Treatise on Hearing: The Temporal Auditory Imaging Theory Inspired by Optics and Communication

A new theory of mammalian hearing is presented, which accounts for the auditory image in the midbrain (inferior colliculus) of objects in the acoustical environment of the listener. It is shown that the ear is a temporal imaging system that comprises three transformations of the envelope functions: cochlear group-delay dispersion, cochlear time lensing, and neural group-delay dispersion. These elements are analogous to the optical transformations in vision of diffraction between the object and the eye, spatial lensing by the lens, and second diffraction between the lens and the retina. Unlike the eye, it is established that the human auditory system is naturally defocused, so that coherent stimuli do not react to the defocus, whereas completely incoherent stimuli are impacted by it and may be blurred by design. It is argued that the auditory system can use this differential focusing to enhance or degrade the images of real-world acoustical objects that are partially coherent. The theory is founded on coherence and temporal imaging theories that were adopted from optics. In addition to the imaging transformations, the corresponding inverse-domain modulation transfer functions are derived and interpreted with consideration to the nonuniform neural sampling operation of the auditory nerve. These ideas are used to rigorously initiate the concepts of sharpness and blur in auditory imaging, auditory aberrations, and auditory depth of field. In parallel, ideas from communication theory are used to show that the organ of Corti functions as a multichannel phase-locked loop (PLL) that constitutes the point of entry for auditory phase locking and hence conserves the signal coherence. It provides an anchor for a dual coherent and noncoherent auditory detection in the auditory brain that culminates in auditory accommodation. Implications on hearing impairments are discussed as well.Comment: 603 pages, 131 figures, 13 tables, 1570 reference

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

BACKGROUND Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS). RESULTS We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently. CONCLUSION Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define

Multidifferential study of identified charged hadron distributions in ZZ-tagged jets in proton-proton collisions at s=\sqrt{s}=13 TeV

Jet fragmentation functions are measured for the first time in proton-proton collisions for charged pions, kaons, and protons within jets recoiling against a $Z$ boson. The charged-hadron distributions are studied longitudinally and transversely to the jet direction for jets with transverse momentum 20 $< p_{\textrm{T}} < 100$ GeV and in the pseudorapidity range $2.5 < \eta < 4$. The data sample was collected with the LHCb experiment at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 1.64 fb$^{-1}$. Triple differential distributions as a function of the hadron longitudinal momentum fraction, hadron transverse momentum, and jet transverse momentum are also measured for the first time. This helps constrain transverse-momentum-dependent fragmentation functions. Differences in the shapes and magnitudes of the measured distributions for the different hadron species provide insights into the hadronization process for jets predominantly initiated by light quarks.Comment: All figures and tables, along with machine-readable versions and any supplementary material and additional information, are available at https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-013.html (LHCb public pages

Study of the B−→Λc+Λˉc−K−B^{-} \to \Lambda_{c}^{+} \bar{\Lambda}_{c}^{-} K^{-} decay

The decay $B^{-} \to \Lambda_{c}^{+} \bar{\Lambda}_{c}^{-} K^{-}$ is studied in proton-proton collisions at a center-of-mass energy of $\sqrt{s}=13$ TeV using data corresponding to an integrated luminosity of 5 $\mathrm{fb}^{-1}$ collected by the LHCb experiment. In the $\Lambda_{c}^+ K^{-}$ system, the $\Xi_{c}(2930)^{0}$ state observed at the BaBar and Belle experiments is resolved into two narrower states, $\Xi_{c}(2923)^{0}$ and $\Xi_{c}(2939)^{0}$, whose masses and widths are measured to be $$m(\Xi_{c}(2923)^{0}) = 2924.5 \pm 0.4 \pm 1.1 \,\mathrm{MeV}, \\ m(\Xi_{c}(2939)^{0}) = 2938.5 \pm 0.9 \pm 2.3 \,\mathrm{MeV}, \\ \Gamma(\Xi_{c}(2923)^{0}) = \phantom{000}4.8 \pm 0.9 \pm 1.5 \,\mathrm{MeV},\\ \Gamma(\Xi_{c}(2939)^{0}) = \phantom{00}11.0 \pm 1.9 \pm 7.5 \,\mathrm{MeV},$$ where the first uncertainties are statistical and the second systematic. The results are consistent with a previous LHCb measurement using a prompt $\Lambda_{c}^{+} K^{-}$ sample. Evidence of a new $\Xi_{c}(2880)^{0}$ state is found with a local significance of $3.8\,\sigma$, whose mass and width are measured to be $2881.8 \pm 3.1 \pm 8.5\,\mathrm{MeV}$ and $12.4 \pm 5.3 \pm 5.8 \,\mathrm{MeV}$, respectively. In addition, evidence of a new decay mode $\Xi_{c}(2790)^{0} \to \Lambda_{c}^{+} K^{-}$ is found with a significance of $3.7\,\sigma$. The relative branching fraction of $B^{-} \to \Lambda_{c}^{+} \bar{\Lambda}_{c}^{-} K^{-}$ with respect to the $B^{-} \to D^{+} D^{-} K^{-}$ decay is measured to be $2.36 \pm 0.11 \pm 0.22 \pm 0.25$, where the first uncertainty is statistical, the second systematic and the third originates from the branching fractions of charm hadron decays.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-028.html (LHCb public pages

GENCODE reference annotation for the human and mouse genomes

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.National Human Genome Research Institute of the National Institutes of Healt

Complex acoustic environments: concepts, methods and auditory perception

Thesis by publication.Bibliography: pages 191-215.1. Introduction -- 2. The ambisonic recordings of typical environments (ARTE) database -- 3. Conversational speech levels and signal-to-noise ratios in realistic conditions -- 4. Complex acoustic environments: review, framework and subjective model -- 5. Exploring the ability of listeners to identify events in realistic environments -- 6. General discussion and conclusions -- Appendices.In everyday life, the ears constantly receive information from the environment that is carried by sound waves. Despite the uncontrolled nature of this information, normal hearing listeners can make sense of the unstructured sounds. In contrast, hearing has mostly been studied using acoustic stimuli that are rigidly controlled. The difference between understanding such artificial stimuli and real-world hearing has produced the distinction of ’complex acoustic environments‘ (CAEs) – a catch-all term for everything that the laboratory-based stimuli are not. However, an exact definition has been elusive, despite growing use in hearing research – especially in research focusing on hearing-impaired individuals, who struggle communicating in cocktail-party like scenarios. In this work, several aspects of CAEs were studied with the intention to understand where the complexity lies. The work consists of four main parts in manuscript form. The first paper presents the Ambisonic Recordings of Typical Environments (ARTE) database, which contains 3D recordings of everyday scenarios. These were the primary stimuli used in all subsequent parts of this work. In the second paper, the speech and noise levels of real conversations were measured at two distances between talkers. The third paper reviews the origins and uses of the CAE concept in literature and presents a framework that summarizes and defines the characteristics that can drive complexity in a given environment. A subset of these characteristics were tested by 65 listeners who listened to the ARTE scenes (also with target speech), while answering a three-stage questionnaire. The analysis revealed that listeners’ perceived complexity is associated with both the loudness and the variability of the scenes. The final paper analyzes the responses of listeners to an open-ended auditory scene analysis task using ARTE, and the observed limitations are discussed. A concluding discussion dissects how the auditory system deals with realistic amounts of acoustic information.1 online resource (xix, 215 pages : illustrations

Complex acoustic environments: concepts, methods and auditory perception

Thesis by publication.Bibliography: pages 191-215.1. Introduction -- 2. The ambisonic recordings of typical environments (ARTE) database -- 3. Conversational speech levels and signal-to-noise ratios in realistic conditions -- 4. Complex acoustic environments: review, framework and subjective model -- 5. Exploring the ability of listeners to identify events in realistic environments -- 6. General discussion and conclusions -- Appendices.In everyday life, the ears constantly receive information from the environment that is carried by sound waves. Despite the uncontrolled nature of this information, normal hearing listeners can make sense of the unstructured sounds. In contrast, hearing has mostly been studied using acoustic stimuli that are rigidly controlled. The difference between understanding such artificial stimuli and real-world hearing has produced the distinction of ’complex acoustic environments‘ (CAEs) – a catch-all term for everything that the laboratory-based stimuli are not. However, an exact definition has been elusive, despite growing use in hearing research – especially in research focusing on hearing-impaired individuals, who struggle communicating in cocktail-party like scenarios. In this work, several aspects of CAEs were studied with the intention to understand where the complexity lies. The work consists of four main parts in manuscript form. The first paper presents the Ambisonic Recordings of Typical Environments (ARTE) database, which contains 3D recordings of everyday scenarios. These were the primary stimuli used in all subsequent parts of this work. In the second paper, the speech and noise levels of real conversations were measured at two distances between talkers. The third paper reviews the origins and uses of the CAE concept in literature and presents a framework that summarizes and defines the characteristics that can drive complexity in a given environment. A subset of these characteristics were tested by 65 listeners who listened to the ARTE scenes (also with target speech), while answering a three-stage questionnaire. The analysis revealed that listeners’ perceived complexity is associated with both the loudness and the variability of the scenes. The final paper analyzes the responses of listeners to an open-ended auditory scene analysis task using ARTE, and the observed limitations are discussed. A concluding discussion dissects how the auditory system deals with realistic amounts of acoustic information.1 online resource (xix, 215 pages : illustrations