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A major challenge in genetics is to identify genetic variants driving natural phenotypic variation. However, current methods of genetic mapping have limited resolution. To address this challenge, we developed a CRISPR-Cas9-based high-throughput genome editing approach that can introduce thousands of specific genetic variants in a single experiment. This enabled us to study the fitness consequences of 16,006 natural genetic variants in yeast. We identified 572 variants with significant fitness differences in glucose media; these are highly enriched in promoters, particularly in transcription factor binding sites, while only 19.2% affect amino acid sequences. Strikingly, nearby variants nearly always favor the same parent's alleles, suggesting that lineage-specific selection is often driven by multiple clustered variants. In sum, our genome editing approach reveals the genetic architecture of fitness variation at single-base resolution and could be adapted to measure the effects of genome-wide genetic variation in any screen for cell survival or cell-sortable markers.
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Edição de Genes/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Saccharomyces cerevisiae/genética , Sistemas CRISPR-Cas , Mapeamento Cromossômico , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Variação Genética/genética , Vetores Genéticos , Genoma , Leveduras/genéticaRESUMO
Cis-regulatory elements such as transcription factor (TF) binding sites can be identified genome-wide, but it remains far more challenging to pinpoint genetic variants affecting TF binding. Here, we introduce a pooling-based approach to mapping quantitative trait loci (QTLs) for molecular-level traits. Applying this to five TFs and a histone modification, we mapped thousands of cis-acting QTLs, with over 25-fold lower cost compared to standard QTL mapping. We found that single genetic variants frequently affect binding of multiple TFs, and CTCF can recruit all five TFs to its binding sites. These QTLs often affect local chromatin and transcription but can also influence long-range chromosomal contacts, demonstrating a role for natural genetic variation in chromosomal architecture. Thousands of these QTLs have been implicated in genome-wide association studies, providing candidate molecular mechanisms for many disease risk loci and suggesting that TF binding variation may underlie a large fraction of human phenotypic variation.
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Imunoprecipitação da Cromatina/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Análise de Sequência de DNA/métodos , Fatores de Transcrição/metabolismo , Predisposição Genética para Doença , Código das Histonas , HumanosRESUMO
Among primates, humans display a unique trajectory of development that is responsible for the many traits specific to our species. However, the inaccessibility of primary human and chimpanzee tissues has limited our ability to study human evolution. Comparative in vitro approaches using primate-derived induced pluripotent stem cells have begun to reveal species differences on the cellular and molecular levels1,2. In particular, brain organoids have emerged as a promising platform to study primate neural development in vitro3-5, although cross-species comparisons of organoids are complicated by differences in developmental timing and variability of differentiation6,7. Here we develop a new platform to address these limitations by fusing human and chimpanzee induced pluripotent stem cells to generate a panel of tetraploid hybrid stem cells. We applied this approach to study species divergence in cerebral cortical development by differentiating these cells into neural organoids. We found that hybrid organoids provide a controlled system for disentangling cis- and trans-acting gene-expression divergence across cell types and developmental stages, revealing a signature of selection on astrocyte-related genes. In addition, we identified an upregulation of the human somatostatin receptor 2 gene (SSTR2), which regulates neuronal calcium signalling and is associated with neuropsychiatric disorders8,9. We reveal a human-specific response to modulation of SSTR2 function in cortical neurons, underscoring the potential of this platform for elucidating the molecular basis of human evolution.
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Fusão Celular , Regulação da Expressão Gênica no Desenvolvimento , Células Híbridas/citologia , Células-Tronco Pluripotentes Induzidas/citologia , Neurogênese/genética , Alelos , Animais , Astrócitos/citologia , Sinalização do Cálcio , Córtex Cerebral/citologia , Feminino , Humanos , Masculino , Neurônios/citologia , Organoides/citologia , Pan troglodytes/genética , Receptores de Somatostatina/genética , Reprodutibilidade dos Testes , Transcrição GênicaRESUMO
Uranyl fluoride (UO2F2) particles (<20 µm) were subjected to first-of-its-kind analysis via simultaneous laser-induced breakdown spectroscopy (LIBS) and laser ablation multi-collector inductively coupled plasma-mass spectrometry (LA-MC-ICP-MS). Briefly, a nanosecond pulsed high-energy laser was focused onto the sample (particle) surface. In a single laser pulse, the UO2F2 particle was excited/ionized within the microplasma volume, and the emission of light was collected via fiber optics such that emission spectroscopy could be employed for the detection of uranium (U) and fluorine (F). The ablated particle was simultaneously transported into the MC-ICP-MS for high precision isotopic (i.e., 234U, 235U, and 238U) analysis. This method, LIBS/LA-MC-ICP-MS was optimized and employed to rapidly measure 80+ UO2F2 particles, which were subjected to different calcination processes, which results in varying degrees of F loss from the individual particles. In measuring the particles, the average F/U ratios for the populations treated at 100 and 500 °C were 2.78 ± 1.28 and 1.01 ± 0.50, respectively, confirming loss of F through the calcination process. The average 235U/238U on the particle populations for the 100 and 500 °C were 0.007262 (22) and 0.007231 (23), which was determined to be <0.2% from the expected value. The 234U/238U ratios on the same particles were 0.000053 (11) and 0.000050 (10) for the 100 and 500 °C, respectively, <10% from the expected value. Notably, each population was analyzed in under 5 min, demonstrating the truly rapid analysis technique presented here.
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Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes between ecotypes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are strongly enriched in genomic regions of repeated marine-freshwater divergence, supporting an important role for these cis-regulatory differences in parallel adaptive evolution of sticklebacks to freshwater habitats. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes across tissues and during development, and support a fundamental role for tissue-specific cis-regulatory changes in rapid adaptation to new environments.
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Smegmamorpha , Animais , Smegmamorpha/genética , Água Doce , Adaptação Fisiológica/genética , Genoma , AclimataçãoRESUMO
Optical sensors and chemometric models were leveraged for the quantification of uranium(VI) (0-100 µg mL-1), europium (0-150 µg mL-1), samarium (0-250 µg mL-1), praseodymium (0-350 µg mL-1), neodymium (0-1000 µg mL-1), and HNO3 (2-4 M) with varying corrosion product (iron, nickel, and chromium) levels using laser fluorescence, Raman scattering, and ultraviolet-visible-near-infrared absorption spectra. In this paper, an efficient approach to developing and evaluating tens of thousands of partial least-squares regression (PLSR) models, built from fused optical spectra or multimodal acquisitions, is discussed. Each PLSR model was optimized with unique preprocessing combinations, and features were selected using genetic algorithm filters. The 7-factor D-optimal design training set contained just 55 samples to minimize the number of samples. The performance of PLSR models was evaluated by using an automated latent variable selection script. PLS1 regression models tailored to each species outperformed a global PLS2 model. PLS1 models built using fused spectra data and a multimodal (i.e., analyzed separately) approach yielded similar information, resulting in percent root-mean-square error of prediction values of 0.9-5.7% for the seven factors. The optical techniques and data processing strategies established in this study allow for the direct analysis of numerous species without measuring luminescence lifetimes or relying on a standard addition approach, making it optimal for near-real-time, in situ measurements. Nuclear reactor modeling helped bound training set conditions and identified elemental ratios of lanthanide fission products to characterize the burnup of irradiated nuclear fuel. Leveraging fluorescence, spectrophotometry, experimental design, and chemometrics can enable the remote quantification and characterization of complex systems with numerous species, monitor system performance, help identify the source of materials, and enable rapid high-throughput experiments in a variety of industrial processes and fundamental studies.
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We measure the thermal conductivity of solid and molten tungsten using steady state temperature differential radiometry. We demonstrate that the thermal conductivity can be well described by application of Wiedemann-Franz law to electrical resistivity data, thus suggesting the validity of Wiedemann-Franz law to capture the electronic thermal conductivity of metals in their molten phase. We further support this conclusion using ab initio molecular dynamics simulations with a machine-learned potential. Our results show that at these high temperatures, the vibrational contribution to thermal conductivity is negligible compared to the electronic component.
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A microextraction liquid sampling system coupled to a quadrupole inductively coupled plasma-mass spectrometer (ICP-MS) was utilized to spatially discern uranium particles, isotopically, on a cellulose-based swipe material (i.e., J-type swipe). These types of swipes are often used by the International Atomic Energy Agency (IAEA) as part of their environmental sampling program. A grid was created such that extraction locations covered the center circle (n = 34 without overlapping). Uranium (U) particulates (<20 µm) of varying U isotopic abundance and chemical form (i.e., uranyl fluoride and uranyl nitrate hexahydrate) were mechanically placed on the swipes in random locations and detected via the microextraction-ICP-MS methodology. Heat maps were subsequently generated to show the placement of the particulate with their respective intensity and isotopic determination. This detection of the uranium particulates, via isotopic determination, agreed with reference values for these materials. Additionally, depleted (235U/238U = 0.002) uranium particulates were placed directly within a clay matrix, on the swipe surface, and subjected to analysis by microextraction-ICP-MS. The mapping of the swipe demonstrated, for the first time, the employment of the microextraction-ICP-MS method for extracting sample from a complex matrix, and correctly identifying the uranium isotopic composition. This example ultimately demonstrates the utility of the methodology for detecting particles of interest in complex matrices.
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Assembly-line polyketide synthases (PKSs) are large and complex enzymatic machineries with a multimodular architecture, typically encoded in bacterial genomes by biosynthetic gene clusters. Their modularity has led to an astounding diversity of biosynthesized molecules, many with medical relevance. Thus, understanding the mechanisms that drive PKS evolution is fundamental for both functional prediction of natural PKSs as well as for the engineering of novel PKSs. Here, we describe a repetitive genetic element in assembly-line PKS genes which appears to play a role in accelerating the diversification of closely related biosynthetic clusters. We named this element GRINS: genetic repeats of intense nucleotide skews. GRINS appear to recode PKS protein regions with a biased nucleotide composition and to promote gene conversion. GRINS are present in a large number of assembly-line PKS gene clusters and are particularly widespread in the actinobacterial genus Streptomyces While the molecular mechanisms associated with GRINS appearance, dissemination, and maintenance are unknown, the presence of GRINS in a broad range of bacterial phyla and gene families indicates that these genetic elements could play a fundamental role in protein evolution.
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Variação Genética , Policetídeo Sintases/genética , Sequências Repetitivas de Ácido Nucleico/genética , Sequência de Bases , Evolução Molecular , Conversão Gênica , Genoma Bacteriano , Família Multigênica , Nucleotídeos/genética , Filogenia , Policetídeo Sintases/química , Domínios Proteicos , Streptomyces/enzimologia , Streptomyces/genéticaRESUMO
Candida albicans is the most common cause of systemic fungal infections in humans and is considerably more virulent than its closest known relative, Candida dubliniensis. To investigate this difference, we constructed interspecies hybrids and quantified mRNA levels produced from each genome in the hybrid. This approach systematically identified expression differences in orthologous genes arising from cis-regulatory sequence changes that accumulated since the two species last shared a common ancestor, some 10 million y ago. We documented many orthologous gene-expression differences between the two species, and we pursued one striking observation: All 15 genes coding for the enzymes of glycolysis showed higher expression from the C. albicans genome than the C. dubliniensis genome in the interspecies hybrid. This pattern requires evolutionary changes to have occurred at each gene; the fact that they all act in the same direction strongly indicates lineage-specific natural selection as the underlying cause. To test whether these expression differences contribute to virulence, we created a C. dubliniensis strain in which all 15 glycolysis genes were produced at modestly elevated levels and found that this strain had significantly increased virulence in the standard mouse model of systemic infection. These results indicate that small expression differences across a deeply conserved set of metabolism enzymes can play a significant role in the evolution of virulence in fungal pathogens.
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Evolução Biológica , Candida/classificação , Candida/genética , Seleção Genética , Alelos , Candida/metabolismo , Candida/patogenicidade , Candidíase/microbiologia , Biologia Computacional/métodos , Perfilação da Expressão Gênica , Regulação Fúngica da Expressão Gênica , Ontologia Genética , Genes Fúngicos , Hibridização Genética , Virulência/genéticaRESUMO
BACKGROUND: Complex surgical back wounds represent significant morbidity in patients who have undergone spinal procedures requiring closure or revision by plastic surgeons. This study aimed to assess the utility of bacterial wound culture data for predicting surgical outcomes of wound management. METHODS: This study is a single-institution retrospective review of consecutive patients who required plastic surgery intervention for wound infection following spinal procedures between the years 2010 and 2021 (n = 70). Statistical analysis was performed for demographics, comorbidities, perioperative laboratory studies, and treatment methods. The primary outcomes of interest were rate of postoperative complications after soft tissue reconstruction and reconstructive failure. The secondary outcome of interest was time to healing in number of days. RESULTS: The overall complication rate after wound closure was 31.4%, with wound infection in 12.9%, seroma in 10%, dehiscence in 12.9%, and hematoma in 1.4%. Increasing number of debridements before wound closure increased the likelihood of a surgical complication of any kind (odds ratio [OR], 1.772; 95% confidence interval [CI], 1.045-3.002). Positive wound cultures before reconstruction were associated with development of seroma only (OR, 0.265; 95% CI, 0.078-0.893). Use of incisional vacuum-assisted closure devices significantly decreased the odds of postoperative wound dehiscence (OR, 0.179; 95% CI, 0.034-0.904) and increased odds of healing (hazard ratio, 3.638; 95% CI, 1.547-8.613). CONCLUSIONS: Positive wound cultures were not significantly associated with negative outcomes after complex closure or reconstruction of infected spinal surgical wounds. This finding emphasizes the importance of clinical judgment with a multidisciplinary approach to complex surgical back wounds over culture data for wound closure timing.
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Infecção da Ferida Cirúrgica , Humanos , Estudos Retrospectivos , Feminino , Masculino , Pessoa de Meia-Idade , Infecção da Ferida Cirúrgica/epidemiologia , Infecção da Ferida Cirúrgica/microbiologia , Infecção da Ferida Cirúrgica/etiologia , Idoso , Adulto , Cicatrização , Procedimentos de Cirurgia Plástica/métodos , Procedimentos de Cirurgia Plástica/efeitos adversos , Complicações Pós-Operatórias/epidemiologia , Complicações Pós-Operatórias/microbiologia , Técnicas de Fechamento de Ferimentos , Resultado do Tratamento , Valor Preditivo dos TestesRESUMO
INTRODUCTION: The immune receptor triggering receptor expressed on myeloid cells 2 (TREM2) is among the strongest genetic risk factors for Alzheimer's disease (AD) and is a therapeutic target. TREM2 multimers have been identified in crystallography and implicated in the efficacy of antibody therapeutics; however, the molecular basis for TREM2 multimerization remains poorly understood. METHODS: We used molecular dynamics simulations and binding energy analysis to determine the effects of AD-associated variants on TREM2 multimerization and validated with experimental results. RESULTS: TREM2 trimers remained stably bound, driven primarily by salt bridge between residues D87 and R76 at the interface of TREM2 units. This salt bridge was disrupted by the AD-associated variants R47H and R98W and nearly ablated by the D87N variant. This decreased binding among TREM2 multimers was validated with co-immunoprecipitation assays. DISCUSSION: This study uncovers a molecular basis for TREM2 forming stable trimers and unveils a novel mechanism by which TREM2 variants may increase AD risk by disrupting TREM2 oligomerization to impair TREM2 normal function. HIGHLIGHTS: Triggering receptor expressed on myeloid cells 2 (TREM2) multimerization could regulate TREM2 activation and function. D87-R76 salt bridges at the interface of TREM2 units drive the formation of stable TREM2 dimers and trimers. Alzheimer's disease (AD)-associated R47H and R98W variants disrupt the D87-R76 salt bridge. The AD-associated D87N variant leads to complete loss of the D87-R76 salt bridge.
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INTRODUCTION: Discrepant data exists regarding the outcomes following total knee arthroplasty (TKA) with a prior anterior cruciate reconstruction (ACLR). The purpose of our study was to compare surgical and medical outcomes in the patients with prior ACLR undergoing TKAs compared to a matched control group of the patients who had undergone TKAs without prior ACLR. We hypothesized that the patients with prior ACLR would have inferior clinical outcomes. MATERIAL/METHODS: We retrospectively queried the PearlDiver-database for patients who underwent TKA following ACLR from 2011 to 2020. We used propensity-score matching to create two cohorts. The two-sided independent t-test and Chi-Squared test were used. RESULTS: We identified 2,174 patients who had prior ACLR before the TKAs. There were another 1,348,870 patients who did not have ACLR before the TKAs. After matching, each group had 2,171 patients. The ACLR-TKA group had significantly lower rates of aseptic revision at 2 years (1.2% vs. 4.0%, OR 0.3, p < 0.01), PJI requiring antibiotic spacer at 2 years (0.3% vs. 0.8%, OR 0.35, p = 0.02), and MUA at 90 days (0.4% vs. 7.5%, OR 0.05, p < 0.01). The rate of wound disruption was lower for the ACLR-TKA group at 90 days (p = 0.03) as were several medical complications including AKI at 90 days (p < 0.01), DVT at 90 days (p < 0.01), pneumonia at 90 days (0.04), and required blood transfusion at 90 days (p < 0.01). CONCLUSION: These results differed from our expectations. Within the limitations of the study, we are unable to determine the factors for the lower complications in the ACLR-TKA group. The data from this study are different from what had been reported in the previous studies.
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Reconstrução do Ligamento Cruzado Anterior , Artroplastia do Joelho , Humanos , Artroplastia do Joelho/métodos , Estudos Retrospectivos , Masculino , Feminino , Reconstrução do Ligamento Cruzado Anterior/métodos , Pessoa de Meia-Idade , Idoso , Complicações Pós-Operatórias/epidemiologia , Reoperação/estatística & dados numéricos , Resultado do Tratamento , Pontuação de Propensão , AdultoRESUMO
A series of quaternary Np(IV) fluorides was synthesized using a mild hydrothermal synthesis approach. The compositions are all of the type NaxMNp6F30, where M = Ti(III), V(III), Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Al(III), and Ga(III) and x = 4 for divalent metals, x = 3 for trivalent metals. The compounds all crystallize in the P-3c1 space group and are isotypic with actinide analogues NaxMAn6F30 (An = Ce, U, Th, Pu). Structure data from the neptunium crystals were combined with data from the other actinide analogues to establish the tetravalent, nine-coordinated ionic radii of neptunium (1.030(2) Å), plutonium (1.014(1) Å), and cerium (1.012(2) Å). Radiation damage studies were also carried out on a surrogate material, the cerium analogue Na3AlCe6F30, which indicates that the structure type has low resistance to amorphization. Density functional theory calculations were carried out to compute the band gaps and enthalpies of formation variations among the isotypic cerium and actinide structures to compare the stability of the structures.
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Perioperative dysfunction of the fibrinolytic system may play a role in adverse outcomes for liver transplant recipients. There is a paucity of data describing the potential impact of the postoperative fibrinolytic system on these outcomes. Our objective was to determine whether fibrinolysis resistance (FR), on postoperative day one (POD-1), was associated with early allograft dysfunction (EAD). We hypothesized that FR, quantified by tissue plasminogen activator thrombelastography, is associated with EAD. Tissue plasminogen activator thrombelastography was performed on POD-1 for 184 liver transplant recipients at a single institution. A tissue plasminogen activator thrombelastography clot lysis at 30 minutes of 0.0% was identified as the cutoff for FR on POD-1. EAD occurred in 32% of the total population. Fifty-nine percent (n=108) of patients were categorized with FR. The rate of EAD was 42% versus 17%, p <0.001 in patients with FR compared with those without, respectively. The association between FR and EAD risk was assessed using multivariable logistic regression after controlling for known risk factors. The odds of having EAD were 2.43 times (95% CI, 1.07-5.50, p =0.03) higher in recipients with FR [model C statistic: 0.76 (95% CI, 0.64-0.83, p <0.001]. An additive effect of receiving a donation after circulatory determination of death graft and having FR in the rate of EAD was observed. Finally, compared with those without FR, recipients with FR had significantly shorter graft survival time ( p =0.03). In conclusion, FR on POD-1 is associated with EAD and decreased graft survival time. Postoperative viscoelastic testing may provide clinical utility in identifying patients at risk for developing EAD, especially for recipients receiving donation after circulatory determination of death grafts.
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Transplante de Fígado , Disfunção Primária do Enxerto , Humanos , Transplante de Fígado/efeitos adversos , Ativador de Plasminogênio Tecidual , Aloenxertos , Disfunção Primária do Enxerto/diagnóstico , Disfunção Primária do Enxerto/epidemiologia , Disfunção Primária do Enxerto/etiologia , Fatores de Risco , Sobrevivência de Enxerto , Morte , Estudos RetrospectivosRESUMO
Low fibrinolytic activity has been associated with pathologic thrombosis and multiple-organ failure. Low fibrinolytic activity has two commonly associated terms, hypofibrinolysis and fibrinolysis shutdown. Hypofibrinolysis is a chronic state of lack of ability to generate an appropriate fibrinolytic response when anticipated. Fibrinolysis shutdown is the shutdown of fibrinolysis after systemic activation of the fibrinolytic system. There has been interchanging of these terms to describe critically ill patients in multiple settings. This is problematic in understanding the pathophysiology of disease processes related to these conditions. There is also a lack of research on the cellular mediators of these processes. The purpose of this article is to review the on and off mechanisms of fibrinolysis in the context of low fibrinolytic states to define the importance in differentiating hypofibrinolysis from fibrinolysis shutdown. In many clinical scenarios, the etiology of a low fibrinolytic state cannot be determined due to ambiguity if a preceding fibrinolytic activation event occurred. In this scenario, the term "low fibrinolytic activity" or "fibrinolysis resistance" is a more appropriate descriptor, rather than using assumptive of hypofibrinolysis and fibrinolysis shutdown, particularly in the acute setting of infection, injury, and surgery.
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Transtornos da Coagulação Sanguínea , Trombose , Humanos , Transtornos da Coagulação Sanguínea/complicações , Relevância Clínica , Fibrinólise/fisiologia , Terapia Trombolítica , Trombose/etiologiaRESUMO
Viscoelastic testing (VET) in liver transplantation (LT) has been used since its origin, in combination with standard laboratory testing (SLT). There are only a few, small, randomized controlled trials that demonstrated a reduction in transfusion rates using VET to guide coagulation management. Retrospective analyses contrasting VET to SLT have demonstrated mixed results, with a recent concern for overtreatment and the increase in postoperative thrombotic events. An oversight of many studies evaluating VET in LT is a single protocol that does not address the different phases of surgery, in addition to pre- and postoperative management. Furthermore, the coagulation spectrum of patients entering and exiting the operating room is diverse, as these patients can have varying anatomic and physiologic risk factors for thrombosis. A single transfusion strategy for all is short sighted. VET in combination with SLT creates the opportunity for personalized resuscitation in surgery which can address the many challenges in LT where patients are at a paradoxical risk for both life-threatening bleeding and clotting. With emerging data on the role of rebalanced coagulation in cirrhosis and hypercoagulability following LT, there are numerous potential roles in VET management of LT that have been unaddressed.
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Transtornos da Coagulação Sanguínea , Transplante de Fígado , Trombose , Humanos , Transplante de Fígado/efeitos adversos , Estudos Retrospectivos , Transtornos da Coagulação Sanguínea/etiologia , Coagulação Sanguínea , Trombose/etiologia , Período Perioperatório/efeitos adversosRESUMO
RNA sequencing has been widely used as an essential tool to probe gene expression. While standard practices have been established to analyze RNA-seq data, it is still challenging to interpret and remove artifactual signals. Several biological and technical factors such as sex, age, batches, and sequencing technology have been found to bias these estimates. Probabilistic estimation of expression residuals (PEER), which infers broad variance components in gene expression measurements, has been used to account for some systematic effects, but it has remained challenging to interpret these PEER factors. Here we show that transcriptome diversity-a simple metric based on Shannon entropy-explains a large portion of variability in gene expression and is the strongest known factor encoded in PEER factors. We then show that transcriptome diversity has significant associations with multiple technical and biological variables across diverse organisms and datasets. In sum, transcriptome diversity provides a simple explanation for a major source of variation in both gene expression estimates and PEER covariates.
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RNA , Transcriptoma , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , RNA/genética , RNA-Seq , Análise de Sequência de RNA , Transcriptoma/genética , Sequenciamento do ExomaRESUMO
A new series of mixed-anion alkali rare earth silicate fluorides with composition Rb2Ln[Si2O6]F (Ln = Y, Eu-Lu) has been synthesized via an alkali chloride/fluoride eutectic flux synthetic route. All synthesized compositions crystallize in the tetragonal space group P42/mnm with a 3D framework consisting of LnO4F2 octahedra, tetrasilicate rings, and 1D channels containing alkali metals. A combination of powder X-ray diffraction, single-crystal X-ray diffraction, and luminescence emission spectroscopy was performed to characterize the reaction products. In addition, density functional theory (DFT) calculations were utilized to calculate the 0 K formation enthalpies of the synthesized phases and of hypothetical trivalent actinide analogues to probe the likelihood of the successful synthesis of such trivalent transuranic containing phases, specifically Am and Cm, in the future.
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BACKGROUND: Each year, children die awaiting LT as the demand for grafts exceeds the available supply. Candidates with public health insurance are significantly less likely to undergo both deceased donor LT and D-LLD LT. ND-LLD is another option to gain access to a graft. The aim of this study was to evaluate if recipient insurance type is associated with likelihood of D-LLD versus ND-LLD LT. METHODS: The SRTR/OPTN database was reviewed for pediatric LDLT performed between January 1, 2014 (Medicaid expansion era) and December 31, 2019 at centers that performed ≥1 ND-LLD LDLT during the study period. A multivariable logistic regression was performed to assess relationship between type of living donor (directed vs. non-directed) and recipient insurance. RESULTS: Of 299 pediatric LDLT, 46 (15%) were from ND-LLD performed at 18 transplant centers. Fifty-nine percent of ND-LLD recipients had public insurance in comparison to 40% of D-LLD recipients (p = .02). Public insurance was associated with greater odds of ND-LLD in comparison to D-LLD upon multivariable logistic regression (OR 2.37, 95% CI 1.23-4.58, p = .01). CONCLUSIONS: ND-LLD allows additional children to receive LTs and may help address some of the socioeconomic disparity in pediatric LDLT, but currently account for only a minority of LDLT and are only performed at a few institutions. Initiatives to improve access to both D-LLD and ND-LLD transplants are needed.