Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase 2 Study of the Safety and Efficacy of Umbralisib in Patients with CLL Who Are Intolerant to BTK or PI3Kδ Inhibitor Therapy.

PURPOSE Intolerance is the most common reason for kinase inhibitor (KI) discontinuation in CLL. Umbralisib a novel, highly selective PI3Kδ/CK1ε inhibitor, is active and well tolerated in CLL patients. This phase 2 trial evaluated umbralisib in CLL patients who are intolerant to prior BTK or PI3K inhibitor therapy. PATIENTS AND METHODS In this phase 2 trial (NCT02742090), umbralisib was initiated at 800 mg oral daily in CLL patients requiring therapy per investigator discretion who were intolerant to prior BTK or PI3K inhibitor therapy, until progression or toxicity. Primary endpoint was progression-free survival (PFS). Secondary endpoints included time to treatment failure and umbralisib safety profile. DNA isolated from buccal swabs was genotyped for polymorphisms in CYP3A4, CYP3A5 and CYP2D6. RESULTS Fifty-one patients were enrolled (44 BTKi and 7 PI3Kδi intolerant). Median age was 70 years (range 48-96), median of 2 prior lines of therapy (1-7), 24% had del17p and/or TP53 mutation, and 65% were IGHV unmutated. Most common AEs leading to prior KI discontinuation were rash (27%), arthralgia (18%), and atrial fibrillation (16%). Median progression free survival (PFS) was 23.5 months (95% CI 13.1-not estimable). 58% of patients were on umbralisib for a longer duration than prior KI. Most common (≥5%) grade ≥3 AEs on umbralisib (all causality) were neutropenia (18%), leukocytosis (14%), thrombocytopenia (12%), pneumonia (12%), and diarrhea (8%). Six patients (12%) discontinued umbralisib due to an AE. Eight patients (16%) had dose reductions and were successfully re-challenged. CONCLUSIONS Umbralisib is safe and effective in this BTK and alternate PI3K inhibitor intolerant CLL population. These are the first prospective data to confirm that switching from a BTK or alternate PI3K inhibitor to umbralisib can result in durable, well tolerated responses.
Hearing Loss in Alzheimer’s Disease Is Associated with Altered Serum Lipidomic Biomarker Profiles

Recent data have found that aging-related hearing loss (ARHL) is associated with the development of Alzheimer’s Disease (AD). However, the nature of the relationship between these two disorders is not clear. There are multiple potential factors that link ARHL and AD, and previous investigators have speculated that shared metabolic dysregulation may underlie the propensity to develop both disorders. Here, we investigate the distribution of serum lipidomic biomarkers in AD subjects with or without hearing loss in a publicly available dataset. Serum levels of 349 known lipids from 16 lipid classes were measured in 185 AD patients. Using previously defined co-regulated sets of lipids, both age- and sex-adjusted, we found that lipid sets enriched in phosphatidylcholine and phosphatidylethanolamine showed a strong inverse association with hearing loss. Examination of biochemical classes confirmed these relationships and revealed that serum phosphatidylcholine levels were significantly lower in AD subjects with hearing loss. A similar relationship was not found in normal subjects. These data suggest that a synergistic relationship may exist between AD, hearing loss and metabolic biomarkers, such that in the context of a pathological state such as AD, alterations in serum metabolic profiles are associated with hearing loss. These data also point to a potential role for phosphatidylcholine, a molecule with antioxidant properties, in the underlying pathophysiology of ARHL in the context of AD, which has implications for our understanding and potential treatment of both disorders.
Physiological responses of date palm (Phoenix dactylifera) seedlings to seawater and flooding.

• In their natural environment along coast lines, date palms are exposed to seawater inundation and, hence, combined stress by salinity and flooding. • To elucidate the consequences of this combined stress on foliar gas exchange and metabolite abundances in leaves and roots, date palm seedlings were exposed to flooding with seawater and its major constituents under controlled conditions. • Seawater flooding significantly reduced CO2 assimilation, transpiration and stomatal conductance, but did not affect isoprene emission. A similar effect was observed upon NaCl exposure. In contrast, flooding with distilled water or MgSO4 did not affect CO2 /H2 O gas exchange or stomatal conductance significantly, indicating that neither flooding itself, nor seawater sulfate, contributed greatly to stomatal closure. Seawater exposure increased Na and Cl contents in leaves and roots, but did not affect sulfate contents significantly. Metabolite analyses revealed reduced abundances of foliar compatible solutes, such as sugars and sugar alcohols, whereas nitrogen compounds accumulated in roots. • Reduced transpiration upon seawater exposure may contribute to controlling the movement of toxic ions to leaves and, therefore, can be seen as a mechanism to cope with salinity. The present results indicate date palm seedlings are tolerant towards seawater exposure to some extent, and highly tolerant to flooding.
Formation of large-area nanostructures on Si and Ge surfaces during low energy ion beam erosion

In this contribution results on self-organized patterns formed during low energy Xe+ ion beam erosion on Si and Ge surfaces are presented. It was found that the evolution of surface patterns depends on ion incidence angle, erosion time, and ion energy. In the case without sample rotation ripple patterns form on the Si and Ge surfaces with a wavelength λ<100nm, for ion energies Eion⩽2000eV at near normal ion incidence (αion∼5°) and at room temperature. The experimental results of a decreasing ripple wavelength with ion incidence angle on Si coincide with the Bradley-Harper [J. Vac. Sci. Technol. A 6, 2390 (1988). ] theory of ripple formation. While the independency of λ from the ion flux suggests that thermally activated surface diffusion can be ruled out as the dominant relaxation mechanism. Experiments reveal that the wavelength of ripples increases with ion energy. With sample rotation at 75° ion incidence angle dot patterns form on the surface with a mean size λ<50nm.
Genome-Wide Identification and Molecular Characterization of the Growth-Regulating Factors-Interacting Factor Gene Family in Tomato

Growth-regulating factors-interacting factor (GIF) proteins play crucial roles in the regulation of plant growth and development. However, the molecular mechanism of GIF proteins in tomato is poorly understood. Here, four SlGIF genes (named SlGRF1a, SlGIF1b, SlGIF2, and SlGIF3) were identified from the tomato genome and clustered into two major clades by phylogenetic analysis. The gene structure and motif pattern analyses showed similar exon/intron patterns and motif organizations in all the SlGIFs. We identified 33 cis-acting regulatory elements (CAREs) in the promoter regions of the SlGIFs. The expression profiling revealed the four GIFs are expressed in various tissues and stages of fruit development and induced by phytohormones (IAA and GA). The subcellular localization assays showed all four GIFs were located in nucleus. The yeast two-hybrid assay indicated various growth-regulating factors (SlGRFs) proteins interacted with the four SlGIF proteins. However, SlGRF4 was a common interactor with the SlGIF proteins. Moreover, a higher co-expression relationship was shown between three SlGIF genes and five SlGRF genes. The protein association network analysis found a chromodomain helicase DNA-binding protein (CHD) and an actin-like protein to be associated with the four SlGIF proteins. Overall, these results will improve our understanding of the potential functions of GIF genes and act as a base for further functional studies on GIFs in tomato growth and development.
Comparative Analysis of User Exposure to the Electromagnetic Radiation Emitted by the Fourth and Fifth Generations of Wi-Fi Communication Devices

A suitable metric to describe human exposure to microwaves emitted by wireless communication devices is still incomplete. By using both theoretical analysis and experimental validation (in controlled and real deployed networks), we analyze and compare the specificity of exposure due to data transmissions in different configurations of fourth and fifth generation wireless fidelity (Wi-Fi) standards in the proximity of a mobile device. Measurements made use of the capability of the amplitude probability density incorporated in a real-time spectrum analyzer, proving its agility of highlighting different user exposure profiles. The results are presented comparatively and indicate that, in Wi-Fi networks, the modulation and coding scheme (MCS) should be used together with the duty cycle for an improved exposure assessment. The present work introduces the emitted energy density per bit in describing the user’s exposure to Wi-Fi signals and proves its superiority in characterizing the true levels of exposure for the IEEE 802.11n and 802.11ac standards of communication.
Unravelling the Features of Success of VIM-Producing ST111 and ST235 Pseudomonas aeruginosa in a Greek Hospital

The objective of this study was to analyze the characteristics that contribute to the successful dissemination of VIM-producing Pseudomonas aeruginosa (P. aeruginosa), belonging to ST111 and ST235, in a Greek hospital. A total of 120 non-repetitive P. aeruginosa, which had meropenem minimal inhibitory concentrations (MICs) greater than 2 mg/L, were studied. VIM-encoding genes were amplified and sequenced within their integrons. Isolates were typed by multilocus sequence typing (MLST). Six VIM-producers, representative of different integron structures and sequence types (STs), were completely sequenced using Illumina platform. Sixty-one P. aeruginosa were confirmed to produce VIM-type carbapenemases. ST111 dominated (n = 34) among VIM-producers, while 15 VIM-producers belonged to ST235. The blaVIM-like genes were located in three integron types, including In59, In595 and In1760, which were integrated into P. aeruginosa chromosomes. Whole genome sequencing (WGS) data demonstrated that ST111 and ST235 MBL producers carried several resistance and virulence genes. Additionally, the presence of type I-C and type I-E clustered regularly interspaced short palindromic repeats (CRISPR)/Cas locus was observed in ST235 and ST395 isolates, respectively. In conclusion, our findings confirmed the clonal spread of ST111 P. aeruginosa, carrying the VIM-2-encoding integron In59, in the University Hospital of Larissa (UHL). In addition, they highlighted the important role of high-risk clones, ST111 and ST235, in the successful dissemination and establishment into hospital settings of clinically important pathogens carrying resistance determinants.
Sensory impairment and all-cause mortality among the elderly adults in China: a population-based cohort study

With age-related functional deterioration, sensory impairment including vision impairment (VI), hearing impairment (HI), and dual sensory impairment (DSI) usually occurred among the elderly population, causing a decrease in functional capacity and quality of life. The study aimed to explore how sensory impairment is associated with the risk of all-cause mortality among the elderly adults in China. We prospectively investigated the association among 37,076 participants enrolled from 1998 to 2019 in the Chinese Longitudinal Healthy Longevity Survey. We also, as a sensitivity analysis, explored the association among 11,365 newly incident sensory impairment participants. Cox regression model with sensory impairment as a time-varying exposure was performed to calculate the hazard ratios (HRs) and 95% confidence intervals (CIs). Compared with participants without sensory impairment, those with VI (HR=1.20, 95% CI: 1.15-1.24), HI (HR=1.26, 95% CI: 1.21-1.31), and DSI (HR: 1.46, 95% CI=1.41-1.52) had significant higher risk of all-cause mortality after adjusting for potential confounders. These associations were robust among subgroup analyses stratified by sex and entry age, and sensitivity analyses performed among newly incident sensory impairment participants. In conclusion, sensory impairment was associated with higher mortality risk among the elderly adults in China.
Childhood trauma moderates morphometric associations between orbitofrontal cortex and amygdala: implications for pathological personality traits

Abstract Background Research has demonstrated that chronic stress exposure early in development can lead to detrimental alterations in the orbitofrontal cortex (OFC)–amygdala circuit. However, the majority of this research uses functional neuroimaging methods, and thus the extent to which childhood trauma corresponds to morphometric alterations in this limbic-cortical network has not yet been investigated. This study had two primary objectives: (i) to test whether anatomical associations between OFC–amygdala differed between adults as a function of exposure to chronic childhood assaultive trauma and (ii) to test how these environment-by-neurobiological effects relate to pathological personality traits. Methods Participants were 137 ethnically diverse adults (48.1% female) recruited from the community who completed a clinical diagnostic interview, a self-report measure of pathological personality traits, and anatomical MRI scans. Results Findings revealed that childhood trauma moderated bilateral OFC–amygdala volumetric associations. Specifically, adults with childhood trauma exposure showed a positive association between medial OFC volume and amygdalar volume, whereas adults with no childhood exposure showed the negative OFC–amygdala structural association observed in prior research with healthy samples. Examination of the translational relevance of trauma-related alterations in OFC–amygdala volumetric associations for disordered personality traits revealed that trauma exposure moderated the association of OFC volume with antagonistic and disinhibited phenotypes, traits characteristic of Cluster B personality disorders. Conclusions The OFC–amygdala circuit is a potential anatomical pathway through which early traumatic experiences perpetuate emotional dysregulation into adulthood and confer risk for personality pathology. Results provide novel evidence of divergent neuroanatomical pathways to similar personality phenotypes depending on early trauma exposure.
Violence and hepatitis C transmission in prison—A modified social ecological model

Background Transmission of hepatitis C virus (HCV) among the prisoner population is most frequently associated with sharing of non-sterile injecting equipment. Other blood-to-blood contacts such as tattooing and physical violence are also common in the prison environment, and have been associated with HCV transmission. The context of such non-injecting risk behaviours, particularly violence, is poorly studied. The modified social-ecological model (MSEM) was used to examine HCV transmission risk and violence in the prison setting considering individual, network, community and policy factors. Methods The Australian Hepatitis C Incidence and Transmission Study in prisons (HITS-p) cohort enrolled HCV uninfected prisoners with injecting and non-injecting risk behaviours, who were followed up for HCV infection from 2004–2014. Qualitative interviews were conducted within 23 participants; of whom 13 had become HCV infected. Deductive analysis was undertaken to identify violence as risk within prisons among individual, network, community, and public policy levels. Results The risk context for violence and HCV exposure varied across the MSEM. At the individual level, participants were concerned about blood contact during fights, given limited scope to use gloves to prevent blood contamination. At the network level, drug debt and informing on others to correctional authorities, were risk factors for violence and potential HCV transmission. At the community level, racial influence, social groupings, and socially maligned crimes like sexual assault of children were identified as possible triggers for violence. At the policy level, rules and regulations by prison authority influenced the concerns and occurrence of violence and potential HCV transmission. Conclusion Contextual concerns regarding violence and HCV transmission were evident at each level of the MSEM. Further evidence-based interventions targeted across the MSEM may reduce prison violence, provide opportunities for HCV prevention when violence occurs and subsequent HCV exposure.
Extensive CFTR Gene Analysis Revealed a Higher Occurrence of Cystic Fibrosis Transmembrane Regulator-Related Disorders (CFTR-RD) among CF Carriers

Background: A wide range of cystic fibrosis (CF)-related conditions are reported in CF carriers, but no study has explored the possibility that such subjects may be affected by cystic fibrosis transmembrane regulator-related disorders (CFTR-RD). No data are available so far on the occurrence of CFTR-RD among CF carriers. Methods: We studied 706 CF carriers—first- and second-degree relatives of CF patients that carried the parental mutation; such subjects were divided in two groups: a first group (353 subjects, group A) performed at first only the analysis of the CFTR proband mutation; we retrospectively evaluated the number of cases that had been diagnosed as CFTR-RD based on subsequent symptoms; a second group (353 subjects, group B) performed extensive CFTR molecular analysis in absence of any reported symptoms, followed by a clinical evaluation in cases that carry a second CFTR mutation; we evaluated the number of cases that prospectively were diagnosed as CFTR-RD. Results: We found seven (2.0%) out of 353 subjects of group A and 24 (6.8%) out of 353 subjects of group B as affected by CFTR-RD (chi square, p = 0.002). Conclusions: A percentage of CF carriers are affected by undiagnosed CFTR-RD. Genetic tasting scanning analysis helps to identify CFTR-RD, some of which may benefit from follow-up and specific therapies improving their outcome.
In Vitro Induction of Trained Innate Immunity by bIgG and Whey Protein Extracts

Bovine immunoglobulin G (bIgG) was previously shown to enhance innate immune responses to toll-like receptor (TLR) stimulation, via induction of trained immunity. In this study, we investigated whether minimally processed dairy streams with high levels of whey proteins as potential infant nutrition ingredients could also induce trained immunity, and to what extent this can be explained by the presence of bIgG. The minimally processed whey ingredients serum protein concentrate (SPC) and whey protein concentrate (WPC) were tested for their ability to induce trained immunity in human peripheral blood monocytes. Both ingredients induced trained immunity as evidenced by an increased production of TNF-α and, to a lesser extent, of IL-6 upon stimulation with TLR ligands. This was comparable to isolated bovine immunoglobulin G (bIgG) that served as positive control. Depletion of bIgG from both whey protein-containing ingredients did not significantly inhibit the induction of trained immunity, suggesting that the streams contain other components in addition to bIgG that are able to induce trained immunity. These results indicate that minimally processed whey ingredients may contribute to protection against infections through enhancing innate immune responsiveness to pathogens.
Hodgkin Reed–Sternberg-Like Cells in Non-Hodgkin Lymphoma

Reed–Sternberg cells (RSCs) are hallmarks of classic Hodgkin lymphoma (cHL). However, cells with a similar morphology and immunophenotype, so-called Reed–Sternberg-like cells (RSLCs), are occasionally seen in both B cell and T cell non-Hodgkin Lymphomas (NHLs). In NHLs, RSLCs are usually present as scattered elements or in small clusters, and the typical background microenviroment of cHL is usually absent. Nevertheless, in NHLs, the phenotype of RSLCs is very similar to typical RSCs, staining positive for CD30 and EBV, and often for B cell lineage markers, and negative for CD45/LCA. Due to different therapeutic approaches and prognostication, it is mandatory to distinguish between cHL and NHLs. Herein, NHL types in which RSLCs can be detected along with clinicopathological correlation are described. Moreover, the main helpful clues in the differential diagnosis with cHL are summarized.
Influenza vaccine failure in the tropics: a retrospective cohort study of waning effectiveness

Abstract Influenza vaccine effectiveness (VE) wanes over the course of a temperate climate winter season but little data are available from tropical countries with year-round influenza virus activity. In Singapore, a retrospective cohort study of adults vaccinated from 2013 to 2017 was conducted. Influenza vaccine failure was defined as hospital admission with polymerase chain reaction-confirmed influenza infection 2–49 weeks after vaccination. Relative VE was calculated by splitting the follow-up period into 8-week episodes (Lexis expansion) and the odds of influenza infection in the first 8-week period after vaccination (weeks 2–9) compared with subsequent 8-week periods using multivariable logistic regression adjusting for patient factors and influenza virus activity. Records of 19 298 influenza vaccinations were analysed with 617 (3.2%) influenza infections. Relative VE was stable for the first 26 weeks post-vaccination, but then declined for all three influenza types/subtypes to 69% at weeks 42–49 (95% confidence interval (CI) 52–92%, P = 0.011). VE declined fastest in older adults, in individuals with chronic pulmonary disease and in those who had been previously vaccinated within the last 2 years. Vaccine failure was significantly associated with a change in recommended vaccine strains between vaccination and observation period (adjusted odds ratio 1.26, 95% CI 1.06–1.50, P = 0.010).
Peptide-Affinity Precipitation of Extracellular Vesicles and Cell-Free DNA Improves Sequencing Performance for the Detection of Pathogenic Mutations in Lung Cancer Patient Plasma

Liquid biopsy is a minimally-invasive diagnostic method that may improve access to molecular profiling for non-small cell lung cancer (NSCLC) patients. Although cell-free DNA (cf-DNA) isolation from plasma is the standard liquid biopsy method for detecting DNA mutations in cancer patients, the sensitivity can be highly variable. Vn96 is a peptide with an affinity for both extracellular vesicles (EVs) and circulating cf-DNA. In this study, we evaluated whether peptide-affinity (PA) precipitation of EVs and cf-DNA from NSCLC patient plasma improves the sensitivity of single nucleotide variants (SNVs) detection and compared observed SNVs with those reported in the matched tissue biopsy. NSCLC patient plasma was subjected to either PA precipitation or cell-free methods and total nucleic acid (TNA) was extracted; SNVs were then detected by next-generation sequencing (NGS). PA led to increased recovery of DNA as well as an improvement in NGS sequencing parameters when compared to cf-TNA. Reduced concordance with tissue was observed in PA-TNA (62%) compared to cf-TNA (81%), mainly due to identification of SNVs in PA-TNA that were not observed in tissue. EGFR mutations were detected in PA-TNA with 83% sensitivity and 100% specificity. In conclusion, PA-TNA may improve the detection limits of low-abundance alleles using NGS.