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Plasma membrane rupture (PMR) in dying cells undergoing pyroptosis or apoptosis requires the cell-surface protein NINJ11. PMR releases pro-inflammatory cytoplasmic molecules, collectively called damage-associated molecular patterns (DAMPs), that activate immune cells. Therefore, inhibiting NINJ1 and PMR may limit the inflammation that is associated with excessive cell death. Here we describe an anti-NINJ1 monoclonal antibody that specifically targets mouse NINJ1 and blocks oligomerization of NINJ1, preventing PMR. Electron microscopy studies showed that this antibody prevents NINJ1 from forming oligomeric filaments. In mice, inhibition of NINJ1 or Ninj1 deficiency ameliorated hepatocellular PMR induced with TNF plus D-galactosamine, concanavalin A, Jo2 anti-Fas agonist antibody or ischaemia-reperfusion injury. Accordingly, serum levels of lactate dehydrogenase, the liver enzymes alanine aminotransaminase and aspartate aminotransferase, and the DAMPs interleukin 18 and HMGB1 were reduced. Moreover, in the liver ischaemia-reperfusion injury model, there was an attendant reduction in neutrophil infiltration. These data indicate that NINJ1 mediates PMR and inflammation in diseases driven by aberrant hepatocellular death.
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Anticorpos Monoclonais , Membrana Celular , Inflamação , Fígado , Fatores de Crescimento Neural , Traumatismo por Reperfusão , Animais , Camundongos , Alanina Transaminase , Alarminas , Anticorpos Monoclonais/imunologia , Aspartato Aminotransferases , Moléculas de Adesão Celular Neuronais/antagonistas & inibidores , Moléculas de Adesão Celular Neuronais/deficiência , Moléculas de Adesão Celular Neuronais/imunologia , Moléculas de Adesão Celular Neuronais/ultraestrutura , Morte Celular , Membrana Celular/patologia , Membrana Celular/ultraestrutura , Concanavalina A , Galactosamina , Hepatócitos/patologia , Hepatócitos/ultraestrutura , Inflamação/patologia , Lactato Desidrogenases , Fígado/patologia , Microscopia Eletrônica , Fatores de Crescimento Neural/antagonistas & inibidores , Fatores de Crescimento Neural/deficiência , Fatores de Crescimento Neural/imunologia , Fatores de Crescimento Neural/ultraestrutura , Infiltração de Neutrófilos , Traumatismo por Reperfusão/patologiaRESUMO
Inorganic-organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties1. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction2,3 and electron microdiffraction4-11. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach14, the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data15-17. We describe the ab initio structure solutions of mithrene (AgSePh)18-20, thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver-silver bonding network that is linked to its divergent optoelectronic properties20. We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.
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Elétrons , Prata , Cristalografia por Raios X , Lasers , Difração de Raios XRESUMO
Ageing of the immune system, or immunosenescence, contributes to the morbidity and mortality of the elderly1,2. To define the contribution of immune system ageing to organism ageing, here we selectively deleted Ercc1, which encodes a crucial DNA repair protein3,4, in mouse haematopoietic cells to increase the burden of endogenous DNA damage and thereby senescence5-7 in the immune system only. We show that Vav-iCre+/-;Ercc1-/fl mice were healthy into adulthood, then displayed premature onset of immunosenescence characterized by attrition and senescence of specific immune cell populations and impaired immune function, similar to changes that occur during ageing in wild-type mice8-10. Notably, non-lymphoid organs also showed increased senescence and damage, which suggests that senescent, aged immune cells can promote systemic ageing. The transplantation of splenocytes from Vav-iCre+/-;Ercc1-/fl or aged wild-type mice into young mice induced senescence in trans, whereas the transplantation of young immune cells attenuated senescence. The treatment of Vav-iCre+/-;Ercc1-/fl mice with rapamycin reduced markers of senescence in immune cells and improved immune function11,12. These data demonstrate that an aged, senescent immune system has a causal role in driving systemic ageing and therefore represents a key therapeutic target to extend healthy ageing.
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Envelhecimento/imunologia , Envelhecimento/fisiologia , Sistema Imunitário/imunologia , Sistema Imunitário/fisiologia , Imunossenescência/imunologia , Imunossenescência/fisiologia , Especificidade de Órgãos/imunologia , Especificidade de Órgãos/fisiologia , Envelhecimento/efeitos dos fármacos , Envelhecimento/patologia , Animais , Dano ao DNA/imunologia , Dano ao DNA/fisiologia , Reparo do DNA/imunologia , Reparo do DNA/fisiologia , Proteínas de Ligação a DNA/genética , Endonucleases/genética , Feminino , Envelhecimento Saudável/imunologia , Envelhecimento Saudável/fisiologia , Homeostase/imunologia , Homeostase/fisiologia , Sistema Imunitário/efeitos dos fármacos , Imunossenescência/efeitos dos fármacos , Masculino , Camundongos , Especificidade de Órgãos/efeitos dos fármacos , Rejuvenescimento , Sirolimo/farmacologia , Baço/citologia , Baço/transplanteRESUMO
Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition and data analysis. We expect that broadly accepted community guidelines and standardized metrics will enhance rigor, data quality and alignment between laboratories. Here we propose best practices, quality controls and data-reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics. Resources and discussion forums are available at https://single-cell.net/guidelines .
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Benchmarking , Proteômica , Benchmarking/métodos , Proteômica/métodos , Reprodutibilidade dos Testes , Proteínas/análise , Espectrometria de Massas em Tandem/métodos , Proteoma/análiseRESUMO
Single-cell proteomics is a powerful approach to precisely profile protein landscapes within individual cells toward a comprehensive understanding of proteomic functions and tissue and cellular states. The inherent challenges associated with limited starting material demand heightened analytical sensitivity. Just as advances in sample preparation maximize the amount of material that makes it from the cell to the mass spectrometer, we strive to maximize the number of ions that make it from ion source to the detector. In isobaric tagging experiments, limited reporter ion generation limits quantitative accuracy and precision. The combination of infrared photoactivation and ion parking circumvents the m/z dependence inherent in HCD, maximizing reporter generation and avoiding unintended degradation of TMT reporter molecules in infrared-tandem mass tags (IR-TMT). The method was applied to single-cell human proteomes using 18-plex TMTpro, resulting in 4-5-fold increases in reporter signal compared to conventional SPS-MS3 approaches. IR-TMT enables faster duty cycles, higher throughput, and increased peptide identification and quantification. Comparative experiments showcase 4-5-fold lower injection times for IR-TMT, providing superior sensitivity without compromising accuracy. In all, IR-TMT enhances the dynamic range of proteomic experiments and is compatible with gas-phase fractionation and real-time searching, promising increased gains in the study of cellular heterogeneity.
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Peptide separations that combine high sensitivity, robustness, peak capacity, and throughput are essential for extending bottom-up proteomics to smaller samples including single cells. To this end, we have developed a multicolumn nanoLC system with offline gradient generation. One binary pump generates gradients in an accelerated fashion to support multiple analytical columns, and a single trap column interfaces with all analytical columns to reduce required maintenance and simplify troubleshooting. A high degree of parallelization is possible, as one sample undergoes separation while the next sample plus its corresponding mobile phase gradient are transferred into the storage loop and a third sample is loaded into a sample loop. Selective offline elution from the trap column into the sample loop prevents salts and hydrophobic species from entering the analytical column, thus greatly enhancing column lifetime and system robustness. With this design, samples can be analyzed as fast as every 20 min at a flow rate of just 40 nL/min with close to 100% MS utilization time and continuously for as long as several months without column replacement. We utilized the system to analyze the proteomes of single cells from a multiple myeloma cell line upon treatment with the immunomodulatory imide drug lenalidomide.
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Proteoma , Análise de Célula Única , Humanos , Proteoma/análise , Nanotecnologia , Proteômica/métodos , Cromatografia Líquida/métodos , Linhagem Celular Tumoral , Lenalidomida/farmacologia , Talidomida/farmacologia , Talidomida/análogos & derivados , Mieloma Múltiplo/metabolismoRESUMO
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.
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Análise de Sequência de Proteína/métodos , Imagem Individual de Molécula/métodos , Espectrometria de Massas/métodos , Nanotecnologia , Proteínas/química , Proteômica/métodos , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodosRESUMO
AIM: To better understand the prevalence of self-reported psychosocial burdens and the unmet needs identified by people with diabetes in relation to routine diabetes visits. METHODS: An English language, online survey was distributed via social media, key stakeholder networks, charity and advocacy groups to adults with type 1 diabetes or type 2 diabetes. Survey items were designed by members of the FDA RESCUE Collaborative Community Governing Committee prior to pilot testing with potential participants. Descriptive statistical analyses were conducted, as well as thematic analyses on free-text responses using NVivo v14. RESULTS: Four hundred and seventy-eight participants completed the survey: 373 (78%) had type 1 diabetes, 346 (73%) identified as a woman and 433 (91%) were white. Most participants had experienced self-reported (rather than diagnosed) anxiety and depression (n = 323 and n = 313, respectively), as well as fear of low blood sugars (n = 294), low mood (n = 290) and diabetes-related distress (n = 257). Sixty-eight percent reported that diabetes had negatively affected self-esteem, 62% reported the feelings of loneliness, but 93% reported that friends/family/work colleagues were supportive when needed. Two hundred and seventy-two percent (57%) reported that their diabetes team had never raised the topic of mental health. The overwhelming majority stated that the best thing their diabetes team could do to help was to simply ask about mental well-being, listen with empathy and without judgement, and practice skills to understand psychosocial issues in diabetes. CONCLUSION: Integrating psychosocial discussions and support within routine healthcare visits is crucial to improve outcomes for people with diabetes. Such a biopsychosocial model of healthcare has long been advocated by regulatory bodies.
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Diabetes Mellitus Tipo 1 , Diabetes Mellitus Tipo 2 , Adulto , Feminino , Humanos , Diabetes Mellitus Tipo 1/epidemiologia , Diabetes Mellitus Tipo 1/psicologia , Diabetes Mellitus Tipo 2/epidemiologia , Diabetes Mellitus Tipo 2/terapia , Emoções , Ansiedade/epidemiologiaRESUMO
Recipients of interpartner aggression often experience internalizing symptoms. However, individual differences exist, and elucidation of factors that attenuate or exacerbate risk are needed to explicate relations and better inform interventions aimed at reducing mental health sequelae of interpartner aggression. Sleep problems compromise coping abilities and are known to exacerbate risk for mental health problems in the context of family risk. We examined whether sleep problems moderated the extent to which the recipients of interpartner aggression experience internalizing symptoms over time. At the first wave, 194 couples participated (M age [women] = 41.81 years, SD = 5.85; M age [men] = 43.75 years, SD = 6.74; 71% White/European American, 26% Black/African American, 3% other race/ethnicity). Two years later, couples returned for a second wave. Psychological and physical forms of interpartner aggression were measured using self- and partner-reports. Sleep duration (minutes) and sleep quality (efficiency) were derived using actigraphy, and subjective sleep/wake problems were also assessed. Individuals self-reported on their own internalizing symptoms. After controlling for autoregressive effects, sleep moderated the extent to which the recipients of interpartner aggression experienced internalizing symptoms longitudinally. Lower sleep efficiency and more subjective sleep/wake problems among women exacerbated the extent to which interpartner aggression forecasted their internalizing symptoms. Lower sleep efficiency among men magnified relations between interpartner aggression and their internalizing symptoms. Findings help understand the multiplicative influence that family risk and sleep problems have on mental health over time.
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Agressão , Transtornos do Sono-Vigília , Masculino , Humanos , Feminino , Adulto , Agressão/psicologia , Etnicidade , Sono , Transtornos do Sono-Vigília/psicologia , BrancosRESUMO
PURPOSE: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic condition with a constellation of symptoms presenting as severe and profound fatigue of ≥ 6 months not relieved by rest. ME/CFS affects health-related quality of life (HRQoL), which can be measured using multi-attribute health state utility (HSU) instruments. The aims of this study were to quantify HSUs for people living with ME/CFS, and to identify an instrument that is preferentially sensitive for ME/CFS. METHODS: Cross-sectional national survey of people with ME/CFS using the AQoL-8D and EQ-5D-5L. Additional questions from the AQoL-8D were used as 'bolt-ons' to the EQ-5D-5L (i.e., EQ-5D-5L-Psychosocial). Disability and fatigue severity were assessed using the De Paul Symptom Questionnaire-Short Form (DSQ-SF). HSUs were generated using Australian tariffs. Mean HSUs were stratified for sociodemographic and clinical factors. Bland-Altman plots were used to compare the three HSU instruments. RESULTS: For the 198 participants, mean HSUs (95% confidence intervals) were EQ-5D-5L: 0.46 (0.42-0.50); AQoL-8D: 0.43 (0.41-0.45); EQ-5D-5L-Psychosocial: 0.44 (0.42-0.46). HSUs were substantially lower than population norms: EQ-5D-5L: 0.89; AQoL-8D: 0.77. As disability and fatigue severity increased, HSUs decreased in all three instruments. Bland-Altman plots revealed interchangeability between the AQoL-8D and EQ-5D-5LPsychosocial. Floor and ceiling effects of 13.5% and 2.5% respectively were observed for the EQ-5D-5L instrument only. CONCLUSIONS: ME/CFS has a profound impact on HRQoL. The AQoL-8D and EQ-5D-5L-Psychosocial can be used interchangeably: the latter represents a reduced participant burden.
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Síndrome de Fadiga Crônica , Qualidade de Vida , Humanos , Qualidade de Vida/psicologia , Estudos Transversais , Austrália , Inquéritos e QuestionáriosRESUMO
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Proteoma , Proteômica , Humanos , Proteoma/metabolismo , Proteômica/métodosRESUMO
BACKGROUND: Music has long been identified as a nonpharmacological tool that can provide benefits for people with dementia, and there is considerable interest in designing technologies to support the use of music in dementia care. However, to ensure that music technologies are appropriately designed for supporting caregivers and people living with dementia, there remains a need to better understand how music is currently used in everyday dementia care at home. OBJECTIVE: This study aims to understand how people living with dementia and their caregivers use music and music technologies in everyday caring, as well as the challenges they experience using music and technology. METHODS: This study used a mixed methods design. First, a survey was administered to 13 people living with dementia and 64 caregivers to understand their use of music and technology. Subsequently, 18 survey respondents (family caregivers: n=12, 67%; people living with dementia: n=6, 33%) participated in focus groups regarding their experiences of using music and technology in care. Interview transcripts were analyzed using reflexive thematic analysis. RESULTS: Most of the survey respondents (people living with dementia: 9/13, 69%; family caregivers: 47/63, 75%) reported using music often or very often in their daily lives. Participants reported a range of technologies used for listening to music, such as CDs, radio, and streaming services. Focus groups highlighted the benefits and challenges of using music and music technologies in everyday care. Participants identified using music and music technologies to regulate mood, provide joy, facilitate social interaction and connection, encourage reminiscence, provide continuity of music use before and after the dementia diagnosis, and make caregiving easier. The challenges of using music technology in everyday caring included difficulties with staying up to date with evolving technology and low self-efficacy with technology for people living with dementia. CONCLUSIONS: This study shows that people with a dementia diagnosis and their caregivers already use music and music technologies to support their everyday care needs. The results suggest opportunities to design technologies that enable easier access to music and to support people living with dementia with recreational and therapeutic music listening as well as music-based activities.
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Cuidadores , Demência , Grupos Focais , Música , Humanos , Demência/psicologia , Cuidadores/psicologia , Música/psicologia , Feminino , Masculino , Idoso , Inquéritos e Questionários , Musicoterapia/métodos , Pessoa de Meia-Idade , Idoso de 80 Anos ou maisRESUMO
We compared three cell isolation and two proteomic sample preparation methods for single-cell and near-single-cell analysis. Whole blood was used to quantify hemoglobin (Hb) and glycated-Hb (gly-Hb) in erythrocytes using targeted mass spectrometry and stable isotope-labeled standard peptides. Each method differed in cell isolation and sample preparation as follows: 1) FACS and automated preparation in one-pot for trace samples (autoPOTS); 2) limited dilution via microscopy and a novel rapid one-pot sample preparation method that circumvented the need for the solid-phase extraction, low-volume liquid handling instrumentation and humidified incubation chamber; and 3) CellenONE-based cell isolation and the same one-pot sample preparation method used for limited dilution. Only the CellenONE device routinely isolated single-cells from which Hb was measured to be 540-660 amol per red blood cell (RBC), which was comparable to the calculated SI reference range for mean corpuscular hemoglobin (390-540 amol/RBC). FACSAria sorter and limited dilution could routinely isolate single-digit cell numbers, to reliably quantify CMV-Hb heterogeneity. Finally, we observed that repeated measures, using 5-25 RBCs obtained from N = 10 blood donors, could be used as an alternative and more efficient strategy than single RBC analysis to measure protein heterogeneity, which revealed multimodal distribution, unique for each individual.
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Hemoglobinas , Proteômica , Proteômica/métodos , Hemoglobinas/análise , Hemoglobinas Glicadas , Eritrócitos/química , Espectrometria de MassasRESUMO
New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.
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Recent developments in mass spectrometry-based single-cell proteomics (SCP) have resulted in dramatically improved sensitivity, yet the relatively low measurement throughput remains a limitation. Isobaric and isotopic labeling methods have been separately applied to SCP to increase throughput through multiplexing. Here we combined both forms of labeling to achieve multiplicative scaling for higher throughput. Two-plex stable isotope labeling of amino acids in cell culture (SILAC) and isobaric tandem mass tag (TMT) labeling enabled up to 28 single cells to be analyzed in a single liquid chromatography-mass spectrometry (LC-MS) analysis, in addition to carrier, reference, and negative control channels. A custom nested nanowell chip was used for nanoliter sample processing to minimize sample losses. Using a 145-min total LC-MS cycle time, â¼280 single cells were analyzed per day. This measurement throughput could be increased to â¼700 samples per day with a high-duty-cycle multicolumn LC system producing the same active gradient. The labeling efficiency and achievable proteome coverage were characterized for multiple analysis conditions.
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Proteômica , Espectrometria de Massas em Tandem , Espectrometria de Massas em Tandem/métodos , Proteômica/métodos , Cromatografia Líquida/métodos , Proteoma/análise , Marcação por IsótopoRESUMO
Src homology-2 domain-containing phosphatase 2 (SHP2) is a ubiquitously expressed phosphatase that is vital for skeletal development and maintenance of chondrocytes, osteoblasts, and osteoclasts. Study of SHP2 function in small animal models has led to insights in phenotypes observed in SHP2-mutant human disease, such as Noonan syndrome. In recent years, allosteric SHP2 inhibitors have been developed to specifically target the protein in neoplastic processes. These inhibitors are highly specific and have great potential for disease modulation in cancer and other pathologies, including bone disorders. In this review, we discuss the importance of SHP2 and related signaling pathways (e.g., Ras/MEK/ERK, JAK/STAT, PI3K/Akt) in skeletal development. We review rodent models of pathologic processes caused by germline mutations that activate SHP2 enzymatic activity, with a focus on the skeletal phenotype seen in these patients. Finally, we discuss SHP2 inhibitors in development and their potential for disease modulation in these genetic diseases, particularly as it relates to the skeleton.
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Neoplasias , Fosfatidilinositol 3-Quinases , Animais , Humanos , Transdução de Sinais , Esqueleto , Esterno/patologia , MutaçãoRESUMO
INTRODUCTION: Refractory hematuria secondary to prostatic disease typically resolves with conservative management; however, this condition may require hospitalization with extensive measures to control life-threatening bleeding. The aim of this study was to report our experience using holmium laser enucleation of the prostate (HoLEP) as an emergency treatment in this clinical setting. METHODS: We conducted a retrospective review of all patients that presented to the emergency department with refractory hematuria of prostatic origin from October 2017 to September 2021, for whom hospitalization and conservative management failed to control bleeding. All emergency HoLEP procedures were performed by a single surgeon. Preoperative and intraoperative parameters, as well as perioperative outcomes, were collected and analyzed. Postoperative outcomes included duration of foley catheterization, length of postoperative hospital stay, and hospital readmissions. RESULTS: A total of 40 emergency HoLEP procedures were performed. Our cohort had a median prostate volume of 110.5 cc and a median resected weight of 81 g. Twenty-seven patients (67.5%) were on anticoagulant or antiplatelet medications on admission. The urethral catheter was removed within 1 day in 95% of patients with a successful trial of void (TOV). Moreover, 92.5% of patients were discharged home within 24 h of their procedure. Two patients (5%) experienced clot retention within one-week post-discharge with a 2.5% overall readmission rate. All postoperative parameters, including International Prostate Symptom Score (IPSS), quality of life (QoL), maximum flow rate (Qmax), and post-void residual volume (PVR), showed significant improvement at 1 year follow up. CONCLUSION: Our experience demonstrates that emergency HoLEP is an effective treatment option for patients with refractory hematuria of prostatic origin. Further studies are warranted to consolidate our results.
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Terapia a Laser , Lasers de Estado Sólido , Hiperplasia Prostática , Ressecção Transuretral da Próstata , Masculino , Humanos , Hiperplasia Prostática/complicações , Hiperplasia Prostática/cirurgia , Hiperplasia Prostática/diagnóstico , Próstata/cirurgia , Qualidade de Vida , Hólmio , Hematúria/etiologia , Hematúria/cirurgia , Lasers de Estado Sólido/uso terapêutico , Assistência ao Convalescente , Alta do Paciente , Ressecção Transuretral da Próstata/métodos , Resultado do Tratamento , Terapia a Laser/métodos , Estudos RetrospectivosRESUMO
Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing-also called metabarcoding-of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.
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DNA Ambiental , Oncorhynchus kisutch , Oncorhynchus mykiss , Animais , Humanos , Ecossistema , Oncorhynchus mykiss/genética , Rios , SalmãoRESUMO
Although single cell RNA-seq has had a tremendous impact on biological research, a corresponding technology for unbiased mass spectrometric analysis of single cells has only recently become available. Significant technological breakthroughs including miniaturized sample handling have enabled proteome profiling of single cells. Furthermore, trapped ion mobility spectrometry (TIMS) in combination with parallel accumulation-serial fragmentation operated in data-dependent acquisition mode (DDA-PASEF) allowed improved proteome coverage from low-input samples. It has been demonstrated that modulating the ion flux in TIMS affects the overall performance of proteome profiling. However, the effect of TIMS settings on the analysis of low-input samples has been less investigated. Thus, we sought to optimize the conditions of TIMS with regard to ion accumulation/ramp times and ion mobility range for low-input samples. We observed that an ion accumulation time of 180 ms and monitoring a narrower ion mobility range from 0.7 to 1.3 V s cm-2 resulted in a substantial gain in the depth of proteome coverage and in detecting proteins with low abundance. We used these optimized conditions for proteome profiling of sorted human primary T cells, which yielded an average of 365, 804, 1116, and 1651 proteins from single, five, ten, and forty T cells, respectively. Notably, we demonstrated that the depth of proteome coverage from a low number of cells was sufficient to delineate several essential metabolic pathways and the T cell receptor signaling pathway. Finally, we showed the feasibility of detecting post-translational modifications including phosphorylation and acetylation from single cells. We believe that such an approach could be applied to label-free analysis of single cells obtained from clinically relevant samples.
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Proteoma , Proteômica , Humanos , Proteoma/análise , Proteômica/métodos , Espectrometria de Mobilidade Iônica/métodos , Espectrometria de Massas/métodos , Processamento de Proteína Pós-TraducionalRESUMO
Single-cell measurements are uniquely capable of characterizing cell-to-cell heterogeneity and have been used to explore the large diversity of cell types and physiological functions present in tissues and other complex cell assemblies. An intriguing application of single-cell proteomics is the characterization of proteome dynamics during biological transitions, like cellular differentiation or disease progression. Time-course experiments, which regularly take measurements during state transitions, rely on the ability to detect dynamic trajectories in a data series. However, in a single-cell proteomics experiment, cell-to-cell heterogeneity complicates the confident identification of proteome dynamics as measurement variability may be higher than expected. Therefore, a critical question for these experiments is how many data points need to be acquired during the time course to enable robust statistical analysis. We present here an analysis of the most important variables that affect statistical confidence in the detection of proteome dynamics: fold change, measurement variability, and the number of cells measured during the time course. Importantly, we show that datasets with less than 16 measurements across the time domain suffer from low accuracy and also have a high false-positive rate. We also demonstrate how to balance competing demands in experimental design to achieve a desired result.