ferret: a Framework for Benchmarking Explainers on Transformers

Many interpretability tools allow practitioners and researchers to explain Natural Language Processing systems. However, each tool requires different configurations and provides explanations in different forms, hindering the possibility of assessing and comparing them. A principled, unified evaluation benchmark will guide the users through the central question: which explanation method is more reliable for my use case? We introduce ferret, an easy-to-use, extensible Python library to explain Transformer-based models integrated with the Hugging Face Hub. It offers a unified benchmarking suite to test and compare a wide range of state-of-the-art explainers on any text or interpretability corpora. In addition, ferret provides convenient programming abstractions to foster the introduction of new explanation methods, datasets, or evaluation metrics

Brivaracetam as Early Add-On Treatment in Patients with Focal Seizures: A Retrospective, Multicenter, Real-World Study

Introduction In randomized controlled trials, add-on brivaracetam (BRV) reduced seizure frequency in patients with drug-resistant focal epilepsy. Most real-world research on BRV has focused on refractory epilepsy. The aim of this analysis was to assess the 12-month effectiveness and tolerability of adjunctive BRV when used as early or late adjunctive treatment in patients included in the BRIVAracetam add-on First Italian netwoRk Study (BRIVAFIRST). Methods BRIVAFIRST was a 12-month retrospective, multicenter study including adult patients prescribed adjunctive BRV. Effectiveness outcomes included the rates of sustained seizure response, sustained seizure freedom, and treatment discontinuation. Safety and tolerability outcomes included the rate of treatment discontinuation due to adverse events (AEs) and the incidence of AEs. Data were compared for patients treated with add-on BRV after 1-2 (early add-on) and >= 3 (late add-on) prior antiseizure medications. Results A total of 1029 patients with focal epilepsy were included in the study, of whom 176 (17.1%) received BRV as early add-on treatment. The median daily dose of BRV at 12 months was 125 (100-200) mg in the early add-on group and 200 (100-200) in the late add-on group (p < 0.001). Sustained seizure response was reached by 97/161 (60.3%) of patients in the early add-on group and 286/833 (34.3%) of patients in the late add-on group (p < 0.001). Sustained seizure freedom was achieved by 51/161 (31.7%) of patients in the early add-on group and 91/833 (10.9%) of patients in the late add-on group (p < 0.001). During the 1-year study period, 29 (16.5%) patients in the early add-on group and 241 (28.3%) in the late add-on group discontinued BRV (p = 0.001). Adverse events were reported by 38.7% and 28.5% (p = 0.017) of patients who received BRV as early and late add-on treatment, respectively. Conclusion Brivaracetam was effective and well tolerated both as first add-on and late adjunctive treatment in patients with focal epilepsy

Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes

Progressive myoclonus epilepsies (PMEs) comprise a group of clinically and genetically heterogeneous rare diseases. Over 70% of PME cases can now be molecularly solved. Known PME genes encode a variety of proteins, many involved in lysosomal and endosomal function. We performed whole-exome sequencing (WES) in 84 (78 unrelated) unsolved PME-affected individuals, with or without additional family members, to discover novel causes. We identified likely disease-causing variants in 24 out of 78 (31%) unrelated individuals, despite previous genetic analyses. The diagnostic yield was significantly higher for individuals studied as trios or families (14/28) versus singletons (10/50) (OR = 3.9, p value = 0.01, Fisher's exact test). The 24 likely solved cases of PME involved 18 genes. First, we found and functionally validated five heterozygous variants in NUS1 and DHDDS and a homozygous variant in ALG10, with no previous disease associations. All three genes are involved in dolichol-dependent protein glycosylation, a pathway not previously implicated in PME. Second, we independently validate SEMA6B as a dominant PME gene in two unrelated individuals. Third, in five families, we identified variants in established PME genes; three with intronic or copy-number changes (CLN6, GBA, NEU1) and two very rare causes (ASAH1, CERS1). Fourth, we found a group of genes usually associated with developmental and epileptic encephalopathies, but here, remarkably, presenting as PME, with or without prior developmental delay. Our systematic analysis of these cases suggests that the small residuum of unsolved cases will most likely be a collection of very rare, genetically heterogeneous etiologies.Peer reviewe

Dopamine Receptor Activation Increases HIV Entry into Primary Human Macrophages

Macrophages are the primary cell type infected with HIV in the central nervous system, and infection of these cells is a major component in the development of neuropathogenesis and HIV-associated neurocognitive disorders. Within the brains of drug abusers, macrophages are exposed to increased levels of dopamine, a neurotransmitter that mediates the addictive and reinforcing effects of drugs of abuse such as cocaine and methamphetamine. In this study we examined the effects of dopamine on HIV entry into primary human macrophages. Exposure to dopamine during infection increased the entry of R5 tropic HIV into macrophages, irrespective of the concentration of the viral inoculum. The entry pathway affected was CCR5 dependent, as antagonizing CCR5 with the small molecule inhibitor TAK779 completely blocked entry. The effect was dose-dependent and had a steep threshold, only occurring above 108 M dopamine. The dopamine-mediated increase in entry required dopamine receptor activation, as it was abrogated by the pan-dopamine receptor antagonist flupenthixol, and could be mediated through both subtypes of dopamine receptors. These findings indicate that the effects of dopamine on macrophages may have a significant impact on HIV pathogenesis. They also suggest that drug-induced increases in CNS dopamine may be a common mechanism by which drugs of abuse with distinct modes of action exacerbate neuroinflammation and contribute to HIV-associated neurocognitive disorders in infected drug abusers

Streptococcus dysgalactiae subsp. equisimilis: two cases of tonsillitis

We described two case reports of S. dysgalactiae subsp. equisimilis tonsillitis occurred from January 2005 to January 2007, among patients who come to our observation during these two years. These patients are paradigmatic of some conditions: adult age, absence of underlying diseases, outbreak of similar pharyngo-tonsillar sympyomatology, unsuccessful oral penicillin therapy, isolation of S. dysgalactiae subsp. equisimilis from throat swab, complete recovery after oral beta-lattamic antibiotic therapy, but total clearance of the microorganism only after oral macrolides administrations. Thus, the intracellular localization of S. dysgalactiae subsp. equismilis, could be in charge of the failure of beta-lattamic antibiotics therapy

Isolation of multidrug-resistant Enterobacter cloacae and comparison among clavulanate-tazobactam and sulbactam-synergy by using a double-disk synergy test

False negative results of double-disk synergy test with Enterobacter cloacae are common, as AmpC-enzymes may mask ESBLs elaboration. We increased the sensitivity of the method by using both clavulanate- and tazobactam/sulbactam; hence, we suggest to use all the three inhibitors to screen ESBLs in AmpC ß-lactamases producing organisms

Effects of probiotic Lactiplantibacillus plantarum IMC 510 supplementation on metabolic factors in otherwise healthy overweight and obese individuals

Aims: Probiotic supplementation approach offers the possibility to shape the gut microbiota (GM), enabling the development of innovative formulations able to improve intestinal well-being and consequently the related body weight modulation and energy metabolism. In the present clinical study, a new potential probiotic supplement based on Lactiplantibacillus plantarum IMC 510 was studied for weight management. Methods and Results: Quantitative characterization by qPCR of representative bacterial groups of GM was used to determine the microbiota modulation at different supplementation periods. Furthermore, measurement of the endpoints linked to weight control (body mass index, body weight, waist circumference) was assessed. Specific questionnaires to evaluate the impact on psychological and physiological point of view were performed. Results showed that after 90 days, Lact. plantarum IMC 510 supplementation brought an improvement in endpoints linked to weight control and healthy status, although no significant changes in the microbiota composition were reported for analysed bacterial groups, except for Lactobacillus spp. and Bifidobacterium spp. Conclusions: We concluded that Lact. plantarum IMC 510 supplementation could be an interesting tool for weight management. More studies are needed to understand the impact on GM, for example, evaluating the production of short-chain fatty acids, since their important role in dietary metabolism. Further research is necessary to better elucidate the relationship between GM and overweight and the mechanism of action by which Lact. plantarum IMC 510 modifies body weight. Significance and Impact of the Study: However, these promising outcomes represent a clear advantage of probiotic supplementation and identify a new potential probiotic as a novel and safe therapeutic approach in the obesity prevention and management

Effects of repetitive transcranial magnetic stimulation on spike-and-wave discharges

Aim of this study was to evaluate the effect of 5 Hz-suprathreshold repetitive transcranial magnetic stimulation (rTMS) on the duration of the spike-and-wave discharges (SWDs) in a patient presenting idiopathic absence seizures. At the moment of the study the patient presented a mild blunting of consciousness due to the high frequency of absences and EEG recordings showed sub-continuous, generalized, symmetrical and synchronous 3c/s SWDs, petit mal status. Trains of 10 stimuli (120% resting motor threshold) were delivered at 5 Hz frequency at the beginning of the SWDs. 5 Hz-rTMS trains significantly changed the EEG activity by reducing the duration of SWDs without changing the intervals between two consecutive discharges. rTMS had not significant after-effects on the epileptic activity and patient's clinical status. Despite the limitations of a single case report, our neurophysiological findings suggest that 5 Hz-suprathreshold rTMS delivered in short trains induces a transitory interference of the ongoing epileptic activity. (c) 2006 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved

Femoral Prosthesis Infection by Rhodotorula mucilaginosa▿

This case report is a case history of a femoral prosthesis infection caused by Rhodotorula mucilaginosa in a human immunodeficiency virus patient. Though the pathogenicity of this organism for bone tissue has been previously reported, this is the first reported case of an orthopedic prosthesis infection by this species of the genus Rhodotorula