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Article ; Online: Automatic recognition of second language speech-in-noise.

Kim, Seung-Eun / Chernyak, Bronya R / Seleznova, Olga / Keshet, Joseph / Goldrick, Matthew / Bradlow, Ann R

JASA express letters

2024 Volume 4, Issue 2

Abstract: Measuring how well human listeners recognize speech under varying environmental conditions (speech intelligibility) is a challenge for theoretical, technological, and clinical approaches to speech communication. The current gold standard-human ... ...

Abstract	Measuring how well human listeners recognize speech under varying environmental conditions (speech intelligibility) is a challenge for theoretical, technological, and clinical approaches to speech communication. The current gold standard-human transcription-is time- and resource-intensive. Recent advances in automatic speech recognition (ASR) systems raise the possibility of automating intelligibility measurement. This study tested 4 state-of-the-art ASR systems with second language speech-in-noise and found that one, whisper, performed at or above human listener accuracy. However, the content of whisper's responses diverged substantially from human responses, especially at lower signal-to-noise ratios, suggesting both opportunities and limitations for ASR--based speech intelligibility modeling.
MeSH term(s)	Humans ; Speech Perception/physiology ; Noise/adverse effects ; Speech Intelligibility/physiology ; Speech Recognition Software ; Recognition, Psychology
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ISSN	2691-1191
ISSN (online)	2691-1191
DOI	10.1121/10.0024877
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: DiffAR

Benita, Roi / Elad, Michael / Keshet, Joseph

Denoising Diffusion Autoregressive Model for Raw Speech Waveform Generation

2023

Abstract: Diffusion models have recently been shown to be relevant for high-quality speech generation. Most work has been focused on generating spectrograms, and as such, they further require a subsequent model to convert the spectrogram to a waveform (i.e., a ... ...

Abstract	Diffusion models have recently been shown to be relevant for high-quality speech generation. Most work has been focused on generating spectrograms, and as such, they further require a subsequent model to convert the spectrogram to a waveform (i.e., a vocoder). This work proposes a diffusion probabilistic end-to-end model for generating a raw speech waveform. The proposed model is autoregressive, generating overlapping frames sequentially, where each frame is conditioned on a portion of the previously generated one. Hence, our model can effectively synthesize an unlimited speech duration while preserving high-fidelity synthesis and temporal coherence. We implemented the proposed model for unconditional and conditional speech generation, where the latter can be driven by an input sequence of phonemes, amplitudes, and pitch values. Working on the waveform directly has some empirical advantages. Specifically, it allows the creation of local acoustic behaviors, like vocal fry, which makes the overall waveform sounds more natural. Furthermore, the proposed diffusion model is stochastic and not deterministic; therefore, each inference generates a slightly different waveform variation, enabling abundance of valid realizations. Experiments show that the proposed model generates speech with superior quality compared with other state-of-the-art neural speech generation systems.
Keywords	Computer Science - Sound ; Computer Science - Computation and Language ; Electrical Engineering and Systems Science - Audio and Speech Processing
Subject code	410
Publishing date	2023-10-02
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impact of dental clearance on bacteremia in hematopoietic cell transplantation.

Zadik, Yehuda / Krasovsky, Andrey / Cohen, Refael / Rettman, Andra / Aframian, Doron J / Avni, Batia / Peretz, Avi / Keshet, Naama

Oral diseases

2024

Language	English
Publishing date	2024-02-29
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	1290529-x
ISSN	1601-0825 ; 1354-523X
ISSN (online)	1601-0825
ISSN	1354-523X
DOI	10.1111/odi.14911
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Article ; Online: Local Alpha1-Antitrypsin Accelerates the Healing of Tympanic Membrane Perforation in Mice.

El-Saied, Sabri / Amar, Amit / Kaplan, Daniel M / Shitrit, Rivka / Kaminer, Benyamin M / Keshet, Aharon / Lewis, Eli C

The Laryngoscope

2024

Abstract: Background: Most tympanic membrane (TM) perforations heal spontaneously, but 10%-20% remain chronic and might lead to impaired hearing and recurrent middle ear infections. Alpha1-antitrypsin (AAT) is a circulating tissue-protective protein that is ... ...

Abstract	Background: Most tympanic membrane (TM) perforations heal spontaneously, but 10%-20% remain chronic and might lead to impaired hearing and recurrent middle ear infections. Alpha1-antitrypsin (AAT) is a circulating tissue-protective protein that is elevated under inflammatory conditions and is currently indicated for genetic AAT deficiency. Recently, AAT has been shown to promote tissue remodeling and inflammatory resolution. Objective: This study aimed to examine the effects of local clinical-grade AAT treatment on tissue repair in a mouse model of acute traumatic TM perforation. Methods: Wild-type mice underwent unilateral TM perforation and were either left untreated or treated locally with human AAT (9 × 10 Results: There were no adverse reactions in hAAT-treated ears throughout the study period. Compared with untreated animals, TM closure occurred earlier in the treated group (days until full closure, median: 4 and 9, respectively). According to gene expression analysis, VEGF, TGFβ, and collagen-5A1 were induced earlier in AAT-treated mice (day 4-5 compared with day 9). Additionally, IL-10 expression levels were higher and IL-6 levels were lower in treated versus untreated mice. Conclusion: A local tissue environment rich in AAT promotes early tissue repair in a perforated TM model both macroscopically and molecularly. Studies are underway to examine TM functionality and recombinant AAT formulations for micro-dosing in the format of a single local application. Level of evidence: NA Laryngoscope, 2024.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	80180-x
ISSN	1531-4995 ; 0023-852X
ISSN (online)	1531-4995
ISSN	0023-852X
DOI	10.1002/lary.31454
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Article ; Online: Differentiation of uniparental human embryonic stem cells into granulosa cells reveals a paternal contribution to gonadal development.

Keshet, Gal / Bar, Shiran / Sarel-Gallily, Roni / Yanuka, Ofra / Benvenisty, Nissim / Eldar-Geva, Talia

Stem cell reports

2023 Volume 18, Issue 4, Page(s) 817–828

Abstract: Genomic imprinting underlies the mammalian requirement for sexual reproduction. Nonetheless, the relative contribution of the two parental genomes during human development is not fully understood. Specifically, a fascinating question is whether the ... ...

Abstract	Genomic imprinting underlies the mammalian requirement for sexual reproduction. Nonetheless, the relative contribution of the two parental genomes during human development is not fully understood. Specifically, a fascinating question is whether the formation of the gonad, which holds the ability to reproduce, depends on equal contribution from both parental genomes. Here, we differentiated androgenetic and parthenogenetic human pluripotent stem cells (hPSCs) into ovarian granulosa-like cells (GLCs). We show that in contrast to biparental and androgenetic cells, parthenogenetic hPSCs present a reduced capacity to differentiate into GLCs. We further identify the paternally expressed gene IGF2 as the most upregulated imprinted gene upon differentiation. Remarkably, while IGF2 knockout androgenetic cells fail to differentiate into GLCs, the differentiation of parthenogenetic cells supplemented with IGF2 is partly rescued. Thus, our findings unravel a surprising essentiality of genes that are only expressed from the paternal genome to the development of the female reproductive system.
MeSH term(s)	Animals ; Humans ; Female ; Human Embryonic Stem Cells ; Genomic Imprinting ; Cell Differentiation/genetics ; Pluripotent Stem Cells ; Parthenogenesis/genetics ; Granulosa Cells ; Mammals
Language	English
Publishing date	2023-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2023.03.004
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Article ; Online: EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq.

Sarel-Gallily, Roni / Keshet, Gal / Kinreich, Shay / Haim-Abadi, Guy / Benvenisty, Nissim

Nature protocols

2023 Volume 18, Issue 12, Page(s) 3881–3917

Abstract: ... as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d. ...

Abstract	Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
MeSH term(s)	Humans ; Female ; Genomic Imprinting ; DNA Methylation ; RNA-Seq ; X Chromosome Inactivation/genetics ; Chromosomes
Language	English
Publishing date	2023-11-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-023-00898-5
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Article ; Online: Familial oral lichen planus: A new risk group for oral cancer?

Czerninski, Rakefet / Awadieh, Zinat / Feldman, Svetlana / Keshet, Naama / Zlotogorski, Abraham / Ramot, Yuval

Oral diseases

2023

Abstract: Objective: The familial type of oral lichen planus (OLP) is rare, with a paucity of data regarding its clinical significance. Our objective was to characterize patients with familial OLP.: Methods: Families with at least two members diagnosed with ... ...

Abstract	Objective: The familial type of oral lichen planus (OLP) is rare, with a paucity of data regarding its clinical significance. Our objective was to characterize patients with familial OLP. Methods: Families with at least two members diagnosed with OLP were included. Clinical and demographic data and medical history were recorded. Results: Twenty families, 19 Jewish and 1 Arab, were identified. Of the Jewish families, 57.8% were non-Ashkenazi, originating mainly from central Asia. Of those with OLP there were 14 males and 23 females with an average age of 49.1. Dyslipidemia, cardiovascular, and thyroid disorders (27.7%, 22.2%, and 16.6%, respectively) were the most common comorbidities. Five patients from five distinct families had oral cancer, two with second primary. Conclusions: To the best of our knowledge, this is the largest study describing familial OLP. The predominant and common ethnicity of the families with multiple members diagnosed with OLP may imply an ethnic tendency. The higher tendency of hypothyroidism and the high percentage of OSCC among familial OLP patients might be connected to familial OLP and the latter suggests that this population is predisposed to malignant transformation. Thus, this group should be considered as a high-risk group.
Language	English
Publishing date	2023-11-20
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	1290529-x
ISSN	1601-0825 ; 1354-523X
ISSN (online)	1601-0825
ISSN	1354-523X
DOI	10.1111/odi.14805
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Article ; Online: Arginine and the metabolic regulation of nitric oxide synthesis in cancer.

Keshet, Rom / Erez, Ayelet

Disease models & mechanisms

2018 Volume 11, Issue 8

Abstract: Nitric oxide (NO) is a signaling molecule that plays important roles in diverse biological processes and thus its dysregulation is involved in the pathogenesis of various disorders. In cancer, NO has broad and sometimes dichotomous roles; it is involved ... ...

Abstract	Nitric oxide (NO) is a signaling molecule that plays important roles in diverse biological processes and thus its dysregulation is involved in the pathogenesis of various disorders. In cancer, NO has broad and sometimes dichotomous roles; it is involved in cancer initiation and progression, but also restricts cancer proliferation and invasion, and contributes to the anti-tumor immune response. The importance of NO in a range of cellular processes is exemplified by its tight spatial and dosage control at multiple levels, including via its transcriptional, post-translational and metabolic regulation. In this Review, we focus on the regulation of NO via the synthesis and availability of its precursor, arginine, and discuss the implications of this metabolic regulation for cancer biology and therapy. Despite the established contribution of NO to cancer pathogenesis, the implementation of NO-related cancer therapeutics remains limited, likely due to the challenge of targeting and inducing its protective functions in a cell- and dosage-specific manner. A better understanding of how arginine regulates the production of NO in cancer might thus support the development of anti-cancer drugs that target this key metabolic pathway, and other metabolic pathways involved in NO production.
MeSH term(s)	Animals ; Antineoplastic Agents/therapeutic use ; Arginine/metabolism ; Humans ; Models, Biological ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Nitric Oxide/biosynthesis
Chemical Substances	Antineoplastic Agents ; Nitric Oxide (31C4KY9ESH) ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2018-08-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1754-8411
ISSN (online)	1754-8411
DOI	10.1242/dmm.033332
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Article ; Online: From actin waves to mechanism and back

Carsten Beta / Leah Edelstein-Keshet / Nir Gov / Arik Yochelis

eLife, Vol

How theory aids biological understanding

2023 Volume 12

Abstract: Actin dynamics in cell motility, division, and phagocytosis is regulated by complex factors with multiple feedback loops, often leading to emergent dynamic patterns in the form of propagating waves of actin polymerization activity that are poorly ... ...

Abstract	Actin dynamics in cell motility, division, and phagocytosis is regulated by complex factors with multiple feedback loops, often leading to emergent dynamic patterns in the form of propagating waves of actin polymerization activity that are poorly understood. Many in the actin wave community have attempted to discern the underlying mechanisms using experiments and/or mathematical models and theory. Here, we survey methods and hypotheses for actin waves based on signaling networks, mechano-chemical effects, and transport characteristics, with examples drawn from Dictyostelium discoideum, human neutrophils, Caenorhabditis elegans, and Xenopus laevis oocytes. While experimentalists focus on the details of molecular components, theorists pose a central question of universality: Are there generic, model-independent, underlying principles, or just boundless cell-specific details? We argue that mathematical methods are equally important for understanding the emergence, evolution, and persistence of actin waves and conclude with a few challenges for future studies.
Keywords	actin ; waves ; pattern formation ; bifurcation ; systems modeling ; chemical signaling ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Exploring the Effect of Ethnicity on Chronic Orofacial Pain: A Comparative Study of Jewish and Arab Israeli Patients.

Yanko, Robert / Badran, Yaara / Leibovitz, Shirley / Sharav, Yair / Vered, Yuval / Keshet, Naama / Rettman, Andra / Aframian, Doron J / Haviv, Yaron

Healthcare (Basel, Switzerland)

2023 Volume 11, Issue 14

Abstract: The relationship between ethnicity and chronic pain has been studied worldwide. The population of Israel includes two main ethnic groups, 75% Jews and 21% Arabs. The purpose of this study was to compare orofacial chronic pain characteristics and ... ...

Abstract	The relationship between ethnicity and chronic pain has been studied worldwide. The population of Israel includes two main ethnic groups, 75% Jews and 21% Arabs. The purpose of this study was to compare orofacial chronic pain characteristics and treatment outcomes between Jewish and Arab Israeli citizens. Two hundred patients admitted to the Orofacial Pain Clinic at Hebrew University-Hadassah School of Dental Medicine between 2017 and 2022 were selected randomly for this historical cohort study. Our cohort included 159 (79.5%) Jews and 41 (20.5%) Arabs. Twenty-six pain-related variables were compared of which only two differed significantly between the two groups, awakening due to pain and mean muscle sensitivity; both indicators were higher in the Arab group (
Language	English
Publishing date	2023-07-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2721009-1
ISSN	2227-9032
ISSN	2227-9032
DOI	10.3390/healthcare11141984
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