bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth impacts in a changing ocean: insights from two coral reef fishes in an extreme environment
Authors: D’Agostino Daniele , Burt John A. , Santinelli Veronica , Vaughan Grace O. , Fowler Ashley , Reader Tom , Taylor Brett M. , Hoey Andrew S. , Cavalcante Georgenes H. , Bauman Andrew G. , Feary David A. 
Published: June 2020

AbstractDetermining the life history consequences for fishes living in extreme and variable environments will be vital in predicting the likely impacts of ongoing climate change on reef fish demography. Here, we compare size-at-age and maximum body size of two common reef fish species (Lutjanus ehrenbergiiandPomacanthus maculosus) between the environmentally extreme Arabian/Persian Gulf (‘Arabian Gulf’) and adjacent comparably benign Oman Sea. Additionally, we use otolith increment width profiles to investigate the influence of temperature, salinity and productivity on the individual growth rates. Individuals of both species showed smaller size-at-age and lower maximum size in the Arabian Gulf compared to conspecifics in the less extreme and less variable environment of the Oman Sea, suggesting a life-history trade-off between size and metabolic demands. Salinity was the best environmental predictor of interannual growth across species and regions, with low growth corresponding to more saline conditions. However, salinity had a weaker negative effect on interannual growth of fishes in the Arabian Gulf than in the Oman Sea, indicating Arabian Gulf populations may be better able to acclimate to changing environmental conditions. Temperature had a weak positive effect on the interannual growth of fishes in the Arabian Gulf, suggesting that these populations may still be living within their thermal windows. Our results highlight the potential importance of osmoregulatory cost in impacting growth, and the need to consider the effect of multiple stressors when investigating the consequences of future climate change on fish demography.
Dynamics of isoflurane-induced vasodilation and blood flow of cerebral vasculature revealed by multi-exposure speckle imaging
Authors: Sullender Colin T. , Richards Lisa M. , He Fei , Luan Lan , Dunn Andrew K. 
Published: June 2020

AbstractBackgroundAnesthetized animal models are used extensively during neurophysiological and behavioral studies despite systemic effects from anesthesia that undermine both accurate interpretation and translation to awake human physiology. The majority of work examining the impact of anesthesia on cerebral blood flow (CBF) has been restricted to before and after measurements with limited spatial resolution.New MethodWe used multi-exposure speckle imaging (MESI), an advanced form of laser speckle contrast imaging (LSCI), to characterize the dynamics of isoflurane anesthesia induction on cerebral vasculature and blood flow in the mouse brain.ResultsThe large anatomical changes caused by isoflurane are depicted with wide-field imagery and video highlighting the induction of general anesthesia. Within minutes of exposure, both vessel diameter and blood flow increased drastically compared to the awake state and remained elevated for the duration of imaging. An examination of the dynamics of anesthesia induction reveals that blood flow increased faster in arteries than in veins or parenchyma regions.Comparison with Existing MethodsMESI offers robust hemodynamic measurements across large fields-of-view and high temporal resolutions sufficient for continuous visualization of cerebrovascular events featuring major changes in blood flow.ConclusionThe large alterations caused by isoflurane anesthesia to the cortical vasculature and CBF are readily characterized using MESI. These changes are unrepresentative of normal physiology and provide further evidence that neuroscience experiments would benefit from transitioning to un-anesthetized awake animal models.
A facile Q-RT-PCR assay for monitoring SARS-CoV-2 growth in cell culture
Authors: Mugisha Christian Shema , Vuong Hung R. , Puray-Chavez Maritza , Kutluay Sebla B. 
Published: June 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the ongoing COVID-19 pandemic, has infected millions within just a few months and is continuing to spread around the globe causing immense respiratory disease and mortality. Assays to monitor SARS-CoV-2 growth depend on time-consuming and costly RNA extraction steps, hampering progress in basic research and drug development efforts. Here we developed a facile Q-RT-PCR assay that bypasses viral RNA extraction steps and can monitor SARS-CoV-2 replication kinetics from a small amount of cell culture supernatants. Using this assay, we screened the activities of a number of entry, SARS-CoV-2- and HIV-1-specific inhibitors in a proof of concept study. In line with previous studies which has shown that processing of the viral Spike protein by cellular proteases and endosomal fusion are required for entry, we found that E64D and apilimod potently decreased the amount of SARS-CoV-2 RNA in cell culture supernatants with minimal cytotoxicity. Surprisingly, we found that macropinocytosis inhibitor EIPA similarly decreased viral RNA in supernatants suggesting that entry may additionally be mediated by an alternative pathway. HIV-1-specific inhibitors nevirapine (an NNRTI), amprenavir (a protease inhibitor), and ALLINI-2 (an allosteric integrase inhibitor) modestly inhibited SARS-CoV-2 replication, albeit the IC50values were much higher than that required for HIV-1. Taken together, this facile assay will undoubtedly expedite basic SARS-CoV-2 research, be amenable to mid-throughput screens to identify chemical inhibitors of SARS-CoV-2, and be applicable to a broad number of RNA and DNA viruses.ImportanceSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the COVID-19 pandemic, has quickly become a major global health problem causing immense respiratory disease and social and economic disruptions. Conventional assays that monitor SARS-CoV-2 growth in cell culture rely on costly and time-consuming RNA extraction procedures, hampering progress in basic SARS-CoV-2 research and development of effective therapeutics. Here we developed a facile Q-RT-PCR assay to monitor SARS-CoV-2 growth in cell culture supernatants that does not necessitate RNA extraction, and is as accurate and sensitive as existing methods. In a proof-of-concept screen, we found that E64D, apilimod, EIPA and remdesivir can substantially impede SARS-Cov-2 replication providing novel insight into viral entry and replication mechanisms. This facile approach will undoubtedly expedite basic SARS-CoV-2 research, be amenable to screening platforms to identify therapeutics against SARS-CoV-2 and can be adapted to numerous other RNA and DNA viruses.
Caudal-rostral progression of alpha motoneurone degeneration in the SOD1G93Amouse model of amyotrophic lateral sclerosis
Authors: Kirby Alastair J , Palmer Thomas , Mead Richard , Ichiyama Ronaldo , Chakrabarty Samit 
Published: June 2020

AbstractMice with transgenic expression of human SOD1G93Aare a widely used model of ALS, with a caudal-rostral progression of motor impairment. Previous studies have quantified the progression of motoneurone (MN) degeneration based on size, even though alpha (α-) and gamma (γ-) MNs overlap in size. Therefore, using molecular markers and synaptic inputs, we quantified the survival of α-MNs and γ-MNs at the lumbar and cervical spinal segments of 3- and 4-month SOD1G93Amice, to investigate whether there is a caudal-rostral progression of MN death. By 3-months, in the cervical and lumbar spinal cord, there was α-MN degeneration with complete γ-MN sparing. At 3-months the cervical spinal cord had more α-MNs per ventral horn than the lumbar spinal cord, in SOD1G93Amice. A similar spatial trend of degeneration was observed in the corticospinal tract, which remained intact in the cervical spinal cord at 3- and 4-months of age. These findings agree with the corticofugal synaptopathy model, that α-MN and CST of the lumbar spinal cord are more susceptible to degeneration in SOD1G93Amice. Hence, there is spatial and temporal caudal-rostral progression of α-MN and CST degeneration in SOD1G93Amice.HighlightsSOD1G93Amice display a caudal-rostral progression of motor impairment.Lumbar spinal cord of SOD1G93Amice has an enhanced susceptibility to degeneration.SOD1G93Amice exhibit a caudal-rostral progression of α-MN and CST degeneration
Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates
Authors: Sang Eric R. , Tian Yun , Gong Yuanying , Miller Laura C. , Sang Yongming 
Published: June 2020

AbstractThe current new coronavirus disease (COVID-19) has caused globally near 0.4/6 million confirmed deaths/infected cases across more than 200 countries. As the etiological coronavirus (a.k.a. SARS-CoV2) may putatively have a bat origin, our understanding about its intermediate reservoir between bats and humans, especially its tropism in wild and domestic animals, are mostly unknown. This constitutes major concerns in public health for the current pandemics and potential zoonosis. Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. Through integration of key immunogenetic factors, including the existence of S-binding-void ACE2 isoforms and the disparity of ACE2 expression upon early innate immune response, we further refine the SARS-CoV2 susceptibility prediction to fit recent experimental validation. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Thus, we propose that domestic animals may be unlikely to play a role as amplifying hosts unless the virus has further species-specific adaptation. These findings may relieve relevant public concerns regarding COVID-19-like risk in domestic animals, highlight virus-host coevolution, and evoke disease intervention through targeting ACE2 molecular diversity and interferon optimization.
Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay
Authors: Brannon A. Rose , Jayakumaran Gowtham , Diosdado Monica , Patel Juber , Razumova Anna , Hu Yu , Meng Fanli , Haque Mohammad , Sadowska Justyna , Murphy Brian J. , Baldi Tessara , Johnson Ian , Ptashkin Ryan , Hasan Maysun , Srinivasan Preethi , Rema Anoop Balakrishnan , Rijo Ivelise , Agarunov Aaron , Won Helen , Perera Dilmi , Brown David N. , Samoila Aliaksandra , Jing Xiaohong , Gedvilaite Erika , Yang Julie L. , Stephens Dennis P. , Dix Jenna-Marie , DeGroat Nicole , Nafa Khedoudja , Syed Aijazuddin , Li Alan , Lebow Emily S. , Bowman Anita S. , Ferguson Donna C. , Liu Ying , Mata Douglas A. , Sharma Rohit , Yang Soo-Ryum , Bale Tejus , Benhamida Jamal K. , Chang Jason C. , Dogan Snjezana , Hameed Meera R. , Hechtman Jaclyn F. , Moung Christine , Ross Dara S. , Vakiani Efsevia , Vanderbilt Chad M. , Yao JinJuan , Razavi Pedram , Smyth Lillian M. , Chandarlapaty Sarat , Iyer Gopa , Abida Wassim , Harding James J. , Krantz Benjamin , O’Reilly Eileen , Yu Helena A. , Li Bob , Rudin Charles , Diaz Luis , Solit David B. , Arcila Maria E. , Ladanyi Marc , Houck-Loomis Brian , Tsui Dana , Berger Michael F. , Zehir Ahmet , Benayed Ryma 
Published: June 2020

AbstractCirculating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 98% fora priorimutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance.
Segmenting surface boundaries using luminance cues: Underlying mechanisms
Authors: DiMattina Christopher , Baker Curtis L. 
Published: June 2020

ABSTRACTSegmenting scenes into distinct surfaces is a basic visual perception task, and luminance differences between adjacent surfaces often provide an important segmentation cue. However, mean luminance differences between two surfaces may exist without any sharp change in albedo at their boundary, but rather from differences in the proportion of small light and dark areas within each surface, e.g. texture elements, which we refer to as aluminance texture boundary. Here we investigate the performance of human observers segmenting luminance texture boundaries. We demonstrate that a simple model involving a single stage of filtering cannot explain observer performance, unless it incorporates contrast normalization. Performing additional experiments in which observers segment luminance texture boundaries while ignoring super-imposed luminance step boundaries, we demonstrate that the one-stage model, even with contrast normalization, cannot explain performance. We then present a Filter-Rectify-Filter (FRF) model positing two cascaded stages of filtering, which fits our data well, and explains observers’ ability to segment luminance texture boundary stimuli in the presence of interfering luminance step boundaries. We propose that such computations may be useful for boundary segmentation in natural scenes, where shadows often give rise to luminance step edges which do not correspond to surface boundaries.
Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review
Authors: Sehmi Prabjot , Cheruiyot Isaac 
Published: June 2020

ABSTRACTCoronavirus disease 2019 (COVID-19) is a rapidly escalating pandemic that has spread to many parts of the world. The disease has already affected over 6 million individuals, with over 400,000 fatalities. Recent studies have confirmed the presence of SARS-CoV-2 nucleic acids in feces of Coronavirus disease 2019 (COVID-19) patients using RT-PCR tests. It is however, still unclear as to whether or not live SARS-CoV-2 virus is actually present in feces of these patients. In this rapid review, we systematically analyzed literature to establish any evidence of live SARS-CoV- 2 virus in fecal samples of COVID-19 patients. We identified 4 studies (one case report, 2 case series and 1 cohort study) where the SARS-CoV-2 was successfully isolated from fecal samples of COVID-19 patients using culture techniques. Therefore, there is some evidence COVID-19 could shed live SARS-CoV-2 virus via the gastro-intestinal tract. Larger studies are needed to corroborate these findings, as well as to determine its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies.
Chest CT Images for COVID-19: Radiologists and Computer-based detection
Authors: Dou Qingli , Liu Jiangping , Zhang Wenwu , Gu Yanan , Hsu Wan-Ting , Ho Kuan-Ching , Tong Hoi Sin , Yu Wing Yan , Lee Chien-Chang 
Published: June 2020

ABSTRACTBackgroundCharacteristic chest computed tomography (CT) manifestation of 2019 novel coronavirus (COVID-19) was added as a diagnostic criterion in the Chinese National COVID-19 management guideline. Whether the characteristic findings of Chest CT could differentiate confirmed COVID-19 cases from other positive nucleic acid test (NAT)-negative patients has not been rigorously evaluated.PurposeWe aim to test whether chest computed tomography (CT) manifestation of 2019 novel coronavirus (COVID-19) can be differentiated by a radiologist or a computer-based CT image analysis system.MethodsWe conducted a retrospective case-control study that included 52 laboratory-confirmed COVID-19 patients and 80 non-COVID-19 viral pneumonia patients between 20 December, 2019 and 10 February, 2020. The chest CT images were evaluated by radiologists in a double blind fashion. A computer-based image analysis system (uAI system, Lianying Inc., Shanghai, China) detected the lesions in 18 lung segments defined by Boyden classification system and calculated the infected volume in each segment. The number and volume of lesions detected by radiologist and computer system was compared with Chi-square test or Mann-Whitney U test as appropriate.ResultsThe main CT manifestations of COVID-19 were multi-lobar/segmental peripheral ground-glass opacities and patchy air space infiltrates. The case and control groups were similar in demographics, comorbidity, and clinical manifestations. There was no significant difference in eight radiologist identified CT image features between the two groups of patients. There was also no difference in the absolute and relative volume of infected regions in each lung segment.ConclusionsWe documented the non-differentiating nature of initial chest CT image between COVID-19 and other viral pneumonia with suspected symptoms. Our results do not support CT findings replacing microbiological diagnosis as a critical criterion for COVID-19 diagnosis. Our findings may prompt re-evaluation of isolated patients without laboratory confirmation.
Diffuse white matter abnormality in very preterm infants reflects reduced brain network efficiency
Authors: Kline Julia E. , Priyanka Illapani Venkata Sita , Li Hailong , He Lili , Parikh Nehal A. 
Published: June 2020

AbstractBetween 50-80% of very preterm infants (≤32 weeks gestational age) exhibit increased white matter signal intensity on T2 MRI at term-equivalent age, known as diffuse white matter abnormality (DWMA). A few studies have linked DWMA with microstructural abnormalities, but the exact relationship remains poorly understood. We used graph theory methods to relate DWMA extent to measures of efficient information processing at term in a representative cohort of 343 very preterm infants. We performed anatomic and diffusion MRI at term and quantified DWMA volume using our novel, semi-automated algorithm. From structural connectomes, we calculated graph theory metrics: local efficiency and clustering coefficient, which measure the ability of groups of nodes to perform specialized processing, and global efficiency, which assesses the ability of brain regions to efficiently combine information. We computed partial correlations between these measures and DWMA volume, adjusted for confounders. Increasing DWMA volume was associated with decreased global efficiency of the entire brain network (r= - 0.27, p= 8.36E-07) and decreased local efficiency and clustering coefficient within individual networks supporting cognitive, linguistic, and motor functions. We show that DWMA is associated with widespread decreased brain network connectivity in very preterm infants, suggesting it is pathologic and likely has adverse developmental consequences.
Evaluation of national responses to COVID-19 pandemic based on Pareto optimality
Authors: Kochańczyk Marek , Lipniacki Tomasz 
Published: June 2020

AbstractCountries worldwide have adopted various strategies to minimize the socio-economic impact of the ongoing COVID-19 pandemic. Stringency and efficacy of imposed measures vary due to diversity of organizational cultures and ingrained societal practices, but also universally reflect the standpoint from which protecting public health and saving economy are seen as contradictory objectives. We analyzed cumulative deaths per capita and cumulative mobility reduction related to the decrease of economic activity in terms of Pareto optimality to show that as long as epidemic suppression is the aim, the trade-off between the death toll and economic loss is illusory: high death toll correlates with deep lockdown and thus, very likely, with severe economic downturn. We explained this effect by analyzing national epidemic trajectories in the mobility reduction vs. reproduction number (R) plane. When the number of daily new infections is high, mobility reduction is the only way to bring R below 1, but when new infections become sporadic, the epidemic can be suppressed by efficient testing complemented by relatively mild restrictions. South American trajectories suggest that lifting mobility restrictions at R > 1 may ultimately lead to the “herd immunity scenario”, in which transient lockdown only adds economic costs to an inevitably high death toll.
Mesoscopic cortical network reorganization during recovery of partial optic nerve injury in GCaMP6s mice
Authors: Groleau Marianne , Nazari-Ahangarkolaee Mojtaba , Vanni Matthieu P. , Higgins Jacqueline L. , Vézina Bédard Anne-Sophie , Sabel Bernhard A. , Mohajerani Majid H. , Vaucher Elvire 
Published: June 2020

AbstractAs the residual vision following a traumatic optic nerve injury can spontaneously recover over time, we explored the plasticity of cortical networks during the early post-optic nerve crush (ONC) phase. Usingin vivowide-field calcium imaging on awake Thy1-GCaMP6s mice, we characterized resting state and evoked cortical activity before, during, and 30 days after ONC. The recovery of monocular visual acuity and depth perception was evaluated at the same time points. Cortical responses to an LED flash decreased in the contralateral hemisphere in the primary visual cortex and in the secondary visual areas following the ONC, but was partially rescued between 3 and 5 days post-ONC, remaining stable thereafter. The connectivity between visual and non-visual regions was disorganized after the crush, as shown by a decorrelation, but correlated activity was restored 30 days after the injury. The number of surviving retinal ganglion cells dramatically dropped and remained low. At the behavioral level, the ONC resulted in visual acuity loss on the injured side and an increase in visual acuity with the non-injured eye. In conclusion, our results show a reorganization of connectivity between visual and associative cortical areas after an ONC, which is indicative of spontaneous cortical plasticity.