bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hippocampal radiotherapy dose constraints for predicting long-term neurocognitive outcomes: mature data from a prospective trial in young patients with brain tumors
Authors: Goda Jayant S , Dutta Debnarayan , Krishna Uday , Goswami Savita , Kothavade Vikas , Kannan Sadhna , Maitre Madan , Bano Nazia , Gupta Tejpal , Jalali Rakesh 
Published: March 2020

Abstract

Background
Hippocampus is considered to be the seat for neurocognitive functions. Avoidance of hippocampus during radiotherapy to brain may serve to preserve various domains of neurocognition. We aimed to derive radiotherapy dose constraints to hippocampi for preserving neurocognition in young patients with brain tumors by measuring various neurocognitive parameters.

Methods
Forty-eight patients with residual/progressive benign or low-grade brain tumors treated with stereotactic conformal radiotherapy (SCRT) to a dose of 54 Gy in 30 fractions underwent prospective neuropsychological assessments at baseline before SCRT and at 6 months and 2, 3, 4, and 5 years. Hippocampi were drawn as per the Radiation Therapy Oncology Group atlas. Longitudinal change in intelligence quotient scores was correlated with hippocampal doses.

Results
Mean volume of bilateral hippocampi was 4.35 cc (range: 2.12–8.41 cc). Craniopharyngioma was the commonest histologic subtype. A drop of &gt;10% in mean full-scale intelligence quotient (FSIQ) scores at 3 and 5 years post SCRT was observed in patients in whom left hippocampus received a mean dose of 30.7 Gy (P = 0.04) and 31 Gy (P = 0.04), respectively. Mean performance quotient (PQ) scores dropped &gt; 10% at 5 years when the left hippocampus received a dose of &gt; 32 Gy (P = 0.03). There was no significant correlation of radiotherapy doses with verbal quotient, or with doses received by the right hippocampus. Multivariate analysis revealed young age (&lt;13 y) and left hippocampus dose predicted for clinically relevant decline in certain neurocognitive domains.

Conclusions
A mean dose of ≤30 Gy to the left hippocampus as a dose constraint for preserving intelligence quotient is suggested.

Key Points
1. Children and young adults with benign and low-grade gliomas survive long after therapy.
2. Higher dose to the hippocampi may result in long-term neurocognitive impairment.
3. Mean dose of &lt;30 Gy to left hippocampus could be used as a pragmatic dose constraint to prevent long-term neurocognitive decline.
Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Authors: Käse Laura , Kraberg Alexandra C , Metfies Katja , Neuhaus Stefan , Sprong Pim A A , Fuchs Bernhard M , Boersma Maarten , Wiltshire Karen H 
Published: March 2020

Abstract
The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations.
Large enhancement of conductivity in a strongly layered type-II superconductor with an artificial pinning array
Authors: Tinh Bui Duc 
Published: March 2020

Abstract
We use the time-dependent Ginzburg–Landau equation to describe a type-II superconductor in a magnetic field in the presence of both strong thermal fluctuations and an artificial pinning array. Thermal fluctuations are represented by the Langevin white noise. The layered structure of the superconductor is taken into accounted with the Lawrence–Doniach model. The self-consistent Gaussian approximation is used to treat the nonlinear interaction term in the time-dependent Ginzburg–Landau equation. In the case of the $\delta $-function model for the pinning centers and the matching field, analytic expressions for the fluctuation electrical and thermoelectric conductivity are obtained. It is found that the fluctuations in electrical and thermoelectric conductivities increase with increasing pinning strength, and when the pinning strength comes near a critical value, the fluctuation conductivity is greatly enhanced. Our result shows that if a pinning array is added to a mixed state superconductor, the original properties of the superconductor are recovered. Physically, in the presence of thermal fluctuations, when the energy scale of the vortex lattice shear fluctuations becomes comparable to the pinning energy scale there is a large enhancement of the fluctuation conductivity in the presence of pinning.
Global transmission network of SARS-CoV-2: from outbreak to pandemic
Authors: Skums Pavel , Kirpich Alexander , Baykal Pelin Icer , Zelikovsky Alex , Chowell Gerardo 
Published: March 2020

AbstractBackgroundThe COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is straining health systems around the world. Although the Chinese government implemented a number of severe restrictions on people’s movement in an attempt to contain its local and international spread, the virus had already reached many areas of the world in part due to its potent transmissibility and the fact that a substantial fraction of infected individuals develop little or no symptoms at all. Following its emergence, the virus started to generate sustained transmission in neighboring countries in Asia, Western Europe, Australia, Canada and the United States, and finally in South America and Africa. As the virus continues its global spread, a clear and evidence-based understanding of properties and dynamics of the global transmission network of SARS-CoV-2 is essential to design and put in place efficient and globally coordinated interventions.MethodsWe employ molecular surveillance data of SARS-CoV-2 epidemics for inference and comprehensive analysis of its global transmission network before the pandemic declaration. Our goal was to characterize the spatial-temporal transmission pathways that led to the establishment of the pandemic. We exploited a network-based approach specifically tailored to emerging outbreak settings. Specifically, it traces the accumulation of mutations in viral genomic variants via mutation trees, which are then used to infer transmission networks, revealing an up-to-date picture of the spread of SARS-CoV-2 between and within countries and geographic regions.Results and ConclusionsThe analysis suggest multiple introductions of SARS-CoV-2 into the majority of world regions by means of heterogeneous transmission pathways. The transmission network is scale-free, with a few genomic variants responsible for the majority of possible transmissions. The network structure is in line with the available temporal information represented by sample collection times and suggest the expected sampling time difference of few days between potential transmission pairs. The inferred network structural properties, transmission clusters and pathways and virus introduction routes emphasize the extent of the global epidemiological linkage and demonstrate the importance of internationally coordinated public health measures.
Phylogenetic analyses suggest independent origins for trichromatic color vision in apes and Old World monkeys
Authors: Toloza-Villalobos Jessica , Opazo Juan C. 
Published: March 2020

AbstractIn catarrhine primates, trichromatic color vision is associated with the presence of three opsin genes that absorb light at three different wavelengths. The OPN1LW and OPN1MW genes are found on the X chromosome. Their proximity and similarity suggest that they originated from a duplication event in the catarrhine ancestor. In this study we use the primate genomes available in public databases to study the duplicative history of the OPN1LW and OPN1MW genes and characterize their spectral sensitivity. Our results reveal a phylogenetic tree that shows a clade containing all X-linked opsin paralogs found in Old World monkeys to be related to a clade containing all X-linked opsin paralogs identified in apes, suggesting that routine trichromacy originated independently in apes and Old World monkeys. Also, we found spectral variability in the X-linked opsin gene of primates. Our study presents a new perspective for the origin of trichromatic color vision in apes and Old World monkeys, not reported so far.
Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens
Authors: Nerli Santrupti , Sgourakis Nikolaos G. 
Published: March 2020

ABSTRACTAs a first step toward the development of diagnostic and therapeutic tools to fight the Coronavirus disease (COVID-19), it is important to characterize CD8+ T cell epitopes in the SARS-CoV-2 peptidome that can trigger adaptive immune responses. Here, we use RosettaMHC, a comparative modeling approach which leverages existing high-resolution X-ray structures from peptide/MHC complexes available in the Protein Data Bank, to derive physically realistic 3D models for high-affinity SARS-CoV-2 epitopes. We outline an application of our method to model 439 9mer and 279 10mer predicted epitopes displayed by the common allele HLA-A*02:01, and we make our models publicly available through an online database (https://rosettamhc.chemistry.ucsc.edu). As more detailed studies on antigen-specific T cell recognition become available, RosettaMHC models of antigens from different strains and HLA alleles can be used as a basis to understand the link between peptide/HLA complex structure and surface chemistry with immunogenicity, in the context of SARS-CoV-2 infection.
Complex naturalistic stimuli are prioritized by attention when maintained in visual working memory
Authors: Rutkowska Natalia , Doradzińska Łucja , Bola Michał 
Published: March 2020

AbstractRecent studies suggest that a stimulus actively maintained in working memory (WM) automatically captures visual attention when subsequently perceived. Such a WM-guidance effect has been consistently observed for stimuli defined by simple features, such as colour or orientation, but studies using more complex stimuli provide inconclusive results. Therefore, we investigated whether the WM-guidance effect occurs also for naturalistic stimuli, whose identity is defined by multiple features and relations among them, specifically for faces and houses. The experiment consisted of multiple blocks in which participants (N = 28) either memorized or merely saw (WM or exposure condition, respectively) a template stimulus and then performed several dot-probe trials, with pairs of stimuli (template and control) presented laterally as distractors and followed by a target-asterisk. Evidence for attentional prioritization of the memorized stimuli was found in the reaction-times (RT) analysis, but not in the analysis of the N2pc ERP component, which raises questions concerning the attentional mechanism involved. Further, in an exploratory ERP analysis we found evidence for a very early (100-200 ms post-stimulus) prioritization specific to the memorized faces, which is in line with the sensory recruitment theory of WM.
Analysis of adaptive immune cell populations and phenotypes in the patients infected by SARS-CoV-2
Authors: Yang Xiaofeng , Dai Tongxin , Zhou Xiaobo , Qian Hongbo , Guo Rui , Lei Lei , Zhang Xingzhe , Zhang Dan , Shi Lin , Cheng Yanbin , Hu Jinsong , Guo Yaling , Zhang Baojun 
Published: March 2020

AbstractCoronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread to most of countries in the world, threatening the health and lives of many people. Unfortunately, information regarding the immunological characteristics in COVID-19 patients remains limited. Here we collected the blood samples from 18 healthy donors (HD) and 38 COVID-19 patients to analyze changes in the adaptive immune cell populations and phenotypes. In comparison to HD, the lymphocyte percentage was slightly decreased, the percentages of CD4 and CD8 T cells in lymphocytes are similar, whereas B cell percentage increased in COVID-19 patients. T cells, especially CD8 T cells, showed an enhanced expression of late activation marker CD25 and exhaustion marker PD-1. Importantly, SARS-CoV-2 induced an increased percentage of T follicular helpher (Tfh)- and germinal center B-like (GCB-like) cells in the blood. However, the parameters in COVD-19 patients remained unchanged across various age groups. Therefore, we demonstrated that the T and B cells can be activated normally and exhibit functional features. These data provide a clue that the adaptive immunity in most people could be primed to induce a significant immune response against SARS-CoV-2 infection upon receiving standard medical care.
Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection
Authors: Chen Xiaoping , Jiang Qunqun , Ma Zhiyong , Ling Jiaxin , Hu Wenjia , Cao Qian , Mo Pingzheng , Yang Rongrong , Gao Shicheng , Gui Xien , Xiong Yong , Li Jinlin , Zhang Yongxi 
Published: March 2020

AbstractBackground & AimsThe coronavirus disease 2019 (COIVD-19) caused by SARS-CoV-2 has been characterized as a pandemic, which causes a serious public health challenge in the world. A very large group of patients infected by HBV has been reported worldwide, especially in China. In order to answer whether specific treatment strategy on the patients coinfected with HBV and SARS-CoV-2, it requires profound understanding of the clinical characteristics on those patients. However, the impacts of SARS-CoV-2 infection on HBV patients remain largely unknown.Approach & ResultsIn this retrospective investigation, we included 123 COVID-19 patients admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from January 5 to March 7, 2020. All enrolled patients are the laboratory confirmed COVID-19 pneumonia cases according to the criteria reported previously. A total of 123 patients were analyzed for their Clinical records, laboratory results including the diagnosis of HBV infection and liver function. Among 123 confirmed COVID-19 patients, the mean age was 51 years old and 59.3% were females (73/123). Fifteen were previously HBV infected patients, 66.7% of them were males (10/15), patients with HBV infection appeared to have a higher incidence of liver cirrhosis and an increased level of total bilirubin. Seven (46.7%) patients with HBV infection were defined as severe cases, while the severity rate was 24.1% for the patients without HBV infection (26/108). The mortality of patients with HBV infection was 13.3% (2/15) compared to 2.8% (3/108) for the patients without HBV infection.ConclusionsSARS-CoV-2 infection may cause Live function damage in COVID-19 cases and the patients with HBV infection are likely to have more severe disease outcome.
Core Outcome Set for Clinical Trials of COVID-19 based on Traditional Chinese and Western Medicine
Authors: Qiu Ruijin , Zhao Chen , Liang Tengxiao , Hao Xuezeng , Huang Ya , Zhang Xiaoyu , Chen Zhao , Wei Xuxu , Zhao Mengzhu , Zhong Changming , Hu Jiayuan , Li Min , Han Songjie , He Tianmai , Chen Jing , Shang Hongcai 
Published: March 2020

AbstractBackgroundDevelopment of a core outcome set (COS) for clinical trials for COVID-19 is urgent because of the pandemic wreaking havoc worldwide and the heterogeneity of outcomes in clinical trials.MethodsA preliminary list of outcomes were developed after a systematic review of protocols of clinical trials for COVID-19. Then, two rounds of the Delphi survey were conducted. Stakeholders were traditional Chinese medicine (TCM) experts, Western medicine (WM) experts, nurses and the public. Patients with confirmed COVID-19 were also invited to participate in a questionnaire written in understandable language. Frontline clinicians, as well as nurse, methodologist, evidence based-medicine researcher, and staff from the Chinese Clinical Trials Registry participated by video conference to vote.ResultsNinety-seven eligible study protocols were identified from 160 clinical trials. Seventy-six outcomes were identified from TCM clinical trials and 126 outcomes were identified from WM clinical trials. Finally, 145 outcomes were included in the first round of the Delphi survey. Then, a COS for clinical trials of TCM and WM was developed. The COS include clinical outcomes (recovery/improvement/progression/death), etiology (SARS-CoV-2 nucleic-acid tests, viral load), inflammatory factor (C-reactive protein), vital signs (temperature, respiration), blood and lymphatic-system parameters (lymphocytes, virus antibody), respiratory outcomes (Pulmonary imaging, blood oxygen saturation, PaO2/FiO2 ratio, arterial blood gas analysis, mechanical ventilation, oxygen intake, pneumonia severity index), clinical efficacy (prevalence of preventing patients with mild-to-moderate disease progressing to severe disease), symptoms (clinical symptom score). Outcomes were recommended according to different types of disease. Outcome measurement instrument/definition were also recommended.ConclusionA COS for COVID-19 may improve consistency of outcome reporting in clinical trials.
Spectral Clustering of Risk Score Trajectories Stratifies Sepsis Patients by Clinical Outcome and Interventions Received
Authors: Liu Ran , Greenstein Joseph L. , Fackler James C. , Bembea Melania M. , Winslow Raimond L. 
Published: March 2020

AbstractSepsis is not a monolithic disease, but a loose collection of symptoms with a diverse range of outcomes. The diverse patterns of sepsis make guideline-driven treatment difficult, as guidelines are based on the needs of the “average” patient. Thus, stratification and subtyping of sepsis patients is of interests, with the ultimate goal of identifying groups of patients who respond similarly to treatment. To do this, we examine the temporal evolution of patient state using our previously-published method for computing patient risk of transition into septic shock. The application of spectral clustering to risk score trajectories reveals that these trajectories diverge into four distinct clusters in the time window following early prediction of septic shock. Patients in these clusters stratify by outcome: the highest-risk group has a 76.5% prevalence of septic shock and 43% mortality, whereas the lowest-risk group has a 10.4% prevalence of septic shock and 18% mortality. These clusters differ also in treatments received, as well as median time to septic shock onset. Data analyses reveal the existence of a rapid (30-60 min) transition in risk at the time of threshold crossing. We hypothesize that this rapid transition occurs as a result of an abrupt failure of compensatory biological systems to cope with infection, resulting in a bifurcation of low to high risk. Such a collapse in compensation, we believe, represents the true onset of septic shock. Thus, what we previously referred to as the pre-shock state represents a potential new data-driven definition of septic shock.
A Social Network Model of the COVID-19 Pandemic
Authors: Zhao Pei Jun 
Published: March 2020

AbstractIn the COVID-19 coronavirus pandemic, currently vaccines and specific anti-viral treatment are not yet available. Thus, preventing viral transmission by case isolation, quarantine, and social distancing is essential to slowing its spread. Here we model social networks using weighted graphs, where vertices represent individuals and edges represent contact. As public health measures are implemented, connectivity in the graph decreases, resulting in lower effective reproductive numbers, and reduced viral transmission. For COVID-19, model parameters were derived from the coronavirus epidemic in China, validated by epidemic data in Italy, then applied to the United States. We calculate that, in the U.S., the public is able to contain viral transmission by limiting the average number of contacts per person to less than 7 unique individuals over each 5 day period. This increases the average social distance between individuals to 10 degrees of separation.
Population-Level Mortality Rates from Novel Coronavirus (COVID-19) in South Korea
Authors: Soneji Samir , Beltrán-Sánchez Hiram , Yang JaeWon , Mann Caroline 
Published: March 2020

ABSTRACTBackgroundSouth Korea was among the first countries to report a case of the novel coronavirus (COVID-19) outside of China. As of 22 March, 2020, South Korea reported 8897 confirmed cases of and 104 deaths from COVID-19.MethodsWe collected the number of laboratory-confirmed cases and deaths in South Korea from the World Health Organization (as of 21 March, 2020) and case distribution and fatality rates by age from the Korean Center for Disease Control and Prevention (as of 22 March, 2020). We estimated population-level mortality rates by fitting a negative binomial regression model with the number of deaths as the outcome and population by age as an offset. We then calculated the age-standardized death rate (ASDR) based on the current COVID-19 figures and for alternative scenarios of increased prevalence.FindingsThe COVID-19 population-level mortality rate (per 100,000 person-years) increased with age: from 0.1 deaths among 30-39 year olds to 9.5 deaths among ≥80 year olds. The ASDR (per 100,000 person-years) was 0.8 deaths. The ASDR would increase to 52.0 deaths at a 1% prevalence (becoming the third leading cause of death) and 155.9 deaths at 3% prevalence (becoming the leading cause of death).InterpretationCurrently, the population-level mortality burden of COVID-19 in South Korea, as measured by the ASDR, was relatively low compared to other causes of death partly due to the low prevalence of COVID-19. If the prevalence increases from another outbreak, the mortality burden could increase substantially and surpass other leading causes.FundingGrant P2C-HD041022, California Center for Population Research, University of California, Los Angeles (US NIH).