bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Fatal Case of Cardiac Contusion After Blunt Chest Injury
Authors: Farkašová Iannaccone Silvia , Ginelliová Alžbeta , Sopková Dorota , Mistríková Lucia , Fröhlichová Lucia , Dettmeyer Reinhard , Farkaš Daniel 
Published: July 2020

Abstract
In this article, we report the autopsy findings of a 48-year-old man who sustained blunt trauma to the thorax. A medical record review revealed no history of cardiac disease. He presented to the hospital with a computed tomography–verified fracture of the left fourth and fifth ribs, and pulmonary and cardiac contusion. He was released from the hospital in stable condition at his own request 7 days later. Because of sudden deterioration, he was readmitted to the hospital the next day. Electrocardiogram detected cardiac arrhythmia on the 15th day after chest trauma. Electrocardiography detected pericardial effusion and severe mitral insufficiency resulting in left ventricular failure. Death was attributed to diffuse alveolar damage–complicating pneumonia due to cardiac contusion with mitral insufficiency occurring 25 days after hospital admission. Internal examination revealed diffuse fibrinous pericarditis, left atrial tear right above the anterior mitral valve leaflet with intrapericardial granulation tissue, and no sign of myocardial damage. Immunohistochemistry showed significantly more CD68-positive macrophages within tissue taken from the heart, a finding indicative of previous atrial and ventricular myocardial contusion. This case report demonstrates that routine hematoxylin and eosin staining may not always reveal significant myocardial damage.
Current and Future MR Contrast Agents
Authors: Lancelot Eric , Raynaud Jean-Sébastien , Desché Pierre 
Published: July 2020

Abstract
This review summarizes 30 years of experience in the development and clinical use of magnetic resonance (MR) contrast agents. Despite their undisputable usefulness for disease diagnosis, gadolinium (Gd)-based contrast agents (GBCAs) have gone through 2 major safety crises. Approximately 10 years ago, the regulatory agencies decided to restrict the use of GBCAs to minimize the risk of nephrogenic systemic fibrosis in patients with severe renal insufficiency. Yet, following the recent discovery of Gd retention in brain, the same agencies adopted different positions ranging from suspension of marketing authorizations, changes in GBCA safety labeling, and performing preclinical and clinical studies to assess the potential long-term consequences of Gd accumulation on motor and cognitive functions. Besides, magnetic resonance imaging (MRI) has benefited from MR technological advances, which provide alternative solutions to increase the MR signal, generate new contrasts on MRI scans, and accelerate their acquisition and analysis. Altogether, GBCAs in combination with new MR techniques have found their place in the diagnostic pathway of various diseases. Despite the large research efforts to identify and develop alternative Gd-free MR agents, manganese- and iron-based contrast agents have failed to reach market approval. In this context, the development of next-generation MR contrast agents should focus on high-stability and high-relaxivity GBCAs, such as gadopiclenol, which offer the possibility to adapt the administered Gd dose to each indication while ensuring an optimal patient safety.
A Standardized Electrode Nomenclature for Stereoelectroencephalography Applications
Authors: Stone Scellig , Madsen Joseph R. , Bolton Jeffrey , Pearl Phillip L. , Chavakula Vamsidhar , Day Emily 
Published: July 2020

Purpose:
Stereoelectroencephalography (SEEG) is widely performed on individuals with medically refractory epilepsy for whom invasive seizure localization is desired. Despite increasing adoption in many centers across the world, no standardized electrode naming convention exists, generating confusion among both clinical and research teams.

Methods:
We have developed a novel nomenclature, named the Standardized Electrode Nomenclature for SEEG Applications system. Concise, unique, informative, and unambiguous labels provide information about entry point, deep targets, and relationships between electrodes. Inter-rater agreement was evaluated by comparing original electrode names from 10 randomly sampled cases (including 136 electrodes) with those prospectively assigned by four additional blinded raters.

Results:
The Standardized Electrode Nomenclature for SEEG Application system was prospectively implemented in 40 consecutive patients undergoing SEEG monitoring at our institution, creating unique electrode names in all cases, and facilitating implantation design, SEEG recording and mapping interpretation, and treatment planning among neurosurgeons, neurologists, and neurophysiologists. The inter-rater percent agreement for electrode names among two neurosurgeons, two epilepsy neurologists, and one neurosurgical fellow was 97.5%.

Conclusions:
This standardized naming convention, Standardized Electrode Nomenclature for SEEG Application, provides a simple, concise, reproducible, and informative method for specifying the target(s) and relative position of each SEEG electrode in each patient, allowing for successful sharing of information in both the clinical and research settings. General adoption of this nomenclature could pave the way for improved communication and collaboration between institutions.
Descriptive epidemiology of 16,780 hospitalized COVID-19 patients in the United States
Authors: Chawla Devika , Rizzo Shemra , Zalocusky Kelly , Keebler Daniel , Chia Jenny , Lindsay Lisa , Yau Vincent , Kamath Tripthi , Tsai Larry 
Published: July 2020

1.ABSTRACTBackgroundDespite the significant morbidity and mortality caused by the 2019 novel coronavirus disease (COVID-19), our understanding of basic disease epidemiology remains limited. This study aimed to describe key patient characteristics, comorbidities, treatments, and outcomes of a large U.S.-based cohort of patients hospitalized with COVD-19 using electronic health records (EHR).MethodsWe identified patients in the Optum De-identified COVID-19 EHR database who had laboratory-confirmed COVID-19 or a presumptive diagnosis between 20 February 2020 and 6 June 2020. We included hospitalizations that occurred 7 days prior to, or within 21 days after, COVID-19 diagnosis. Among hospitalized patients we describe the following: vital statistics and laboratory results on admission, relevant comorbidities (using diagnostic, procedural, and revenue codes), medications (NDC, HCPC codes), ventilation, intensive care unit (ICU) stay, length of stay (LOS), and mortality.FindingsWe identified 76,819 patients diagnosed with COVID-19, 16,780 of whom met inclusion criteria for COVID-related hospitalization. Over half the cohort was over age 50 (74.5%), overweight or obese (77.2%), or had hypertension (56.6%). At admission, 30.3% of patients presented with fever (>38° C) and 32.3% had low oxygen saturation (<90%). Among the 16,099 patients with complete hospital records, we observed that 58.9% had hypoxia, 23.4% had an ICU stay during hospitalization, 18.1% were ventilated, and 16.2% died. The median LOS was 6 days (IQR: 4, 11).InterpretationTo our knowledge, this is the largest descriptive study of patients hospitalized with COVID-19 in the United States. We report summary statistics of key clinical outcomes that provide insights to better understand COVID-19 disease epidemiology.
Prophylaxis with tetracyclines in ARDS: Potential therapy for COVID-19-induced ARDS?
Authors: Byrne James D. , Shakur Rameen , Collins Joy E. , Becker Sarah , Young Cameron C. , Boyce Hannah , Traverso Giovanni 
Published: July 2020

AbstractThere is an immediate need for therapies related to coronavirus disease 2019 (COVID-19), especially candidate drugs that possess anti-inflammatory and immunomodulatory effects with low toxicity profiles. We hypothesized the application of pleiotropic tetracyclines as potential therapeutic candidates. Here, we present a retrospective multi-institutional cohort study evaluating ventilatory status in patients who had taken a tetracycline antibiotic within a year prior to diagnosis of acute respiratory distress syndrome (ARDS). The primary outcomes were the need for mechanical ventilation and duration of mechanical ventilation. The secondary outcome was the duration of intensive care unit (ICU) stay. Data was evaluated using logistic regression and treatment effects regression models. Minocycline or doxycycline treatment within a year prior to ARDS diagnosis was associated with a 75% reduced likelihood for mechanical ventilation during hospital stay. Furthermore, tetracycline antibiotic therapy corresponded to significant reductions in duration of mechanical ventilation and ICU stay in ARDS patients. These data suggest tetracyclines may provide prophylactic benefit in reducing ventilatory support for ARDS patients and support further evaluation in a randomized prospective trial.
Identifying Sepsis Subphenotypes via Time-Aware Multi-Modal Auto-Encoder
Authors: Yin Changchang , Liu Ruoqi , Zhang Dongdong , Zhang Ping 
Published: July 2020

ABSTRACTSepsis is a heterogeneous clinical syndrome that is the leading cause of mortality in hospital intensive care units (ICUs). Identification of sepsis subphenotypes may allow for more precise treatments and lead to more targeted clinical interventions. Recently, sepsis subtyping on electronic health records (EHRs) has attracted interest from healthcare researchers. However, most sepsis subtyping studies ignore the temporality of EHR data and suffer from missing values. In this paper, we propose a new sepsis subtyping framework to address the two issues. Our subtyping framework consists of a novel Time-Aware Multi-modal auto-Encoder (TAME) model which introduces time-aware attention mechanism and incorporates multi-modal inputs (e.g., demographics, diagnoses, medications, lab tests and vital signs) to impute missing values, a dynamic time wrapping (DTW) method to measure patients’ temporal similarity based on the imputed EHR data, and a weighted k-means algorithm to cluster patients. Comprehensive experiments on real-world datasets show TAME outperforms the baselines on imputation accuracy. After analyzing TAME-imputed EHR data, we identify four novel subphenotypes of sepsis patients, paving the way for improved personalization of sepsis management.CCS CONCEPTS•Applied computing → Health informatics; • Social and professional topics → Medical records; • Mathematics of computing → Time series analysis.ACM Reference FormatChangchang Yin, Ruoqi Liu, Dongdong Zhang, and Ping Zhang. 2020. Identifying Sepsis Subphenotypes via Time-Aware Multi-Modal Auto-Encoder.
Accounting for small-study effects using a bivariate trim and fill meta-analysis procedure
Authors: Luo Chongliang , Marks-Anglin Arielle , Duan Rui , Lin Lifeng , Hong Chuan , Chu Haitao , Chen Yong 
Published: July 2020

AbstractIn meta-analyses, small-study effects (SSE) refer to the phenomenon that smaller studies show different, often larger, treatment effects than larger studies, which may lead to incorrect, commonly optimistic estimates of treatment effects. Visualization tools such as funnel plots have been widely used to investigate the SSE in univariate meta-analyses. The trim and fill procedure is a non-parametric method to identify and adjust for SSE and is widely used in practice due to its simplicity. However, most visualization tools and SSE bias correction methods have been focusing on univariate outcomes. For a meta-analysis with multiple outcomes, the estimated number of trimmed studies by trim and fill for different outcomes may be different, leading to inconsistent conclusions. In this paper, we propose a bivariate trim and fill procedure to account for SSE in a bivariate meta-analysis. Based on a recently developed visualization tool of bivariate meta-analysis, known as the galaxy plot, we develop a sensible data-driven imputation algorithm for SSE bias correction. The method relies on the symmetry of the galaxy plot and assumes that some studies are suppressed based on a linear combination of outcomes. The studies are projected along a particular direction and the univariate trim and fill method is used to estimate the number of trimmed studies. Compared to the univariate method, the proposed method yields consistent conclusion about SSE and trimmed studies. The proposed approach is validated using simulated data and is applied to a meta-analysis of efficacy and safety of antidepressant drugs.
A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry
Authors: Singh Praveen , Chakraborty Rahul , Marwal Robin , V S Radhakrishan , Bhaskar Akash kumar , Vashisht Himanshu , Dhar Mahesh S , Pradhan Shalini , Ranjan Gyan , Imran Mohamed , Raj Anurag , Sharma Uma , Singh Priyanka , Lall Hemlata , Dutta Meena , Garg Parth , Ray Arjun , Dash Debasis , Sivasubbu Sridhar , Gogia Hema , Madan Preeti , Kabra Sandhya , Singh Sujeet K , Agrawal Anurag , Rakshit Partha , Kumar Pramod , Sengupta Shantanu 
Published: July 2020

AbstractIn the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 minute gradient run with 100% specificity and 90.4 % sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.
Evaluating the neuroprotective impact of senolytic drugs on human vision
Authors: El-Nimri Nevin W. , Moore Spencer M. , Zangwill Linda M. , Proudfoot James A. , Weinreb Robert N. , Skowronska-Krawczyk Dorota , Baxter Sally L. 
Published: July 2020

ABSTRACTGlaucoma, a chronic neurodegenerative disease of retinal ganglion cells (RGCs), is a leading cause of irreversible blindness worldwide. Its management currently focuses on lowering intraocular pressure to slow disease progression. However, disease-modifying, neuroprotective treatments for glaucoma remain a major unmet need. Recently, senescent cells have been observed in glaucomatous eyes, exposing a potential pathway for alternative glaucoma therapies. Prior studies demonstrated that targeting senescent RGCs for removal (i.e., a senolytic approach) protected healthy RGCs and preserved visual function in a mouse ocular hypertension model. However, the effects of senolytic drugs on vision in human patients are unknown. Here, we used existing clinical data to conduct a retrospective cohort study in 28 human glaucoma patients who had been exposed to senolytics. Senolytic exposure was not associated with decreased visual acuity, elevated intraocular pressure, or documentation of senolytic-related adverse ocular effects by treating ophthalmologists. Additionally, patients exposed to senolytics (n=9) did not exhibit faster progression of glaucomatous visual field damage compared to matched glaucoma patients (n=26) without senolytic exposure. These results suggest that senolytic drugs do not carry significant ocular toxicity and provide further support for additional evaluation of the potential neuroprotective effects of senolytics on glaucoma and other neurodegenerative diseases.
Mutational analysis unveils the temporal and spatial distribution of G614 genotype of SARS-CoV-2in different Indian states and its association with case fatality rate of COVID-19
Authors: Kumar Ballamoole Krishna , Venkatraja Bakilapadavu , Prithvisagar Kattapuni Suresh , Rai Praveen , Rohit Anusha , Hegde Madhura Nagesh , Karunasagar Indrani , Karunasagar Iddya 
Published: July 2020

AbstractPan genomic analysis of the global SARS-CoV-2 isolates has resulted in the identification of several regions of increased genetic variation but there is absence of research on its association with the clinical outcome. The present study fills the vacuum and does mutational analysis of genomic sequence of Indian SARS-CoV-2 isolates. Results reveal the existence of non-synonymous G614 spike protein mutation in 61.45% of the total study genome along with three other mutations. Further, temporal variation in the frequencies of G614 genotype in the country is observed. The examination of the probable association of G614 genotype with COVID-19 severity shows that CFR G614 genotype in India is positively and strongly correlated. It appears that the clinical outcome of the COVID-19 cases in India are significantly and adversely affected by the increasing trend in the G614 genotype; which needs to be addressed combining both laboratory experiments and epidemiological investigations.
Mineralisation of theCallorhinchusvertebral column (Holocephali; Chondrichthyes)
Authors: Pears Jacob , Johanson Zerina , Trinajstic Kate , Dean Mason , Boisvert Catherine 
Published: July 2020

AbstractChondrichthyes (Elasmobranchii and Holocephali) are distinguished by their largely cartilaginous endoskeleton that comprises an uncalcified core overlain by a mineralised layer; in the Elasmobranchii (sharks, skates, rays) this mineralisation takes the form of calcified polygonal tiles known as tesserae. In recent years, these skeletal tissues have been described in ever increasing detail in sharks and rays but those of Holocephali (chimaeroids) have been less well-described, with conflicting accounts as to whether or not tesserae are present. During embryonic ontogeny in holocephalans, cervical vertebrae fuse to form a structure called the synarcual. The synarcual mineralises early and progressively, anteroposteriorly and dorsoventrally, and therefore presents a good skeletal structure in which to observe mineralised tissues in this group. Here we describe the development and mineralisation of the synarcual in an adult and stage 36 elephant shark embryo (Callorhinchus milii). Small, discrete, but irregular blocks of cortical mineralisation are present in stage 36, similar to what has been described recently in embryos of other chimaeroid taxa such asHydrolagus, while inCallorhinchusadults, the blocks of mineralisation have become more irregular, but remain small. This differs from fossil members of the holocephalan crown group (Edaphodon), as well as from stem group holocephalans (e.g., Symmorida,Helodus, Iniopterygiformes), where tessellated cartilage is present, with tesserae being notably larger than inCallorhinchusand showing similarities to elasmobranch tesserae, for example with respect to polygonal shape.
A CRISPR/Cas9 vector system for neutrophil-specific gene disruption in zebrafish
Authors: Wang Yueyang , Hsu Alan Y. , Walton Eric M. , Syahirah Ramizah , Wang Tianqi , Zhou Wenqing , Ding Chang , Lemke Abby Pei , Tobin David M. , Deng Qing 
Published: July 2020

AbstractTissue-specific knockout techniques are widely applied in biological studies to probe the tissue-specific roles of specific genes in physiology, development, and disease. CRISPR/Cas9 is a widely used technology to perform fast and efficient genome editing in vitro and in vivo. Here, we report a robust CRISPR-based gateway system for tissue-specific gene inactivation in zebrafish. A transgenic fish line expressing Cas9 under the control of a neutrophil-restricted promoter was constructed. As proof of principle, we transiently disruptedrac2orcdk2in neutrophils using plasmids driving the expression of sgRNAs from U6 promoters. Loss of therac2orcdk2gene in neutrophils resulted in significantly decreased cell motility, which could be restored by re-expressing Rac2 or Cdk2 in neutrophils in the corresponding knockout background. The subcellular location of Rac activation and actin structure and stress in the context of neutrophil migration was determined in both the wild-type andrac2knockout neutrophilsin vivo. In addition, we evaluated an alternative approach where the Cas9 protein is ubiquitously expressed while the sgRNA is processed by ribozymes and expressed in a neutrophil-restricted manner. Cell motility was also reduced uponrac2sgRNA expression. Together, our work provides a potent tool that can be used to advance the utility of zebrafish in identification and characterization of gene functions in neutrophils.
The ABCD Stop Signal Data: Response to Bissett et al.
Authors: Garavan H , Chaarani B , Hahn S , Allgaier N , Juliano A , Yuan DK , Orr C , Watts R , Wager TD , Ruiz de Leon O , Hagler DJ , Potter A 
Published: July 2020

AbstractThis paper responds to a recent critique by Bissett and colleagues (Bissett et al., eLife, In Press) of the fMRI Stop task being used in the Adolescent Brain Cognitive DevelopmentSMStudy (ABCD Study®). The critique focuses primarily on a design feature of the task that the authors contend lead to a violation of race model assumptions (i.e., that the Go and Stop processes are fully independent) which are relevant to the calculation of the Stop Signal Reaction Time, a measure of the inhibition process. Bissett and colleagues also raise a number of secondary concerns. In this response we note that satisfying race model assumptions is a pernicious challenge for Stop task designs but also that the race model is quite robust against violations of its assumptions. Most importantly, while Bissett et al. raise conceptual concerns with the task we focus here on analyses of both the performance and the neuroimaging data and we conclude that the concerns appear to have minimal impact on the neuroimaging data (the validity of which do not rely on race model assumptions) and have far less of an impact on the performance data than the critique suggests. We note that Bissett et al. did not apply any performance-based exclusions to the data they analyzed, that a number of the trial coding errors that they flagged were already identified and corrected in the ABCD annual data releases, that a number of the secondary concerns reflect sensible design decisions and, indeed, that their own computational modeling of the ABCD Stop task suggests the problems they identify have just a modest impact on the rank ordering of individual differences in subject performance. In this paper, we list some adjustments that have been made to the task and some new flags that are now added to the annual, curated data releases. We stress that the ABCD data are fully available to the scientific community who are empowered to apply whatever inclusion and exclusion criteria they deem appropriate for their analyses and we conclude that the ABCD Stop task yields valuable data that researchers can use to track adolescent neurodevelopment.
Altered Thalamocortical Signaling in a Mouse Model of Parkinson’s Disease
Authors: Swanson Olivia K. , Richard David , Maffei Arianna 
Published: July 2020

AbstractActivation of the primary motor cortex (M1) is important for the execution of skilled movements and motor learning, and its dysfunction contributes to the pathophysiology of Parkinson’s disease (PD). A well accepted idea in PD research, albeit not tested experimentally, is that loss of midbrain dopamine leads to decreased activation of M1 by the motor thalamus (Mthal). Here, we report that midbrain dopamine loss reduced Mthal input in a laminar- and cell type-specific fashion and induced laminar-specific changes in intracortical synaptic transmission. As a result, M1 activation by Mthal was decreased, but M1 output was increased. Our results demonstrate that loss of midbrain dopaminergic neurons alters thalamocortical activation of M1, and provide novel insights into circuit mechanisms for motor cortex dysfunction in a mouse model of PD.