bluuebunny/crossref_metadata_2025_split huggingface dataset:
SoundChunk: A free open-source and user oriented R package for acoustic data management, sound detection and extraction
Authors: Villain Avelyne S. , Renaud-Goud Paul 
Published: August 2023

AbstractIn a standard bioacoustic experiment setting, after data collection and before data analysis lies a time-consuming process that consists in extracting and labeling sounds of interest (chunks) from usually long recording files, collected through spreading PAM (Passive Acoustic Monitoring) for instance, and storing them in a structured and exploitable way based on both the meta-data of the initial recordings and the label data.SoundChunkis a user-oriented package in R that aims at providing tools for any R user so that they can go efficiently and comfortably through this process. Usually, the tasks include detecting, labeling, and extracting sound from audio files. With the recent advance of Machine Learning, especially Convolutional Neural Networks, some of these tasks are integrated in the ML framework; however, the learning phase relies on labeled chunks that need to be created.Three types of data are involved in the process: (i) WAVE files, whether they come from the initial recordings or are generated by chunk extraction, (ii) meta-data describing the conditions in which the initial WAVE files were recorded, (iii) label track files, whether they are automatically generated or manually input, that contain timed information about audio files.SoundChunkprovides utilities to sanely manipulate each of these three categories and combine them into easy-to-use chunks along with their meta-data.We expose functionalities that: (i) clean and restructure label tracks that are readable by softwares likeAudacity, (ii) chop long recordings into small fixed-size slices, (iii) detect chunks both interactively (so that robust detection settings can be found on a subset of the recordings) and automatically (so that the detection is applied across all recordings), (iii) dispatch chunks into structured folder(s), according to their meta-data.MaintainersThe team is open for suggestions and contributions. Contact:soundchunknfeat@proton.me(currently: ASV, PRG).UsersThis document is available as a vignette once the package is loaded an may be used on a set of example data (Villain and Renaud-Goud 2023).
Human Plasma-Like Medium (HPLM) inducesCryptococcus neoformans in vivocell morphologies
Authors: Mozo Eduardo G , Ross Orlando , Yuecel Raif , Dambuza Ivy M. , Mukaremera Liliane 
Published: August 2023

ABSTRACTThe fungal pathogenCryptococcus neoformans (C. neoformans)forms yeast cells of different sizes and morphological characteristics during infection. These features are usually not seen in standard laboratoryin vitroconditions. Here, we describein vivocell morphologies whenC. neoformansis grown in human plasma-like medium at 37°C-5% CO2. We observed mixed-size populations of cells less than 1 μm up to 16.8 μm cell diameter, increased capsule size, high chitin and DNA content in larger cells. Our findings show serum is not required for HPLM-inducedC. neoformanscellular heterogeneity. Thus, this new method offers an opportunity to investigate factors ofC. neoformansthat mediate pathogenesis or host-pathogen interactions in a physiologically relevant setting.IMPORTANCEDescription of newin vitroculture condition using the human plasma-like medium that supports the formation of the full range ofin vivocell morphologies ofC. neoformans.
Robust acidic pH and digestive enzyme stability of anti-SarsCov2 IgY antibodies: Implications for treatment of viral transmission thru gastrointestinal, ocular, nasal and skin tissues
Authors: Battula Sanjana , Saranya K , Meher Kranti , Arpitha Reddy R.N , Kadiyala Gopi , Iyer Subramanian , Vangala Subrahmanyam , Chandran Satish , Saxena Uday 
Published: August 2023

AbstractThere are many paths for the transmission of SarsCov2 virus. The main routes are nasal and oral and the droplets carrying the virus can also be transmitted thru ocular and skin tissues. The gastrointestinal (small intestine), nasal, ocular and skin tissues all present an acidic pH milieu and therefore any treatment with antibodies thru these routes has to have the antibodies remain active at acid pH as well as be resistant to typical protease digestion.To this end we profiled our anti-SarasCov2 receptor binding domain IgY antibodies for retention of activity at acidic and basic pHs and trypsin digestion. We find that the IgY are strongly resistant to denaturation at acid pH as well as not digested by trypsin. Our data strongly support the use of these IgY in treatment of viral transmission thru the GI, nasal, ocular and skin all tissues where the pH is acidic. We also provide an enabling platform to rapidly asses the suitability of any antibody or protein therapeutic for use at acidic pH.
Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension
Authors: Seo Hwa-seon , Yu Deli , Popov Ivan , Tao Jiahui , Angermeier Allyson , Sha Bingdong , Axelrod Jeffrey D. , Chang Chenbei , Wang Jianbo 
Published: August 2023

AbstractConvergent extension (CE) is a fundamental morphogenetic process where oriented cell behaviors lead to polarized extension of diverse tissues. In vertebrates, regulation of CE requires both non-canonical Wnt, its co-receptor Ror, and “core members” of the planar cell polarity (PCP) pathway. PCP was originally identified as a mechanism to coordinate the cellular polarity in the plane of static epithelium, where core proteins Frizzled (Fz)/ Dishevelled (Dvl) and Van Gogh-like (Vangl)/ Prickel (Pk) partition to opposing cell cortex. But how core PCP proteins interact with each other to mediate non-canonical Wnt/ Ror signaling during CE is not clear. We found previously that during CE, Vangl cell-autonomously recruits Dvl to the plasma membrane but simultaneously keeps Dvl inactive. In this study, we show that non-canonical Wnt induces Dvl to transition from Vangl to Fz. PK inhibits the transition, and functionally synergize with Vangl to suppress Dvl during CE. Conversely, Ror is required for the transition, and functionally antagonizes Vangl. Biochemically, Vangl interacts directly with both Ror and Dvl. Ror and Dvl do not bind directly, but can be cofractionated with Vangl. We propose that Pk assists Vangl to function as an unconventional adaptor that brings Dvl and Ror into a complex to serves two functions: 1) simultaneously preventing both Dvl and Ror from ectopically activating non-canonical Wnt signaling; and 2) relaying Dvl to Fz for signaling activation upon non-canonical Wnt induced dimerization of Fz and Ror.
Drug mode of action and resource constraints modulate antimicrobial resistance evolution
Authors: Delaney Oscar , Letten Andrew D. , Engelstädter Jan 
Published: August 2023

AbstractOne of the key characteristics of an antibiotic drug is its mode of action: bacteriostatic or bactericidal. The effect of drug mode of action on the evolution of resistance has been surprisingly underinvestigated to date. We present a theoretical model comparing the efficacy of bacteriostatic and bactericidal drugs, and drugs of intermediate type, at preventing the evolutionary rescue of an initially susceptible bacterial population in a patient. Our results suggest that in resource-abundant environments bacteriostatic drugs are best, as they constrain cell divisions and thus cause fewer resistance mutations to occur. When multiple drugs are employed, using one bacteriostatic and one bactericidal drug is usually optimal, because the cell division rate cannot fall below zero, so there are diminishing returns to bacteriostatic activity from two drugs. We also provide a web-based simulation engine for other researchers to intuitively explore related dynamics without requiring programming expertise.
DNA barcoding revealed a high percentage of mislabeling in commercial fish products: the first empirical survey in South Texas
Authors: Tommasi Rita B. , Lamia Sanjana M. , Van Dysocheata , Estrada Isaiah , Kuchler Zoen L. , Ramsey Dean , Tamang Jyoti , Kaneko Gen , Ehsan Hashimul 
Published: August 2023

AbstractSeafood mislabeling is a widespread problem that have produced a growing distrust of seafood industry. In this study, we examined the prevalence of mislabeling in fish samples from regional markets in the greater Houston area and close-by coastal communities. A total of 63 fish fillet samples were purchased, labeled, and stored at -20°C in individual packages until DNA extraction. DNA fragments of roughly 700 base pairs encoding cytochrome oxidase I (COI) were PCR-amplified from each DNA sample. With 99.6–100% nucleotide identity in the GenBank and BOLD databases, all samples were correctly identified at the species level. The scientific names identified by DNA barcoding were matched with legally acceptable market names using the US Food and Drug Administration (FDA) Seafood List. Out of the 63 samples examined, 13 samples (20.6%) were mislabeled. Moreover, 24 samples (38.1%) did not use the acceptable market names, indicating that the FDA policy is poorly implemented in seafood industry. The first DNA barcoding survey this area warranted the need of continuous monitoring and the dissemination of the regulation combined with taxonomic knowledge.
Clinical pattern and diagnostic of comorbidity of respiratory tuberculosis and viral pneumonia caused by Herpesvirus Simplex, Human Cytomegalovirus and SARS-CoV-2 in patients with late-stage HIV infection with immunodeficiency
Authors: Mishin V. Yu. , Mishina A.V. , Shashenkov I. V. 
Published: August 2023

AbstractAimTo study features of social status, clinical pattern and diagnosis in cases of comorbidity of respiratory tuberculosis and viral pneumonia caused byHerpesvirus Simplexof type 1,Human CytomegalovirusandSARS-CoV-2in patients with late-stage HIV infection with immunodeficiency.Materials and methodsThe prospective study included 25 patients with comorbid condition of respiratory tuberculosis withMycobacterium tuberculosisin excreta, herpesvirus and coronavirus pneumonia, and 21 patients with respiratory tuberculosis as well as cytomegalovirus and coronavirus pneumonia (1a and 2a main groups) and, respectively, 25 and 21 similar patients, but without coronavirus pneumonia (1b and 2b comparison group) in the late stages of HIV infection with immunodeficiency. For the etiological diagnosis of herpesvirus- and cytomegalovirus pneumonia, the PCR test was used for recognition of DNA ofHerpesvirus Simplexof type 1 andHuman Cytomegalovirusin the diagnostic material of respiratory tract and for the etiological diagnosis of coronavirus pneumonia, the PCR for recognition of RNA was used to revealSARS–CoV-2. Statistical analysis of the data was performed by the use of the Microsoft Office Excel 2019 software for calculation of group mean, standard error of mean and confidence interval.ResultsThe comorbidity of respiratory tuberculosis, herpes-, cytomegalo- and coronavirus pneumonia in patients with late-stage HIV infection in the phase of progression and in the absence of ART was characterized by severe immunodeficiency and generalization of tuberculosis with multiple extrapulmonary lesions. The results displayed similarity of clinical manifestations and visualization of changes in CT-picture in cases of comorbidity the diseases which hampers their recognition due to simultaneous combination of several pathologies with similar clinical manifestations that requires a complex etiological diagnosis of the specific diseases to prescribe a timely comprehensive treatment and reduce lethality in this severe contingent of patients.ConclusionPatients with respiratory tuberculosis and HIV infection registered in the office of tuberculosis care for HIV-infected individuals in the antituberculosis dispensary represent a group of high risk from COVID-19 infection and CVP disease, and, in cases of combination with severe immunodeficiency, HVP and CMVP, the patients should be regularly subjected to preventive studies for timely detection of COVID-19 for the purpose of their emergency isolation and treatment.
Sexual health in women with Parkinson’s disease: Motor, non-motor, and social impacts
Authors: Nobrega Kátia Cirilo Costa , da Silva Nascimento Isaíra Almeida Pereira , Souza Bruno Rafael Antunes , Gonçalves Raissa Amorim , Martins Thalyta Silva , Santos Geovanna Ferreira , de Almeida da Silva Bruno Eron , Helene André Frazão , Roque Antonio Carlos , Savica Rodolfo , Piemonte Maria Elisa Pimentel 
Published: August 2023

AbstractBackgroundSexual dysfunction (SD) is a common non-motor symptom (NMS) in people with Parkinson’s disease (PwPD). Sexual health (SH) depends on several biological, mental, and social factors that PD may affect. Despite its prevalence and relevance for quality of life, SD in women with Parkinson’s disease (WwPD) is poorly understood, and research in this area is scarce.ObjectivesTo investigate the impact of motor, non-motor, and social aspects on the SH of WwPD.MethodsWe conducted a cross-sectional study of 100 women (mean age 54.45±8.31, mean H&Y stage 1.70±0.71). The following data were collected for each person (used tests/scales indicated within parentheses and defined in Glossary): (1) demographic information and global cognitive capacity (T-MoCA); (2) non-motor aspects of daily life experiences (MDS-UPDRS, part I); (3) motor aspects of daily life experiences (MDS-UPDRS, part II); (4) fatigue (FSS); (5) self-esteem (RSES); (6) sleep disorder (PDSS); (7) couple relationship quality (CRQ) (DAS); (8) depressive signals (BDI); (8) short-term sexual health (FSFI); and (9) long-term sexual health (SQ-F).ResultsOur results suggest that depressive symptoms, preserved cognitive status, and CRQ are predictive factors in the sexual health of WwPD. Age, disease onset, duration, postmenopausal, Levodopa dosage, motor disability, and fatigue were not correlated with SH.ConclusionOur findings emphasize the need to assess the sexual functioning of WwPD to investigate which motor, non-motor, and social aspects may be involved in SD so that measures can be implemented in clinical practice.
Dance or disappear: Strategic sexual signalling in female Peninsular rock agama
Authors: Sridharan Aravind , Lawrence Swapna , Isvaran Kavita 
Published: August 2023

AbstractSexual signalling has largely been studied in the context of indirect competition among males through displays and mate choice by females. Historically, sexual signalling in females was expected to be of limited consequence. However, there is growing evidence of sexual signalling in females and its value in the context of sexual selection. Here, we test how females strategize the use of sexual signals in a socially polygynous lizard,Psammophilus dorsalis. We evaluated key hypotheses for how females should modulate their signalling, including male quality and mate availability. We simulate male quality using artificial male models to individually tagged, and intensely monitored wild female lizards, measuring their strategic investment in sexual signalling. We found that females invest more in signalling towards high quality males and increased their investment towards the later part of the only breeding season. Contrary to what is typically expected in a polygynous mating system, females not only invest in costly and elaborate sexual signals, they also modulate their usage to maximise their benefits and minimise their costs. Even in polygynous mating systems, dispersed distribution of individuals can result in females experiencing limitation in mate availability, resulting in costly sexual signalling.
Evidence of target-mediated miRNA degradation inDrosophilaovarian cell culture
Authors: Akulenko Natalia , Mikhaleva Elena , Marfina Sofya , Kornyakov Dmitry , Bobrov Vlad , Arapidi Georgij , Shender Victoria , Ryazansky Sergei 
Published: August 2023

AbstractTarget-mediated miRNA degradation (TDMD) is a recently discovered process of post-transcriptional regulation of miRNA stability in animals. TDMD is induced by the formation of the non-canonical duplex of Ago-bound miRNAs with the specialized RNA target, and, as suggested for human cell culture, this complex is recognized by the ZSWIM8 receptor protein of the Cullin-RING-ligase complex CRL3. CRL3 ubiquitinates Ago, resulting in proteolysis of Ago and degradation of the released miRNAs. To date, the molecular mechanism of the TDMD process was not studied in other animal species. Here we investigated protein Dora, theDrosophilaortholog of ZSWIM8, in the culture ofDrosophilaovarian somatic cells (OSC). We show that Dora in OSCs localizes in protein granules that are not related to P-and GW-bodies. The knock-out ofDoraup-regulates multiple miRNAs, including miR-7-5p. Also, we show that Dora associates with proteins of the CRL3 complex, and the depletion of its main component Cul3 up-regulates miR-7-5p. We concluded that the mechanism of TDMD is conserved in humans andDrosophila. The knock-out ofDoraalso down-regulates the putative protein-coding targets of miRNAs. One of them isTomfrom the Brd-C gene family, which is known to repress the Notch signaling pathway. Indeed, in cells lacking Dora, we have observed the down-regulation ofcut, the marker of the activated Notch pathway. This data indicates that TDMD in OSCs may contribute to modulation of the Notch pathway.
Influence of pseudo-green water on growth, colouration, and survival in European lobster (Homarus gammarus) larvae
Authors: Bell Matt E , Grady Julie O , Domech Paula C , Frontaura Erik R , Hinchcliffe James , Davies Simon J , McCusker Stephen , Wan Alex H L 
Published: August 2023

AbstractWith the depletion of European lobster (Homarus gammarus) wild stocks from historic overexploitation, the attention has turned towards restocking, stock enhancement programs and farming potential. The early life larval stages of the European lobster present a major barrier to hatchery production efforts due to low survival rates. Green water techniques are rapidly growing due to their ability to improve nutrition quality. This study explores the potential benefits of using pseudo-green water. This is determined by adding microalgae to the rearing environment of larvae by analysing the effects on growth and survival. The commonly used algal species:Tetraselmis suecica(TS),Dunaliella salina(DS), andNannochloropsissp. (N) were added as monoculture or mixture treatments to a controlled European lobster larvae-rearing environment over thirteen days. The trial consisted of seven permutations of algal treatments (TS, DS, N, TS+DS, TS+N, DS+N, and TS+DS+N) and one control group, with clear water conditions using length measurements, survival rates and colouration to determine treatment impacts at the end of the trial. Results indicate that mixtures of algal species outperformed monocultures and clear water regarding growth performance.Nannochloropsissp. is of significant benefit to growth performance. Algal mixes containingNannochloropsissp. resulted in significantly better growth thanD.salinamonoculture treatment. There were no significant differences in survival rates between treatment groups.
Microbial cell factory optimisation using genome-wide host-pathway interaction screens
Authors: Cachera Paul , Kurt Nikolaj Can , Røpke Andreas , Strucko Tomas , Mortensen Uffe H. , Jensen Michael K. 
Published: August 2023

AbstractThe ubiquity of genetic interactions in living cells challenges the concept of parts orthogonality, which is a cornerstone of synthetic biology. Parts, such as heterologously expressed genes, draw from shared pools of limited cellular resources and interactions between parts themselves and their host are inevitable. Instead of trying to eliminate or disregard these interactions, we propose to leverage them to promote desirable phenotypes. We recently described CRI-SPA, a method for high-throughput genome-wide gene delivery and screening of host:pathway interactions inSaccharomyces cerevisiae. In this study, we combine this method with biosensor-based high-throughput screening and high-density colony image analysis to identify lead engineering targets for optimisingcis-cis-muconic acid (CCM) production in yeast cell factories. Using the biosensor screen, we phenotype >9,700 genotypes for their interaction with the heterologously expressed CCM biosynthesis pathway, including both gene knock-out and overexpression, and identify novel metabolic targets belonging to sulphur assimilation and methionine synthesis, as well as cellular redox homeostasis, positively impacting CCM biosynthesis by up to 280%. Our genome-wide exploration of host pathway interaction opens novel strategies for the metabolic engineering of yeast cell factories.
Inhibiting NINJ1-dependent plasma membrane rupture protects against inflammasomeinduced blood coagulation and inflammation
Authors: Cui Jian , Li Hua , Ye Dien , Zhang Guoying , Zhang Yan , Yang Ling , Sim Martha M.S. , Wood Jeremy P. , Wei Yinan , Li Zhenyu , Wu Congqing 
Published: August 2023

AbstractSystemic blood coagulation accompanies inflammation during severe infection like sepsis and COVID. We’ve previously established a link between pyroptosis, a vital defense mechanism against infection, and coagulopathy. During pyroptosis, the formation of gasdermin-D (GSDMD) pores on the plasma membrane leads to the release of tissue factor (TF)-positive microvesicles (MVs) that are procoagulant. Mice lacking GSDMD release fewer TF MVs. However, the specific mechanisms leading from activation of GSDMD to MV release remain unclear. Plasma membrane rupture (PMR) in pyroptosis was recently reported to be actively mediated by the transmembrane protein Ninjurin-1 (NINJ1). Here we show that NINJ1 promotes procoagulant MV release during pyroptosis. Haploinsuffciency or glycine inhibition of NINJ1 limited the release of procoagulant MVs and inflammatory cytokines and partially protected against blood coagulation and lethality triggered by bacterial flagellin. Our findings suggest a crucial role for NINJ1-dependent PMR in inflammasome-induced blood coagulation and inflammation.
Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells
Authors: Gilmore Rachel B. , Gorka Dea , Stoddard Christopher E. , Cotney Justin L. , Chamberlain Stormy J 
Published: August 2023

AbstractAngelman Syndrome (AS) and Prader-Willi Syndrome (PWS), two distinct neurodevelopmental disorders, result from loss of expression from imprinted genes in the chromosome 15q11-13 locus most commonly caused by a megabase-scale deletion on either the maternal or paternal allele, respectively. Each occurs at an approximate incidence of 1/15,000 to 1/30,000 live births and has a range of debilitating phenotypes. Patient-derived induced pluripotent stem cells (iPSCs) have been valuable tools to understand human-relevant gene regulation at this locus and have contributed to the development of therapeutic approaches for AS. Nonetheless, gaps remain in our understanding of how these deletions contribute to dysregulation and phenotypes of AS and PWS. Variability across cell lines due to donor differences, reprogramming methods, and genetic background make it challenging to fill these gaps in knowledge without substantially increasing the number of cell lines used in the analyses. Isogenic cell lines that differ only by the genetic mutation causing the disease can ease this burden without requiring such a large number of cell lines. Here, we describe the development of isogenic human embryonic stem cell (hESC) lines modeling the most common genetic subtypes of AS and PWS. These lines allow for a facile interrogation of allele-specific gene regulation at the chromosome 15q11-q13 locus. Additionally, these lines are an important resource to identify and test targeted therapeutic approaches for patients with AS and PWS.