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The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Elementos Facilitadores Genéticos , Regiões Promotoras Genéticas , Elementos Facilitadores Genéticos/genética , Regiões Promotoras Genéticas/genética , Animais , Humanos , Ativação Transcricional/genética , Regulação da Expressão Gênica/genética , Cromatina/metabolismo , Cromatina/genéticaRESUMO
Dysregulated mTORC1 signaling alters a wide range of cellular processes, contributing to metabolic disorders and cancer. Defining the molecular details of downstream effectors is thus critical for uncovering selective therapeutic targets. We report that mTORC1 and its downstream kinase S6K enhance eIF4A/4B-mediated translation of Wilms' tumor 1-associated protein (WTAP), an adaptor for the N6-methyladenosine (m6A) RNA methyltransferase complex. This regulation is mediated by 5' UTR of WTAP mRNA that is targeted by eIF4A/4B. Single-nucleotide-resolution m6A mapping revealed that MAX dimerization protein 2 (MXD2) mRNA contains m6A, and increased m6A modification enhances its degradation. WTAP induces cMyc-MAX association by suppressing MXD2 expression, which promotes cMyc transcriptional activity and proliferation of mTORC1-activated cancer cells. These results elucidate a mechanism whereby mTORC1 stimulates oncogenic signaling via m6A RNA modification and illuminates the WTAP-MXD2-cMyc axis as a potential therapeutic target for mTORC1-driven cancers.
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Adenosina/análogos & derivados , Alvo Mecanístico do Complexo 1 de Rapamicina/metabolismo , Estabilidade de RNA , Adenosina/metabolismo , Animais , Sequência de Bases , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , Fatores de Iniciação em Eucariotos/metabolismo , Células HEK293 , Humanos , Masculino , Camundongos , Modelos Biológicos , Biossíntese de Proteínas , Proteínas Proto-Oncogênicas c-myc/metabolismo , Fatores de Processamento de RNA/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Proteínas Quinases S6 Ribossômicas/metabolismo , Transdução de SinaisRESUMO
BACKGROUND: Invasive mechanical ventilation in critically ill adults involves adjusting the fraction of inspired oxygen to maintain arterial oxygen saturation. The oxygen-saturation target that will optimize clinical outcomes in this patient population remains unknown. METHODS: In a pragmatic, cluster-randomized, cluster-crossover trial conducted in the emergency department and medical intensive care unit at an academic center, we assigned adults who were receiving mechanical ventilation to a lower target for oxygen saturation as measured by pulse oximetry (Spo2) (90%; goal range, 88 to 92%), an intermediate target (94%; goal range, 92 to 96%), or a higher target (98%; goal range, 96 to 100%). The primary outcome was the number of days alive and free of mechanical ventilation (ventilator-free days) through day 28. The secondary outcome was death by day 28, with data censored at hospital discharge. RESULTS: A total of 2541 patients were included in the primary analysis. The median number of ventilator-free days was 20 (interquartile range, 0 to 25) in the lower-target group, 21 (interquartile range, 0 to 25) in the intermediate-target group, and 21 (interquartile range, 0 to 26) in the higher-target group (P = 0.81). In-hospital death by day 28 occurred in 281 of the 808 patients (34.8%) in the lower-target group, 292 of the 859 patients (34.0%) in the intermediate-target group, and 290 of the 874 patients (33.2%) in the higher-target group. The incidences of cardiac arrest, arrhythmia, myocardial infarction, stroke, and pneumothorax were similar in the three groups. CONCLUSIONS: Among critically ill adults receiving invasive mechanical ventilation, the number of ventilator-free days did not differ among groups in which a lower, intermediate, or higher Spo2 target was used. (Supported by the National Heart, Lung, and Blood Institute and others; PILOT ClinicalTrials.gov number, NCT03537937.).
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Estado Terminal , Oxigênio , Respiração Artificial , Adulto , Humanos , Estado Terminal/terapia , Mortalidade Hospitalar , Unidades de Terapia Intensiva , Oxigênio/administração & dosagem , Oxigênio/sangue , Oxigênio/uso terapêutico , Respiração Artificial/métodos , Cuidados Críticos/métodos , Estudos Cross-Over , Serviço Hospitalar de Emergência , Centros Médicos Acadêmicos , OximetriaRESUMO
Rationale: Among mechanically ventilated critically ill adults, the PILOT (Pragmatic Investigation of Optimal Oxygen Targets) trial demonstrated no difference in ventilator-free days among lower, intermediate, and higher oxygen-saturation targets. The effects on long-term cognition and related outcomes are unknown.Objectives: To compare the effects of lower (90% [range, 88-92%]), intermediate (94% [range, 92-96%]), and higher (98% [range, 96-100%]) oxygen-saturation targets on long-term outcomes.Methods: Twelve months after enrollment in the PILOT trial, blinded neuropsychological raters conducted assessments of cognition, disability, employment status, and quality of life. The primary outcome was global cognition as measured using the Telephone Montreal Cognitive Assessment. In a subset of patients, an expanded neuropsychological battery measured executive function, attention, immediate and delayed memory, verbal fluency, and abstraction.Measurements and Main Results: A total of 501 patients completed follow-up, including 142 in the lower, 186 in the intermediate, and 173 in the higher oxygen target groups. Median (interquartile range) peripheral oxygen saturation values in the lower, intermediate, and higher target groups were 94% (91-96%), 95% (93-97%), and 97% (95-99%), respectively. Telephone Montreal Cognitive Assessment score did not differ between lower and intermediate (adjusted odds ratio [OR], 1.36 [95% confidence interval (CI), 0.92-2.00]), intermediate and higher (adjusted OR, 0.90 [95% CI, 0.62-1.29]), or higher and lower (adjusted OR, 1.22 [95% CI, 0.83-1.79]) target groups. There was also no difference in individual cognitive domains, disability, employment, or quality of life.Conclusions: Among mechanically ventilated critically ill adults who completed follow-up at 12 months, oxygen-saturation targets were not associated with cognition or related outcomes.
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Estado Terminal , Respiração Artificial , Adulto , Humanos , Estado Terminal/terapia , Qualidade de Vida , Unidades de Terapia Intensiva , Oxigênio , CogniçãoRESUMO
Using cryo-electron microscopy and molecular characterization, David Sabatini and colleagues provide crucial new insights that validate and expand their model of how amino acids are sensed and signal at the lysosome to activate mechanistic target of rapamycin complex 1 (mTORC1) and cell growth-regulating processes. This work also reveals new therapeutic opportunities for mTORC1-driven diseases.
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Microscopia Crioeletrônica , Transdução de Sinais , Aminoácidos , Lisossomos/metabolismo , Alvo Mecanístico do Complexo 1 de Rapamicina/metabolismoRESUMO
INTRODUCTION: Understanding the pneumococcal serotypes causing community-acquired pneumonia (CAP) is essential for evaluating the impact of pneumococcal vaccines. METHODS: We conducted a prospective surveillance study of adults aged ≥18 years hospitalized with CAP at 3 hospitals in Tennessee and Georgia between 1 September 2018 and 31 October 2022. We assessed for pneumococcal etiology with cultures, the BinaxNOW urinary antigen detection test, and serotype-specific urinary antigen detection assays that detect 30 pneumococcal serotypes contained in the investigational pneumococcal conjugate vaccine V116, as well as licensed vaccines PCV15 and PCV20 (except serotype 15B). The distribution of pneumococcal serotypes was calculated based on serotype-specific urinary antigen detection results. RESULTS: Among 2917 hospitalized adults enrolled with CAP, 352 (12.1%) patients had Streptococcus pneumoniae detected, including 51 (1.7%) patients with invasive pneumococcal pneumonia. The 8 most commonly detected serotypes were: 3, 22F, 19A, 35B, 9N, 19F, 23A, and 11A. Among 2917 adults with CAP, 272 (9.3%) had a serotype detected that is contained in V116, compared to 196 (6.7%) patients with a serotype contained in PCV20 (P < .001), and 168 (5.8%) patients with a serotype contained in PCV15 (P < .001). A serotype contained in V116 but not PCV15 or PCV20 was detected in 120 (4.1%) patients, representing 38.0% of serotype detections. CONCLUSIONS: Approximately 12% of adults hospitalized with CAP had S. pneumoniae detected, and approximately one-third of the detected pneumococcal serotypes were not contained in PCV15 or PCV20. Development of new pneumococcal vaccines with expanded serotype coverage has the potential to prevent a substantial burden of disease.
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Infecções Comunitárias Adquiridas , Hospitalização , Vacinas Pneumocócicas , Pneumonia Pneumocócica , Sorogrupo , Streptococcus pneumoniae , Humanos , Infecções Comunitárias Adquiridas/epidemiologia , Infecções Comunitárias Adquiridas/microbiologia , Pneumonia Pneumocócica/epidemiologia , Pneumonia Pneumocócica/microbiologia , Pneumonia Pneumocócica/prevenção & controle , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/isolamento & purificação , Masculino , Feminino , Pessoa de Meia-Idade , Estudos Prospectivos , Tennessee/epidemiologia , Adulto , Idoso , Prevalência , Georgia/epidemiologia , Hospitalização/estatística & dados numéricos , Vacinas Pneumocócicas/administração & dosagem , Adulto Jovem , Adolescente , Idoso de 80 Anos ou mais , Índice de Gravidade de DoençaRESUMO
Diuresis to achieve decongestion is a central aim of therapy in patients hospitalized for acute decompensated heart failure (ADHF). While multiple approaches have been tried to achieve adequate decongestion rapidly while minimizing adverse effects, no single diuretic strategy has shown superiority, and there is a paucity of data and guidelines to utilize in making these decisions. Observational cohort studies have shown associations between urine sodium excretion and outcomes after hospitalization for ADHF. Urine chemistries (urine sodium ± urine creatinine) may guide diuretic titration during ADHF, and multiple randomized clinical trials have been designed to compare a strategy of urine chemistry-guided diuresis to usual care. This review will summarize current literature for diuretic monitoring and titration strategies, outline evidence gaps, and describe the recently completed and ongoing clinical trials to address these gaps in patients with ADHF with a particular focus on the utility of urine sodium-guided strategies.
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Diurese , Diuréticos , Insuficiência Cardíaca , Sódio , Humanos , Insuficiência Cardíaca/tratamento farmacológico , Insuficiência Cardíaca/urina , Insuficiência Cardíaca/fisiopatologia , Diurese/efeitos dos fármacos , Sódio/urina , Diuréticos/uso terapêutico , Diuréticos/administração & dosagem , Doença AgudaRESUMO
OBJECTIVE: Growing research indicates that daily stress is associated with poorer same-day cognitive performance, for example, memory and attention. However, it is unclear whether this relationship holds across diverse ages and engagement in physical activity (PA), or whether these factors might buffer the relationship between daily stress and subjective cognitive function. METHODS: Ecological momentary assessment data were collected from adults aged 25 to 88 years across British Columbia, Canada. For 14 days, participants ( N = 204) wore a triaxial physical activity monitor, reported stressor occurrence in mobile surveys four times per day, and rated their subjective attention and memory at the end of each day. RESULTS: Multilevel models evaluated daily stressor occurrence as a predictor of subjective attention and memory, with same-day PA engagement and age as moderators. Subjective attention and memory were lower on days when a stressor had occurred, compared to stressor-free days. Neither PA nor age moderated the within-person associations of daily stressors with subjective cognition. CONCLUSION: The lack of stress-buffering effects for same-day PA and age raises questions about the contexts in which PA promotes cognitive functioning and about age-related processes underlying stress and cognition. Future work could examine the mechanisms that might explain the link between daily stress and cognition function, as well as the associations of different intensity and forms of physical activity on stress across age groups.
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Atenção , Cognição , Avaliação Momentânea Ecológica , Exercício Físico , Estresse Psicológico , Humanos , Idoso , Pessoa de Meia-Idade , Feminino , Masculino , Adulto , Idoso de 80 Anos ou mais , Exercício Físico/fisiologia , Cognição/fisiologia , Atenção/fisiologia , Memória/fisiologia , Colúmbia Britânica , Fatores Etários , Envelhecimento/fisiologiaRESUMO
OBJECTIVE: Abundant research has linked nightly sleep as an antecedent of daily psychosocial experiences; however, less is known about sleep's influence on daily expectations of these experiences. Therefore, this research examined the day-to-day associations of sleep quality, duration, and efficiency with next-day expectations for stress(ors) and positive experiences, as well as whether these expectations were related to end-of-day reports of physical symptoms. METHODS: In Study 1, U.S. adults ( n = 354; ages 19 to 74) completed twice-daily diaries for 10 weekdays about sleep, expectations for encountering daily stressors and positive events, and physical symptoms. In Study 2, adults in Canada ( n = 246; ages 25 to 87) wore a sleep watch for 14 consecutive days and completed mobile surveys 5×/day about sleep, stressfulness and pleasantness expectations, and physical symptoms. RESULTS: Multilevel models indicated that self-reported sleep quality and duration, but not efficiency, were associated with lower next-day expectations for stressors (Study 1) and stressfulness (Study 2). Self-reported sleep quality (Study 1) and all sleep indices (Study 2) predicted greater next-day expectations for positive events and pleasantness, respectively. For actigraphy-assessed sleep (Study 2), only longer-than-usual actigraphic sleep duration was associated with lower stressfulness expectations, whereas both sleep duration and efficiency were positively linked with daily pleasantness expectations. Only pleasantness expectations (Study 2)-but not daily stressfulness and event expectations (Study 1)-predicted end-of-day physical symptoms. CONCLUSION: Findings suggest the importance of sleep on expectations of next-day stress and positive experiences, of which may have implications for daily physical health.
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Qualidade do Sono , Estresse Psicológico , Humanos , Masculino , Adulto , Feminino , Pessoa de Meia-Idade , Idoso , Adulto Jovem , Idoso de 80 Anos ou mais , Estados Unidos , Canadá , Actigrafia , Sono/fisiologiaRESUMO
New phases or new phenomena are often observed near-zero temperature phase transitions. These new effects represent nature's way of avoiding quantum critical phase transitions. Here, we look at the quantum tricritical point (QTCP), the special case where two transitions are driven to zero temperature at the same time. Unlike the case of quantum critical points, the avoidance of quantum tricritical points has yet to be demonstrated. Using chemical substitution and a magnetic field, we drive LaCrSb_{3} toward a quantum tricritical point. For the first time near a QTCP, we observe the emergence of a new magnetic phase and the avoidance of the QTCP via a first order phase transition.
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Although the progression of non-alcoholic fatty liver disease (NAFLD) from steatosis to steatohepatitis (NASH) and cirrhosis remains poorly understood, a critical role for dysregulated innate immunity has emerged. We examined the utility of ALT-100, a monoclonal antibody (mAb), in reducing NAFLD severity and progression to NASH/hepatic fibrosis. ALT-100 neutralizes eNAMPT (extracellular nicotinamide phosphoribosyltransferase), a novel damage-associated molecular pattern protein (DAMP) and Toll-like receptor 4 (TLR4) ligand. Histologic and biochemical markers were measured in liver tissues and plasma from human NAFLD subjects and NAFLD mice (streptozotocin/high-fat diet-STZ/HFD, 12 weeks). Human NAFLD subjects (n = 5) exhibited significantly increased NAMPT hepatic expression and significantly elevated plasma levels of eNAMPT, IL-6, Ang-2, and IL-1RA compared to healthy controls, with IL-6 and Ang-2 levels significantly increased in NASH non-survivors. Untreated STZ/HFD-exposed mice displayed significant increases in NAFLD activity scores, liver triglycerides, NAMPT hepatic expression, plasma cytokine levels (eNAMPT, IL-6, and TNFα), and histologic evidence of hepatocyte ballooning and hepatic fibrosis. Mice receiving the eNAMPT-neutralizing ALT-100 mAb (0.4 mg/kg/week, IP, weeks 9 to 12) exhibited marked attenuation of each index of NASH progression/severity. Thus, activation of the eNAMPT/TLR4 inflammatory pathway contributes to NAFLD severity and NASH/hepatic fibrosis. ALT-100 is potentially an effective therapeutic approach to address this unmet NAFLD need.
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Hepatopatia Gordurosa não Alcoólica , Humanos , Camundongos , Animais , Hepatopatia Gordurosa não Alcoólica/metabolismo , Receptor 4 Toll-Like/metabolismo , Interleucina-6/metabolismo , Fígado/metabolismo , Cirrose Hepática/metabolismoRESUMO
People who use substances commonly experience sleep disruptions, affecting the regulation of physical and mental health, and presenting a significant barrier to treatment success. Sleep impairments are noted in all phases of substance use; however, differences between subjective versus objective methods used to measure sleep quality have been reported. While polysomnography is the gold-standard for sleep measurement, recent advances in actigraphy may help address the discordance between subjective and objective sleep reports. This systematic review examined emerging evidence (2016-present) for sleep impairment in people who use substances, with the twofold goal of: (1) identifying whether sleep outcomes vary across substance type (alcohol, nicotine, cannabis, cocaine, methamphetamine and opioids); and (2) contrasting results from subjective and objective measures. While some differences between subjective and objective sleep were noted, there was overwhelming evidence of clinically relevant sleep impairment in people who use alcohol, nicotine, cocaine, methamphetamine and opioids, with less consistent results for cannabis. Gaps in the literature are identified and future recommendations are presented, including utilization of common methodological frameworks, identification of mechanisms, and closer examination of sleep across stages of substance use and the interconnection between sleep and return to use.
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STUDY OBJECTIVE: To examine the association between the neuromuscular blocking agent received (succinylcholine versus rocuronium) and the incidences of successful intubation on the first attempt and severe complications during tracheal intubation of critically ill adults in an emergency department (ED) or ICU. METHODS: We performed a secondary analysis of data from 2 multicenter randomized trials in critically ill adults undergoing tracheal intubation in an ED or ICU. Using a generalized linear mixed-effects model with prespecified baseline covariates, we examined the association between the neuromuscular blocking agent received (succinylcholine versus rocuronium) and the incidences of successful intubation on the first attempt (primary outcome) and severe complications during tracheal intubation (secondary outcome). RESULTS: Among the 2,440 patients in the trial data sets, 2,339 (95.9%) were included in the current analysis; 475 patients (20.3%) received succinylcholine and 1,864 patients (79.7%) received rocuronium. Successful intubation on the first attempt occurred in 375 patients (78.9%) who received succinylcholine and 1,510 patients (81.0%) who received rocuronium (an adjusted odds ratio of 0.87; 95% CI 0.65 to 1.15). Severe complications occurred in 67 patients (14.1%) who received succinylcholine and 456 patients (24.5%) who received rocuronium (adjusted odds ratio, 0.88; 95% CI 0.62 to 1.26). CONCLUSION: Among critically ill adults undergoing tracheal intubation, the incidences of successful intubation on the first attempt and severe complications were not significantly different between patients who received succinylcholine and patients who received rocuronium.
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Although it is an effective HIV prevention method, pre-exposure prophylaxis (PrEP) is underutilized in the Southern US. Many people who use drugs (PWUD) have increased susceptibility to HIV which could be lessened by using PrEP. Potential barriers to PrEP use include lack of awareness of PrEP, low knowledge about HIV prevention, low self-efficacy for HIV prevention, inaccurate risk perceptions, and anticipated stigma. The current study examined predisposing, enabling, and reinforcing factors that may predict interest in PrEP. The purpose of the current study was to explore factors associated with interest in and willingness to use daily oral and long acting injectable PrEP among sexually active adult PWUD. The data were collected from adult participants (n = 270) residing in Harris County, TX, who self-reported problematic substance use and who reported oral, anal, or vaginal sex in the six months prior to completing the survey. The survey was distributed and completed online via Qualtrics Panels in March of 2022 and included measures of PrEP and HIV knowledge, PrEP stigma, sexual health self-efficacy, experiences of discrimination, health literacy, and medical mistrust. The majority of participants reported circumstances or behaviors that increased their susceptibility to HIV. Findings indicated that PrEP user stereotypes and PrEP anticipated disapproval by others were associated with interest in using daily oral PrEP and willingness to use long acting injectable PrEP. These results provide insight into reasons for low PrEP uptake among PWUD who live in a high HIV prevalence jurisdiction. Implications for HIV prevention intervention are discussed.
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Infecções por HIV , Conhecimentos, Atitudes e Prática em Saúde , Profilaxia Pré-Exposição , Humanos , Masculino , Feminino , Infecções por HIV/prevenção & controle , Infecções por HIV/epidemiologia , Infecções por HIV/psicologia , Profilaxia Pré-Exposição/estatística & dados numéricos , Adulto , Estudos Transversais , Pessoa de Meia-Idade , Aceitação pelo Paciente de Cuidados de Saúde/estatística & dados numéricos , Aceitação pelo Paciente de Cuidados de Saúde/psicologia , Transtornos Relacionados ao Uso de Substâncias/epidemiologia , Transtornos Relacionados ao Uso de Substâncias/psicologia , Estigma Social , Prevalência , Comportamento Sexual/psicologia , Comportamento Sexual/estatística & dados numéricos , Adulto Jovem , Fármacos Anti-HIV/uso terapêutico , Inquéritos e QuestionáriosRESUMO
OBJECTIVE: To investigate the correlation between bone metabolism markers, bone mineral density (BMD), and sarcopenia. METHODS: A total of 331 consecutive patients aged ≥ 60 years who were hospitalized between November 2020 and December 2021 were enrolled. Participants were divided into sarcopenia and non-sarcopenia groups according to the Asian Working Group on Sarcopenia criteria (AWGS, 2019). The clinical data, bone metabolism markers (ß-CTX, N-MID, and TP1NP), and BMD were compared between the two groups. RESULTS: Age, ß-CTX, and N-MID of the sarcopenia group were higher than those of the non-sarcopenia group (P < 0.05), but the BMD T values were lower than those of the non-sarcopenia group (P < 0.05). Binary logistic regression analysis showed that increased femoral neck BMD (FNBMD) was a protective factor for sarcopenia, while increased ß-CTX was a risk factor. Pearson/Spearman correlation analysis showed that the diagnostic indices of sarcopenia were positively correlated with FNBMD and negatively correlated with ß-CTX and N-MID. Multiple linear regression analysis revealed that BMI and FNBMD significantly positively affected muscle strength and appendicular skeletal muscle mass (ASM). The FNBMD significantly positively affected physical performance, while ß-CTX significantly negatively affected muscle strength, ASM, and physical performance. CONCLUSION: Increased FNBMD may be a protective factor against sarcopenia, and increased ß-CTX may be a risk factor. The FNBMD significantly positively affected the diagnostic indices of sarcopenia, while ß-CTX significantly negatively affected them. BMD and bone metabolism marker levels may be considered in early screening for sarcopenia.
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Biomarcadores , Densidade Óssea , Sarcopenia , Humanos , Sarcopenia/diagnóstico , Sarcopenia/metabolismo , Feminino , Masculino , Densidade Óssea/fisiologia , Idoso , Biomarcadores/análise , Pessoa de Meia-Idade , Pró-Colágeno/sangue , Músculo Esquelético/metabolismo , Fragmentos de Peptídeos/sangue , Colágeno Tipo I/sangue , Osso e Ossos/metabolismo , Força Muscular/fisiologiaRESUMO
Accurate DNA sequencing is crucial in biomedicine. Underlying the most accurate methods is the assumption that a mutation is true if altered bases are present on both strands of the DNA duplex. We now show that this assumption can be wrong. We establish that current methods to prepare DNA for sequencing, via 'End Repair/dA-Tailing,' may substantially resynthesize strands, leading amplifiable lesions or alterations on one strand to become indiscernible from true mutations on both strands. Indeed, we discovered that 7-17% and 32-57% of interior 'duplex base pairs' from cell-free DNA and formalin-fixed tumor biopsies, respectively, could be resynthesized in vitro and potentially introduce false mutations. To address this, we present Duplex-Repair, and show that it limits interior duplex base pair resynthesis by 8- to 464-fold, rescues the impact of induced DNA damage, and affords up to 8.9-fold more accurate duplex sequencing. Our study uncovers a major Achilles' heel in sequencing and offers a solution to restore high accuracy.
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Neoplasias da Mama/genética , DNA/análise , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Feminino , Humanos , Estrutura MolecularRESUMO
Kinases play important roles in diverse cellular processes, including signaling, differentiation, proliferation, and metabolism. They are frequently mutated in cancer and are the targets of a large number of specific inhibitors. Surveys of cancer genome atlases reveal that kinase domains, which consist of 300 amino acids, can harbor numerous (150 to 200) single-point mutations across different patients in the same disease. This preponderance of mutations-some activating, some silent-in a known target protein make clinical decisions for enrolling patients in drug trials challenging since the relevance of the target and its drug sensitivity often depend on the mutational status in a given patient. We show through computational studies using molecular dynamics (MD) as well as enhanced sampling simulations that the experimentally determined activation status of a mutated kinase can be predicted effectively by identifying a hydrogen bonding fingerprint in the activation loop and the αC-helix regions, despite the fact that mutations in cancer patients occur throughout the kinase domain. In our study, we find that the predictive power of MD is superior to a purely data-driven machine learning model involving biochemical features that we implemented, even though MD utilized far fewer features (in fact, just one) in an unsupervised setting. Moreover, the MD results provide key insights into convergent mechanisms of activation, primarily involving differential stabilization of a hydrogen bond network that engages residues of the activation loop and αC-helix in the active-like conformation (in >70% of the mutations studied, regardless of the location of the mutation).
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Quinase do Linfoma Anaplásico/química , Aprendizado de Máquina , Simulação de Dinâmica Molecular , Mutação , Quinase do Linfoma Anaplásico/deficiência , Ativação Enzimática/genética , Humanos , Conformação Proteica em alfa-HéliceRESUMO
BACKGROUND: Data collected from hospitals are usually partially annotated by radiologists due to time constraints. Developing and evaluating deep learning models on these data may result in over or under estimation PURPOSE: We aimed to quantitatively investigate how the percentage of annotated lesions in CT images will influence the performance of universal lesion detection (ULD) algorithms. METHODS: We trained a multi-view feature pyramid network with position-aware attention (MVP-Net) to perform ULD. Three versions of the DeepLesion dataset were created for training MVP-Net. Original DeepLesion Dataset (OriginalDL) is the publicly available, widely studied DeepLesion dataset that includes 32 735 lesions in 4427 patients which were partially labeled during routine clinical practice. Enriched DeepLesion Dataset (EnrichedDL) is an enhanced dataset that features fully labeled at one or more time points for 4145 patients with 34 317 lesions. UnionDL is the union of the OriginalDL and EnrichedDL with 54 510 labeled lesions in 4427 patients. Each dataset was used separately to train MVP-Net, resulting in the following models: OriginalCNN (replicating the original result), EnrichedCNN (testing the effect of increased annotation), and UnionCNN (featuring the greatest number of annotations). RESULTS: Although the reported mean sensitivity of OriginalCNN was 84.3% using the OriginalDL testing set, the performance fell sharply when tested on the EnrichedDL testing set, yielding mean sensitivities of 56.1%, 66.0%, and 67.8% for OriginalCNN, EnrichedCNN, and UnionCNN, respectively. We also found that increasing the percentage of annotated lesions in the training set increased sensitivity, but the margin of increase in performance gradually diminished according to the power law. CONCLUSIONS: We expanded and improved the existing DeepLesion dataset by annotating additional 21 775 lesions, and we demonstrated that using fully labeled CT images avoided overestimation of MVP-Net's performance while increasing the algorithm's sensitivity, which may have a huge impact to the future CT lesion detection research. The annotated lesions are at https://github.com/ComputationalImageAnalysisLab/DeepLesionData.
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Algoritmos , Aprendizado Profundo , Interpretação de Imagem Radiográfica Assistida por Computador , Tomografia Computadorizada por Raios X , Humanos , Tomografia Computadorizada por Raios X/métodos , Interpretação de Imagem Radiográfica Assistida por Computador/métodos , Processamento de Imagem Assistida por Computador/métodos , Neoplasias/diagnóstico por imagem , Bases de Dados Factuais , Redes Neurais de ComputaçãoRESUMO
Objective: The intellectualized versions of the Montreal Cognitive Assessment Scale (MoCA) and the Mini-mental State Examination (MMSE) (i-MoCA/i-MMSE) were developed. The validity of this system was evaluated in a clinical sample through comparing with the manual-based assessments. Methods: A total of 88 patients [aged (66.82±11.37) years, 30 males and 58 females] were enrolled in the outpatient clinic of Xuanwu Hospital of Capital Medical University with complaints of cognitive decline, from February to October 2023. All participants completed manual-based and intellectualized assessments in a randomized order, with an interval of 2 weeks to control for the practice effect. The reliability of the intellectualized version of assessments was evaluated based on the manual-based version using the Concordance correlation coefficient (CCC). The difference between the intellectualized and the manual-based assessments was tested by the Repeated ANCOVA with demographic information controlled. The accuracy of evaluation of the i-MoCA and i-MMSE was analyzed by the Receiver Operating Characteristic (ROC) analysis. Results: High concordance was observed between the intellectualized version and the manual-based assessments (CCCMoCA=0.87, CCCMMSE=0.83). Controlling for basic demographic information, there was no significant difference in the scores of the intellectualized version and the manual-based assessments (all P>0.05). The accuracy of i-MoCA in screening patients with cognitive impairment was 94.3% (sensitivity=94.6%, specificity=78.1%), while the accuracy of i-MMSE in screening patients with cognitive impairment was 94.9% (sensitivity=94.9%, specificity=77.6%). In addition, the majority of subdomains measured by the cognitive assessments exhibited high consistency across the intellectualized the manual-based versions (CCCMoCA=0.32-0.78; CCCMMSE=0.54-0.79). Conclusion: Both the i-MoCA and i-MMSE showed high consistency and diagnostic accuracy with the manual-based versions in terms of overall cognitive function and subdomains.
Assuntos
Disfunção Cognitiva , Feminino , Humanos , Masculino , Instituições de Assistência Ambulatorial , Cognição , Disfunção Cognitiva/diagnóstico , Testes Neuropsicológicos , Reprodutibilidade dos TestesRESUMO
Objective: To investigate pathological features and differential diagnosis in the gonads with disorder of sex development. Methods: Thirty-six cases of clinically diagnosed hermaphroditism with gonadal biopsy in the Department of Pathology, the Seventh Medical Center of People's Liberation Army General Hospital from April 2007 to July 2021, were collected. All biopsy pathological sections were reviewed, and the gonadal cases with abnormal pathological morphology were screened out. The clinical and imaging data and karyotype of these cases were reviewed. Additional immunohistochemical staining was performed and relevant literature was reviewed. Results: Seven cases of ovotesticular disorder of sex development (OTDSD) were identified, which were characterized by the presence of testicular and ovarian differentiation in the same individual. All patients were under 15 years old and presented with abnormal appearance of external genitalia, and the ratio of male to female was 2â¶5. Ultrasonography showed testicular structure in all female patients and cryptorchidism in all male patients. The most common karyotype was 46, XX. One case with undifferentiated gonadal tissue (UGT) and one case with streak gonads were screened out. UGT germ cells were neither in seminiferous tubules nor in follicles, but randomly distributed in an ovarial-type interstitial background, sometimes accompanied by immature sex cords. Streak gonads resembled UGT without germ cells. FOXL2 was positive in granulosa cells, but negative in Sertoli cells. SOX9 expression was opposite. OCT4 was weakly positively/negatively expressed in oocytes and positively expressed in the germ nuclei of UGT. Conclusions: Four differentiation patterns need to be identified in the gonadal biopsy: ovarian differentiation, testicular differentiation, undifferentiated gonadal tissue and streak gonad. The positive expression of SOX9 indicates testicular differentiation, while the positive expression of FOXL2 confirms ovarian differentiation, and the expression of both markers in the same tissue indicates ovotestis differentiation. It is very important to identify UGT, because that has a high probability of developing into gonadoblastoma in the future.