid species. In this manuscript, we describe a novel algorithm to perform reference‐free variant detection and genotyping from GBS reads. Nonexact searches on a dynamic hash table of consensus sequences allow for efficient read clustering and sorting. This algorithm was integrated in the Next Generation Sequencing Experience Platform (NGSEP) to integrate the state‐of‐the‐art variant detector already implemented in this tool. We performed benchmark experiments with three different empirical data sets of plants and animals with different population structures and ploidies, and sequenced with different GBS protocols at different read depths. These experiments show that NGSEP has comparable and in some cases better accuracy and always better computational efficiency compared to existing solutions. We expect that this new development will be useful for many research groups conducting population genetic studies in a wide variety of species.
Mutual Information and Categorical Perception

Categorical perception refers to the enhancement of perceptual sensitivity near category boundaries, generally along dimensions that are informative about category membership. However, it remains unclear exactly which dimensions are treated as informative and why. This article reports a series of experiments in which subjects were asked to learn statistically defined categories in a novel, unfamiliar 2D perceptual space of shapes. Perceptual discrimination was tested before and after category learning of various features in the space, each defined by its position and orientation relative to the maximally informative dimension. The results support a remarkably simple generalization: The magnitude of improvement in perceptual discrimination of each feature is proportional to the mutual information between the feature and the category variable. This finding suggests a rational basis for categorical perception in which the precision of perceptual discrimination is tuned to the statistical structure of the environment.
Sedation strategy and ICU delirium: a multicentre, population-based propensity score-matched cohort study

Objectives We examined the relationship between dominant sedation strategy, risk of delirium and patient-centred outcomes in adults admitted to intensive care units (ICUs). Design Retrospective propensity-matched cohort study. Setting Mechanically ventilated adults (≥ 18 years) admitted to four Canadian hospital medical/surgical ICUs from 2014 to 2016 in Calgary, Alberta, Canada. Participants 2837 mechanically ventilated adults (≥ 18 years) requiring admission to a medical/surgical ICU were evaluated for the relationship between sedation strategy and delirium. Interventions None. Primary and secondary outcome measures The primary exposure was dominant sedation strategy, defined as the sedative infusion, including midazolam, propofol or fentanyl, with the longest duration before the first delirium assessment. The primary outcome was ‘ever delirium’ identified using the Intensive Care Delirium Screening Checklist. Secondary outcomes included mortality, length of stay (LOS), ventilation duration and days with delirium. The cohort was analysed in two propensity score (patient characteristics and therapies received) matched cohorts (propofol vs fentanyl and propofol vs midazolam). Results 2837 patients (60.7% male; median age 57 years (IQR 43–68)) were considered for propensity matching. In propensity score-matched cohorts(propofol vs midazolam, n=712; propofol vs fentanyl, n=1732), the odds of delirium were significantly higher with midazolam (OR 1.46 (95% CI 1.06 to 2.00)) and fentanyl (OR 1.22 (95% CI 1.00 to 1.48)) compared with propofol dominant sedation strategies. Dominant sedation strategy with midazolam and fentanyl were associated with a longer duration of ventilation compared with propofol. Fentanyl was also associated with increased ICU mortality (OR 1.50, 95% CI 1.07 to 2.12)) ICU and hospital LOS compared with a propofol dominant sedation strategy. Conclusions We identified a novel association between fentanyl dominant sedation strategies and an increased risk of delirium, a composite outcome of delirium or death, duration of mechanical ventilation, ICU LOS and hospital LOS. Midazolam dominant sedation strategies were associated with increased delirium risk and mechanical ventilation duration.
Learning walks in an Australian desert ant, Melophorus bagoti.

The Central Australian ant Melophorus bagoti is the most thermophilic ant in Australia and forages solitarily in the summer months during the hottest period of the day. For successful navigation, desert ants of many species are known to integrate a path and learn landmark cues around the nest. Ants perform a series of exploratory walks around the nest before their first foraging trip, during which they are presumed to learn about their landmark panorama. Here, we studied 15 naïve M. bagoti ants transitioning from indoor work to foraging outside the nest. In three to four consecutive days, they performed 3 to 7 exploratory walks before heading off to forage. Naïve ants increased the area of exploration around the nest and the duration of trips over successive learning walks. In their first foraging walk, the majority of the ants followed a direction explored on their last learning walk. During learning walks, the ants stopped and performed stereotypical orientation behaviours called pirouettes. They performed complete body rotations with stopping phases as well as small circular walks without stops known as voltes. After just one learning walk, these desert ants could head in the home direction from locations 2 m from the nest, although not from locations 4 m from the nest. These results suggest gradual learning of the visual landmark panorama around the foragers' nest. Our observations show that M. bagoti exhibit similar characteristics in their learning walks as other desert ants of the genera Ocymyrmex and Cataglyphis.
Evidence of psychological and biological effects of structured Mindfulness‐Based Interventions for cancer patients and survivors: A meta‐review

A large number of studies have been conducted exploring the effects of mindfulness programs on health outcomes, such as psychological and biological outcomes. However, there is substantial heterogeneity among studies and, consequently, in the systematic reviews/meta‐analyses. Since clinical practice is massively informed by evidence on review studies, our main objective was to summarize the reported evidence regarding the effects of structured mindfulness‐based programs on psychological, biological, and quality‐of‐life outcomes in cancer patients.
Assessing the Effects of Healthy and Neuropathological Aging on Personality with the Iowa Scales of Personality Change

ABSTRACT Personality changes in older adults with brain disease may be confounded by effects of normal aging. In this cross-sectional study, ratings with the Iowa Scales of Personality Change for 62 healthy older adults (OA-H, aged 60+) were compared to matched older adults with brain diseases (OA-BD). OA-H did not show any significant personality changes from middle age to older adulthood. However, between 10% and 20% of OA-H developed a disturbance in Lack of Stamina, Inflexibility, Lability, and Lack of Insight. Otherwise, the pattern of findings suggesting normal aging effects on personality disturbances in clinical groups are generally minimal.
Colpodella sp. (ATCC 50594) Life Cycle: Myzocytosis and Possible Links to the Origin of Intracellular Parasitism

Colpodella species are free living bi-flagellated protists that prey on algae and bodonids in a process known as myzocytosis. Colpodella species are phylogenetically related to Apicomplexa. We investigated the life cycle of Colpodella sp. (ATCC 50594) to understand the timing, duration and the transition stages of Colpodella sp. (ATCC 50594). Sam-Yellowe’s trichrome stains for light microscopy, confocal and differential interference contrast (DIC) microscopy was performed to identify cell morphology and determine cross reactivity of Plasmodium species and Toxoplasma gondii specific antibodies against Colpodella sp. (ATCC 50594) proteins. The ultrastructure of Colpodella sp. (ATCC 50594) was investigated by transmission electron microscopy (TEM). The duration of Colpodella sp. (ATCC 50594) life cycle is thirty-six hours. Colpodella sp. (ATCC 50594) were most active between 20–28 h. Myzocytosis is initiated by attachment of the Colpodella sp. (ATCC 50594) pseudo-conoid to the cell surface of Parabodo caudatus, followed by an expansion of microtubules at the attachment site and aspiration of the prey’s cytoplasmic contents. A pre-cyst formed at the conclusion of feeding differentiates into a transient or resting cyst. Both DIC and TEM microscopy identified asynchronous and asymmetric mitosis in Colpodella sp. (ATCC 50594) cysts. Knowledge of the life cycle and stages of Colpodella sp. (ATCC 50594) will provide insights into the development of intracellular parasitism among the apicomplexa.