bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined impacts of climate and land use change and the future restructuring of Neotropical bat biodiversity
Authors: Gonçalves Fernando , Sales Lilian P. , Galetti Mauro , Pires Mathias M. 
Published: July 2021

AbstractForecasting the effects of global change on biodiversity is necessary to anticipate the threats operating at different scales in space and time. Climate change may create unsuitable environmental conditions, forcing species to move to persist. However, land-use changes create barriers that limit the access of some species to future available habitats. Here, we project the impacts of climate and land-use change on 228 Neotropical bat species by forecasting changes in environmental suitability, while accounting for the effect of habitat type specialization and simulating dispersal across suitable patches. We also identify the most vulnerable ecoregions and those that may offer future stable refugia. We further investigate potential functional changes by analysing the response of different trophic guilds. We found that the range contraction of habitat specialists, especially frugivores, was more frequent and stronger under all simulated scenarios. Projected changes differ markedly across ecoregions. While the Amazon region is likely to undergo high turnover rates in bat composition, the Andean grassland, Cerrado and Chaco might experience the greatest losses. The expansion of habitat generalists, which forage in open areas and commonly establish large colonies in manmade structures, coupled with the range contraction of habitat specialists is projected to homogenize bat communities across the Neotropics. Overall, dispersal will likely be the key for the future of Neotropical bat diversity. Therefore, safeguarding the refugia highlighted here, by expanding and connecting the existing network of protected areas, for example, may allow species to move in response to global change.
Mesalamine Reduces Intestinal ACE2 Expression Without Modifying SARS-CoV-2 Infection or Disease Severity in Mice
Authors: Alvarado David M. , Son Juhee , Thackray Larissa B. , Diamond Michael S. , Ding Siyuan , Ciorba Matthew A. ,   the IBD Investigators Group at Washington University
Published: July 2021

AbstractIntroductionCoronavirus Disease 2019 (COVID-19) is an ongoing public health crisis that has sickened or precipitated death in millions. The etiologic agent of COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), infects the intestinal epithelium, and can induce GI symptoms similar to the human inflammatory bowel diseases (IBD). An international surveillance epidemiology study (SECURE-IBD) reported that the standardized mortality ratio trends higher in IBD patients (1.5-1.8) and that mesalamine/sulfasalazine therapy correlates with poor outcome. The goal of our study was to experimentally address the relationship between mesalamine and SARS-CoV-2 entry, replication, and/or pathogenesis.MethodsViral infection was performed with a chimeric vesicular stomatitis virus expressing SARS-CoV-2 spike protein and EGFP (VSV-SARS-CoV-2) and SARS-CoV-2 virus derived from an infectious cDNA clone of 2019n-CoV/USA_WA1/2020. Primary human ileal spheroids derived from healthy donors were grown as 3D spheroids or on 2D transwells. We assessed the effect of 10 mM mesalamine (Millipore Sigma) on viral RNA levels, as well as the expression of the SARS-CoV-2 receptor angiotensin II-converting enzyme 2 (ACE2), Transmembrane Serine Protease 2 (TMPRSS2), TMPRSS4, Cathepsin B (CTSB) and CTSL by qRT-PCR. 8-12 week old K18-ACE2 were treated orally with PBS or mesalamine at 200 mg/kg daily. Mice were inoculated intranasally with 1×103 FFU of SARS-CoV-2. Mice were weighed daily and viral titers were determined 7 days post infection (dpi) by qRT-PCR. For the intestinal viral entry model, VSV-SARS-CoV-2 was injected into a ligated intestinal loop of anesthetized K18-ACE2 mice and tissues were harvested 6 hours post-infection.ResultsWe found no change in viral RNA levels in human intestinal epithelial cells in response to mesalamine. Expression of ACE2 was reduced following mesalamine treatment in enteroids, while CTSL expression was increased. Mice receiving mesalamine lost weight at similar rates compared to mice receiving vehicle control. Mesalamine treatment did not change viral load in the lung, heart, or intestinal tissues harvested at 7 dpi. Pretreatment with mesalamine did not modulate intestinal entry of the chimeric VSV-SARS-CoV-2 in K18-ACE2 mice.ConclusionsMesalamine did not alter viral entry, replication, or pathogenesis in vitro or in mouse models. Mesalamine treatment reduced expression of the viral receptor ACE2 while concurrently increasing CTSL expression in human ileum organoids.
Biocompatible soft hydrogel lens as topical implants for diabetic retinopathy
Authors: Sadasivam Rajkumar , Packirisamy Gopinath , Goswami Mayank 
Published: July 2021

AbstractFashioned contact lenses can be converted into novel drug delivery vehicles. Ocular disease like diabetic retinopathy is a major microvascular complication where its early diagnosis and treatment is still a mystery to clinicians. Delivery of pharmaceuticals to the posterior part of eye is quite difficult, with exemption from the injectable formulations. Drug loaded hydrogel like contact lens implants can be utilized in place of commercial contact lens. Such hydrogel lens implants are developed with precise manner in which they are to be inserted as implants in the mice models. The present work is the preliminary outcome of our ongoing research work where the polymerized lens implant can be used as payload carrier for retinopathy. The aim is to propose such appropriate implants suitable for in vivo mice models.
Slow-rising and fast-falling dopaminergic dynamics jointly adjust negative prediction error in the ventral striatum
Authors: Shikano Yu , Yagishita Sho , Tanaka Kenji F. , Takata Norio 
Published: July 2021

AbstractThe greater the reward expectations are, the more different the brain’s physiological response will be. Although it is well-documented that better-than-expected outcomes are encoded quantitatively via midbrain dopaminergic (DA) activity, it has been less addressed experimentally whether worse-than-expected outcomes are expressed quantitatively as well. We show that larger reward expectations upon unexpected reward omissions are associated with the preceding slower rise and following larger decrease (DA dip) in the DA concentration at the ventral striatum of mice. We set up a lever press task on a fixed ratio (FR) schedule requiring five lever presses as an effort for a food reward (FR5). The mice occasionally checked the food magazine without a reward before completing the task. The percentage of this premature magazine entry (PME) increased as the number of lever presses approached five, showing rising expectations with increasing proximity to task completion, and hence greater reward expectations. Fiber photometry of extracellular DA dynamics in the ventral striatum using a fluorescent protein (genetically encoded GPCR-activation-based-DA sensor: GRABDA2m) revealed that the slow increase and fast decrease in DA levels around PMEs were correlated with the PME percentage, demonstrating a monotonic relationship between the DA dip amplitude and degree of expectations. Computational modeling of the lever press task implementing temporal difference errors and state transitions replicated the observed correlation between the PME frequency and DA dip amplitude in the FR5 task. Taken together, these findings indicate that the DA dip amplitude represents the degree of reward expectations monotonically, which may guide behavioral adjustment.
SARS-CoV-2 Exploits Sexually Dimorphic and Adaptive IFN and TNFa Signaling to Gain Entry into Alveolar Epithelium
Authors: Wang Yan , Gurrapu Sreeharsha , Chen Hong , Laudato Sara , Caggiano Emily , Jiang Yan , Ling Hsiang-Hsi , Giancotti Filippo G. 
Published: July 2021

AbstractInfection of the alveolar epithelium constitutes a bottleneck in the progression of COVID-19 to SARS presumably due to the paucity of viral entry receptors in alveolar epithelial type 1 and 2 cells. We have found that the male alveolar epithelial cells express twice as many ACE2 and TMPRSS2 entry receptors as the female ones. Intriguingly, IFN and TNF-α signaling are preferentially active in male alveolar cells and induce binding of the cognate transcription factors to the promoters and lung-active enhancers ofACE2andTMPRSS2. Cotreatment with IFN-I and III dramatically increases expression of the receptors and viral entry in alveolar epithelial cells. TNFα and IFN-II, typically overproduced during the cytokine storm, similarly collaborate to induce these events. Whereas JAK inhibitors suppress viral entry induced by IFN-I/III, simultaneous inhibition of IKK/NF-κB is necessary to block viral entry induced by TNFα and IFN-II. In addition to explaining the increased incidence of SARS in males, these findings indicate that SARS-Cov-2 hijacks epithelial immune signaling to promote infection of the alveolar epithelium and suggest that JAK inhibitors, singly and in combination with NF-KB inhibitors, may exhibit efficacy in preventing or treating COVID-19 SARS.
Mitochondrial DNA variation across 56,434 individuals in gnomAD
Authors: Laricchia Kristen M. , Lake Nicole J. , Watts Nicholas A. , Shand Megan , Haessly Andrea , Gauthier Laura , Benjamin David , Banks Eric , Soto Jose , Garimella Kiran , Emery James ,   Genome Aggregation Database Consortium, Rehm Heidi L. , MacArthur Daniel G. , Tiao Grace , Lek Monkol , Mootha Vamsi K. , Calvo Sarah E. 
Published: July 2021

ABSTRACTDatabases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, genetic databases such as the Genome Aggregation Database (gnomAD) have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three technical challenges: (i) detecting homoplasmic and heteroplasmic variants, present respectively in all or a fraction of mtDNA molecules, (ii) circular mtDNA genome, and (iii) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded samples prone to NUMT misalignment (few mtDNA copies per cell), cell line artifacts (many mtDNA copies per cell), or with contamination and we reported variants with heteroplasmy greater than 10%. We applied this pipeline to 56,434 whole genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. Importantly, we report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mitochondrial population allele frequencies are publicly available at gnomad.broadinstitute.org and will aid in diagnostic interpretation and research studies.
Characterization of BLUF-photoreceptors present in Acinetobacter nosocomialis
Authors: Abatedaga Inés , Mora Bárbara Pérez , Tuttobene Marisel , Müller Gabriela , Biancotti Daiana , Borsarelli Claudio D. , Valle Lorena , Mussi Maria A. 
Published: July 2021

AbstractAcinetobacter nosocomialis is a Gram-negative opportunistic pathogen, whose ability to cause disease in humans is well recognized. Blue light has been shown to modulate important physiological traits related to persistence and virulence in this microorganism. In this work, we characterized the three Blue Light sensing Using FAD (BLUF) domain-containing proteins encoded in the A. nosocomialis genome, which account for the only “traditional” light sensors present in this microorganism. By focusing on a light-modulated bacterial process such as motility, the temperature dependence of light regulation was studied, as well as the expression pattern and spectroscopic characteristics of the different A. nosocomialis BLUFs. Our results show that the three BLUF-containing proteins encode active photoreceptors, despite only two of them are stable in the light-regulatory temperature range when expressed recombinantly. In vivo, only the A. baumannii’s ortholog AnBLUF65 is expressed, which is active in a temperature range from 15 °C to 37 °C. In turn, AnBLUF46 is an active photoreceptor between 15 °C to 32 °C in vitro, but is not expressed in A. nosocomialis in the conditions tested. Intra-protein interactions were analyzed using 3D models built based on A. baumanni’s photoreceptor, to support spectroscopic data and profile intra-protein residue interactions. A general scheme is presented on how hydrophobic/aromatic interactions may contribute to the stability of dark/light- adapted states, indicating the importance of these interactions in BLUF photoreceptors.
Differential mitochondrial protein interaction profile between human translocator protein and its A147T polymorphism variant
Authors: Asih Prita R , Poljak Anne , Kassiou Michael , Ke Yazi D , Ittner Lars M 
Published: July 2021

AbstractThe translocator protein (TSPO) has been implicated in mitochondrial transmembrane cholesterol transport, brain inflammation, and other mitochondrial functions. It is upregulated in glial cells during neuroinflammation in Alzheimer’s disease. High affinity TSPO imaging radioligands are utilized to visualize neuroinflammation. However, this is hampered by the common A147T polymorphism which compromises ligand binding. Furthermore, this polymorphism has been linked to increased risk of neuropsychiatric disorders, and possibly reduces TSPO protein stability. Here, we used immunoprecipitation coupled to mass-spectrometry (IP-MS) to establish a mitochondrial protein binding profile of wild-type (WT) TSPO and the A147T polymorphism variant. Using mitochondria from human glial cells expressing either WT or A147T TSPO, we identified 30 WT TSPO binding partners, yet only 23 for A147T TSPO. Confirming that A147T polymorphism of the TSPO might confer loss of function, we found that one of the identified interactors of WT TSPO, 14-3-3 theta (YWHAQ), a protein involved in regulating mitochondrial membrane proteins, interacts much less with A147T TSPO. Our data presents a network of mitochondrial interactions of TSPO and its A147T polymorphism variant in human glial cells and indicate functional relevance of A147T in mitochondrial protein networks.
Female Bengalese finches recognize their father’s song as sexually attractive
Authors: Fujii Tomoko G. , Okanoya Kazuo 
Published: July 2021

AbstractBirdsong is an important communication signal used in mate choice. In some songbirds, only males produce songs while females do not. Female birds are sensitive to inter- and intra-species song variation. Some aspects of female song preference depend on developmental experiences. For example, in Bengalese finches and zebra finches, adult females prefer the song to which they were exposed early in life, such as the father’s song. However, it is unclear whether such song preference in females is sexually motivated. The purpose of our study is to test if female Bengalese finches recognize their father’s song as sexually attractive. We measured copulation solicitation displays during playbacks of the father’s song vs. unfamiliar conspecific songs and found that across individuals, the father’s song elicited more displays than other songs. In addition, we analyzed if a bird’s response to a given song could be predicted by the level of similarity of that song to the father’s song. The results suggest that preference for the father’s song in this species is actually relevant to mate choice. Although more precise control is necessary in future studies to elucidate the process of preference development, our results imply the significance of early-life experience in shaping female song preference.
Evaluation of the sensitivity and specificity of three diagnostic tests for Coxiella burnetii infection in cattle and buffaloes in Punjab (India) using Bayesian latent class analysis
Authors: Meletis E. , Keshavamurthy R. , Singh B.B. , Aulakh R.S. , Dhand N.K. , Kostoulas P. 
Published: July 2021

AbstractQ Fever is a zoonotic disease of significant animal and public health concern, caused by Coxiella burnetii (C. burnetii), an obligate intracellular bacterium. This study was done to evaluate the sensitivity (Se) and specificity (Sp) of three diagnostic methods to diagnose C. burnetii infection in cattle and buffaloes in Punjab, India: an indirect ELISA method applied in serum samples and a trans-Polymerase Chain Reaction (trans-PCR) technique applied in milk samples and genital swabs. Bayesian Latent Class Models were developed following the STARD-BLCM reporting guidelines. Conditional independence was assumed between the tests, given (i) the different biological principle of ELISA and trans-PCR and (ii) the fact that the trans-PCR was performed on different tissues. The ELISA method in the serum samples showed the highest Se of 0.97 (95% Probability Intervals (PIs): 0.93; 0.99) compared to the trans-PCR method applied in milk samples 0.76 (0.62; 0.87) and genital swabs 0.7 (0.55; 0.82). The Sps of all tests were high, with trans-PCR in genital swabs recording the highest Sp of 0.99 (0.98; 1), while the Sp of trans-PCR in milk samples and ELISA in serum samples were 0.98 (0.96; 0.99) and 0.95 (0.93; 0.97) respectively. The study results show that none of the applied tests are perfect, therefore, a testing regimen based on the diagnostic characteristic of the tests may be considered for diagnosis of C. burnetii.
Vision-based monitoring and measurement of bottlenose dolphins’ daily habitat use and kinematics
Authors: Gabaldon Joaquin , Zhang Ding , Lauderdale Lisa , Miller Lance , Johnson-Roberson Matthew , Barton Kira , Shorter K. Alex 
Published: July 2021

AbstractThis research presents a framework to enable computer-automated observation and monitoring of bottlenose dolphins (Tursiops truncatus) in a professionally managed environment. Results from this work provide insight into the dolphins’ movement patterns, kinematic diversity, and how changes in the environment affect their dynamics. Fixed overhead cameras were used to collect ∼100 hours of observations, recorded over multiple days including time both during and outside of formal training sessions. Animal locations were estimated using convolutional neural network (CNN) object detectors and Kalman filter post-processing. The resulting animal tracks were used to quantify habitat use and animal dynamics. Additionally, Kolmogorov-Smirnov analyses of the swimming kinematics were used for high-level behavioral mode classification. The detectors achieved a minimum Average Precision of 0.76. Performing detections and post-processing yielded 1.24×107estimated dolphin locations. Animal kinematic diversity was found to be lowest in the morning and peaked immediately before noon. Regions of the habitat displaying the highest activity levels correlated to locations associated with animal care specialists, conspecifics, or enrichment. The work presented here demonstrates that CNN object detection is not only viable for large-scale marine mammal tracking, it also enables automated analyses of dynamics that provide new insight into animal movement and behavior.
Virulence and antimicrobial resistance profile of non-typhoidalSalmonella entericaserovars recovered from poultry processing environments at wet markets in Dhaka, Bangladesh
Authors: Siddiky Nure Alam , Sarker Md Samun , Khan Md. Shahidur Rahman , Rahman Md. Tanvir , Kafi Md. Abdul , Samad Mohammed A. 
Published: July 2021

AbstractThe rapid emergence of virulent and multidrug-resistant (MDR) non-typhoidalSalmonella(NTS)entericaserovars are a growing public health concern globally. The present study focused on the assessment of the pathogenicity and antimicrobial resistance (AMR) profiling of NTSentericaserovars isolated from chicken processing environments at wet markets in Dhaka, Bangladesh. A total number of 870 samples consisting of carcass dressing water (CDW), chopping board swabs (CBS), and knife swabs (KS) were collected from 29 wet markets. The prevalence ofSalmonellawas found to be 20% in CDW, 19.31% in CBS and 17.58% in KS, respectively. Meanwhile, the MDRSalmonellawas found to be 72.41%, 73.21% and 68.62% in CDW, CBS, and KS, respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namelyinvA,agfA,IpfA,hilA,sivH,sefA,sopE, andspvC. TheS. Enteritidis and untypedSalmonellaisolate harbored all virulence genes whileS. Typhimurium isolates carried six virulence genes exceptsefA andspvC. Phenotypic resistance revealed decreased susceptibility to ciprofloxacin, streptomycin, ampicillin, tetracycline, gentamycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanic acid and azithromycin. Genotypic resistance showed higher prevalence of plasmid mediatedblaTEM followed bytetA,sul1,sul2,sul3, andstrA/B genes. Harmonic and symmetrical trend was observed among the phenotypic and genotypic resistance patterns of the isolates. The research findings anticipate that MDR and virulent NTSentericaserovars are prevailing in the wet market environments which can easily enter into the human food chain. There was a resilient and significant correlation existent among the phenotypic and genotypic resistance patterns and virulence genes ofSalmonellaisolate recovered from carcass dressing water, chopping board swabs, and knife swabs (p< 0.05), respectively.