cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Inference of genetic effects via Approximate Message Passing
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people.
Epistylis irregularis Stiller 1940
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis irregularis

description: Epistylis irregularis Stiller, 1940
Locality of the original isolate: USA
Habit: epibiont
Host: Cyclopidae
Reference: Stiller (1940)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on pages 282-283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
Additional file 1: Figure S1. of Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon
Creators: name: Amselem, Joelle
name: Vigouroux, Marielle
name: Oberhaensli, Simone
name: Brown, James
name: Bindschedler, Laurence
name: Skamnioti, Pari
name: Wicker, Thomas
name: Spanu, Pietro
name: Quesneville, Hadi
name: SacristĂĄn, Soledad
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Alignment of nucleotide sequences of Avra10 gene and Satine ORF1. (PDF 131 kb)
Recent Advances in Scalable Energy-Efficient and Trustworthy Spiking Neural Networks: From Algorithms to Technology
Creators: Souvik Kundu
Rui-Jie Zhu
Akhilesh Jaiswal
Peter A. Beerel
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Neuromorphic computing and, in particular, spiking neural networks (SNNs) have become an attractive alternative to deep neural networks for a broad range of signal processing applications, processing static and/or temporal inputs from different sensory modalities, including audio and vision sensors. In this paper, we start with a description of recent advances in algorithmic and optimization innovations to efficiently train and scale low-latency, and energy-efficient spiking neural networks (SNNs) for complex machine learning applications. We then discuss the recent efforts in algorithm-architecture co-design that explores the inherent trade-offs between achieving high energy-efficiency and low latency while still providing high accuracy and trustworthiness. We then describe the underlying hardware that has been developed to leverage such algorithmic innovations in an efficient way. In particular, we describe a hybrid method to integrate significant portions of the model’s computation within both memory components as well as the sensor itself. Finally, we discuss the potential path forward for research in building deployable SNN systems identifying key challenges in the algorithm-hardware-application co-design space with an emphasis on trustworthiness.
MOESM1 of EpiMINE, a computational program for mining epigenomic data
Creators: name: SriGanesh Jammula
name: Pasini, Diego
Publisher: name: Figshare
Year: 2016
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Computational Biology

description: Additional file 1. Contains two supplementary figures and corresponding legends: Figure S1 provides a graphical description of the quantification workflow. Figure S2 provides a comparison of differences in different modes of quantification, annotation of differentially regulated ROI and quantification of different ChIPs in Suz12 binding regions.
Epistylis jaerae Precht 1935
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis jaerae

description: Epistylis jaerae Precht, 1935
Locality of the original isolate: Baltic countries
Habit: epibiont
Host: Jaera marina
Reference: Precht (1935)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
ARCHITECTURAL UNDERSTANDING OF UTOPIANISM
Creators: name: Farshad, Armin
Publisher: name: Zenodo
Year: 2023
Subjects: Utopia
Ideal City
Future Architecture

description: ARCHITECTURAL UNDERSTANDING OF UTOPIANISM presentation under the supervision of Dr. Asli Varon presented at Bahcesehir University in Jan 2023 by Armin Farshad

Abstract : 

To reach a better world and society, utopianism is one of the approaches that many experts follow. In contrast, many others believe that this is a nonprofitable effort to escape from reality and responsibilities. Meanwhile, in 2010, Reinhold Martin presented a critical view of Utopianism as a revision to extract valuable and positive elements from utopian traditions. The direct translation of utopias into real life might face risks and dangers that theorists and practitioners should consider when examining ideological practices to find a solution for contemporary issues. Utopian imaginary and real contexts have various relationships. Different modes and platforms of relations need to be considered to perceive this difference. Most utopianism frameworks concentrate on varieties including formal, functional, and conceptual categories (Levitas, 2013). This research aims to answer the main research question of “How can bring more reality into the conceptuality of utopias?” and to find the architectural utopianism conceptual framework. By investigating existing data and related articles, utopianism is understood, and then concentrating on the architectural features of the utopia derived from examples and utopias of experts.

Keywords: Utopia, Ideal City, Future Architecture
Training Ultra-Low-Latency Spiking Neural Networks from Scratch
Creators: Gourav Datta
Zeyu Liu
Peter Beerel
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Spiking Neural networks (SNN) have emerged as an attractive spatio-temporal computing paradigm for a wide range of low-power vision tasks. However, state-of-the-art (SOTA) SNN models either incur multiple time steps which hinder their deployment in real-time use cases or increase the training complexity significantly. To mitigate this concern, we present a training framework (from scratch) for SNNs with ultra-low (down to 1) time steps that leverages the Hoyer regularizer. We calculate the threshold for each BANN layer as the Hoyer extremum of a clipped version of its activation map. The clipping value is determined through training using gradient descent with our Hoyer regularizer. We evaluate the efficacy of our training framework on large-scale vision tasks, including traditional and event-based image recognition and object detection. Our experiments demonstrate up to 34× increase in compute efficiency with a marginal accuracy/mAP drop compared to non-spiking networks. Finally, we implement our framework in the Lava-DL library, thereby enabling the deployment of our SNN models in the Loihi neuromorphic chip.
Epistylis jaroschenkow Shubernetzki 1978
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis jaroschenkow

description: Epistylis jaroschenkow i Shubernetskii, 1978
Locality of the original isolate: Russia
Habit: epibiont
Host: Oligochaeta
References: Shubernetskii (1978); Schödel (2018)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
title: "Ritratto d'uomo", Antonello di Antonio detto Antonello da Messina, inv. 396 (ITA/EN)
title: Scheda catalogo digitale Borghese
titleType: AlternativeTitle
Creators: name: Riccobono, Emiliano
name: Galleria Borghese
Publisher: name: Galleria Borghese
Year: 2024

description: Pubblicazione delle schede delle opere conservate nel museo ed estratte dal catalogo digitale di Galleria Borghese, nelle due versioni esistenti online, in italiano e inglese.

Collegamento al catalogo digitale:

ITA: https://www.collezionegalleriaborghese.it/

EN: https://www.collezionegalleriaborghese.it/en
Additional file 2: of Relationship between’ patient’s rights charter’ and patients’ satisfaction in gynecological hospitals
Creators: name: Farzianpour, Fereshteh
name: Foroushani, Abbas Rahimi
name: Niusha Shahidi Sadeghi
name: Saeede Ansari Nosrati
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Marine Biology
subject: Science Policy

description: Questionnaire for patient,s satisfaction. (DOCX 46 kb)
Additional file 7: Figure S4. of Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses
Creators: name: Troy, Niamh
name: Elysia Hollams
name: Holt, Patrick
name: Bosco, Anthony
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Biological pathways enriched in the WGCNA modules in the CD4 T cell responses to HDM from HDM sensitized atopics without asthma. Data analysis by Cluster Profiler using reactome database. (PDF 72Â kb)
Dryinus gharaeii Olmi 2005
Creators: name: Derafshan, Hossein Ali
name: Rakhshani, Ehsan
name: Olmi, Massimo
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ampulicidae
Dryinus
Dryinus gharaeii

description: Dryinus gharaeii Olmi, 2005
Material examined. Holotype, ♀, IRAN: Ilam Prov., Chogasabz Region, Ilam, 1.IX.2003, Babak Gharaei leg. (MOLC).
Distribution. Iran: Ilam (Olmi 2005).
Hosts. Unknown.
Remarks. Dryinus gharaeii is very different from the most common Western Palaearctic species of group 3, D. niger (Kieffer, 1904), based on the morphology of the chela, as follows:
1 Enlarged claw with one row of proximal and medial lamellae (Fig. 2 A)............................. D. gharaeii Olmi
- Enlarged claw with one or more small lamellae situated near distal apex (Fig. 165 in Olmi 1999)........ D. niger (Kieffer)
description: Published as part of Derafshan, Hossein Ali, Rakhshani, Ehsan & Olmi, Massimo, 2016, A review of the genus Dryinus Latreille, 1804 (Hymenoptera, Chrysidoidea, Dryinidae) from Iran, with description of a new species, pp. 411-420 in Zootaxa 4117 (3) on page 412, DOI: 10.11646/zootaxa.4117.3.8, http://zenodo.org/record/267649
Epistylis jaworowskii Kahl 1935
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis jaworowskii

description: Epistylis jaworowskii Kahl, 1935
Locality of the original isolate: Germany
Habit: epibiont
Host: Stechmucken larvae
Reference: Kahl (1935)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
Additional file 1: of Quantitative analysis of insulin-like growth factor 2 receptor and insulin-like growth factor binding proteins to identify control mechanisms for insulin-like growth factor 1 receptor phosphorylation
Creators: name: Tian, Dan
name: Mitchell, Isaiah
name: Kreeger, Pamela
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology

description: Detailed methods including the full set of differential equations and assumptions used in the model, experimental methods for determination of several rates and initial conditions, experimental methods for validation of the IGF2R knockdown and overexpression, and tables of both experimentally-determined and model-fitted rates and initial conditions. (DOCX 80Â kb)
EFFICIENT VIDEO AND AUDIO PROCESSING WITH LOIHI 2
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Loihi 2 is a fully event-based neuromorphic processor that supports a wide range of synaptic connectivity configurations and temporal neuron dynamics. Loihi 2's temporal and event-based paradigm is naturally well-suited to processing data from an event-based sensor, such as a Dynamic Vision Sensor (DVS) or a Silicon Cochlea. However, this begs the question: How general are signal processing efficiency gains on Loihi 2 versus conventional computer architectures? For instance, how efficiently can Loihi 2 process a \textit{standard} temporal input datastream, such as a frame-based video or a streaming audio waveform? In this work, we address this question by designing and benchmarking efficient audio and video applications on Loihi 2. We utilize the wide variety of powerful dynamics supported by the flexible neuron programming on Loihi 2, such as Leaky Integrate and Fire, Adaptive Leaky Integrate and Fire, Resonate and Fire, and Sigma-Delta encapsulation. We find that these powerful neuron dynamics, when matched with appropriate synaptic connectivity such as hardware-accelerated convolutions, enable highly efficient processing for a variety of tasks on standard audio and video on Loihi 2.
BNMTRANS: A BRAIN NETWORK SEQUENCE-DRIVEN MANIFOLD-BASED TRANSFORMER FOR COGNITIVE IMPAIRMENT DETECTION USING EEG
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Early identification of mild cognitive impairment (MCI) is crucial for the prevention of Alzheimer’s disease. As neurodegenerative
diseases progress, the synchronous activity observed in electroencephalography (EEG) - which indicates functional connectivity -
may change due to the deterioration of the neural system. Thus, developing geometric learning to decode the functional brain structure is essential. Techniques such as graph neural networks and Riemannian manifolds have demonstrated potential in analyzing data with non-Euclidean properties. However, existing methodologies remain insufficient for detecting cognitive impairment effectively. This paper proposes the Brain Network sequence-driven Manifoldbased Transformer (BNMTrans) to identify MCI patterns from EEG data. BNMTrans leverages its strengths by extracting features from sequential brain networks through the self-attention mechanism, guided by the geometric correlations within the Riemannian manifold. Benefiting from the integration of long-term temporal dynamics and structural relationships, this approach outperforms others in EEG feature comparisons and state-of-the-art evaluations based on clinical data from 89 subjects (46 MCI/43 healthy controls) at a local hospital. Our work has significance for both MCI clinical management and technical progression in the EEG field.
Οι συνέπειες της πανδημίας στην ψυχική υγεία των παιδιών και των εφήβων
Creators: name: Σαμψωνίδου, Ιωάννα Ανέστη
Publisher: name: Aristotle University of Thessaloniki
Year: 2024
Subjects: Ψυχική υγεία, Έφηβοι
Αγχώδεις διαταραχές
Κατάθλιψη
Ενδοοικογενειακή βία
Κακοποίηση
Mental Health, Adolescents
Anxiety Disorders
Depression
Domestic Violence
Abuse

description: Η παρούσα συστηματική ανασκόπηση στοχεύει στη μελέτη των συνεπειών της πανδημίας COVID-19 στην ψυχική υγεία των παιδιών και των εφήβων. Για την επιλογή των κατάλληλων μελετών αξιοποιήθηκαν οι βάσεις δεδομένων PubMed και Google Scholar και καθορίστηκαν τα κριτήρια ένταξης και αποκλεισμού από την ανασκόπηση. Συμπεριλήφθηκαν μελέτες που είχαν γραφτεί στην Αγγλική γλώσσα, με δείγμα που ξεπερνούσε τους διακόσιους (200) συμμετέχοντες, αποτελούμενο από παιδιά, εφήβους και νεαρούς ενήλικες 11 έως 21 ετών. Επίσης, τα άρθρα που αξιοποιήθηκαν ήταν αυτά στα οποία υπήρχε πρόσβαση στο πλήρες κείμενο. Η ηλεκτρονική έρευνα κατέληξε σε δύο χιλιάδες τετρακόσιες ογδόντα (2480) καταγραφές, από τις οποίες τελικά επιλέχθηκαν οι δεκαοκτώ (18) που πληρούσαν όλα τα κριτήρια ένταξης. Οι έρευνες που τελικά συμπεριλήφθηκαν στην παρούσα συστηματική ανασκόπηση είχαν διεξαχθεί τη χρονολογική περίοδο 2020-2023. Από τις δεκαοκτώ (18) δημοσιεύσεις οι δεκατέσσερις (14) κατέληξαν ότι κατά τη διάρκεια της πανδημίας του COVID-19 αυξήθηκαν τα ποσοστά των αγχώδων διαταραχών και των καταθλιπτικών συμπτωμάτων στους εφήβους, και ταυτόχρονα παρατηρήθηκε όξυνση της ενδοοικογενειακής βίας και της κακοποίησης.
description: This study aims to investigate the consequences of COVID-19 in mental health of children, adolescents and young adults. Databases, PubMed and Google Scholar were used for the selection of the appropriate studies and the inclusion and exclusion criteria were determined. Inclusion criteria included that studies had to be written in English, the study sample had to be larger than 200 participants aged between 11 to 21, consisting of adolescents, and access to the full text of the study was required. The electronic search resulted in 2480 papers, from which eighteen studies were selected, which met the inclusion criteria. The specific papers were published between 2020 and 2023. Of the eighteen publications, fourteen found a positive association of the COVID-19 pandemic with anxiety disorders, depression and domestic violence. According to the results of most researches we could conclude that during the COVID-19 pandemic the percentage of anxiety disorders and depressive symptoms in teenagers increased. Moreover, during the pandemic there was an exacerbation of domestic violence and abuse.
Epistylis kolbi Nenninger 1948
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis kolbi

description: Epistylis kolbi Nenninger, 1948
Locality of the original isolate: Germany
Habit: epibiont
Host: crustaceans
Reference: Nenninger (1948)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
Towards ASR robust spoken language understanding through in-context learning with word confusion networks
Creators: Kevin Everson
Yi Gu
Huck Yang
Prashanth Gurunath Shivakumar
Guan-Ting Lin
Jari Kolehmainen
Ivan Bulyko
Ankur Gandhe
Shalini Ghosh
Wael Hamza
Hung-yi Lee
Ariya Rastrow
Andreas Stolcke
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: In the realm of spoken language understanding (SLU), numerous natural language understanding (NLU) methodologies have been adapted by supplying large language models (LLMs) with transcribed speech instead of conventional written text. In real-world scenarios, prior to input into an LLM, an automated speech recognition (ASR) system generates an output transcript hypothesis, where inherent errors can degrade subsequent SLU tasks. Here we introduce a method that utilizes the ASR system’s lattice output instead of relying solely on the top hypothesis, aiming to encapsulate speech ambiguities and enhance SLU outcomes. Our in-context learning experiments, covering spoken question answering and intent classification, underline the LLM’s resilience to noisy speech transcripts with the help of word confusion networks from lattices, bridging the SLU performance gap between using the top ASR hypothesis and an oracle upper bound. Additionally, we delve into the LLM’s robustness to varying ASR performance conditions and scrutinize the aspects of in-context learning which prove the most influential.
Common-slope modeling of late reverberation
Creators: Georg Götz
Sebastian J. Schlecht
Ville Pulkki
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: The decaying sound field in rooms is typically described by energy decay functions (EDFs). Late reverberation can deviate considerably from the ideal diffuse field, for example, in multiple connected rooms or non-uniform absorption material distributions. This paper proposes the common-slope model of late reverberation. The model describes spatial and directional late reverberation as linear combinations of exponential decays called common slopes. Its fundamental idea is that common slopes have decay times that are invariant across space and direction, while their amplitudes vary across both. We explore different approaches for determining the common slopes for large EDF sets describing different source-receiver configurations of the same environment. Among the presented approaches, the k-means clustering of decay times is the most general. Our evaluation shows that the common-slope model introduces only a small error between the modeled and the true EDF, while being considerably more compact than the traditional multi-exponential model. The amplitude variations of the common slopes yield interpretable room acoustic analyses. The common-slope model has potential applications in all fields relying on late reverberation models, such as source separation, dereverberation, echo cancellation, and parametric spatial audio rendering.
Epistylis lalinensis Qi 2009
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis lalinensis

description: Epistylis lalinensis Qi et al., 2009
Locality of the original isolate: China
Habit: epibiont
Host: Bellamya
Reference: Qi et al. (2009)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
title: Explaining Variation in Individual Aging, Its Sources, and Consequences: A Comprehensive Conceptual Model of Human Aging
Creators: name: Rothermund, Klaus
name: Englert, Christoph
name: Gerstorf, Denis
Publisher: name: Humboldt-Universität zu Berlin
Year: 2023
Subjects: subject: Buffering mechanisms
subject: Psychological adaptation
subject: Biological sources of aging
subject: Subjective experiences of aging
subject: Aging
subject: 150 Psychologie

description: We define aging as a characteristic deterioration in one (or more) observable attributes of an organism that typically occurs during later life. With this narrow functional definition, we gain the freedom to separate aging from other processes of age-related change (e.g., maturation, growth, illness, terminal decline). We introduce a structural model that distinguishes between (1) the phenomenon of aging, (2) the subjective experience of aging, (3) sources of aging, and (4) consequences of aging. A core focus of the model is on the role of buffering mechanisms of biological repair and personal adaptation that regulate the relations between sources of aging, aging proper, and its consequences. The quality and level of functioning of these buffering mechanisms also varies across the life span, which directly affects the sources of aging, resulting in either resilience against or accelerated aging, and thus can be considered to be a major source of the variation in aging processes among different individuals. External factors comprising attributes of the physical environment and sociocultural characteristics are considered as contexts in which aging occurs. These contextual factors are assumed to feed into the various components of the model. Our model provides an interdisciplinary account of human aging, its sources and consequences, and also its subjective experience, by integrating biological, psychological, lifestyle, and sociocultural factors, and by specifying their interrelations and interactions. The model provides a comprehensive understanding of individual human aging, its underlying processes, and modulating factors. It allows for the derivation of empirically testable hypotheses, and it helps practitioners to identify elements that lend themselves to targeted intervention efforts aimed at increasing the resilience of individuals against aging and buffering its negative consequences.
title: Gaze Behavior Reveals Expectations of Potential Scene Changes
Creators: name: Roth, Nicolas
name: McLaughlin, Jasper
name: Obermayer, Klaus
name: Rolfs, Martin
Publisher: name: Humboldt-Universität zu Berlin
Year: 2024
Subjects: subject: top-down attention
subject: static vs. dynamic
subject: animacy
subject: free-viewing
subject: real-world scenes
subject: spatiotemporal expectations
subject: 150 Psychologie

description: This publication is with permission of the rights owner (Sage) freely accessible.
description: Even if the scene before our eyes remains static for some time, we might explore it differently compared with how we examine static images, which are commonly used in studies on visual attention. Here we show experimentally that the top-down expectation of changes in natural scenes causes clearly distinguishable gaze behavior for visually identical scenes. We present free-viewing eye-tracking data of 20 healthy adults on a new video dataset of natural scenes, each mapped for its potential for change (PfC) in independent ratings. Observers looking at frozen videos looked significantly more often at the parts of the scene with a high PfC compared with static images, with substantially higher interobserver coherence. This viewing difference peaked right before a potential movement onset. Established concepts like object animacy or salience alone could not explain this finding. Images thus conceal experience-based expectations that affect gaze behavior in the potentially dynamic real world.
Dynamics of EEG Microstates Change Across the Spectrum of Disorders of Consciousness
Creators: name: Manasova, Dragana
name: Sanz Perl, Yonatan
name: Bruno, Nicolas Marcelo
name: Valente, Melanie
name: Rohaut, Benjamin
name: Tagliazucchi, Enzo
name: Naccache, Lionel
name: Raimondo, Federico
name: Sitt, Jacobo D.
Publisher: name: Forschungzentrum Jülich
Year: 2024

description: doi:10.1101/2024.05.30.596582
description: As a response to the environment and internal signals, brain networks reorganize on asub-second scale. To capture this reorganization in patients with disorders ofconsciousness and understand their residual brain activity, we investigated thedynamics of electroencephalography (EEG) microstates. We analyze EEG microstatemarkers to quantify the periods of semi-stable topographies and the large-scalecortical networks they may reflect. To achieve this, EEG samples are clustered intofour groups and then fit back into each time sample. We then obtain a time series ofmaps with different frequencies of occurrence and duration. One such occurrence of amap with a given duration is called a microstate. The goal of this work is to study thedynamics of these topographical patterns across patients with disorders ofconsciousness. Using the microstate time series, we calculate static and dynamicmarkers. In contrast to the static, the dynamic metrics depend on the specific temporalsequences of the maps. The static measure Ratio of Total Time covered (RTT) showsdifferences between healthy controls and patients, however, no differences wereobserved between the groups of patients. In contrast, some dynamic markers captureinter-patient group differences. The dynamic markers we investigated are MeanMicrostate Durations (MMD), Microstate Duration Variances (MDV), MicrostateTransition Matrices (MTM), and Entropy Production (EP). The MMD and MDVdecrease with the state of consciousness, whereas the MTM non-diagonal transitionsand EP increase. In other words, DoC patients have slower and closer to equilibrium(time-reversible) brain dynamics. In conclusion, static and dynamic EEG microstatemetrics differ across consciousness levels, with the latter capturing the subtitlerdifferences between groups of patients with disorders of consciousness.
Hydrometra argentina Berg 1879
Creators: name: Cianferoni, Fabio
name: Buzzetti, Filippo Maria
Publisher: name: Zenodo
Year: 2012
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Hydrometridae
Hydrometra
Hydrometra argentina

description: Hydrometra argentina Berg, 1879
Hydrometra argentina Berg 1879: 182.
Hydrometra mensor White 1879: 267.
Limnobates chilensis Reed 1901: 70.
Hydrometra kirkaldyana Torre-Bueno 1926: 104. Hydrometra husseyi Torre-Bueno 1926: 111. H. argentina: Moreira et al. 2009: 70.
Material examined. ECUADOR: Manabi, Puerto Lopez, Aguas Blancas, ex aguas sulfureas, 24.XI.2006, G. Onore legit, 1 3 macropterous, FMB.
Notes. Described from Argentina, this species is widespread in South and Central America. This is the first record of this species in Ecuador.
description: Published as part of Cianferoni, Fabio & Buzzetti, Filippo Maria, 2012, The genus Hydrometra Latreille in Ecuador with description of a new species (Hemiptera: Heteroptera: Gerromorpha: Hydrometridae), pp. 55-62 in Zootaxa 3274 on page 56, DOI: 10.5281/zenodo.213988
Hydrometra caraiba Guerin-Meneville 1857
Creators: name: Cianferoni, Fabio
name: Buzzetti, Filippo Maria
Publisher: name: Zenodo
Year: 2012
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Hydrometridae
Hydrometra
Hydrometra caraiba

description: Hydrometra caraiba Guérin-Méneville, 1857
Hydrometra caraiba Guérin-Méneville 1857: 413. Hydrometra agenor Kirkaldy 1902: 280. Hydrometra championiana Torre-Bueno 1926: 119. H. agenor: Torre-Bueno 1926: 124.
H. agenor: Hungerford & Evans 1934: 101. H. caraiba: Drake & Lauck 1959: 50.
H. caraiba: Nieser 1970: 143.
H. caraiba: Froeschner 1981: 39.
H. caraiba: Moreira et al. 2009: 72.
H. caraiba: Heckman 2011: 261.
Material examined. ECUADOR: Esmeraldas, Montalvo, La Mayronga, 95 m, 0°53’27,2”N 79°13’2,5”W, 14- 17.XI.2004, F.M. Buzzetti & G. Carotti legit, 1 3 macropterous, FMB.
Notes. Kirkaldy (1902) described H. agenor from Guayaquil, but Drake & Lauck (1959) synonymized it with H. caraiba. Widespread from the Caribbean to South America.
description: Published as part of Cianferoni, Fabio & Buzzetti, Filippo Maria, 2012, The genus Hydrometra Latreille in Ecuador with description of a new species (Hemiptera: Heteroptera: Gerromorpha: Hydrometridae), pp. 55-62 in Zootaxa 3274 on page 56, DOI: 10.5281/zenodo.213988
Hydrometra williamsi Hungerford & Evans 1934
Creators: name: Cianferoni, Fabio
name: Buzzetti, Filippo Maria
Publisher: name: Zenodo
Year: 2012
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Hydrometridae
Hydrometra
Hydrometra williamsi

description: Hydrometra williamsi Hungerford & Evans, 1934
Hydrometra williamsi Hungerford & Evans 1934: 97. H. williamsi: Drake & Lauck 1959: 52.
H. williamsi: Froeschner 1981: 39.
H. williamsi: Heckman 2011: 263.
Material examined. ECUADOR: Napo, WP 10, E. S. Yasuni transecto, 2-5.V.2002, F.M. Buzzetti legit, 1 3 apterous, FMB.
Notes. Known only from Ecuador.
description: Published as part of Cianferoni, Fabio & Buzzetti, Filippo Maria, 2012, The genus Hydrometra Latreille in Ecuador with description of a new species (Hemiptera: Heteroptera: Gerromorpha: Hydrometridae), pp. 55-62 in Zootaxa 3274 on page 56, DOI: 10.5281/zenodo.213988
VOXTLM: UNIFIED DECODER-ONLY MODELS FOR CONSOLIDATING SPEECH RECOGNITION, SYNTHESIS AND SPEECH, TEXT CONTINUATION TASKS
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: We propose a decoder-only language model, VoxtLM, that can perform four tasks: speech recognition, speech synthesis, text generation, and speech continuation. VoxtLM integrates text vocabulary with discrete speech tokens from self-supervised speech features and uses special tokens to enable multitask learning. Compared to a single-task model, VoxtLM exhibits a significant improvement in speech synthesis, with improvements in both speech intelligibility from 28.9 to 5.6 and objective quality from 2.68 to 3.90. VoxtLM also improves speech generation and speech recognition performance over the single-task counterpart. Further, VoxtLM is trained with publicly available data and training recipes and model checkpoints are open-sourced to make fully reproducible work.
title: Antimicrobial Activity Screening of Recombinant and Synthetic Varasin a Defensin from the Hard Tick Dermacentor variabilis Against Various Bacteria
Creators: name: Sharp, Julia A.
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2007

description: Hematophagous arthropods, such as ticks and mosquitoes, rely on their innate immune system for defense against pathogens ingested in a blood meal as well as those acquired through injury. In response to pathogen recognition, the production of antimicrobial peptides, such as defensin, is typically upregulated. Varisin, a defensin, is thought to be a key component in the immunocompetence of the hard tick D. variabilis against Borrelia burgdorferi, the causative agent of Lyme disease. To study the antimicrobial effects of varisin, recombinant varisin was expressed by both insect cells and E coli. Purification of the protein followed by enterokinase treatment yielded a protein identified by Western blotting as varisin. However, neither recombinant protein was bactericidal against M. luteus, a bacterium with known susceptibility to varisin. The lack of activity is possibly the result of varisin aggregates forming prior to their interaction with the target cell. Synthetic varisin was shown to inhibit the growth of 13 out of 14 Gram-positive bacteria and 2 out of 20 Gram-negative bacteria via well-diffusion and microtiter inhibition assays. Studies of varisin are essential to further our understanding of the innate immune response as well as providing possible insight into treatment or preventative measures for bacterial illness.
Epistylis laxipes Dumas 1930
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis laxipes

description: Epistylis laxipes Dumas, 1930
Locality of the original isolate: France
Habit: epibiont
Host: Planorbis
Reference: Dumas (1930)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
Additional file 5: of Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development
Creators: name: VenĂ¸, Morten
name: Hansen, Thomas
name: VenĂ¸, Susanne
name: Clausen, Bettina
name: Grebing, Manuela
name: Finsen, Bente
name: Holm, Ida
name: JĂ¸Rgen Kjems
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Hematology
subject: 110309 Infectious Diseases
subject: Plant Biology

description: RT-PCR validation of hot-spot circRNA isoforms. RT-PCR with divergent primers showing multiple circRNA isoforms for the host genes TMEFF1, NDFIP2 and TLK1. Gel images show the sizes of back-spliced amplicons from RT-PCR. On the right, the expected size of circRNAs from RNA-seq is shown, with font size indicating general expression level. (PDF 203 kb)
AUGSUMM: TOWARDS GENERALIZABLE SPEECH SUMMARIZATION USING SYNTHETIC LABELS FROM LARGE LANGUAGE MODELS
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: Abstractive speech summarization (SSUM) aims to generate humanlike summaries from speech. Given variations in information captured
and phrasing, recordings can be summarized in multiple ways. Therefore, it is more reasonable to consider a probabilistic distribution
of all potential summaries rather than a single summary. However, conventional SSUM models are mostly trained and evaluated
with a single ground-truth (GT) human-annotated deterministic summary for every recording. Generating multiple human references
would be ideal to better represent the distribution statistically, but impractical because annotation is expensive. We tackle this challenge
by proposing AugSumm, a method to leverage large language models (LLMs) as a proxy for human annotators to generate augmented
summaries for training and evaluation. First, we explore prompting strategies to generate synthetic summaries from Chat-
GPT. We validate the quality of synthetic summaries using multiple metrics including human evaluation, where we find that summaries
generated using AugSumm are perceived more valid to humans. Second, we develop methods to utilize synthetic summaries
in training and evaluation. Experiments on How2 demonstrate that pre-training on synthetic summaries and fine-tuning on GT summaries
improves ROUGE-L by 1 point on both GT and AugSummbased test sets. AugSumm summaries are available at https://github.com/Jungjee/AugSumm.
Additional file 5: Figure S9. of Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Creators: name: Hénaff, Elizabeth
name: Zapata, Luís
name: Casacuberta, Josep
name: Ossowski, Stephan
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Space Science
subject: Medicine
subject: Biotechnology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: A) characteristic signature of Illumina short read mapping in the case of a target site duplication generated by the insertion of a mobile element. B) Example of a TEI with TSD in Ler-1 compared to Columbia-0: IGV screenshots and BLAT alignments of Illumina and PacBio sequences, mapped to the reference, respectively. Jitterbug calls the breakpoint as the position with highest softclipped reads support, which can be either side of the TSD, 5’ in the first example and 3’ in the second. BLAT reports the 3’ position on the forward (reference) strand as the breakpoint. The difference in breakpoint position determined by these two methods in many cases corresponds to either zero or the length of the TSD. (PDF 15 kb)
Additional file 1: of Urinary chitinase 3-like protein 1 for early diagnosis of acute kidney injury: a prospective cohort study in adult critically ill patients
Creators: name: Loor, Jorien De
name: Decruyenaere, Johan
name: Demeyere, Kristel
name: Nuytinck, Lieve
name: Hoste, Eric AJ
name: Meyer, Evelyne
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology

description: Supplemental data. This file provides all details on the study methods (Supplemental Text S1 and Tables S3A-F) and on additional analyses not included in the manuscript (Supplemental Text S2, Tables S4A-I and Figure Legends S1-S4). It also contains the Supplemental Tables S1, S2, S5-S8, to which we refer in the manuscript. (PDF 628 kb)
In operando NMR investigations of advanced aqueous CO2RR systems
Creators: name: Kochs, Johannes Florian
name: Robens, Elisabeth
name: Jovanovic, Sven
name: Schleker, Peter Philipp Maria
name: Eichel, Rüdiger-A.
name: Granwehr, Josef
name: Martini, Katerine Antil
Publisher: name: Forschungzentrum Jülich
Year: 2024

description: 5th ELECTRA Symposium, Jülich, RWTH Aachen, Germany, 11 Sep 2024 - 12 Sep 2024
Epistylis leucoa Ehrenberg 1838
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis leucoa

description: Epistylis leucoa Ehrenberg, 1838
Locality of the original isolate: Germany
Habit: epibiont
Host: Carex
Reference: Ehrenberg (1838)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971
Additional file 8: Figure S7. of Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Creators: name: HĂŠnaff, Elizabeth
name: LuĂ­S Zapata
name: Casacuberta, Josep
name: Ossowski, Stephan
Publisher: name: Figshare
Year: 2015
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Percent of TEI flanking sequences masked by RepeatMasker. On average, 80 % of the sequences flanking RetroSeq TEI (red) are masked, compared to 10 % for Jitterbug (black). (PDF 19 kb)
https://sigport.org/events/documents/ieee-icassp-2024
Publisher: name: IEEE Signal Processing Society
Year: 2024

description: We propose a decoder-only language model, VoxtLM, that can perform four tasks: speech recognition, speech synthesis, text generation, and speech continuation. VoxtLM integrates text vocabulary with discrete speech tokens from self-supervised speech features and uses special tokens to enable multitask learning. Compared to a single-task model, VoxtLM exhibits a significant improvement in speech synthesis, with improvements in both speech intelligibility from 28.9 to 5.6 and objective quality from 2.68 to 3.90. VoxtLM also improves speech generation and speech recognition performance over the single-task counterpart. Further, VoxtLM is trained with publicly available data and training recipes and model checkpoints are open-sourced to make fully reproducible work.
Epistylis limnophili Biegel 1954
Creators: name: Porto, Ana Victoria Dunke
name: Rigo, Francine Vargas
name: Warren, Alan
name: Utz, Laura R. P.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Chromista
Ciliophora
Oligohymenophorea
Peritrichida
Epistylididae
Epistylis
Epistylis limnophili

description: Epistylis limnophili (Kahl, 1935) Biegel, 1954
Locality of the original isolate: Germany
Habit: epibiont
Host: caddisfly
References: Kahl (1935); Biegel (1954)
description: Published as part of Porto, Ana Victoria Dunke, Rigo, Francine Vargas, Warren, Alan & Utz, Laura R. P., 2024, Checklist of species in the genus Epistylis (Ciliophora, Peritrichia): the first step for a taxonomic revision, pp. 269-299 in Zootaxa 5415 (2) on page 283, DOI: 10.11646/zootaxa.5415.2.3, http://zenodo.org/record/10692971