bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrical Determinants of Tinnitus Extinction in a Cochlear Implant Patient
Authors: Muller Leah , Gilbert Melanie , Jiam Nicole T. , Limb Charles J. , Tward Aaron D. 
Published: December 2022

Hypothesis
Electrical tinnitus suppression by cochlear implants requires stimulation of a subset of neural elements in the cochlea.

Background
Tinnitus is the phantom perception of sound in the ears and is a known correlate of hearing loss. Cochlear implants restore hearing and are known to lessen or extinguish tinnitus. The amount of electrical charge required and the number and location of electrodes required to extinguish tinnitus with a cochlear implant are factors that remain poorly understood.

Methods
In a subject with single-sided deafness, with tinnitus in the deaf ear, we enabled single electrodes and groups of electrodes along the cochlea and increased the current until tinnitus was diminished or extinguished. We recorded the subject's perception of these changes using loudness scaling of both the electrical stimuli and the tinnitus.

Results
Tinnitus could be extinguished with individual electrodes and more effectively extinguished by activating a greater number of electrodes. Tinnitus suppression and loudness growth of the electrical stimuli were imperfectly correlated.

Conclusion
Tinnitus suppression in this cochlear implant patient was achieved by electrically stimulating multiple distinct portions of the cochlea, and the cochlear neural substrate for tinnitus suppression may be distinct from that for auditory perception.
Hearing Preservation and Spatial Hearing Outcomes After Cochlear Implantation in Children With TMPRSS3 Mutations
Authors: Peng Z. Ellen , Garcia Alejandro , Godar Shelly P. , Holt Jeffrey R. , Lee Daniel J. , Litovsky Ruth Y. 
Published: December 2022

Objective
Investigate hearing preservation and spatial hearing outcomes in children with TMPRSS3 mutations who received bilateral cochlear implantation.

Study Design and Methods
Longitudinal case series report. Two siblings (ages, 7 and 4 yr) with TMPRSS3 mutations with down-sloping audiograms received sequential bilateral cochlear implantation with hearing preservation with low-frequency acoustic amplification and high-frequency electrical stimulation. Spatial hearing, including speech perception and localization, was assessed at three time points: preoperative, postoperative of first and second cochlear implant (CI).

Results
Both children showed low-frequency hearing preservation in unaided, acoustic-only audiograms. Both children demonstrated improvements in speech perception in both quiet and noise after CI activations. The emergence of spatial hearing was observed. Each child's overall speech perception and spatial hearing when listening with bilateral CIs were within the range or better than published group data from children with bilateral CIs of other etiology.

Conclusion
Bilateral cochlear implantation with hearing preservation is a viable option for managing hearing loss for pediatric patients with TMPRSS3 mutations.
Experience with Telemedicine in a Tertiary Academic Otologic Clinic During the COVID-19 Pandemic
Authors: Xie Katherine Z. , Gottlich Harrison C. , Antezana Luis A. , Yeakel Sarah , Nassiri Ashley M. , Moore Eric J. , Carlson Matthew L. 
Published: December 2022

Objective
To examine the utility of telemedicine in a tertiary otologic practice.

Study Design
Retrospective case series.

Setting
Tertiary neurotology clinic.

Patients
Consecutive adult patients presenting via video visit between January 2020 and January 2021.

Intervention(s)
Televideo modality to conduct visits with patients seeking evaluation for new concerns, second opinions, or routine follow-up for established conditions.

Main Outcome Measure(s)
Success of the televideo visit defined by the televideo visit being sufficient for determining a definitive plan and not requiring deferment of recommendations for a subsequent in-person visit.

Results
A total of 102 televideo visits were performed among 100 unique patients. Of those, 92 (90.2%) visits were for second opinions or evaluation of new concerns, most commonly for vestibular schwannoma (n = 32, 31.4%), followed by sensorineural hearing loss (n = 20, 19.6%). Other visits were conducted for early postoperative follow-up and established general follow-up. In 91.2% of cases (n = 93), patients were successfully evaluated and provided recommendations from the initial video visit. All visits with patients having a diagnosis of meningioma (n = 7), and nearly all with vestibular Schwannoma (97%, n = 31) and sensorineural hearing loss (95%, n = 19) were successful. Of the 79 patients offered surgery as one potential treatment option, 31 patients underwent surgery at our institution by time of review. Patients with unsuccessful visits (n = 9, 8.8%) were advised to schedule additional in-person diagnostic imaging, vestibular testing, or cochlear implant candidacy evaluation to establish a more definitive care plan.

Conclusion
Virtual televideo visits were successful for a high percentage of selected patients seen at a tertiary neurotology practice, particularly those seeking evaluation of vestibular schwannoma or sensorineural hearing loss.
Myosin Mutations and Sudden Sensorineural Hearing Loss: Results of Whole Exome Sequencing
Authors: Sharma Rahul K. , Drusin Madeleine , Hostyk Joseph , Baugh Evan H. , Aggarwal Vimla S. , Goldstein David , Kim Ana H. 
Published: December 2022

Objective
Idiopathic sudden sensorineural hearing loss (ISSNHL) affects 66,000 patients per year in the United States. Genetic mutations have been associated with progressive hearing loss; however, genetic mutations associated with ISSNHL have not been identified.

Methods
A prospective cohort study of adults older than 18 years presenting with ISSNHL at a tertiary academic medical center. Whole exome sequencing (WES) was conducted using Genome Analysis Toolkit best practices. An automated diagnostic screen employing a variety of models for pathogenicity was conducted across all genes with no specific targets. Candidate pathogenic variants were reviewed by a team of geneticists and clinicians. Variants were crossed-referenced with 92 known hearing loss associated genes.

Results
Twenty-nine patients with SSNHL were screened using WES. The average age of patients was 53 ± 17.1 years, and most patients were White (62%) and men (55%). The mean pure tone average was 64.8 ± 31.3 dB for the affected ear. Using a 0.1% allele frequency screen, 12 (41%) cases had a mutation in any of the nine selected myosin genes. When we restrict to singletons (allele frequency = 0%), 21% (n = 6) of cases have qualifying variants, whereas only 3.8% (n = 481) of 12,577 healthy controls carry qualifying variants (p < 0.01). Most mutations (80%) were missense mutations. Of the novel mutations, one was a frameshift mutation, and two were a stop-gained function. Three were missense mutations.

Conclusion
Myosin mutations may be associated with ISSNHL. However, larger population screening is needed to confirm the association of myosin mutation with ISSNHL and steroid responsiveness.
Antimicrobial properties of English churchyard lichens.
Authors: Taylor J A , Fourie T , Powell M , Chianella I 
Published: December 2022

The emergence of multidrug resistant bacteria has driven the need for novel antibiotics. Our investigations have focussed on lichens as they naturally produce a wide range of unique and very effective defence chemicals. The aim of this study was to evaluate the antimicrobial properties of British churchyard lichens. Crude extracts from ten common lichen species were tested against six bacteria and two fungi by disc diffusion susceptibility testing. Extracts showed inhibition of Gram positive bacteria and dermatophytic fungi. Diploica canescence and Pertusaria amara showed the most potent antimicrobial activity.
Erythrobacter aurantius sp. nov., isolated from intertidal seawater in Taizhou
Authors: Zhang Yu , Hua Jia , Ying Jun-Jie , Dong Han , Li Hao , Xamxidin Maripat , Han Bing-Nan , Sun Cong , Xu Lin 
Published: December 2022

A Gram-stain-negative, aerobic, chemoheterotrophic and rod-shaped strain, designated as C5T, was isolated from intertidal surface seawater in Taizhou, Zhejiang Province, PR China and characterized using a polyphasic taxonomic approach. Strain C5T could produce carotenoids and bacteriochlorophyll a. Growth was observed at 20–45 °C, at pH 6.0–9.0 and with 0–8.0 % (w/v) NaCl. The 16S rRNA gene sequence identity analysis revealed that strain C5T was the most closely related to

Qipengyuania nanhaisediminis

CGMCC 1.7715T (98.8%) and

Erythrobacter litoralis

DSM 8509T (98.7%). The phylogenetic reconstruction based on core genes demonstrated that strain C5T was clustered into the members of the genus

Erythrobacter

. The average nucleotide identity and digital DNA–DNA hybridization values between strain C5T and

Erythrobacter

type strains were lower than 76 and 25 %, respectively. The predominant and minor respiratory quinones were identified as ubiquinone-10 and ubiquinone-9. The major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and iso-C18 : 0. Polar lipids included phosphatidylethanolamine, phosphatidylglycerol, a glycosphingolipid and an unidentified aminolipid. Based on the genetic, chemotaxonomic and phenotypic data, strain C5T is concluded to represent a novel species in the genus

Erythrobacter

, for which the name Erythrobacter aurantius sp. nov. is proposed. The type strain is C5T (=MCCC 1K05108T=KCTC 92307T).
Machine learning identifies a COVID-19-specific phenotype in university students using a mental health app
Authors: Shvetcov Artur , Whitton Alexis , Kasturi Suranga , Zheng Wu-Yi , Beames Joanne , Ibrahim Omar , Han Jin , Hoon Leonard , Mouzakis Kon , Gupta Sunil , Venkatesh Svetha , Christensen Helen , Newby Jill 
Published: December 2022

AbstractAdvances in smartphone technology have allowed people to access mental healthcare via digital apps from wherever and whenever they choose. University students experience a high burden of mental health concerns. Although these apps improve mental health symptoms, user engagement has remained low. Studies have shown that users can be subgrouped based on unique characteristics that just-in-time adaptive interventions (JITAIs) can use to improve engagement. To date, however, no studies have examined the effect of the COVID-19 pandemic on these subgroups. Here, we use machine learning to examine user subgroup characteristics across three COVID-19-specific timepoints: during lockdown, immediately following lockdown, and three months after lockdown ended. We demonstrate that there are three unique subgroups of university students who access mental health apps. Two of these, with either higher or lower mental well-being, were defined by characteristics that were stable across COVID-19 timepoints. The third, situational well-being, had characteristics that were timepoint-dependent, suggesting that they are highly influenced by traumatic stressors and stressful situations. This subgroup also showed feelings and behaviours consistent with burnout. Overall, our findings clearly suggest that user subgroups are unique: they have different characteristics and therefore likely have different mental healthcare goals. Our findings also highlight the importance of including questions and additional interventions targeting traumatic stress(ors), reason(s) for use, and burnout in JITAI-style mental health apps to improve engagement.
Spatially and temporally varying selection influence species boundaries in two sympatricMimulus
Authors: Tataru Diana , Wheeler Emma C. , Ferris Kathleen G. 
Published: December 2022

AbstractSpatially and temporally varying selection can maintain genetic variation within and between populations, but it is less known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely relatedMimulusspecies. Using repeated reciprocal transplant experiments with advanced generation hybrids we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation inMimulus guttatusandMimulus laciniatusbetween two years with dramatically different water availability. We found strong divergent habitat mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence.
Investigation of Soft Magnetic Material Cores in Transcranial Magnetic Stimulation Coils and the Effect of Changing Core Shapes on the Induced Electric Field in Small Animals
Authors: Tashli Mohannad , Weistroffer George , Mhaskar Aryan , Kumbhare Deepak , Baron Mark S. , Hadimani Ravi L. 
Published: December 2022

AbstractTranscranial magnetic stimulation (TMS) is a safe, effective and non-invasive treatment for several psychiatric and neurological disorders. Lately, there has been a surge in research utilizing this novel technology in treating other neurological and psychiatric ailments. The application of TMS on several neurological disorders requires the induced electric and magnetic fields to be focused and targeted to a small region in the brain. TMS of a focal cortical territory will ensure modulation of specific brain circuitry without affecting unwanted surrounding regions. This can be achieved by altering the properties of the magnetic core material used for the TMS system. In this study, soft ferromagnetic materials having high permeability, high saturation magnetization and low coercivity have been investigated as TMS coil cores in finite element simulations. Also, magnetic field measurements have been carried out using different cores in the TMS coil.Finite element analysis of the rat head model is carried out using Sim4life software while investigating variations associated with changing the ferromagnetic core material and shape in the coil. Materials proposed for the analysis in this study include Iron Cobalt Vanadium alloy (Fe-Co-V) also known as Permendur, Carbon Steel (AISI 1010) and Manganese Zinc ferrites (MnZn ferrites). Simulation results indicated significant magnetic field distribution variation when introducing a ferromagnetic core in TMS coil, concentrating the magnetic field to the targeted region in the rat head model without stimulating adjacent regions. It was observed that the v-tip sharpened core attained the highest magnetic field and best focality among other cores in simulations and experimentally.
BioNetGMMFit: Estimating Parameters of a BioNetGen Model from Time-Stamped Snapshots of Single Cells
Authors: Wu John , Stewart William CL , Jayaprakash Ciriyam , Das Jayajit 
Published: December 2022

AbstractBackgroundMechanistic models are commonly employed to describe signaling and gene regulatory kinetics in single cells and cell populations. Recent advances in single-cell technologies have produced multidimensional datasets where snapshots of copy numbers (or abundances) of a large number of proteins and mRNA are measured across time in single cells. The availability of such datasets presents an attractive scenario where mechanistic models are validated against experiments, and estimated model parameters enable quantitative predictions of signaling or gene regulatory kinetics. To empower the systems biology community to easily estimate parameters accurately from multidimensional single-cell data, we have merged a widely used rule-based modeling software package BioNetGen, which provides a user-friendly way to code for mechanistic models describing biochemical reactions, and the recently introduced CyGMM, that uses cell-to-cell differences to improve parameter estimation for such networks, into a single software package: BioNetGMMFit.ResultsBioNetGMMFit provides parameter estimates of the model, supplied by the user in the BioNetGen markup language (BNGL), which yield the best fit for the observed single-cell, timestamped data of cellular components. Furthermore, for more precise estimates, our software generates confidence intervals around each model parameter. BioNetG-MMFit is capable of fitting datasets of increasing cell population sizes for any mechanistic model specified in the BioNetGen markup language.ConclusionBy streamlining the process of developing mechanistic models for large single-cell datasets, BioNetGMMFit provides an easily-accessible modeling framework designed for scale and the broader biochemical signaling community.
Biodiversity and local interaction complexity promote sustainable fisheries in large food webs
Authors: Werner Alexandra , Albert Georg , Brose Ulrich , Gauzens Benoit 
Published: December 2022

AbstractOn a global scale, fisheries harvest an estimated 96 million tonnes of fish biomass annually, making them one of the most important drivers of marine ecosystem biodiversity. Yet little is known about the interactions between fisheries and the dynamics of complex food webs in which the harvested species are embedded. We have developed a synthetic model that combines resource economics with complex food webs to examine the direct effects of fishing on exploited species and the indirect impact on other species in the same community. Our model analyses show that the sensitivity of the targeted species increases with its trophic level and decreases with its local interaction complexity (i.e. its number of interactions with prey, predators, and competitors). In addition, we also document a strikingly positive effect of community species richness on the resilience of the harvested species to this disturbance. The indirect effects on other species show specific patterns of spreading across trophic modules that differ systematically from how other disturbances spread across ecological networks. While these results call for further research on how human resource exploitation in general and fishery in particular affect ecological dynamics and biodiversity in naturally complex systems, they also allow for some cautious conclusions. Taken together, our results suggest that the sustainability concerning fishery yield and ecosystem integrity can be maximised by focusing the harvest on low trophic level species with a high local interaction complexity in high biodiversity ecosystems. In this sense, our complex network approach offers a promising avenue for integrating the necessities of generating economic revenue with the protection of natural biodiversity.
Evo-Scope: Fully automated assessment of correlated evolution on phylogenetic trees
Authors: Godfroid Maxime , Coluzzi Charles , Lambert Amaury , Glaser Philippe , Rocha Eduardo P. C. , Achaz Guillaume 
Published: December 2022

AbstractCorrelated evolution describes how multiple biological traits evolve together. Recently developed methods provide increasingly detailed results of correlated evolution, sometimes at elevated computational costs.Here, we presentevo-scope, a fast and fully-automated pipeline with minimal input requirements to compute correlation between discrete traits evolving on a phylogenetic tree. Notably, we improve two of our previously developed tools that efficiently compute statistics of correlated evolution to characterize the nature, such as synergy or antagonism, and the strength of the interdependence between the traits.Furthermore, we improved the running time and implemented several additional features, such as genetic mapping, Bayesian Markov Chain Monte Carlo estimation, consideration of missing data and phylogenetic uncertainty.As an application, we scan a published penicillin resistance data set ofStreptococcus pneumoniaeand characterize genetic mutations that correlate with antibiotic resistance. The pipeline is accessible both as a self-contained github repository (https://github.com/Maxime5G/EvoScope) and through a graphical galaxy interface (https://galaxy.pasteur.fr/u/maximeg/w/evoscope).
Taxonomically mixed blue musselMytiluspopulations are spatially heterogeneous and temporally unstable in the subarctic Barents Sea
Authors: Marchenko Julia , Khaitov Vadim , Katolikova Marina , Sabirov Marat , Malavenda Sergey , Gantsevich Michael , Basova Larisa , Genelt-Yanovsky Evgeny , Strelkov Petr 
Published: December 2022

AbstractSubarctic populations of blue mussels represented by “cryptic” speciesMytilus edulis(ME) andM. trossulus(MT) have been studied less intensively than Arctic and boreal populations. Ecological features ofMEandMTin sympatry are poorly known everywhere. The knowledge about mussels at the northeasternmost boundary of the Atlantic littoral communities on Murman coast of the Barents Sea is based on data obtained 50-100 years ago. Our study provides the first insight into the long-term dynamics of the Barents Sea mussels, the habitat segregation ofMEandMT, and the interannual dynamics of their mixed settlements. The Tyuva Inlet (Kola Bay), which is 3 km long, was used as the study site. Mussels were found everywhere in the littoral and the sublittoral down to a depth of 4 m. Their characteristic habitats were sandbanks, littoral rocks, sublittoral kelp forests and “the habitat of the mussel bed” in the freshened top of the inlet. The main spatial gradients explaining the variability of demographics of the settlements (abundance, age structure, size) were associated with the depth and the distance from the inlet top.MEandMTwere partially segregated by depth:MEdominated in the sublittoral andMT, in the littoral. In addition,MEdominated both in the littoral and in the sublittoral parts of the mussel bed. The ratio of species in the mixed settlements varied over time: between 2004 and 2010 the proportions ofMTdecreased everywhere, by 22 % on average. Historical data indicate that the abundance of the Murman mussels declined sharply between the 1960s and the 1970s, which coincided with the cooling of the Arctic. It seems that the populations have not completely recovered in the abnormally warm recent decades. The habitat distribution of mussels apparently changed with time, too: unlike today, in the 20th century mussels were rarely observed in kelps. We suggest that the spatial and temporal dynamics of subarctic mussels can be partly explained by the competition betweenMEandMTcombined with their differing sensitivity to environmental factors.