Evaluating Semantic Parsing against a Simple Web-based Question Answering Model

Semantic parsing shines at analyzing complex natural language that involves composition and computation over multiple pieces of evidence. However, datasets for semantic parsing contain many factoid questions that can be answered from a single web document. In this paper, we propose to evaluate semantic parsing-based question answering models by comparing them to a question answering baseline that queries the web and extracts the answer only from web snippets, without access to the target knowledge-base. We investigate this approach on COMPLEXQUESTIONS, a dataset designed to focus on compositional language, and find that our model obtains reasonable performance (35 F1 compared to 41 F1 of state-of-the-art). We find in our analysis that our model performs well on complex questions involving conjunctions, but struggles on questions that involve relation composition and superlatives.Comment: *sem 201

Accelerating the Global Aggregation of Local Explanations

Local explanation methods highlight the input tokens that have a considerable impact on the outcome of classifying the document at hand. For example, the Anchor algorithm applies a statistical analysis of the sensitivity of the classifier to changes in the token. Aggregating local explanations over a dataset provides a global explanation of the model. Such aggregation aims to detect words with the most impact, giving valuable insights about the model, like what it has learned in training and which adversarial examples expose its weaknesses. However, standard aggregation methods bear a high computational cost: a na\"ive implementation applies a costly algorithm to each token of each document, and hence, it is infeasible for a simple user running in the scope of a short analysis session. % We devise techniques for accelerating the global aggregation of the Anchor algorithm. Specifically, our goal is to compute a set of top-$k$ words with the highest global impact according to different aggregation functions. Some of our techniques are lossless and some are lossy. We show that for a very mild loss of quality, we are able to accelerate the computation by up to 30$\times$, reducing the computation from hours to minutes. We also devise and study a probabilistic model that accounts for noise in the Anchor algorithm and diminishes the bias toward words that are frequent yet low in impact

Complexity, connectivity, and duplicability as barriers to lateral gene transfer

Laterally transferred genes are shown to be less involved in protein-protein interactions, and essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent

Bridge over Troubled Water: Spelling Accuracy of Novel Phonemes in Arabic among Native Hebrew‑Speaking Pupils in a Bilingual—Arabic‑Hebrew—Elementary School

Previous studies of the Neve Shalom/Wahat al‑Salam/Oasis of Peace Bilingual School have focused mainly on the socio‑cultural and political aspects of the school. The current study explores spelling accuracy of novel phonemes. Four tasks were created for the 2nd‑4th grades for the purpose of this study, all dealing with phonemic aspects and phoneme‑grapheme correspondences. Compared with the poor results of previous studies dealing with spelling accuracy among Hebrew L1 pupils in non‑bilingual settings, the results of the current study show significantly higher scores in all grades for all the tasks. It is assumed that the most significant factor affecting higher scores as of the second grade is the unique pedagogical setting implemented at Neve Shalom a few years ago. It advocates mutual learning of L1/L2 pupils mentored by L1 teachers without translation and without separate lessons for Hebrew and Arabic speakers, as had been previously accepted at Neve Shalom, and still is in other Arabic‑Hebrew settings in Israel. The results of the current study may also indicate that early exposure to Arabic in a bilingual setting also enhances linguistic knowledge.Les recherches antérieures menées à l’école élémentaire bilingue de Neve‑Shalom avaient comme principal objectif l’étude des aspects socio‑culturels et politiques de cette école. Cette recherche‑ci a examiné l’épellation de phonèmes arabes inconnus parmi des locuteurs natifs de l’hébreu. L’étude comprenait quatre tâches destinées aux élèves de CE1‑CM1, permettant d’examiner différents aspects du savoir phonémique et des relations graphème‑phonème. En comparaison de recherches semblables au sein de locuteurs natifs de l’hébreu dans des écoles unilingues, les résultats dans cette étude étaient meilleurs dans les quatre tâches. Nous formulons l’hypothèse que la raison principale de ces excellents résultats serait à attribuer à la pédagogie unique de l’école bilingue à cette époque. Les principes de cette pédagogie étaient : un enseignement commun par une enseignante arabophone et une autre hébréophone dans chaque classe, à chaque cours, sans traduction et sans cours de langue distincts (comme cela se pratique habituellement dans la plupart des écoles bilingues). Les résultats de l’étude semblent révéler l’importance de l’exposition précoce à l’arabe dans un environnement bilingue comme moyen de renforcement du savoir linguistique des élèves.מחקרים קודמים שנעשו בבית הספר הדו-לשוני נוה שלום התמקדו בהיבטים סוציו-תרבותיים ופוליטיים בעיקר. המחקר הנוכחי בדק את סוגיית האיות של פונמות בערבית לא מוכרות בקרב דוברי עברית. המחקר כלל ארבע מטלות שיועדו לתלמידי כיתות ב’-ד’, לבדיקת היבטים שונים של ידע פונמי וקשרי גרפמה-פונמה. לעומת מחקרים דומים בקרב דוברי עברית כשפת אם בבתי ספר שאינם דו-לשוניים, התוצאות במחקר זה היו גבוהות יותר באופן מובהק בכל המטלות. החוקרים משערים שהגורם המשמעותי ביותר שתרם להישגים גבוהים אלה היה הפדגוגיה הבית ספרית הייחודית שננקטה באותה עת בבית הספר. עיקרי התפיסה היו: הוראה משותפת של מורות דוברות עברית וערבית בכל כיתה, בכל שיעור, ללא תרגום, וללא שיעורי שפה נפרדים (כפי שמקובל במרבית בתי הספר הדו-לשוניים). ממצאי המחקר עשויים להצביע על חשיבות החשיפה המוקדמת לערבית בסביבה דו-לשונית כאמצעי לחיזוק הידע הלשוני של התלמידים

Systematic identification of edited microRNAs in the human brain

Adenosine-to-inosine (A-to-I) editing modifies RNA transcripts from their genomic blueprint. A prerequisite for this process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Editing of miRNAs has the potential to add another layer of complexity to gene regulation pathways, especially if editing occurs within the miRNA–mRNA recognition site. Thus, it is of interest to study the extent of this phenomenon. Current reports in the literature disagree on its extent; while some reports claim that it may be widespread, others deem the reported events as rare. Utilizing a next-generation sequencing (NGS) approach supplemented by an extensive bioinformatic analysis, we were able to systematically identify A-to-I editing events in mature miRNAs derived from human brain tissues. Our algorithm successfully identified many of the known editing sites in mature miRNAs and revealed 17 novel human sites, 12 of which are in the recognition sites of the miRNAs. We confirmed most of the editing events using in vitro ADAR overexpression assays. The editing efficiency of most sites identified is very low. Similar results are obtained for publicly available data sets of mouse brain-regions tissues. Thus, we find that A-to-I editing does alter several miRNAs, but it is not widespread

Diffuse Facial Hyperpigmentation as a Presenting Sign of Lupus Erythematosus: Three Cases and Review of the Literature

Lupus erythematosus (LE) is an autoimmune disorder commonly affecting the skin; cutaneous lesions may indicate systemic involvement, warranting further evaluation. Photosensitivity, which may result in hyperpigmentation, is a well-known feature of the disease. In contrast, the prevalence of primary hyperpigmentation as a presenting sign of LE is not well established. Here, we compare 3 unique cases of diffuse facial hyperpigmentation as the primary manifestation of LE (cutaneous or systemic) and review previously reported cases. Our data highlight the need for considering LE in the differential diagnosis of facial hyperpigmentation and substantiate the importance of this unique lupus variant in early diagnosis and patient evaluation

The Chloroplast Envelope Protease FTSH11 – Interaction With CPN60 and Identification of Potential Substrates

FTSH proteases are membrane-bound, ATP-dependent metalloproteases found in bacteria, mitochondria and chloroplasts. The product of one of the 12 genes encoding FTSH proteases in Arabidopsis, FTSH11, has been previously shown to be essential for acquired thermotolerance. However, the substrates of this protease, as well as the mechanism linking it to thermotolerance are largely unknown. To get insight into these, the FTSH11 knockout mutant was complemented with proteolytically active or inactive variants of this protease, tagged with HA-tag, under the control of the native promoter. Using these plants in thermotolerance assay demonstrated that the proteolytic activity, and not only the ATPase one, is essential for conferring thermotolerance. Immunoblot analyses of leaf extracts, isolated organelles and sub-fractionated chloroplast membranes localized FTSH11 mostly to chloroplast envelopes. Affinity purification followed by mass spectrometry analysis revealed interaction between FTSH11 and different components of the CPN60 chaperonin. In affinity enrichment assays, CPN60s as well as a number of envelope, stroma and thylakoid proteins were found associated with proteolytically inactive FTSH11. Comparative proteomic analysis of WT and knockout plants, grown at 20°C or exposed to 30°C for 6 h, revealed a plethora of upregulated chloroplast proteins in the knockout, some of them might be candidate substrates. Among these stood out TIC40, which was stabilized in the knockout line after recovery from heat stress, and three proteins that were found trapped in the affinity enrichment assay: the nucleotide antiporter PAPST2, the fatty acid binding protein FAP1 and the chaperone HSP70. The consistent behavior of these four proteins in different assays suggest that they are potential FTSH11 substrates

Examining the synergistic effects of a cognitive control video game and a home-based, self-administered non-invasive brain stimulation on alleviating depression : the DiSCoVeR trial protocol

Funding Information: Open Access funding enabled and organized by Projekt DEAL. The DisCoVeR project is funded by ERA NET NEURON. The NEURON ‘Network of European Funding for Neuroscience Research is established under the organization of the ERA-NET ‘European Research Area Networks’ of the European Commission. National funding agencies are the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung [BMBF]) for LMU Munich, the Ministry of Health (MOH) for HUJI and Hadassah, the Swiss National Science Foundation (SNSF) for UNIGE and EPFL and the State Education and Development Agency (VIAA) of Latvia for RSU. Funding Information: This project was funded by the European Research Area Network (ERA-NET) NEURON 2018 Mental Disorders program. Publisher Copyright: © 2022, The Author(s).Enhanced behavioral interventions are gaining increasing interest as innovative treatment strategies for major depressive disorder (MDD). In this study protocol, we propose to examine the synergistic effects of a self-administered home-treatment, encompassing transcranial direct current stimulation (tDCS) along with a video game based training of attentional control. The study is designed as a two-arm, double-blind, randomized and placebo-controlled multi-center trial (ClinicalTrials.gov: NCT04953208). At three study sites (Israel, Latvia, and Germany), 114 patients with a primary diagnosis of MDD undergo 6 weeks of intervention (30 × 30 min sessions). Patients assigned to the intervention group receive active tDCS (anode F3 and cathode F4; 2 mA intensity) and an action-like video game, while those assigned to the control group receive sham tDCS along with a control video game. An electrode-positioning algorithm is used to standardize tDCS electrode positioning. Participants perform their designated treatment at the clinical center (sessions 1-5) and continue treatment at home under remote supervision (sessions 6-30). The endpoints are feasibility (primary) and safety, treatment efficacy (secondary, i.e., change of Montgomery-Åsberg Depression Rating Scale (MADRS) scores at week six from baseline, clinical response and remission, measures of social, occupational, and psychological functioning, quality of life, and cognitive control (tertiary). Demonstrating the feasibility, safety, and efficacy of this novel combined intervention could expand the range of available treatments for MDD to neuromodulation enhanced interventions providing cost-effective, easily accessible, and low-risk treatment options.ClinicalTrials.gov: NCT04953208.publishersversionPeer reviewe