Miracle-dz/UniFAR-FTUs huggingface dataset:
Apraclonidine Is Better Than Cocaine for Detection of Horner Syndrome

Background: In suspected cases of Horner syndrome pharmacological confirmation is often required before embarking on further investigations. There are two drugs currently used for this purpose that are commercially available for topical administration: cocaine (2–10%) and apraclonidine (0.5–1.0%). Aims: To evaluate and compare the effects of both drugs in normal eyes and eyes with Horner syndrome Methods: This is a retrospective study looking at the outcome of 660 consecutive pharmacological tests with these two drugs in one tertiary referral center over 14 years. Eyes were categorized as “normal” or “Horner syndrome” based on non-pharmacological criteria (pupillometric and clinical evidence). Pupil diameters in the dark and in bright light were measured by pupillometry before and 40 min after administration of the test drug (either 4% cocaine or 0.5% apraclonidine). Results: Cocaine dilated the normal pupil (measured in bright light: mean +2.1 mm, range −0.4 to +3.9 mm; 95% lower limit +0.5 mm); the extent of this response was not significantly affected by patient age or pupil size, but was 50% less in brown eyes compared with blue or green eyes, and 20% less if the measurements were made in the dark. In eyes with Horner syndrome cocaine had significantly less mydriatic effect (mean +0.7 mm, range −0.7 to +2.9 mm). Apraclonidine constricted the normal pupil (measured in the dark: mean −0.4 mm, range −1.3 to +0.8 mm; 95% upper limit +0.1 mm); eye color made no difference but the response was significantly greater in younger patients and larger pupils and significantly less if measured in bright lighting conditions. In eyes with Horner syndrome apraclonidine dilated the pupil (mean +0.6, range −0.4 to +2.3 mm). Applying the 95% limits identified from my normative data, I estimate the sensitivity of each drug test for detection of Horner syndrome at 40% for cocaine (criterion for abnormal: mydriasis ≤0.5 mm when measured in the dark) compared with 93% for apraclonidine (criterion for abnormal: mydriasis ≥0.1 mm when measured in the dark). Conclusions: Apraclonidine is a more sensitive test than cocaine for detection of Horner syndrome, and should be adopted as the new gold standard in routine clinical practice. However, caution is needed when using this drug within hours of a suspected sympathetic lesion, or in infants under 1 year of age.
Chronic Low-Level Vagus Nerve Stimulation Improves Long-Term Survival in Salt-Sensitive Hypertensive Rats

Chronic hypertension (HTN) affects more than 1 billion people worldwide, and is associated with an increased risk of cardiovascular disease. Despite decades of promising research, effective treatment of HTN remains challenging. This work investigates vagus nerve stimulation (VNS) as a novel, device-based therapy for HTN treatment, and specifically evaluates its effects on long-term survival and HTN-associated adverse effects. HTN was induced in Dahl salt-sensitive rats using a high-salt diet, and the rats were randomly divided into two groups: VNS (n = 9) and Sham (n = 8), which were implanted with functional or non-functional VNS stimulators, respectively. Acute and chronic effects of VNS therapy were evaluated through continuous monitoring of blood pressure (BP) and ECG via telemetry devices. Autonomic tone was quantified using heart rate (HR), HR variability (HRV) and baroreflex sensitivity (BRS) analysis. Structural cardiac changes were quantified through gross morphology and histology studies. VNS significantly improved the long-term survival of hypertensive rats, increasing median event-free survival by 78% in comparison to Sham rats. Acutely, VNS improved autonomic balance by significantly increasing HRV during stimulation, which may lead to beneficial chronic effects of VNS therapy. Chronic VNS therapy slowed the progression of HTN through an attenuation of SBP and by preserving HRV. Finally, VNS significantly altered cardiac structure, increasing heart weight, but did not alter the amount of fibrosis in the hypertensive hearts. These results suggest that VNS has the potential to improve outcomes in subjects with severe HTN.
Optimal Design of the Band Structure for Beam Lattice Metamaterials

Sonic or acoustic metamaterials may offer a mechanically robust and highly customizable solution to open large band gaps in the low-frequency dispersion spectrum of beam lattice materials. Achieving the largest possible stop bandwidth at the lowest possible center frequency may be a challenging multi-objective optimization issue. The paper presents a first effort of analysis, systematization and synthesis of some recent multi-disciplinary studies focused on the optimal spectral design of beam lattice materials and metamaterials. The design parameter vector is a finite set including all the microstructural properties characterizing the periodic material and the local resonators. Numerical algorithms are employed as leading methodology for solving various instances of the optimization problem. Methodological alternatives, based on perturbation methods and computational modeling, are also illustrated. Some optimal results concerning the dispersion spectrum of hexachiral, tetrachiral and anti-tetrachiral materials and metamaterials are summarized. The concluding remarks are accompanied by preliminary ideas to overcome some operational issues in solving the optimization problem.
Sub-dimensions of Alcohol Use Disorder in Alcohol Preferring and Non-preferring Rats, a Comparative Study

Recent animal models of alcohol use disorder (AUD) are centered in capturing individual vulnerability differences in disease progression. Here, we used genetically selected Marchigian Sardinian alcohol-preferring (msP) and Wistars rats to apply a multidimensional model of AUD adapted from a previously described DSM-IV/DSM-5 multisymptomatic cocaine addiction model. As proof of concept, we hypothesized that msP rats, genetically selected for excessive drinking, would be more prone to develop dependence-like behavior compared to Wistars. Before exposure of animals to alcohol, we monitored basal anxiety in the elevated plus maze (EPM). Animals were then trained in prolonged operant alcohol self-administration, consisting of 30-min daily sessions for 60 days in total. Each session consisted of two 10-min periods of alcohol reinforcement separated by 10-min interval of non-reinforcement. Following training, we applied three criteria of individual vulnerability for AUD: (1) persistence of lever pressing for alcohol when it was not available; (2) motivation for alcohol in a progressive ratio (PR) schedule of reinforcement; and (3) resistance to punishment when alcohol delivery was anticipated by a foot-shock (0.3 mA). We obtained four groups corresponding to the number of criteria met (0–3 crit). Rats in the 0crit and 1crit groups were characterized as resilient, whereas rats in the 2crit and 3crit groups were characterized as prone to develop a dependent-like phenotype. As predicted, the 2–3crit groups were enriched with msP rats while the 0–1crit groups were enriched in Wistar rats. In further analysis, we calculated the global addiction score (GAS) per subject by the sum of the normalized score (z-score) of each criterion. Results showed GAS was highly correlated with animal distribution within the 3 criteria. Specifically, GAS was negative in the 0–1crit groups, and positive in the 2–3crit groups. A positive correlation between basal anxiety and quantity of alcohol intake was detected in msP rats but not Wistars. In conclusion, we demonstrated that the 0/3criteria model is a suitable approach to study individual differences in AUD and that msP rats, selected for excessive-alcohol drinking, show a higher propensity to develop AUD compared to non-preferring Wistars.
Effectiveness of Robot-Assisted Upper Limb Training on Spasticity, Function and Muscle Activity in Chronic Stroke Patients Treated With Botulinum Toxin: A Randomized Single-Blinded Controlled Trial

Background: The combined use of Robot-assisted UL training and Botulinum toxin (BoNT) appear to be a promising therapeutic synergism to improve UL function in chronic stroke patients. Objective: To evaluate the effects of Robot-assisted UL training on UL spasticity, function, muscle strength and the electromyographic UL muscles activity in chronic stroke patients treated with Botulinum toxin. Methods: This single-blind, randomized, controlled trial involved 32 chronic stroke outpatients with UL spastic hemiparesis. The experimental group (n = 16) received robot-assisted UL training and BoNT treatment. The control group (n = 16) received conventional treatment combined with BoNT treatment. Training protocols lasted for 5 weeks (45 min/session, two sessions/week). Before and after rehabilitation, a blinded rater evaluated patients. The primary outcome was the Modified Ashworth Scale (MAS). Secondary outcomes were the Fugl-Meyer Assessment Scale (FMA) and the Medical Research Council Scale (MRC). The electromyographic activity of 5 UL muscles during the “hand-to-mouth” task was explored only in the experimental group and 14 healthy age-matched controls using a surface Electromyography (EMGs). Results: No significant between-group differences on the MAS and FMA were measured. The experimental group reported significantly greater improvements on UL muscle strength (p = 0.004; Cohen's d = 0.49), shoulder abduction (p = 0.039; Cohen's d = 0.42), external rotation (p = 0.019; Cohen's d = 0.72), and elbow flexion (p = 0.043; Cohen's d = 1.15) than the control group. Preliminary observation of muscular activity showed a different enhancement of the biceps brachii activation after the robot-assisted training. Conclusions: Robot-assisted training is as effective as conventional training on muscle tone reduction when combined with Botulinum toxin in chronic stroke patients with UL spasticity. However, only the robot-assisted UL training contributed to improving muscle strength. The single-group analysis and the qualitative inspection of sEMG data performed in the experimental group showed improvement in the agonist muscles activity during the hand-to-mouth task. Clinical Trial Registration: www.ClinicalTrials. gov, identifier: NCT03590314
Cell Wall Surface Properties of Kluyveromyces marxianus Strains From Dairy-Products

Thirty-three Kluyveromyces marxianus strains were tested for the ability to form biofilm and mat structures in YPD and whey and for cell surface hydrophobicity. To identify genes potentially involved in adhesion properties, a RT-qPCR analysis was performed. Eight strains were able to adhere on polystyrene plates in both media and formed a mature mat structure. These strains showed a different level of hydrophobicity ranging from 55 to 66% in YPD and from 69 to 81% in whey. Four K. marxianus orthologs genes (FLO11, STE12, TPK3, and WSC4), known from studies in other yeast to be involved in biofilm formation, have been studied. FLO11 and STE12 showed the highest fold changes in all conditions tested and especially in whey: 15.05 and 11.21, respectively. TPK3 was upregulated only in a strain, and WSC4 in 3 strains. In YPD, fold changes were lower than in whey with STE12 and FLO11 genes showing the highest fold changes. In mat structures FLO11 and STE12 fold changes ranged from 3.6–1.3 to 2–1.17, respectively. Further studies are necessary to better understand the role of these genes in K. marxianus adhesion ability.
A Genome-Wide Screen Identifies Factors Involved in S. aureus-Induced Human Neutrophil Cell Death and Pathogenesis

Staphylococcus aureus is a commensal organism in approximately 30% of the human population and colonization is a significant risk factor for invasive infection. As a result of this, there is a great need to better understand how S. aureus overcomes human immunity. Neutrophils are essential during the innate immune response to S. aureus, yet this microorganism uses multiple evasion strategies to avoid killing by these immune cells, perhaps the most catastrophic of which is the rapid induction of neutrophil cell death. The aim of this study was to better understand the mechanisms underpinning S. aureus-induced neutrophil lysis, and how this contributes to pathogenesis in a whole organism model of infection. To do this we screened the genome-wide Nebraska Transposon Mutant Library (NTML) in the community acquired methicillin resistant S. aureus strain, USA300, for decreased ability to induce neutrophil cell lysis. Out of 1,920 S. aureus mutants, a number of known regulators of cell lysis (including the master regulators accessory gene regulator A, agrA and Staphylococcus exoprotein expression protein S, saeS) were identified in this blinded screen, providing validity to the experimental system. Three gene mutations not previously associated with cell death: purB, lspA, and clpP were found to be significantly attenuated in their ability to induce neutrophil lysis. These phenotypes were verified by genetic transductants and complemented strains. purB and clpP were subsequently found to be necessary for bacterial replication and pathogenesis in a zebrafish embryo infection model. The virulence of the clpP mutant was restored in a neutrophil-depleted zebrafish model, suggesting the importance of ClpP in mechanisms underpinning neutrophil immunity to S. aureus. In conclusion, our work identifies genetic components underpinning S. aureus pathogenesis, and may provide insight into how this commensal organism breaches innate immune barriers during infection.
Non-destructive 3D Microtomography of Cerebral Angioarchitecture Changes Following Ischemic Stroke in Rats Using Synchrotron Radiation

A better understanding of functional changes in the cerebral microvasculature following ischemic injury is essential to elucidate the pathogenesis of stroke. Up to now, the simultaneous depiction and stereological analysis of 3D micro-architectural changes of brain vasculature with network disorders remains a technical challenge. We aimed to explore the three dimensional (3D) microstructural changes of microvasculature in the rat brain on 4, 6 hours, 3 and 18 days post-ischemia using synchrotron radiation micro-computed tomography (SRμCT) with a per pixel size of 5.2 μm. The plasticity of angioarchitecture was distinctly visualized. Quantitative assessments of time-related trends after focal ischemia, including number of branches, number of nodes, and frequency distribution of vessel diameter, reached a peak at 6 h and significantly decreased at 3 days and initiated to form cavities. The detected pathological changes were also proven by histological tests. We depicted a novel methodology for the 3D analysis of vascular repair in ischemic injury, both qualitatively and quantitatively. Cerebral angioarchitecture sustained 3D remodeling and modification during the healing process. The results might provide a deeper insight into the compensatory mechanisms of microvasculature after injury, suggesting that SRμCT is able to provide a potential new platform for deepening imaging pathological changes in complicated angioarchitecture and evaluating potential therapeutic targets for stroke.
Suppressor of Cytokine Signaling 3 (SOCS3) Degrades p65 and Regulate HIV-1 Replication

Human Immunodeficiency Virus-1 (HIV-1) is known to induce the expression of SOCS3 which is a negative feed-back regulator of inflammatory responses. Here, we demonstrate that reactivation of latent HIV-1 leads to degradation of SOCS3 at early time points. Interestingly, SOCS3 degradation following transfection of HIV-1 RNA as well as polyIC in THP-1 cells further confirmed the role of viral RNA signaling in SOCS3 biology. Degradation of SOCS3 contributes toward viral RNA induced inflammatory responses. NF-κB signaling is also induced upon HIV-1 infection which leads to the production of pro-inflammatory cytokines to control the viral spread. Further investigations revealed that SOCS3 inhibits the expression and activity of p65 by interacting with it and inducing its ubiquitin-dependent proteasomal degradation. SH2 domain was critical for SOCS3-p65 interaction and p65 degradation. We also found that expression of SOCS3 promotes HIV-1 replication. Thus, HIV-1 downregulates SOCS3 in early phase of infection to promote inflammatory responses for large production of activated cells which are suitable for viral spread and induces SOCS3 later on to limit inflammatory responses and ensure viral survival.
Differences in Characteristics of Error-Related Potentials Between Individuals With Spinal Cord Injury and Age- and Sex-Matched Able-Bodied Controls

Background: Non-invasive brain-computer interfaces (BCI) represent an emerging technology for enabling persons with impaired or lost grasping and reaching functions due to high spinal cord injury (SCI) to control assistive devices. A major drawback of BCIs is a high rate of false classifications. The robustness and performance of BCIs might be improved using cerebral electrophysiological correlates of error recognition (error-related potentials, ErrPs). As ErrPs have never been systematically examined in subjects with SCI, this study compares the characteristics of ErrPs in individuals with SCI with those of able-bodied control subjects. Methods: ErrPs at FCz and Cz were analyzed in 11 subjects with SCI (9 male, median age 28 y) and in 11 sex- and age-matched controls. Moving a shoulder joystick according to a visual cue, subjects received feedback about the match/mismatch of the performed movement. ErrPs occurring after “error”-feedback were evaluated by comparing means of voltage values within three consecutive time windows after feedback (wP1, wN1, wP2 containing peak voltages P1, N1, P2) using repeated-measurement analysis of variance. Results: In the control group, mean voltage values for the “error” and “correct” feedback condition differed significantly around N1 (FCz: 254 ms, Cz: 252 ms) and P2 (FCz: 347 ms, Cz: 345 ms), but not around P1 (FCz: 181 ms, Cz: 179 ms). ErrPs of the control and the SCI group showed similar morphology, however mean amplitudes of ErrPs were significantly smaller in individuals with SCI compared to controls for wN1 (FCz: control = −1.55 μV, SCI = −0.27 μV, p = 0.02; Cz: control = −1.03 μV, SCI = 0.11 μV, p = 0.04) and wP2 (FCz: control = 2.79 μV, SCI = 1.29 μV, p = 0.011; Cz: control = 2.12 μV, SCI = 0.81 μV, p = 0.003). Mean voltage values in wP1, wN1, and wP2 did not correlate significantly with either chronicity after or level of injury. Conclusion: The morphology of ErrPs in subjects with and without SCI is comparable, however, with reduced mean amplitude in wN1 and wP2 in the SCI group. Further studies should evaluate whether ErrP-classification can be used for online correction of false BCI-commands in individuals with SCI.
A New Panel-Based Next-Generation Sequencing Method for ADME Genes Reveals Novel Associations of Common and Rare Variants With Expression in a Human Liver Cohort

We developed a panel-based NGS pipeline for comprehensive analysis of 340 genes involved in absorption, distribution, metabolism and excretion (ADME) of drugs, other xenobiotics, and endogenous substances. The 340 genes comprised phase I and II enzymes, drug transporters and regulator/modifier genes within their entire coding regions, adjacent intron regions and 5′ and 3′UTR regions, resulting in a total panel size of 1,382 kbp. We applied the ADME NGS panel to sequence genomic DNA from 150 Caucasian liver donors with available comprehensive gene expression data. This revealed an average read-depth of 343 (range 27–811), while 99% of the 340 genes were covered on average at least 100-fold. Direct comparison of variant annotation with 363 available genotypes determined independently by other methods revealed an overall accuracy of >99%. Of 15,727 SNV and small INDEL variants, 12,022 had a minor allele frequency (MAF) below 2%, including 8,937 singletons. In total we found 7,273 novel variants. Functional predictions were computed for coding variants (n = 4,017) by three algorithms (Polyphen 2, Provean, and SIFT), resulting in 1,466 variants (36.5%) concordantly predicted to be damaging, while 1,019 variants (25.4%) were predicted to be tolerable. In agreement with other studies we found that less common variants were enriched for deleterious variants. Cis-eQTL analysis of variants with (MAF ≥ 2%) revealed significant associations for 90 variants in 31 genes after Bonferroni correction, most of which were located in non-coding regions. For less common variants (MAF < 2%), we applied the SKAT-O test and identified significant associations to gene expression for ADH1C and GSTO1. Moreover, our data allow comparison of functional predictions with additional phenotypic data to prioritize variants for further analysis.
Using Floating-Gate Memory to Train Ideal Accuracy Neural Networks

Floating-gate silicon-oxygen-nitrogen-oxygen-silicon (SONOS) transistors can be used to train neural networks to ideal accuracies that match those of floating-point digital weights on the MNIST handwritten digit data set when using multiple devices to represent a weight or within 1% of ideal accuracy when using a single device. This is enabled by operating devices in the subthreshold regime, where they exhibit symmetric write nonlinearities. A neural training accelerator core based on SONOS with a single device per weight would increase energy efficiency by <inline-formula> <tex-math notation="LaTeX">$120\times $ </tex-math></inline-formula>, operate <inline-formula> <tex-math notation="LaTeX">$2.1\times $ </tex-math></inline-formula> faster, and require <inline-formula> <tex-math notation="LaTeX">$5\times $ </tex-math></inline-formula> lower area than an optimized SRAM-based ASIC.
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities

Abstract Motivation Deep learning architectures have recently demonstrated their power in predicting DNA- and RNA-binding specificity. Existing methods fall into three classes: Some are based on convolutional neural networks (CNNs), others use recurrent neural networks (RNNs) and others rely on hybrid architectures combining CNNs and RNNs. However, based on existing studies the relative merit of the various architectures remains unclear. Results In this study we present a systematic exploration of deep learning architectures for predicting DNA- and RNA-binding specificity. For this purpose, we present deepRAM, an end-to-end deep learning tool that provides an implementation of a wide selection of architectures; its fully automatic model selection procedure allows us to perform a fair and unbiased comparison of deep learning architectures. We find that deeper more complex architectures provide a clear advantage with sufficient training data, and that hybrid CNN/RNN architectures outperform other methods in terms of accuracy. Our work provides guidelines that can assist the practitioner in choosing an appropriate network architecture, and provides insight on the difference between the models learned by convolutional and recurrent networks. In particular, we find that although recurrent networks improve model accuracy, this comes at the expense of a loss in the interpretability of the features learned by the model. Availability and implementation The source code for deepRAM is available at https://github.com/MedChaabane/deepRAM. Supplementary information Supplementary data are available at Bioinformatics online.