bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 3-step Mechanical Digestion Method to Harvest Adipose-derived Stromal Vascular Fraction
Authors: Tiryaki Tunc , Condé-Green Alexandra , Cohen Steven R. , Canikyan Serli , Kocak Polen 
Published: February 2020

Background:
Adipose stromal vascular fraction (SVF) isolation with enzymatic digestion is the gold standard, but is expensive, having practical and legal concerns. The alternative mechanical SVF isolation methods provide lower cell yields as they employ either centrifugation, emulsification, or digestion steps alone. We combined mechanical processing with buffer incubation and centrifugation steps into an isolation method called “mechanical digestion” and compared the cell yields with that of enzymatic digestion.

Methods:
A total of 40-mL lipoaspirate was harvested from 35 women undergoing liposuction and was submitted to conventional enzymatic digestion for SVF isolation or mechanical digestion using a closed unit harnessing 3 ports with blades, followed by buffer incubation and centrifugation. Culture of the SVFs and flow cytometry were performed.

Results:
The SVF cell yield obtained by enzymatic digestion was significantly higher 3.38 × 106/mL (±3.63; n = 35) than that obtained by mechanical digestion 1.34 × 106/mL (±1.69; n = 35), P = 0.015. The average cell viability was 82.86% ± 10.68 after enzymatic digestion versus 85.86% ± 5.74 after mechanical digestion, which was not significant. Mechanical digested SVF expressed 2-fold higher stem cell surface markers compared with enzymatically digested SVF. Mechanical digestion was less time consuming, cost effective, and did not require a specific laboratory environment.

Conclusions:
Mechanically digested SVF was comparable to enzymatically digested SVF in terms of stromal cell composition and viability. With mechanical digestion, we can isolate 30%–50% SVF cells of that isolated with enzymatic digestion. Further studies are warranted to determine the clinical outcomes.
Absent Internal Mammary Recipient Vein in Autologous Breast Reconstruction
Authors: Muto Mayu , Satake Toshihiko , Masuda Yuma , Kobayashi Saya , Tamura Shihoko , Kobayashi Shinji , Ohtake Tohru , Maegawa Jiro 
Published: February 2020

Summary:
The internal mammary vessels (IMA/Vs) have been used as the first-choice recipient vessels for microsurgical anastomosis and flap inset in autologous breast reconstruction owing to their ease of access and use compared with the thoracodorsal vessels (TDA/Vs). Herein, we report two cases of deep inferior epigastric perforator flap breast reconstructions in which the recipient internal mammary vein (IMV) was lacking. In the first case, a 50-year-old patient underwent delayed two-stage reconstruction, and in the second, a 45-year-old patient underwent delayed reconstruction because of capsular contracture following breast implant reconstruction. Neither patient received preoperative radiation therapy. During IMA/V preparation, we could not find the internal mammary vein (IMV) around the internal mammary artery (IMA) despite careful dissection. No internal mammary lymph node adenopathy and vascular encasement from metastasis were noted. Intraoperative indocyanine green angiography revealed absence of IMV, which was presumed to be congenital. Therefore, microsurgical anastomosis was performed to connect the deep inferior epigastric vessels to the thoracodorsal vessel. The postoperative course was uneventful in both cases. Although many anatomical studies have revealed different locations, diameters, branching patterns, and perforators of the IMA/V, absent IMV has been reported very rarely. In autologous breast reconstruction, plastic surgeons should be prepared for the possibility of the absence of IMV.
Pharmacotherapy in Critically Ill Children: A Retrospective Review of 17,199 Admissions
Authors: Gaetani Melany , Frndova Helena , Seto Winnie , Parshuram Christopher 
Published: February 2020

Objectives:
Despite the ubiquitous role of pharmacotherapy in the care of critically ill children, descriptions of the extent of pharmacotherapy in critical illness are limited. Greater understanding of drug therapy can help identify clinically important associations and assist in the prioritization of efforts to address knowledge gaps. The objectives of this study were to describe the diversity, volume, and patterns of pharmacotherapy in critically ill children.

Design:
A retrospective cohort study was performed with patient admissions to the ICU between July 31, 2006, and July 31, 2015.

Setting:
The study took place at a single, free-standing, pediatric, quaternary center.

Patients:
Eligible patient admissions were admitted to the ICU for more than 6 hours and received one or more drug administration. There were a total 17,482 patient-admissions and after exclusion of 283 admissions (2%) with no documented enteral or parenteral drug administration, 17,199 eligible admissions were studied.

Interventions:
None.

Measurements and Main Results:
The 17,199 eligible admissions were admitted to the ICU for 2,208,475 hours and received 515 different drugs. The 1,954,171 administrations were 894,709 (45%) enteral administrations, 998,490 (51%) IV injections and 60,972 (3%) infusions. Infusions were administered for 4,476,538 hours. Twelve-thousand two-hundred seventy-three patients (71%) were administered five or more different drugs on 80,943 of patient days (75%). The 10 most commonly administered drugs comprised of 834,441 administrations (43%).

Conclusions:
Drug administration in the ICU is complex, involves many medications, and the potential for drug interaction and reaction is compounded by the volume and diversity of therapies routinely provided in ICU. Further evaluation of polytherapy could be used to improve outcomes and enhance the safety of pharmacotherapy in critically ill children.
Clinically oriented system-based embryology; a significant course in clinical practice
Authors: Moghadam Samira , Gharebaghi Hamid , Mohamadi Mohamad Javad , Farokhi Ahmad , Ghorbanlou Mehrdad , Arianmanesh Mitra 
Published: February 2020

AbstractIntroductionEmbryology is a branch of medical sciences in developmental biology. Since the knowledge of embryology is of special significance for medical students, this study was conducted with the purpose of elucidating the viewpoint of medical students of Zanjan University of Medical Sciences in Iran on the application of embryology courses in fulfilling clinical purposes.MethodsThis cross-sectional study was conducted in 2018-2019 with a census method on all clinical medical students (trainees and interns). To collect medical students’ opinions, the researcher-designed questionnaire was used. The validity of the questionnaire was confirmed by embryology experts by content validity ratio (CVR) and factor analysis and the reliability of the questionnaire Cronbach’s alpha coefficient (0.9), respectively. Data were analyzed by SPSS (version 24) and Lisrel software. Values with P<0.05 were considered significant.ResultsDescriptive statistics in the field of general and system-based embryology demonstrated that the topics of birth defects and development of body cavities (diaphragm development) have the most influence on clinical practice of medical students.ConclusionsIt seems that more focus on system-based embryology courses leads to a better performance of medical students in clinical courses.
Molecular malaria surveillance using a novel protocol for extraction and analysis of nucleic acids retained on used rapid diagnostic tests
Authors: Guirou Etienne A. , Schindler Tobias , Hosch Salome , Donfack Olivier Tresor , Yoboue Charlene Aya , Krähenbühl Silvan , Deal Anna , Cosi Glenda , Gondwe Linda , Mwangoka Grace , Masuki Heavenlight , Salim Nahya , Mpina Maxmillian , Said Jongo , Abdulla Salim , Hoffman Stephen L. , Nlavo Bonifacio Manguire , Maas Carl , Falla Carlos Cortes , Phiri Wonder P. , Garcia Guillermo A. , Tanner Marcel , Daubenberger Claudia 
Published: February 2020

AbstractThe use of malaria rapid diagnostic tests (RDTs) as a source for nucleic acids that can be analyzed via nucleic acid amplification techniques has several advantages, including minimal amounts of blood, sample collection, simplified storage and shipping conditions at room temperature. We have systematically developed and extensively evaluated a procedure to extract total nucleic acids from used malaria RDTs. The co-extraction of DNA and RNA molecules from small volumes of dried blood retained on the RDTs allows detection and quantification of P. falciparum parasites from asymptomatic patients with parasite densities as low as 1 Pf/µL blood using reverse transcription quantitative PCR. Based on the extraction protocol we have developed the ENAR (Extraction of Nucleic Acids from RDTs) approach; a complete workflow for large-scale molecular malaria surveillance. Using RDTs collected during a malaria indicator survey we demonstrated that ENAR provides a powerful tool to analyze nucleic acids from thousands of RDTs in a standardized and high-throughput manner. We found several, known and new, non-synonymous single nucleotide polymorphisms in the propeller region of the kelch 13 gene among isolates circulating on Bioko Island, Equatorial Guinea.
Tracking and Predicting COVID-19 Epidemic in China Mainland
Authors: Sun Haoxuan , Qiu Yumou , Yan Han , Huang Yaxuan , Zhu Yuru , Chen Song Xi 
Published: February 2020

AbstractBy proposing a varying coefficient Susceptible-Infected-Removal model (vSIR), we track the epidemic of COVID-19 in 30 provinces in China and 15 cities in Hubei province, the epicenter of the outbreak. It is found that the spread of COVID-19 has been significantly slowing down within the two weeks from January 27 to February 10th with 87.0% and 84.3% reductions in the reproduction numberR0among the 30 provinces and 15 Hubei cities, respectively. This suggests the extreme control measures implemented since January 23, which include cutting off Wuhan and many other cities and towns, a great public awareness and high level of self isolation at home, have contributed to a substantial decline in the reproductivity of the COVID-19 in China. We predict that Hubei province will reach its peak between February 20 and 22, 2020, and if the removal rate can be increased to 0.1, the epidemic outside Hubei province will end in May 2020, and inside Hubei in early June.
Clustering of CD3ζ is sufficient to initiate T cell receptor signaling
Authors: Ma Yuanqing , Lim Yean J , Benda Aleš , Goyette Jesse , Gaus Katharina 
Published: February 2020

AbstractT cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of CD3ζ chains in a light controlled manner. We showed that spatial clustering of the CD3ζ intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of CD3ζ, Zap70, PLCγ, ERK and initiated Ca2+flux. In reconstituted COS-7 cells, only Lck expression was required to initiate CD3ζ phosphorylation upon CD3ζ clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed CD3ζ clusters at the plasma membrane. Taken together, our data suggest that clustering of the TCR can initialize proximal TCR signaling and thus constitute a biophysical mechanism of TCR triggering.
Spatial maps in piriform cortex during olfactory navigation
Authors: Poo Cindy , Agarwal Gautam , Bonacchi Niccolò , Mainen Zachary 
Published: February 2020

SummaryOdors are a fundamental part of the sensory environment used by animals to inform behaviors such as foraging and navigation1, 2. Primary olfactory (piriform) cortex is thought to be dedicated to encoding odor identity3–8. Here, using neural ensemble recordings in freely moving rats performing a novel odor-cued spatial choice task, we show that posterior piriform cortex neurons also carry a robust spatial map of the environment. Piriform spatial maps were stable across behavioral contexts independent of olfactory drive or reward availability, and the accuracy of spatial information carried by individual neurons depended on the strength of their functional coupling to the hippocampal theta rhythm. Ensembles of piriform neurons concurrently represented odor identity as well as spatial locations of animals, forming an “olfactory-place map”. Our results reveal a previously unknown function for piriform cortex in spatial cognition and suggest that it is well-suited to form odor-place associations and guide olfactory cued spatial navigation.
Genome editing enables reverse genetics of multicellular development in the choanoflagellateSalpingoeca rosetta
Authors: Booth David S. , King Nicole 
Published: February 2020

AbstractIn a previous study, we established a forward genetic screen to identify genes required for multicellular development in the choanoflagellate,Salpingoeca rosetta(Levin et al., 2014). Yet, the paucity of reverse genetic tools for choanoflagellates has hampered direct tests of gene function and impeded the establishment of choanoflagellates as a model for reconstructing the origin of their closest living relatives, the animals. Here we establish CRISPR/Cas9-mediated genome editing inS. rosettaby engineering a selectable marker to enrich for edited cells. We then use genome editing to disrupt the coding sequence of aS. rosettaC-type lectin gene,rosetteless, and thereby demonstrate its necessity for multicellular rosette development. This work advancesS. rosettaas a model system in which to investigate how genes identified from genetic screens and genomic surveys function in choanoflagellates and evolved as critical regulators of animal biology.
A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology
Authors: Marken John P. , Xiao Fangzhou , Murray Richard M. 
Published: February 2020

AbstractMuch of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system’s structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator.
The stability and ABA import activity of NRT1.2 inArabidopsisare regulated by CEPR2 via phosphorylation modification
Authors: Zhang Lei , Yu Zipeng , Xu Yang , Yu Miao , Ren Yue , Zhang Shizhong , Yang Guodong , Huang Jinguang , Yan Kang , Zheng Chengchao , Wu Changai 
Published: February 2020

AbstractAbscisic acid (ABA) transport plays important role in systematic plant responses to environmental factors. Here, we showed that C-terminally encoded peptide receptor 2 (CEPR2) directly interacted with the ABA transporter NRT1.2. Using transgenic seedlings, we demonstrated that NRT1.2 positively regulated the ABA response, and that CEPR2 acted on NRT1.2 epistatically and negatively. Under normal conditions, CEPR2 phosphorylated NRT1.2 at least at serine 292 to promote the degradation of NRT1.2. However, ABA and serine 292 nonphospharylation strongly inhibited the degradation of NRT1.2, indicating that ABA-inhibited the phosphorylation of NRT1.2. Transport assays in yeast andXenopusoocytes showed that nonphosphorylated NRT1.2 had high levels of ABA-import activity, but phosphorylated NRT1.2 did not import ABA. Analyses of complementnrt1.2mutants by mimicking nonphospharylated and phospharylated NRT1.2 confirmed that nonphospharylated NRT1.2S292Ahad high stability and ABA import activityin planta. Further experiments indicated that NRT1.2 was degraded via the 26S proteasome and vacuolar degradation pathways. UBC32, UBC33, and UBC34 interacted with, and mediated the ubiquitination of NRT1.2. UBC32, UBC33, and UBC34 acted on NRT1.2 epistatically and negativelyin planta. Thus, our results suggested the existence of novel plant mechanisms regulating NRT1.2 stability and ABA import activity in response to environmental conditions.
Commonalities and differences in the Oxidative Phosphorylation of Mitochondria and Neuronal Membranes
Authors: Ravera Silvia , Bartolucci Martina , Calzia Daniela , Morelli Alessandro M. , Panfoli Isabella 
Published: February 2020

ABSTRACTMitochondria are considered the exclusive site of aerobic metabolism. However, in recent years, the functional expression of the oxidative phosphorylation (OxPhos) machinery has been reported in several other membranous structures, including the plasma membrane, endoplasmic reticulum, nucleus, myelin sheath and disks of rod outer segments. Thus, to underline commonalities and differences between extra-mitochondrial and mitochondrial aerobic metabolism, we characterized the aerobic ATP synthesis in isolated myelin sheath (IM) and rod outer segment (OS) disks, using mitochondria-enriched fractions, as a positive control. Oxygen consumption and ATP synthesis were evaluated in the presence of conventional (pyruvate + malate or succinate) and unconventional (NADH) substrates. ATP synthesis was also assayed in the presence of 10-100 µM ATP in the assay medium. Data show that IM and OS disks consumed oxygen and synthesized ATP both in the presence of conventional and unconventional respiratory substrates, while the mitochondria-enriched fraction did not utilize NADH. Only in mitochondria, ATP synthesis was progressively lost in the presence of increasing ATP concentrations. Conversely, only myelin sheath and rod OS disks produced ATP at a later time or after the removal of respiratory substrates, reflecting their ability to accumulate energy and this opens up exciting perspectives in the study of sleep. Thus, these data suggest that the extramitochondrial OxPhos in IM and rod OS displays a different behavior concerning the classic mitochondrial aerobic metabolism, representing a possible basic molecular process involved in the physiology of the nervous system.Significance StatementMitochondria are considered the cell powerhouse, being the site of the oxidative phosphorylation (OxPhos), which produces the major part of cellular chemical energy by oxygen consumption. However, proteomics, microscopy, and biochemical analyses have described the ectopic functional expression of the OxPhos machinery also in other membranous structures, such as isolated myelin (IM) and rod outer segments (OS). The results reported in this work shows that, although the proteins involved in IM and rod OS OxPhos appear the same expressed in mitochondria, the comparison of mitochondrial and extramitochondrial OxPhos display some differences, opening a new scenario about the energy metabolism modulation.Graphical Abstract
Estimation of the number of synapses in the hippocampus and brain-wide by volume electron microscopy and genetic labeling
Authors: Santuy Andrea , Tomás-Roca Laura , Rodríguez José-Rodrigo , González-Soriano Juncal , Zhu Fei , Qiu Zhen , Grant Seth GN , DeFelipe Javier , Merchan-Perez Angel 
Published: February 2020

AbstractDetermining the number of synapses that are present in different brain regions is crucial to understand brain connectivity as a whole. Membrane-associated guanylate kinases (MAGUKs) are a family of scaffolding proteins that are expressed in excitatory glutamatergic synapses. We used genetic labeling of two of these proteins (PSD95 and SAP102), and Spinning Disc confocal Microscopy (SDM), to estimate the number of fluorescent puncta in the CA1 area of the hippocampus. We also used FIB-SEM, a three-dimensional electron microscopy technique, to calculate the actual numbers of synapses in the same area. We then estimated the ratio between the three-dimensional densities obtained with FIB-SEM (synapses/μm3) and the bi-dimensional densities obtained with SDM (puncta/100 μm2). Given that it is impractical to use FIB-SEM brain-wide, we used previously available SDM data from other brain regions and we applied this ratio as a conversion factor to estimate the minimum density of synapses in those regions. We found the highest densities of synapses in the isocortex, olfactory areas, hippocampal formation and cortical subplate. Low densities were found in the pallidum, hypothalamus, brainstem and cerebellum. Finally, the striatum and thalamus showed a wide range of synapse densities.
Modality-specific dysfunctional neural processing of social-abstract and non-social-concrete information in schizophrenia
Authors: He Yifei , Steines Miriam , Sammer Gebhard , Nagels Arne , Kircher Tilo , Straube Benjamin 
Published: February 2020

AbstractSchizophrenia is characterized by marked communication dysfunctions encompassing potential impairments in the processing of social-abstract and non-social-concrete information, especially in everyday situations where multiple modalities are present in the form of speech and gesture. To date, the neurobiological basis of these deficits remains elusive. In a functional magnetic resonance imaging (fMRI) study, 17 patients with schizophrenia or schizoaffective disorder, and 18 matched controls watched videos of an actor speaking, gesturing (unimodal), and both speaking and gesturing (bimodal) about social or non-social events in a naturalistic way. Participants were asked to judge whether each video contains person-related (social) or object-related (non-social) information. When processing social-abstract content, patients showed reduced activation in the medial prefrontal cortex (mPFC) only in the gesture but not in the speech condition. For non-social-concrete content, remarkably, reduced neural activation for patients in the left postcentral gyrus and the right insula was observed only in the speech condition. Moreover, in the bimodal conditions, patients displayed improved task performance and comparable activation to controls in both social and non-social content. To conclude, patients with schizophrenia displayed modality-specific aberrant neural processing of social and non-social information, which is not present for the bimodal conditions. This finding provides novel insights into dysfunctional multimodal communication in schizophrenia, and may have potential therapeutic implications.