Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of fungal gamma-linolenic acid and beta-carotene containing prefermented feed on immunity and gut of broiler chicken

ABSTRACT Gamma‐linolenic acid (GLA) is a fatty acid from the ω‐6 family. It is able to deliver a wide range of health benefits arising from its anti‐inflammatory effects. An insufficient supply of GLA from agricultural and animal sources resulted in the development of a fermentation technique using lower filamentous fungi, which have the ability to accumulate high concentrations of GLA and beta‐carotene during solid‐state fermentation of cereals. The goal of this study was to observe the influence of the addition of prefermented cereal product, containing high amounts of GLA and beta‐carotene, into the feed of broiler chickens on their immune status, and also the number of lactic acid bacteria and enterobacteria in gut content, which has never been studied before. Immunostimulation in the GLA group was manifested by a significant increase in the oxidative burst of phagocytes, CD4+CD8‐ lymphocytes in blood, and the CD4: CD8 ratio. Upregulation of gene expression for IgA in the GLA group indicates that the B‐lymphocytes were stimulated at a local gut level. In the caecum, increased mRNA expression for mucin‐2 and insulin‐like growth factor was observed in the GLA group, which could contribute mainly to the protection of the intestinal mucosa and to better growth and regeneration of skeletal muscles. Improved immune activation and protection of the intestinal mucosa were subsequently reflected in a change of the microbial composition in gut contents; a significant reduction of enterobacteria occurred after GLA administration. We can conclude that prefermented cereals containing fungal GLA and beta‐carotene represent a low‐cost supplement for broiler diet having a beneficial health effect.
Framingham vascular age is associated with worse cognitive performance in the middle-aged and elderly

ABSTRACT “Normal” age-related cognitive decline has been associated with cardiovascular risk factors. Framingham Vascular Age is age-normed cardiovascular risk which may help communicate risk to patients and identify those at relatively higher risk. We aim to assess the association between Framingham Vascular Age and cognition. 346 “healthy” participants (57±10 years) without neuropsychiatric disorders or clinical manifestations of cardiovascular disease were studied. Cognition was evaluated using the Brief Memory and Executive Test and Framingham Vascular Age was calculated. The association between Framingham Vascular Age and cognitive performance was determined through General Linear Models to control for covariates. Framingham Vascular age was associated with poorer Memory and Executive Function/Processing Speed indices (p= 0.019 and p<0.001, respectively). We conclude Framingham Vascular Age is associated with worse Executive Function/Processing Speed and Memory. Vascular Age may help identify patients at higher risk of age-related cognitive decline with implications for communicating the morbidity associated with cardiovascular risk.
Thrombospondin receptor α2δ-1 promotes synaptogenesis and spinogenesis via postsynaptic Rac1

Astrocytes control excitatory synaptogenesis by secreting thrombospondins (TSPs), which function via their neuronal receptor, the calcium channel subunit &agr;2&dgr;-1. &agr;2&dgr;-1 is a drug target for epilepsy and neuropathic pain; thus the TSP–&agr;2&dgr;-1 interaction is implicated in both synaptic development and disease pathogenesis. However, the mechanism by which this interaction promotes synaptogenesis and the requirement for &agr;2&dgr;-1 for connectivity of the developing mammalian brain are unknown. In this study, we show that global or cell-specific loss of &agr;2&dgr;-1 yields profound deficits in excitatory synapse numbers, ultrastructure, and activity and severely stunts spinogenesis in the mouse cortex. Postsynaptic but not presynaptic &agr;2&dgr;-1 is required and sufficient for TSP-induced synaptogenesis in vitro and spine formation in vivo, but an &agr;2&dgr;-1 mutant linked to autism cannot rescue these synaptogenesis defects. Finally, we reveal that TSP–&agr;2&dgr;-1 interactions control synaptogenesis postsynaptically via Rac1, suggesting potential molecular mechanisms that underlie both synaptic development and pathology.
Advanced cerebral amyloid angiopathy and small vessel disease are associated with psychosis in Alzheimer’s disease

Psychotic symptoms may occur in any dementia, including Alzheimer’s disease (AD), but are particularly common in Lewy body dementia (LBD). The mechanisms of psychotic symptoms are largely unknown. Psychosis has been found to be associated with more severe AD and Lewy body pathology in patients with AD and cerebrovascular disease-related vasculopathy.1 One form of vascular pathology, cerebral amylod angiopathy (CAA), is defined as deposits of amyloid in the vessel walls that increase risk of haemorrhage and ischaemia. CAA contributes to neurodegeneration, but its relation to clinical symptoms and course in dementia is not fully understood.2 The aim of this study was to investigate the postmortem pathological correlates of severe psychotic symptoms in moderate AD and LBD, which were followed annually from the time of diagnosis until death. This is a 12-year prospective follow-up study of dementia ending in neuropathological examination. The 223 patients of the dementia study in Western Norway (Demvest) were diagnosed as mild dementia and followed annually with standardised clinical assessments until death. Patient were diagnosed according to standardised clinical criteria for AD3 and DLB4 or Parkinson's disease dementia (PDD) (both combined as LBD) and mild dementia defined as Mini Mental Status Examination (MMSE) score of at least 20 or a Clinical Dementia Rating scale(CDR) global score=1. The procedures are described in detail elsewhere.5 All comparisons are between groups are based on pathological defined diagnosis. The validated Norwegian 12-item Neuropsychiatric Inventory (NPI) was used to assess neuropsychiatric symptoms. Presence of severe psychosis was based on the first 5 years after diagnosis and MMSE value above 10. NPI score of >4 on either item 1 (delusions) or 2 (hallucinations) was used as clinical significant cut-off. …
Ex situ normothermic machine perfusion of donor livers using a haemoglobin‐based oxygen carrier: a viable alternative to red blood cells

With interest we have read the systematic review by Eshmuminov et al. regarding porcine and human liver normothermic machine perfusion (NMP) [1]. The authors focused on studies using red blood cells (RBC) as oxygen carrier in the perfusion fluid and excluded studies using perfusion solutions based on artificial oxygen carriers. In their review, the authors state "We excluded studies using artificial oxygen carriers. Results of studies with synthetic hemoglobin based oxygen carriers (HBOC) were disappointing, even with stopping of the ongoing clinical trials by FDA due to safety reasons". This article is protected by copyright. All rights reserved.
Brain Development and Heart Function after Systemic Single-Agent Chemotherapy in a Mouse Model of Childhood Leukemia Treatment

Purpose: Chemotherapy for childhood acute lymphoblastic leukemia (ALL) can cause late-appearing side effects in survivors that affect multiple organs, including the heart and brain. However, the complex ALL treatment regimen makes it difficult to isolate the causes of these side effects and impossible to separate the contributions of individual chemotherapy agents by clinical observation. Using a mouse model, we therefore assessed each of eight representative, systemically-administered ALL chemotherapy agents for their impact on postnatal brain development and heart function. Experimental Design: Mice were treated systemically with a single chemotherapy agent at an infant equivalent age, then allowed to age to early adulthood (9 weeks). Cardiac structure and function were assessed using in vivo high-frequency ultrasound, and brain anatomy was assessed using high-resolution volumetric ex vivo MRI. In addition, longitudinal in vivo MRI was used to determine the time course of developmental change after vincristine treatment. Results: Vincristine, doxorubicin, and methotrexate were observed to produce the greatest deficiencies in brain development as determined by volumes measured on MRI, whereas doxorubicin, methotrexate, and l-asparaginase altered heart structure or function. Longitudinal studies of vincristine revealed widespread volume loss immediately following treatment and impaired growth over time in several brain regions. Conclusions: Multiple ALL chemotherapy agents can affect postnatal brain development or heart function. This study provides a ranking of agents based on potential toxicity, and thus highlights a subset likely to cause side effects in early adulthood for further study.
Characterization of carbapenemase-producing Enterobacteriaceae from colonized patients in a university hospital in Madrid, Spain, during the R-GNOSIS project depicts increased clonal diversity over time with maintenance of high-risk clones

Objectives To describe the incidence and microbiological features of carbapenemase-producing Enterobacteriaceae (CPE) from colonized patients in a Spanish university hospital during a cluster-randomized study [the Resistance of Gram-Negative Organisms: Studying Intervention Strategies (R-GNOSIS) project] on isolation strategies for faecal ESBL carriers. Methods From March 2014 to March 2016, 15 556 rectal swabs from 8209 patients admitted in two surgical wards and two medical wards were collected and seeded on ESBL and CPE chromogenic agars. Carbapenemase characterization (PCR and sequencing) was performed, and antibiotic susceptibility (MIC), clonality (PFGE and MLST) and diversity (Simpson diversity index estimation) were determined. Results One hundred and ninety-eight CPE isolates, mainly Klebsiella pneumoniae (53.5%) and Escherichia coli (19.2%), were identified in 162 patients (2%). Prevalence of CPE carriage remained unchanged over time. Overall, amikacin (9.6%), tigecycline (9.6%) and colistin (0.5%) showed low non-susceptibility. The most frequent carbapenemase was OXA-48 (64.1%), followed by VIM-1 (26.8%), NDM-1 (5.3%) and KPC-3 (3.5%), and these were co-produced with ESBLs in 43.9%. OXA-48 plus CTX-M-15 was the most frequent association. Two major K. pneumoniae clones were identified (OXA-48-CTX-M-15-ST11 and VIM-1-SHV-12-ST54) with considerable genetic diversity among the remaining isolates, including OXA-48-E. coli. Species diversity tended to decrease from 0.75 in the first 6 months of the study to 0.43 in the final months. The emergence of new clones (i.e. OXA-48-Kluyvera spp. and NDM-1-K. pneumoniae ST437 and ST101) and displacement of other particular clones were also demonstrated. Conclusions We describe a polyclonal and changeable CPE population over time. Coexistence of worldwide disseminated clones, such as ST11-OXA-48- K. pneumoniae, with unrelated and emerging OXA-48-E. coli clones, depicts a disturbing CPE epidemiology in our institution.
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries

Summary Large-scale peptide mass spectrometry (MS)/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a comprehensive set of spectra for identification and quantification of proteins. We have developed a novel web-based R-package (iSwathX) for combining reference libraries that is compatible with different DIA analysis software. This open-source web GUI automates the process of normalization and combination of spectral libraries and provides a user-friendly method for performing library format conversions, analysis and visualizations, with no need for programing familiarity. Availability and implementation iSwathX is freely accessible at https://biolinfo.shinyapps. io/iSwathX with the R-package and Shiny source code available from GitHub (https://github.com/znoor/iSwathX). Supplementary information Supplementary data are available at Bioinformatics online.
The association of health-related quality of life with unmet supportive care needs and sociodemographic factors in low-income Latina breast cancer survivors: a single-centre pilot study

Abstract Purpose: Determine correlations between health-related quality of life (HRQOL), supportive care need, and sociodemographic factors in low-income Latina breast cancer survivors. Methods: A descriptive, survey-based, cross-sectional study was completed with 102 low-income Latina breast cancer survivors at a major public safety net hospital. Correlation coefficients were calculated between number of unmet supportive care needs (per Supportive Care Needs Survey), HRQOL (per SF-36), and sociodemographic variables. Results: Unmet supportive care needs were correlated with lower HRQOL in all domains (r > −0.40; p < 0.0001). Lower income was significantly associated with lower HRQOL (r > 0.21; p < 0.05) and more supportive care needs (r = −0.22; p < 0.05). Multimorbidity was significantly associated with decreased HRQOL (r > −0.23; p < 0.05) and greater supportive care need (r = 0.19; p < 0.05). Conclusions: Identifying and addressing unmet supportive care needs may improve HRQOL in low-income Latina breast cancer survivors. Rehabilitation interventions that address barriers to accessing supportive care related to low SES and multimorbidity may also improve health outcomes in this population. The dual effect of multimorbidity on both quality of life and level of supportive care need in this population warrants further investigation. Implications for rehabilitation Screening for unmet supportive care needs may be an important step in improving health-related quality of life during cancer rehabilitation. Challenges accompanying multimorbidity and lower socioeconomic status may prevent low-income cancer patients from accessing adequate supportive care. Rehabilitation interventions for socioeconomically disadvantaged cancer survivors should compensate for both socioeconomic status and the presence of comorbidities in order to reduce disparities in quality of life during survivorship.
Effects of Larval Density and Support Substrate in Liquid Diet on Productivity and Quality of Artificially Reared Anastrepha ludens (Diptera: Tephritidae)

Abstract The larval developmental environment can affect the quality of artificially reared insects used in pest control programs that apply the sterile insect technique. We used a liquid larval diet lacking corncob fractions (an ingredient which may be contaminated by toxins that inhibit larval development and drastically reduce insect production in mass-rearing facilities) to examine quality indicators of Anastrepha ludens (Loew) (Diptera: Tephritidae) as a function of larval density (1–5 larvae per ml of diet) and on two types of supporting materials (synthetic sponge and carpet felt) compared with a standard solid diet with corncob fractions inoculated with a fixed quantity of A. ludens eggs. Pupal weight and adult emergence of A. ludens reared on a liquid artificial diet were negatively and positively density dependent, respectively. One tray of solid diet produced an average (95% CI) of 689.5 (594.4, 794.3) pupae, whereas one tray of liquid diet with synthetic sponge and carpet felt produced an average of 266.0 (208.7, 332.9) and 43.7 (23.2, 73.9) pupae, respectively. Pupal weight and adult emergence of flies reared on the solid diet were atypically low probably due to the type of rearing tray used, whereas pupal weight and adult emergence on liquid diet were equal to, or exceeded 20 mg and a proportion of 0.93, respectively. The highest proportion of adults capable of flight was observed in the liquid diet with carpet felt. The potential causes by which larval density and support substrate affected productivity and quality of A. ludens reared on liquid diet are discussed.
Atrioventricular optimization in cardiac resynchronization therapy with quadripolar leads: should we optimize every pacing configuration including multi-point pacing?

Aims This study aims to define an atrioventricular (AV) delay optimization method for cardiac resynchronization therapy (CRT) with a quadripolar left ventricular (LV) lead based on intrinsic conduction intervals. Methods and results Heart failure patients with a left bundle branch block underwent CRT implantation with a quadripolar LV lead. Invasive LV pressure-volume loops were recorded during four biventricular and three multi-point pacing (MPP) settings, using four patient-specific paced AV delays. Haemodynamic response was defined as change in stroke work (Δ%SW) compared to intrinsic rhythm and was related to the following conduction intervals: right atrial pacing to right ventricular sensing interval (RAp-RVs), Q to LV sensing interval normalized to QRS duration (QLV/QRSd), PR-interval, and P-wave duration. In 44 patients, the largest Δ%SW (104 ± 76%) occurred at a paced AV delay of 128 ± 32 ms, at 47 ± 9% of RAp-RVs. Optimal AV delay of biventricular pacing (126 ± 26 ms) did not differ from MPP (126 ± 21 ms, P = 0.29). Intra-class correlation coefficient between optimal AV delays of different pacing configurations was 0.64 (0.45-0.78, P < 0.001). Although not statistically significant, Δ%SW at 50% of RAp-RVs (98 ± 74%) was closer to the maximal achievable Δ%SW increase than a fixed interval of 120 ms (96 ± 73%, P = 0.60). RAp-RVs, QLV/QRSd, PR interval, and P-wave duration were associated with the optimal AV delay in univariate analysis, but only RAp-RVs remained significantly associated in multivariate analysis (R = 0.69). Conclusion The AV delay that provides highest haemodynamic response is similar for various LV pacing configurations and for MPP. An AV delay ∼50% of RAp-RVs creates an acute haemodynamic response close to the maximal patient-specific response.
Meeting report: Consensus recommendations for a research agenda to address immunosuppressant nonadherence in organ transplantation

Despite advances in the field of transplantation, immunosuppressant medication nonadherence (NA) remains a primary contributor to suboptimal long‐term outcomes. Due to the multidimensional and multifactorial causes of medication NA, studies to date have focused on individual differing facets or single point barriers of NA with relative success. However, these successes have not proven to be sustainable, partly due to the intense resources needed for continued viability. This article provides a summary of a 2‐day meeting held in April 2017 (Chicago, IL) prior to the American Transplant Congress in which a multidisciplinary group convened to identify the unmet research needs related to medication NA in transplantation. Thought leaders in the field presented the past, present, and future directions of medication NA with the primary outcome of designing, developing, and ranking targeted interventions into a dynamic research agenda to identify which interventions maintained effects over time. Break‐out sessions were created based on the five World Health Organization (WHO) dimensions of adherence. Participants were then organized into the newly formed AST Transplant Pharmacy Adherence Consortium (AST TPAC) research group. This meeting report summarizes the content of the symposium, and the development, background, and future directions of the AST TPAC.
Invasion of midgut epithelial cells by a persistently transmitted virus is mediated by sugar transporter 6 in its insect vector

Insect transmission is obligatory for persistently transmitted viruses because the vector insect is the only means of virus spread in nature. The insect midgut is the first major barrier limiting virus acquisition, but the mechanisms by which viruses are able to cross the cell membrane and then infect the midgut epithelial cells of the insect have not been elucidated completely. Here, we found that the outer capsid or nucleocapsid protein (NP) of three viruses can interact and colocalize with sugar transporter 6 that is highly expressed in the midgut of Laodelphax striatellus (LsST6). In contrast, LsST6 did not interact with the NP of rice grassy stunt virus, which cannot be transmitted by the same planthopper. LsST6 not only altered the cellular location of viral proteins and then colocalized with them in the cell membrane, but also mediated the entry of rice stripe virus (RSV) particles into Spodoptera frugiperda 9 (Sf9) cells that expressed the heterologous gene LsST6. We further showed that RSV particles initially bound to the cell membrane of midgut epithelial cells where it colocalized with LsST6, and then invaded the cytoplasm. When LsST6 expression was knocked down, viral titre, acquisition percentage and transmission efficiency of the treated insect decreased significantly, but virus replication was not affected. This work thus uncovered a strategy by which LsST6 mediates viral entry into midgut epithelial cells and leads to successful transmission by the insect vector.
Cotton Fleahopper Damage on Water-Stressed Cotton

Cotton fleahopper, Pseudatomoscelis seriatus, can cause excessive loss of cotton squares, resulting in reduced yield and harvest delays. Field testing during drought conditions provided opportunity to assess insect activity in a high contrast of dryland and irrigated conditions. Plant water stress affected natural cotton fleahopper populations (South Texas study: increasing more in irrigated plots) and water stressed plants were more sensitive to equal cotton fleahopper pressure (High Plains study: lint loss and possibly boll load decreasing more in low irrigation plots). As seen last year, plant development stage at the time of initial cotton fleahopper infestation was crucial, with early squaring cotton having higher densities than cotton at early bloom in the infestation (South Texas study). For field application, detection of fleahoppers in early planted cotton may serve as early warning of cotton fleahoppers in later-planted cotton. As the infestation progresses, fleahoppers may persist better in cotton with low water stress. But the greatest potential for yield decline from cotton fleahopper was when cotton was water stressed and infestations occurred during pre-bloom squaring. Understanding how water stress contributes to cotton fleahopper fluctuations may allow better estimation of cotton risk from cotton fleahopper damage.
freesurfer: Connecting the Freesurfer software with R

We present the package freesurfer, a set of R functions that interface with Freesurfer, a commonly-used open-source software package for processing and analyzing structural neuroimaging data, specifically T1-weighted images. The freesurfer package performs operations on nifti image objects in R using command-line functions from Freesurfer, and returns R objects back to the user. freesurfer allows users to process neuroanatomical images and provides functionality to convert and read the output of the Freesurfer pipelines more easily, including brain images, brain surfaces, and Freesurfer output tables.
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

Abstract The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation of the multispecies coalescent, using transmodel Markov chain Monte Carlo to calculate the posterior probabilities of different species trees. BPP is suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here, we provide a practical guide to the use of BPP in species tree estimation. BPP is a command-line program that runs on linux, macosx, and windows. This protocol shows how to use both BPP 3.4 (http://abacus.gene.ucl.ac.uk/software/) and BPP 4.0 (https://github.com/bpp/).