bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Surgical Approach to Abdominal Sacrocolpopexy and Concurrent Hysterectomy: Trends for the Past Decade
Authors: Winkelman William D. , Modest Anna M. , Richardson Monica L. 
Published: May 2020

Objective
The aim of the study was to understand the surgical trends and 30-day complications of patients undergoing an abdominal sacrocolpopexy with a concurrent hysterectomy.

Methods
This is a retrospective cohort study of surgical cases from the American College of Surgeons National Surgical Quality Improvement Program from 2010 to 2017 who underwent an abdominal sacrocolpopexy and a concurrent hysterectomy.

Results
There were 9327 surgical cases of an abdominal sacrocolpopexy with a concurrent hysterectomy of which 7772 (83.3%) were minimally invasive and 1555 (16.7%) were through a laparotomy. The proportion of patients undergoing a laparotomy decreased by 2.4% per year from 2010 to 2018 (R
2 = 0.77). Among minimally invasive procedures, 4359 (46.7%) involved a concurrent supracervical hysterectomy and 4968 (53.3%) involved a concurrent total hysterectomy. Among minimally invasive procedures, patients who had a concurrent supracervical hysterectomy both had a longer operative time and were more likely to be admitted at least 2 days postoperatively compared with those who had a concurrent total hysterectomy (P < 0.001 for both).

Conclusions
Patients undergoing an abdominal sacrocolpopexy and concurrent hysterectomy are increasingly likely to undergo surgery in a minimally invasive approach. The Food and Drug Administration safety communication on electric power morcellation did not impact this trend. Although complication rates are low, regardless of the type of concurrent hysterectomy, some complications, such as blood transfusions and surgical site infections, seem to be highest for those undergoing a concurrent total hysterectomy despite the fact that a concurrent supracervical hysterectomy may be associated with a longer operative time and longer hospital admission.
Open tracheostomy for COVID-19–positive patients: A method to minimize aerosolization and reduce risk of exposure
Authors: Prabhakaran Kartik , Malcom Ryan , Choi James , Chudner Alexandra , Moscatello Augustine , Panzica Peter , Latifi Rifat , Rhee Peter 
Published: May 2020

BACKGROUND
The COVID-19 virus is highly contagious, and thus there is a potential of infecting operating staff when operating on these patients. This case series describes a method of performing open tracheostomy for COVID-19 patients while minimizing potential aerosolization of the virus using typically available equipment and supplies.

METHODS
This is a case series of 18 patients who were COVID-19–positive and underwent open tracheostomy in the operating room under a negative pressure plastic hood created using readily available equipment and supplies. Patients had to be intubated for at least 14 days, be convalescing from their cytokine storm, and deemed to survive for at least 14 more days. Other indications for tracheostomy were altered mental status, severe deconditioning, respiratory failure and failed extubation attempts.

RESULTS
There were 14 men and 4 women with severe SARS-CoV2 infection requiring long-term intubation since March 23 or later. The mean age was 61.7 years, body mass index was 32.6, and the pretracheostomy ventilator day was 20.4 days. The indications for tracheostomy were altered mental status, severe deconditioning and continued respiratory with hypoxia. Failed extubation attempt rate was 16.7% and hemodialysis rate was 38.9%. All patients were hemodynamically stable, without any evidence of accelerating cytokine storm. To date there was one minor bleeding due to postoperative therapeutic anticoagulation.

CONCLUSION
This report describes a method of performing open tracheostomy with minimal aerosolization using readily available equipment and supplies in most hospitals.

LEVEL OF EVIDENCE
Therapeutic/care management, Level V.
A dynamic model for Covid-19 in Brazil
Authors: Filho Rubens Lichtenthäler , Lichtenthäler Daniel Gomes 
Published: May 2020

1AbstractA dynamic model for the current coronavirus outbreak is presented. The most important parameters are identified which determine the number of cases progression. Results of a numerical simulation are compared with existing data of the number of COVID-19 cases and deaths in Sao Paulo and Brazil. On the basis of these results we display the effect of social distancing measures taken so far, which flattened the infection curve. A simple three steps procedure is proposed to predict changes in the evolution of the epidemics and we discuss the importance of serological representative surveys to relate the epidemic time to the real time. A criteria to start relaxing social distance measures is suggested.
Mitochondrial nucleoid organization and biogenesis of complex I require mTERF18/SHOT1 and ATAD3 inArabidopsis thaliana
Authors: Kim Minsoo , Schulz Vincent , Brings Lea , Schoeller Theresa , Kühn Kristina , Vierling Elizabeth 
Published: May 2020

AbstractMitochondria play critical roles in eukaryotes in ATP generation through oxidative phosphorylation (OXPHOS) and also produce both damaging and signaling reactive oxygen species (ROS). Originating from endosymbiosis, mitochondria have their own reduced genomes that encode essential subunits of the OXPHOS machinery. MTERF (Mitochondrial Transcription tERmination Factor-related) proteins have been shown to be involved in organelle gene expression by interacting with organellar DNA or RNA in multicellular eukaryotes. We previously identified mutations inArabidopsis thaliana MTERF18/SHOT1that enable plants to better tolerate heat and oxidative stresses, presumably due to low ROS and reduced oxidative damage. To understand molecular mechanisms leading toshot1phenotypes, we investigated mitochondrial defects ofshot1mutants and targets of the SHOT1 protein.shot1mutants have problems accumulating OXPHOS complexes that contain mitochondria-encoded subunits, with complex I and complex IV most affected. SHOT1 binds specific mitochondrial DNA sequences and localizes to mitochondrial nucleoids, which are diffuse inshot1mutants. Furthermore, three homologues of mammalian ATAD3A proteins, which are suggested to be involved in mitochondrial nucleoid organization, were identified as SHOT1-interacting proteins (designated SHOT1 BINDING ATPASES (SBA)1, 2 and 3). Importantly, disrupting SBA function also disrupts nucleoids, compromises accumulation of complex I and enhances heat tolerance. We conclude that proper nucleoid organization is critical for correct expression and accumulation of complex I, and propose that nucleoid disruption results in unique changes in mitochondrial metabolism and signaling that lead to heat tolerance.SignificanceIn all eukaryotes, mitochondria are critical organelles that supply chemical energy for life, which is produced by the oxidative phosphorylation (OXPHOS) machinery on the inner mitochondrial membrane. The OXPHOS machinery comprises multiple protein complexes with subunits encoded by both nuclear and mitochondrial genes. Nuclear-encoded mTERF proteins are important for expression of mitochondrial genes, interacting with mitochondrial DNA or RNA. Our study reveals that the Arabidopsis mTERF18/SHOT1 protein interacts with mtDNA and homologs of human ATAD3A proteins, and that both proteins are critical for mitochondrial nucleoid organization and accumulation of OXPHOS Complex I. Further, the data indicate nucleoid disruption leads to unique mitochondrial and cellular responses such that mutant plants have enhanced heat tolerance.
Single-soma transcriptomics of tangle-bearing neurons in Alzheimer’s disease reveals the signatures of tau-associated synaptic dysfunction
Authors: Otero-Garcia Marcos , Xue Yue-Qiang , Shakouri Tamara , Deng Yongning , Morabito Samuel , Allison Thomas , Lowry William E. , Kawaguchi Riki , Swarup Vivek , Cobos Inma 
Published: May 2020

AbstractAggregation of hyperphosphorylated tau in neurofibrillary tangles (NFTs) is closely associated with neuronal death and cognitive decline in Alzheimer’s disease (AD). To define the signatures that distinguish between aggregation-prone and resistant cell states in AD, we developed a FACS-based method for the high-throughput isolation and transcriptome profiling of individual cells with cytoplasmic aggregates and profiled 63,110 somas from human AD brains. By comparing NFT-bearing and NFT-free somas within and across neuronal subtypes, we identified the cell-type-specific and shared states. NFT-bearing neurons shared a marked upregulation of genes associated with synaptic transmission, including a core set of 63 genes enriched for synaptic vesicle cycle and transsynaptic signaling, whereas glucose metabolism and oxidative phosphorylation changes were highly neuronal-subtype-specific. Apoptosis was modestly enriched in NFT-bearing neurons despite the strong link between tau and cell death. Our datasets provide a resource for investigating tau-mediated neurodegeneration and a platform for biomarker and drug target discovery.
Plasmacytoid dendritic cell expansion defines a distinct subset of RUNX1 mutated acute myeloid leukemia
Authors: Xiao Wenbin , Chan Alexander , Waarts Michael R. , Mishra Tanmay , Liu Ying , Cai Sheng F. , Yao Jinjuan , Gao Qi , Bowman Robert L. , Koche Richard , Csete Isabelle S. , Baik Jeeyeon , Yanis Sophia , Famulare Christopher , Patel Minal , Arcila Maria E. , Stahl Maximilian , Rampal Raajit K. , Tallman Martin S. , Zhang Yanming , Dogan Ahmet , Goldberg Aaron D. , Roshal Mikhail , Levine Ross L. 
Published: May 2020

AbstractPlasmacytoid dendritic cells (pDC) are the principal natural type I interferon producing dendritic cells. Neoplastic expansion of pDCs and pDC precursors leads to blastic plasmacytoid dendritic cell neoplasm (BPDCN) and clonal expansion of mature pDCs has been described in chronic myelomonocytic leukemia (CMML). The role of pDC expansion in acute myeloid leukemia (AML) is poorly studied. Here we characterize AML patients with pDC expansion (pDC-AML), which we observe in approximately 5% of AML. pDC-AML often possess crosslineage antigen expression and have adverse risk stratification with poor outcome. RUNX1 mutations are the most common somatic alterations in pDC-AML (>70%) and are much more common than in AML without PDC expansion. We demonstrate that pDCs are clonally related to, and originate from, leukemic blasts in pDC-AML. We further demonstrate that leukemic blasts from RUNX1-mutated AML upregulate a pDC transcriptional program, poising the cells towards pDC differentiation and expansion. Finally, tagraxofusp, a targeted therapy directed to CD123, reduces leukemic burden and eliminates pDCs in a patient-derived xenograft model. In conclusion, pDC-AML is characterized by a high frequency of RUNX1 mutations and increased expression of a pDC transcriptional program. CD123 targeting represents a potential treatment approach for pDC-AML.
Post-reactivation mifepristone impairs generalisation of strongly-conditioned contextual fear memories
Authors: Flavell Charlotte R. , Gascoyne Rebecca M. , Lee Jonathan L. C. 
Published: May 2020

AbstractThe efficacy of pharmacological disruption of fear memory reconsolidation depends on several factors, including memory strength and age. We built on previous observations that systemic treatment with the nootropic nefiracetam potentiates cued fear memory destabilization to facilitate mifepristone-induced reconsolidation impairment. Here, we applied nefiratecam and mifepristone to strongly-conditioned, 1-week old contextual fear memories in male rats. Unexpectedly, the combined treatment did not result in impairment of contextual fear expression. However, mifepristone did reduce freezing to a novel context. These observations suggest that strong and established contextual fear memories do undergo destabilization without the need for pharmacological facilitation, and that impairments in strong context fear memory reconsolidation can manifest as a reduction in generalization.
Ion Identity Molecular Networking in the GNPS Environment
Authors: Schmid Robin , Petras Daniel , Nothias Louis-Félix , Wang Mingxun , Aron Allegra T. , Jagels Annika , Tsugawa Hiroshi , Rainer Johannes , Garcia-Aloy Mar , Dührkop Kai , Korf Ansgar , Pluskal Tomáš , Kameník Zdeněk , Jarmusch Alan K. , Caraballo-Rodríguez Andrés Mauricio , Weldon Kelly , Nothias-Esposito Melissa , Aksenov Alexander A. , Bauermeister Anelize , Orio Andrea Albarracin , Grundmann Carlismari O. , Vargas Fernando , Koester Irina , Gauglitz Julia M. , Gentry Emily C. , Hövelmann Yannick , Kalinina Svetlana A. , Pendergraft Matthew A. , Panitchpakdi Morgan W. , Tehan Richard , Le Gouellec Audrey , Aleti Gajender , Russo Helena Mannochio , Arndt Birgit , Hübner Florian , Hayen Heiko , Zhi Hui , Raffatellu Manuela , Prather Kimberly A. , Aluwihare Lihini I. , Böcker Sebastian , McPhail Kerry L. , Humpf Hans-Ulrich , Karst Uwe , Dorrestein Pieter C. 
Published: May 2020

AbstractMolecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.
CommDivMap: Modelling and mapping species richness at different spatial scales
Authors: Miller Julia E , Steinke Dirk 
Published: May 2020

Summary1. Modern ecosystem models have the potential to greatly enhance our capacity to predict community responses to change, but they demand comprehensive spatial distribution information, creating the need for new approaches to gather and synthesize biodiversity data.2. Metabarcoding or metagenomics can generate comprehensive biodiversity data sets at species-level resolution but they are limited to point samples.3. CommDivMap contains a number of functions that can be used to turn OTU tables resulting from metabarcoding runs of bulk samples into species richness maps. We tested the method on a series of arthropod bulk samples obtained from various experimental agricultural plots.4. The script runs smoothly and is reasonably fast. We hope that our assemble first, predict later approach to statistical modelling of species richness will set the stage for the transition from data-rich but finite sets of point samples to spatially continuous biodiversity maps.
Viscoelastic mapping of mouse brain tissue: relation to structure and age
Authors: Antonovaite Nelda , Hulshof Lianne A. , Hol Elly M. , Wadman Wytse J. , Iannuzzi Davide 
Published: May 2020

AbstractThere is growing evidence that mechanical factors affect brain functioning. However, brain components responsible for regulating the physiological mechanical environment and causing mechanical alterations during maturation are not completely understood. To determine the relationship between structure and stiffness of the brain tissue, we performed high resolution viscoelastic mapping by dynamic indentation of hippocampus and cerebellum of juvenile brain, and quantified relative area covered by immunohistochemical staining of NeuN (neurons), GFAP (astrocytes), Hoechst (nuclei), MBP (myelin), NN18 (axons) of juvenile and adult mouse brain slices. When compared the mechanical properties of juvenile mouse brain slices with previously obtained data on adult slices, the latter was ~ 20-150% stiffer, which correlates with an increase in the relative area covered by astrocytes. Heterogeneity within the slice, in terms of storage modulus, correlates negatively with the relative area of nuclei and neurons, as well as myelin and axons, while the relative area of astrocytes correlates positively. Several linear regression models are suggested to predict the mechanical properties of the brain tissue based on immunohistochemical stainings.
Bifurcated Hydrogen Bonds and the Fold Switching of Lymphotactin
Authors: Khatua Prabir , Ray Alan J , Hansmann Ulrich H. E. 
Published: May 2020

AbstractLymphotactin (Ltn) exists under physiological conditions in an equilibrium between two interconverting structures with distinct biological functions. Using Replica-Exchange-with-Tunneling we study the conversion between the two folds. Unlike previously proposed, we find that the fold switching does not require unfolding of Lymphotactin, but proceeds through a series of intermediates that remain partially structured. This process relies on two bifurcated hydrogen bonds that connect theβ2andβ3strands and eases the transition between the hydrogen bond pattern by which the central three-strandedβ-sheet in the two forms differ.
Autoregulation of Many Yeast Ribosomal Proteins Discovered by Efficient Search for Feedback Regulation
Authors: Roy Basab , Granas David , Bragg Fredrick , Cher Jonathan A. Y. , White Michael A. , Stormo Gary D. 
Published: May 2020

AbstractPost-transcriptional autoregulation of gene expression is common in bacterial systems but many fewer examples are known in eukaryotes. We used the yeast collection of genes fused to GFP as a rapid screen for examples of feedback regulation in ribosomal proteins by overexpressing a non-regulatable version of a gene and observing the effects on the expression of the GFP-fused version. We tested 95 ribosomal protein genes and found that 21 of them showed at least a three-fold repression. Two genes,RPS22BandRPL1B, showed over a 10-fold repression. In both cases the cis-regulatory segment resides in the 5’ UTR of the gene as shown by placing that segment of the mRNA upstream of GFP alone and demonstrating it is sufficient to cause repression of GFP when the protein is over-expressed. Further analyses showed that the intron in the 5’ UTR ofRPS22Bis required for regulation, presumably because the protein inhibits splicing that is necessary for translation. The 5’ UTR ofRPL1Bcontains a sequence and structure motif that is conserved in the binding sites of Rpl1 orthologs from bacteria to mammals, and mutations within the motif eliminate repression.
The Dynamics of Plant Nutation
Authors: Raja Vicente , Silva Paula L. , Holghoomi Roghaieh , Calvo Paco 
Published: May 2020

AbstractIn this article we advance a cutting-edge methodology for the study of the dynamics of plant movements of nutation. Our approach, unlike customary kinematic analyses of shape, period, or amplitude, is based on three typical signatures of adaptively controlled processes and motions, as reported in the biological and behavioral dynamics literature: harmonicity, predictability, and complexity. We illustrate the application of a dynamical methodology to the bending movements of shoots of common beans (Phaseolus vulgarisL.) in two conditions: with and without a support to climb onto. The results herewith reported support the hypothesis that patterns of nutation are influenced by the presence of a support to climb in their vicinity. The methodology is in principle applicable to a whole range of plant movements.
Sequential sequestrations increase the incorporation and retention of multiple growth factors in mineralized collagen scaffolds
Authors: Tiffany Aleczandria S. , Dewey Marley J. , Harley Brendan A.C. 
Published: May 2020

ABSTRACTTrauma induced injuries of the mouth, jaw, face, and related structures present unique clinical challenges due to their large size and complex geometry. Growth factor signaling coordinates the behavior of multiple cell types following an injury, and effective coordination of growth factor availability within a biomaterial can be critical for accelerating bone healing. Mineralized collagen scaffolds are a class of degradable biomaterial whose biophysical and compositional parameters can be adjusted to facilitate cell invasion and tissue remodeling. Here we describe the use of modified simulated body fluid treatments to enable sequential sequestration of bone morphogenic protein 2 and vascular endothelial growth factor into mineralized collagen scaffolds for bone repair. We report the capability of these scaffolds to sequester growth factors from solution without additional crosslinking treatments and show high levels of retention for individual and multiple growth factors that can be layered into the material via sequential sequestration steps. Sequentially sequestering growth factors allows prolonged release of growth factorsin vitroand suggests the potential to improve healing of large-scale bone injury modelsin vivo. Future work will utilize this sequestration method to induce cellular activities critical to bone healing such as vessel formation and cell migration.
Targeting the latent human cytomegalovirus reservoir with virus specific nanobodies
Authors: De Groof Timo W.M. , Elder Elizabeth G. , Heukers Raimond , Lim Eleanor Y. , Wills Mark , Sinclair John H. , Smit Martine J. 
Published: May 2020

AbstractLatent reservoirs of viral pathogens are significant barriers to eradication of these viruses. During latency, herpesviruses maintain their genome, with little gene expression, making latent infections refractory to current treatments targeting viral replication. In the case of human cytomegalovirus (HCMV), sporadic reactivation events are well controlled by the immune system. However, in immunocompromised or immunosuppressed individuals, HCMV reactivation often results in morbidity in solid organ and stem cell transplant patients. Clearance of the latent reservoir could lower the incidence and severity of HCMV-associated disease. Here, we develop a virus specific nanobody (VUN100b) that partially inhibits signaling of the viral receptor US28. VUN100b treatment partially reverses latency without fully reactivating the virus. Moreover, VUN100b treatment drives recognition and killing of latently infected monocytes by autologous cytotoxic T lymphocytes from HCMV-seropositive individuals. This study shows the potential of VUN100b as a therapy to clear the HCMV latent reservoir of transplant patients.
Global view on virus infection in non-human primates and implication for public health and wildlife conservation
Authors: Liu Zhijin 
Published: May 2020

AbstractThe pandemic outbreak and rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not only a threat for humans, but potentially also for many animals. Research has revealed that SARS-CoV-2 and other coronaviruses have been transmitted from animals to humans andvice versa, and across animal species, and hence, attracted public attention concerning host-virus interactions and transmission ways. Non-human primates (NHPs), as our evolutionary closest relatives, are susceptible to human viruses, and a number of pathogens are known to circulate between humans and NHPs. Here we generated global statistics of virus infection in NHPs (VI-NHPs). In total, 121 NHP species from 14 families have been reported to be infected by 139 DNA and RNA viruses from 23 virus families; 74.8 percent of viruses in NHPs have also been found in humans, indicative of the high potential for cross species transmission of these viruses. The top ten NHP species with high centrality in the NHP-virus network are two apes (Pan troglodytes, Pongo pygmaeus), seven Old World monkeys (Macaca mulatta, M. fascicularis, Papio cynocephalus, Lophocebus albigena, Chlorocebus aethiops, Cercopithecus ascanius, C. nictitans) and a lemur (Propithecus diadema). Besides apes, there is a high risk of virus circulation between humans and Old World monkeys, given the wide distribution of many Old World monkey species and their frequent contact with humans. We suggest epidemiological investigations in NHPs, specifically in Old World monkeys with close contact to humans, and other effective measures to prevent this potential circular transmission.