bluuebunny/crossref_metadata_2025_split huggingface dataset:
Awareness With Paralysis in Mechanically Ventilated Patients in the Emergency Department and ICU: A Systematic Review and Meta-Analysis*
Authors: Pappal Ryan D. , Roberts Brian W. , Winkler Winston , Yaegar Lauren H. , Stephens Robert J. , Fuller Brian M. 
Published: January 2021

OBJECTIVE:
Awareness with paralysis is a devastating complication for mechanically ventilated patients and can carry long-term psychologic sequelae. Hundreds of thousands of patients require mechanical ventilation in the emergency department and ICU annually, yet awareness has only been rigorously examined in the operating room (incidence ~0.1%). This report collates the global literature regarding the incidence of awareness with paralysis outside of the operating room.

DATA SOURCES:
We searched OvidMedline, Embase, Scopus, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, ClinicalTrials.gov, conference proceedings, and reference lists.

STUDY SELECTION:
Randomized or nonrandomized studies (except single case studies) reporting on awareness with paralysis in the emergency department or ICU were eligible.

DATA EXTRACTION:
Two independent reviewers screened abstracts for eligibility.

DATA SYNTHESIS:
The search identified 4,454 potentially eligible studies. Seven studies (n = 941 patients) were included for analysis. A random effects meta-analysis of proportions along with multiple subgroup analyses was performed. Significant between-study heterogeneity in reporting of awareness with paralysis was noted, and the quality of the evidence was low. Analyses stratified by: 1) good-quality studies and 2) use of the modified Brice questionnaire to detect awareness revealed estimates of 3.4% (95% CI, 0–10.2%) and 1.9% (95% CI, 1.0–3.0%), respectively.

CONCLUSIONS:
The incidence of awareness with paralysis in mechanically ventilated patients in the emergency department and ICU, as evaluated in a small number of qualifying studies from this comprehensive systematic review, appears much higher than that reported from the operating room. Given the clinical and statistical heterogeneity, caution is warranted in the interpretation of these findings. Further high-quality studies are needed to both define the true incidence and to target the prevention of awareness with paralysis in this vulnerable patient cohort.
Iatrogenic Arsenism Characterized by Palmoplantar Hyperkeratosis and Diffused Skin Cancers for Over Decades
Authors: Tian Cui-cui , Hu Feng-Qiu , Lu Sha , Tan Guo-Zhen , Wang Liangchun 
Published: January 2021

Abstract:
Chronic arsenism usually occurs after a long-term unawareness of arsenic exposure from environment, occupation, food, and water. We here reported 3 cases with diffused arsenic keratosis and skin cancers derived from long-term arsenic medication ingestion. In these cases, hyperkeratotic skin lesions were initially found on palms and soles, slowly progressed to every part of the skin and lasted maximally for over 30 years. Skin cancers were diagnosed and removed intermittently within decades, but with no malignancies in other organs. Oral retinoids combing with topical 5- fluorouracil and photodynamic treatment yielded a desirable outcome.
Dermal Regeneration Templates in Maxillo-Facial District: A Multipurpose Aid
Authors: Spallaccia Fabrizio , Benedetti Simone , Massarelli Mauro , Paparo Francesco , Rivaroli Andrea , Vellone Valentino 
Published: January 2021

Abstract
Since 1980s, the use of dermal regeneration templates (DRT) for reconstructive purposes has been described in Literature.1 The authors present their experience of 13 patients treated with integra dermal regeneration template and a single-stage surgery for different indications like oncologic reconstruction, trauma injuries, and preprosthetic surgery in the maxillo-facial district.
The authors retrospectively reviewed a total of 13 patients treated with DRT at Maxillo-Facial Department of S. Maria Hospital in Terni.
Inclusion criteria included the presence of a defect nonapproachable primarily or by secondary intention with an easy locoregional flap reconstruction, a complete clinical record, and a minimum 6 months follow-up.
A total of 12 patients underwent surgical reconstruction with DRT at the S. Maria Hospital from June 2018 to February 2020.
During follow-up, all patients in which intraoral reconstruction was performed showed first signs of re-mucosization and neovascularization after 10 days.
Only in 1 patient (8%) a seroma underneath the silicon sheet was observed. Afterward, the patient healed correctly with no other complications.
Dermal regeneration template represents an option that should be considered in the head and neck district reconstruction, especially for intraoral defects where, thanks to its long-term functional results and limited alternatives, should represent a relevant choice.
Extending influenza surveillance to detect non-influenza respiratory viruses of public health relevance: analysis of surveillance data, 2015-2019, Belgium
Authors: Subissi Lorenzo , Bossuyt Nathalie , Reynders Marijke , Gérard Michèle , Dauby Nicolas , Lacor Patrick , Daelemans Siel , Lissoir Bénédicte , Holemans Xavier , Magerman Koen , Jouck Door , Bourgeois Marc , Delaere Bénédicte , Quoilin Sophie , Van Gucht Steven , Thomas Isabelle , Barbezange Cyril 
Published: January 2021

AbstractBACKGROUNDSeasonal influenza-like illness (ILI) affects millions of people yearly. Severe acute respiratory infections (SARI), mainly caused by influenza, are a leading cause of hospitalisation and mortality. Increasing evidence indicates that non-influenza respiratory viruses (NIRVs) also contribute to the burden of SARI. In Belgium, SARI surveillance by a network of sentinel hospitals is ongoing since 2011.AIMHere, we report the results of using in-house multiplex PCRs for the detection of a flexible panel of viruses in respiratory ILI and SARI samples and the estimated incidence rates of SARI associated to each virus.METHODSILI was defined as an infection with onset of fever and cough or dyspnoea. SARI was defined as an infection requiring hospitalization with onset of fever and cough or dyspnoea within the previous 10 days. Samples were collected during four winter seasons and tested by multiplex RT-qPCRs for influenza virus and NIRVs. Using catchment population estimates, incidence rates of SARI associated to each virus were calculated.RESULTSOne third of the SARI cases were positive for NIRVs, reaching 49.4% among children under fifteen. In children under five, incidence rates of NIRV-associated SARI were double that of influenza (103.4 versus 57.6 per 100000 person-months), with NIRV co-infections, respiratory syncytial viruses, human metapneumoviruses and picornaviruses contributing the most (33.1, 13.6, 15.8 and 18.2 per 100000 person-months, respectively).CONCLUSIONEarly testing for NIRVs could be beneficial to clinical management of SARI patients, especially in children under five, for whom the burden of NIRV-associated disease exceeds that of influenza.
Type 2 Diabetes Modifies Skeletal Muscle Gene Expression Response to Gastric Bypass Surgery
Authors: Barberio Matthew D. , Dohm G. Lynis , Pories Walter J. , Gadaleta Natalie A. , Houmard Joseph A. , Nadler Evan P. , Hubal Monica J. 
Published: January 2021

AbstractRoux-en-Y gastric bypass (RYGB) is an effective treatment for type 2 diabetes mellitus (T2DM) which can result in remission of clinical symptoms, yet mechanisms for improved skeletal muscle health are poorly understood. We sought to define the impact of existing T2DM on RYGB-induced muscle transcriptome changes.MethodsVastus lateralis biopsy transcriptomes were generated pre- and 1-yr post-RYGB in black adult females with (T2D; n = 5, age=51±6 yr, BMI=53.0±5.8 kg/m2) and without (CON; n = 7,43±6 yr,51.0±9.2 kg/m2) T2DM. Insulin, glucose, and HOMA-IR were measured in blood at the same time points. ANCOVA detected differentially expressed genes (p< 0.01, Fold change<|1.2|), which were used to identify enriched biological pathways.ResultsPre-RYGB, 95 probes were downregulated with T2D including subunits of mitochondrial complex I. Post-RYGB, the T2D group had normalized gene expression when compared to their non-diabetic counterparts with only 3 probes remaining significantly different. In the T2D, we identified 52 probes upregulated from pre- to post-RYGB, including NDFUB7 and NDFUA1.ConclusionBlack females with T2DM show extensive down regulation of genes across aerobic metabolism pathways prior to RYGB, which resolves 1 year post-RYGB and is related to improvements in clinical markers. These data support efficacy of RYGB for improving skeletal muscle health, especially in patients with T2DM.
REACT-1 round 8 interim report: SARS-CoV-2 prevalence during the initial stages of the third national lockdown in England
Authors: Riley Steven , Wang Haowei , Eales Oliver , Walters Caroline E. , Ainslie Kylie E. C. , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul 
Published: January 2021

AbstractBackgroundHigh prevalence of SARS-CoV-2 virus in many northern hemisphere populations is causing extreme pressure on healthcare services and leading to high numbers of fatalities. Even though safe and effective vaccines are being deployed in many populations, the majority of those most at-risk of severe COVID-19 will not be protected until late spring, even in countries already at a more advanced stage of vaccine deployment.MethodsThe REal-time Assessment of Community Transmission study-1 (REACT-1) obtains throat and nose swabs from between 120,000 and 180,000 people in the community in England at approximately monthly intervals. Round 8a of REACT-1 mainly covers a period from 6th January 2021 to 15th January 2021. Swabs are tested for SARS-CoV-2 virus and patterns of swab-positivity are described over time, space and with respect to individual characteristics. We compare swab-positivity prevalence from REACT-1 with mobility data based on the GPS locations of individuals using the Facebook mobile phone app. We also compare results from round 8a with those from round 7 in which swabs were collected from 13th November to 24th November (round 7a) and 25th November to 3rd December 2020 (round 7b).ResultsIn round 8a, we found 1,962 positives from 142,909 swabs giving a weighted prevalence of 1.58% (95% CI, 1.49%, 1.68%). Using a constant growth model, we found no strong evidence for either growth or decay averaged across the period; rather, based on data from a limited number of days, prevalence may have started to rise at the end of round 8a. Facebook mobility data showed a marked decrease in activity at the end of December 2020, followed by a rise at the start of the working year in January 2021. Between round 7b and round 8a, prevalence increased in all adult age groups, more than doubling to 0.94% (0.83%, 1.07%) in those aged 65 and over. Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with increased prevalence. Both healthcare and care home workers, and other key workers, had increased odds of swab-positivity compared to other workers.ConclusionDuring the initial 10 days of the third COVID-19 lockdown in England in January 2021, prevalence of SARS-CoV-2 was very high with no evidence of decline. Until prevalence in the community is reduced substantially, health services will remain under extreme pressure and the cumulative number of lives lost during this pandemic will continue to increase rapidly.
Correlates of Sleep and Arousal via Matrix Methods
Authors: Sorooshyari Siamak K. , Lecea Luis de 
Published: January 2021

AbstractConventional computational modeling of sleep and arousal are primarily brain-centric in restricting attention to data from the nervous system. While such a view is warranted, the importance of considering the coupling of peripheral systems in the causes and effects of sleep are being increasingly recognized. An analysis is presented that has the capability to incorporate neural recordings of different modalities as well as data from the metabolic and immune systems. We formulate a matrix-based approach for inference of the arousal state based on the activity level of cell types that will comprise the matrix components. While the presented computations are intended to predict sleep/arousal, it is anticipated that a scrutiny of the structure of the matrices will provide insight into the dynamics of the constituent systems. A model is also proposed to consider the interaction of the signals recorded across the neural, metabolic, and immune systems in leading to the arousal state.
Selection maintains protein interactome resilience in the long-term evolution experiment withEscherichia coli
Authors: Maddamsetti Rohan 
Published: January 2021

AbstractMost cellular functions are carried out by a dynamic network of interacting proteins. An open question is whether the network properties of protein interactomes represent phenotypes under natural selection. One proposal is that protein interactomes have evolved to be resilient, such that they tend to maintain connectivity when proteins are removed from the network. This hypothesis predicts that interactome resilience should be maintained by natural selection during long-term experimental evolution. I tested this prediction by modeling the evolution of protein-protein interaction (PPI) networks in Lenski’s long-term evolution experiment withEscherichia coli(LTEE). In this test, I removed proteins affected by nonsense, insertion, deletion, and transposon mutations in evolved LTEE strains, and measured the resilience of the resulting networks. I compared the rate of change of network resilience in each LTEE population to the rate of change of network resilience for corresponding randomized networks. The evolved PPI networks are significantly more resilient than networks in which random proteins have been deleted.Moreover, the evolved networks are generally more resilient than networks in which the random deletion of proteins was restricted to those disrupted in LTEE. These results suggest that evolution in the LTEE has favored PPI networks that are, on average, more resilient than expected from the genetic variation across the evolved strains. My findings therefore support the hypothesis that selection maintains protein interactome resilience over evolutionary time.Significance StatementUnderstanding how protein-protein interaction (PPI) networks evolve is a central goal of evolutionary systems biology. One property that has been hypothesized to be important for PPI network evolution is resilience, which means that networks tend to maintain connectivity even after many nodes (proteins in this case) have been removed. This hypothesis predicts that PPI network resilience should be maintained during long-term experimental evolution. Consistent with this prediction, I found that the PPI networks that evolved over 50,000 generations of Lenski’s long-term evolution experiment withE. coliare more resilient than expected by chance.
Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms
Authors: Orabi Baraa , McConeghy Brian , Chauve Cedric , Hach Faraz 
Published: January 2021

AbstractAlternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective target of personalized cancer therapeutics. However, detecting AS events remains a challenging task, especially if these AS events are not pre-annotated. This is exacerbated by the fact that existing transcriptome annotation databases are far from being comprehensive, especially with regard to cancer-specific AS. Additionally, traditional sequencing technologies are severely limited by the short length of the generated reads, that rarely spans more than a single splice junction site. Given these challenges, transcriptomic long-read (LR) sequencing presents a promising potential for the detection and discovery of AS.We present Freddie, a computational annotation-independent isoform discovery and detection tool. Freddie takes as input transcriptomic LR sequencing of a sample and computes a set of isoforms for the given sample. Freddie takes as input the genomic alignment of the transcriptomic LRs generated by a splice aligner. It then partitions the reads to sets that can be processed independently and in parallel. For each partition, Freddie segments the genomic alignment of the reads into canonical exon segments. The goal of this segmentation is to be able to represent any potential isoform as a subset of these canonical exons. This segmentation is formulated as an optimization problem and is solved with a Dynamic Programming algorithm. Then, Freddie reconstructs the isoforms by jointly clustering and error-correcting the reads using the canonical segmentation as a succinct representation. The clustering and error-correcting step is formulated as an optimization problem – the Minimum Error Clustering into Isoforms (MErCi) problem – and is solved using Integer Linear Programming (ILP).We compare the performance of Freddie on simulated datasets with other isoform detection tools with varying dependence on annotation databases. We show that Freddie outperforms the other tools in its recall, including those given the complete ground truth annotation. In terms of false positive rate, Freddie performs comparably to the other tools. We also run Freddie on a transcriptomic LR dataset generated in-house from a prostate cancer cell line. Freddie detects a potentially novel Androgen Receptor isoform that includes novel intron retention. We cross-validate this novel intron retention using orthogonal publicly available short-read RNA-seq datasets.AvailabilityFreddie is open source and available athttps://bitbucket.org/baraaorabi/freddie
Uncovering the Gene Regulatory Networks Underlying Macrophage Polarization Through Comparative Analysis of Bulk and Single-Cell Data
Authors: Carvalho Klebea , Rebboah Elisabeth , Jansen Camden , Williams Katherine , Dowey Andrew , McGill Cassandra , Mortazavi Ali 
Published: January 2021

SummaryGene regulatory networks (GRNs) provide a powerful framework for studying cellular differentiation. However, it is less clear how GRNs encode cellular responses to everyday microenvironmental cues. Macrophages can be polarized and potentially repolarized based on environmental signaling. In order to identify the GRNs that drive macrophage polarization and the heterogeneous single-cell subpopulations that are present in the process, we used a high-resolution time course of bulk and single-cell RNA-seq and ATAC-seq assays of HL-60-derived macrophages polarized towards M1 or M2 over 24 hours. We identified transient M1 and M2 markers, including the main transcription factors that underlie polarization, and subpopulations of naive, transitional, and terminally polarized macrophages. We built bulk and single-cell polarization GRNs to compare the recovered interactions and found that each technology recovered only a subset of known interactions. Our data provide a resource to study the GRN of cellular maturation in response to microenvironmental stimuli in a variety of contexts in homeostasis and disease.
RNAStructViz: Graphical base pairing analysis
Authors: Schmidt Maxie Dion , Kirkpatrick Anna , Heitsch Christine 
Published: January 2021

AbstractSummaryWe present a new graphical tool for RNA secondary structure analysis. The central feature is the ability to visually compare/contrast up to three base pairing configurations for a given sequence in a compact, standardized circular arc diagram layout. This is complemented by a built-in CT-style file viewer and radial layout substructure viewer which are directly linked to the arc diagram window via the zoom selection tool. Additional functionality includes the computation of some numerical information, and the ability to export images and data for later use. This tool should be of use to researchers seeking to better understand similarities and differences between structural alternatives for an RNA sequence.Availability and implementationhttps://github.com/gtDMMB/RNAStructViz/wikiAuthor contactsmschmidt34@gatech.edu,akirkpatrick3@gatech.edu, andheitsch@math.gatech.edu
Large-scale calcium imaging with a head-mounted axial scanning 3D fluorescence microscope
Authors: Hayashi Yuichiro , Kobayakawa Ko , Kobayakawa Reiko 
Published: January 2021

SummaryMiniaturized fluorescence microscopes are becoming more important for deciphering the neural codes underlying various brain functions. With gradient index (GRIN) lenses, these devices enable recording neuronal activity in deep brain structures. However, to minimize any damage to brain tissues and local circuits, the diameter of the GRIN lens should be 0.5–1 mm, resulting in a small field of view. Volumetric imaging capability might increase the number of neurons imaged through the lenses considering the three-dimensional (3D) structure of neural circuits in the brain. To observe 3D calcium dynamics, we developed a miniaturized microscope with an electrically tunable lens and a novel CNMF-based neural signal extraction algorithm for wide-field 3D imaging data. By combining the hardware and software, approximately 1000 neurons were imaged from the cortices of freely behaving mice. Compared with the state-of-the-art 2D imaging technique, the proposed 3D method imaged 1.7–2.6 times more cells with a higher separation of cellular signals.
New insights on folliculogenesis and follicular placentation in marine viviparous fish black rockfish (Sebastes schlegelii)
Authors: Xu Xiaojie , Liu Qinghua , Wang Xueying , Qi Xin , Zhou Li , Liu Haoming , Li Jun 
Published: January 2021

AbstractIn viviparous fish, a considerable degree of variation in placental structures have been described. However, no distinct structures are reported in Scorpaenidae. In this study, we demonstrate a new type of folliculogenesis and follicular placentation inSebastes schlegelii. Before copulation, the germinal epithelium gradually surrounds the oocytes and develops to individually follicles with a stalk-like structure hanging on the ovigerous lamella, which ensures each follicle have access to spermatozoa after copulation. From stage V to early gestation, thecyp17-Ihighly expressed accompanied bycyp19a1asignals disappearance, and 11-ketotestosterone level keeps rising and peaks at blastula stage, while 17β-estradiol declines to the bottom. Meanwhile, the theca cells rapidly proliferate and invade outwards forming a highly hypertrophied and folded microvillous placenta. This unbalance of hormone might be an important factor driving the theca cells proliferation and invasion. Additionally, some conserved genes related to mammalian placentation are significantly high expression in follicular placenta suggesting the high convergence in vertebrate placenta evolution.