Biology subjects

Inbar, M.

Publications and source records attributed to Inbar, M..

6 recordsLinked to original sources

bioRxiv2026

Improved deconvolution of circulating tumor DNA from ultra-low-pass whole-genome methylation sequencing using CelFiE-ISH

Liquid biopsy using ultra-low-pass whole-genome sequencing (ULP-WGS, [~]0.25x coverage) is a promising tool to detect circulating tumor DNA (ctDNA) for cancer management, and the use of the native Oxford Nanopore (ONT) sequencing platform adds DNA methylation to the set of detectable features. Here, we test the performance of methylation-based cell-type deconvolution in ULP-WGS samples from diverse epithelial malignancies and investigate several new computational strategies using our CelFiE-ISH deconvolution framework. We find that incorporating larger numbers of markers restricted to the epithelial cell lineage can reduce the cancer fraction limit of detection down to 1.7-3.1%, matching or exceeding the 3% floor of established copy-number alteration (CNA) benchmarks. Our study provides a useful strategy for analysis of ULP-WGS ONT data and indicates that marker selection remains a key challenge for analyzing methylation-based cancer datasets.

genomics↗

bioRxiv2024

A universal of speech timing: Intonation units form low frequency rhythms and balance cross-linguistic syllable rate variability

Intonation units (IUs) are a universal building-block of human speech. They are found cross-linguistically and are tied to important language functions such as the pacing of information in discourse and swift turn-taking. We study the rate of IUs in 48 languages from every continent and from 27 distinct language families. Using a novel analytic method to annotate natural speech recordings, we identify a low-frequency rate of IUs across the sample, with a peak at 0.6 Hz, and little variation between sexes or across the life span. We find that IU rate is only weakly related to speech rate quantified at the syllable level (SR), and crucially, that cross-linguistic variation in IU rate is smaller than cross-linguistic variation in SR. Since SR was shown to be inversely related to information density quantified at the syllable level, we suggest that across languages, IUs are more balanced than syllables in their information content.

animal behavior and cognition↗

bioRxiv2023

Intonation Units in spontaneous speech evoke a neural response

Spontaneous speech is produced in chunks called Intonation Units (IUs). IUs are defined by a set of prosodic cues and occur in all human languages. Linguistic theory suggests that IUs pace the flow of information and serve as a window onto the dynamic focus of attention in speech processing. IUs provide a promising and hitherto unexplored theoretical framework for studying the neural mechanisms of communication, thanks to their universality and their consistent temporal structure across different grammatical and socio-cultural conditions. In this article, we identify a neural response unique to the boundary defined by the IU. We measured the EEG of participants who listened to different speakers recounting an emotional life event. We analyzed the speech stimuli linguistically, and modeled the EEG response at word offset using a GLM approach. We find that the EEG response to IU-final words differs from the response to IU-nonfinal words when acoustic boundary strength is held constant. To the best of our knowledge, this is the first time this is demonstrated in spontaneous speech under naturalistic listening conditions, and under a theoretical framework that connects the prosodic chunking of speech, on the one hand, with the flow of information during communication, on the other. Finally, we relate our findings to the body of research on rhythmic brain mechanism in speech processing by comparing the topographical distributions of neural speech tracking in model-predicted and empirical EEG. This qualitative comparison suggests that IU-related neural activity contributes to the previously characterized delta-band neural speech tracking.

neuroscience↗

bioRxiv2022

The dynamics of speciation in the gall-forming aphid Geoica spp. within and among Pistacia host tree species

Trees of the genus Pistacia serve as obligate hosts for gall-forming aphids (Hemiptera, Aphididae, Fordini). Each aphid species induces a characteristic gall on a single Pistacia host species. The genus Geoica (Fordini) induce similar spherical closed galls on the lower side of the leaflets midvein, on different Pistacia species. Two species of Pistacia trees that harbor Geoica galls grow naturally in Israel: P. palaestina and P. atlantica. We analyzed the phylogeny and the genetic structure of the Geoica species complex in Israel, and assessed the genetic differentiation and the level of host plant specificity of the aphids between P. atlantica and P. palaestina. We found that the splitting of the genus between P. atlantica and P. palaestina is estimated to have occurred 24-25 Ma (the Oligocene/Miocene boundary). Five different haplotypes suggesting five different species have been further speciating among Geoica spp., galling on P. atlantica, and an additional three species, on P. palaestina. Accession Numbers (COI sequences)MW452548 - Pp-Q-7d-Gamla - Haplotype-VI MW452549 - Pp-Q-10b-Gamla - Haplotype-VII MW452550 - Pp-A-1a-Mezar - Haplotype-VII MW452551 - Pp-S-6c-Sasa - Haplotype-VI MW452552 - Pp-New Hermon-2-5 - Haplotype-VIII MW452553 - Pa-Q-10a-II Gamla - Haplotype-IV MW452554 - Pa-Q-5d Gamla - Haplotype-II MW452555 - Pa-A-2f Mezar - Haplotype-IV MW452556 - Pa-E-13 Anafa - Haplotype-III MW452557 - Pa-K-10a Adolam - Haplotype-IV MW452558 - Pa-K-3a Adolam - Haplotype-II MW452559 - Pa-N-2a Nizana - Haplotype-I MW452560 - Pa-Z-1-3 Hazeva - Haplotype-I MW452561 - Pa-SL-3-3 Jordan-Sela - Haplotype-V

genetics↗

bioRxiv2020

Biological activity of Ajuga iva extracts against the African cotton leafworm Spodoptera littoralis

The African cotton leafworm Spodoptera littoralis, a major crop pest worldwide, is controlled by chemical insecticides, leading to serious resistance problems. Ajuga plants contain phytoecdysteroids (analogs of arthropod steroid hormones that regulate metamorphoses) and clerodanes (diterpenoids exhibiting antifeedant activity). We analyzed phytoecdysteroids and clerodanes in leaf extracts of the Israeli Ajuga iva by LC-TOF-MS and TLC, and their efficiency at reducing S. littoralis fitness. Castor bean leaves were smeared with an aqueous suspension of dried methanolic crude extract of phytoecdysteroid and clerodanes from A. iva leaves (50, 100 and 250 {micro}g/{micro}l). First and third instars of S. littoralis larvae were fed with 1 treated leaf for 3 and 4 days, respectively. Mortality, larval weight gain, relative growth rate and survival were compared to feeding on control leaves. To evaluate and localize A. iva crude leaf extract activity in the insect gut, we used DAPI and phalloidin staining. Crude extract of A. iva leaves (50, 100 and 250 {micro}g/{micro}l) significantly increased mortality of first instar S. littoralis larvae (36%, 70% and 87%, respectively) compared to controls (6%). Third instar larval weight gain decreased significantly (by 52%, 44% and 30%, respectively), as did relative growth rate (-0.05 g/g day, compared to the relevant controls). S. littoralis larvae were further affected at later stages, with few survivors. Insect-gut staining showed that 250 {micro}g/{micro}l crude leaf extract reduces gut size, with relocation of nuclei and abnormal actin-filament organization. Our results demonstrate the potential of A. iva extract for alternative, environmentally safe insect-pest control. Key MessageInsects cause severe damage to numerous crops and their control relies on pesticides. Green control is becoming increasingly popular due to concerns about the negative impacts of pesticides on the environment. Phytoecdysteroids are found in Ajuga plants and affect a wide range of insects at very low concentrations. Here we demonstrate that crude extract from Ajuga iva alters the development of Spodoptera littoralis. Phytoecdysteroids may therefore be beneficial in IPM programs.

plant biology↗

bioRxiv2019

Sequences of Intonation Units Form a 1 Hz Rhythm

Studies of speech processing investigate the relationship between temporal structure in speech stimuli and neural activity. Despite clear evidence that the brain tracks speech at low frequencies (~1 Hz), it is not well understood what linguistic information gives rise to this rhythm. Here, we harness linguistic theory to draw attention to Intonation Units (IUs), a fundamental prosodic unit of human language, and characterize their temporal structure as captured in the speech envelope, an acoustic representation relevant to the neural processing of speech. IUs are defined by a specific pattern of syllable delivery, together with resets in pitch and articulatory force. Linguistic studies of spontaneous speech indicate that this prosodic segmentation paces new information in language use across diverse languages. Therefore, IUs provide a universal structural cue for the cognitive dynamics of speech production and comprehension. We study the relation between IUs and periodicities in the speech envelope, applying methods from investigations of neural synchronization. Our sample includes recordings from every-day speech contexts of over 100 speakers and six languages. We find that sequences of IUs form a consistent low-frequency rhythm and constitute a significant periodic cue within the speech envelope. Our findings allow to predict that IUs are utilized by the neural system when tracking speech, and the methods we introduce facilitate testing this prediction given physiological data.

neuroscience↗