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1.
PLoS Biol ; 22(5): e3002405, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38713717

RESUMO

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.


Assuntos
Genoma , Software , Animais , Genoma/genética , Alinhamento de Sequência/métodos , Genômica/métodos , Algoritmos , Estados Unidos , Humanos , Eucariotos/genética , Bases de Dados Genéticas , National Library of Medicine (U.S.) , Anotação de Sequência Molecular/métodos
2.
Rhinology ; 2024 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-38752541

RESUMO

BACKGROUND: Orbital apex syndrome (OAS) is a condition characterised by lesions within the orbital apex, leading to various ophthalmologic symptoms. This study aimed to analyse the clinical characteristics and treatment strategies of OAS with respect to aetiology. METHODS: This retrospective analysis utilised data from 5 medical institutions between 2013 and 2022. Patients who were diagnosed with OAS were initially enrolled, but patients who failed to follow up at least 1 month were excluded. The prevalence of initial ophthalmologic symptoms and visual improvement after treatment was compared according to aetiology. Factors related to visual improvement were analysed. RESULTS: Among 73 enrolled patients, the leading aetiology was tumours, followed by fungal infections and inflammation. Visual impairment and proptosis were prevalent in tumour-related OAS cases. Inflammation-related OAS exhibited a higher likelihood of painful eye movements and ophthalmoplegia. Ptosis was most frequently observed in fungal infection-related OAS. Notably, fungal infections emerged as the sole significant factor negatively impacting vision progression. In inflammation-related OAS, the time interval between symptom onset and the administration of steroids was longer in patients without visual improvement, even though there was no statistically significant difference. CONCLUSIONS: Tumours were the predominant cause of OAS. Visual impairment was a common manifestation in tumour-related OAS, while fungal infections were strongly associated with a poor visual prognosis. The timely administration of steroids might be helpful for improving vision in patients with inflammation-related OAS. However, further studies are needed to enhance understanding and management of OAS.

3.
Fish Shellfish Immunol ; 150: 109625, 2024 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-38740231

RESUMO

The mucosal surfaces of fish, including their intestines, gills, and skin, are constantly exposed to various environmental threats, such as water quality fluctuations, pollutants, and pathogens. However, various cells and microbiota closely associated with these surfaces work in tandem to create a functional protective barrier against these conditions. Recent research has shown that incorporating specific feed ingredients into fish diets can significantly boost their mucosal and general immune response. Among the various ingredients being investigated, insect meal has emerged as one of the most promising options, owing to its high protein content and immunomodulatory properties. By positively influencing the structure and function of mucosal surfaces, insect meal (IM) has the potential to enhance the overall immune status of fish. This review provides a comprehensive overview of the potential benefits of incorporating IM into aquafeed as a feed ingredient for augmenting the mucosal immune response of fish.

4.
Results Chem ; 72024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38560090

RESUMO

Phospholipase D3 (PLD3) and D4 (PLD4) are endolysosomal exonucleases of ssDNA and ssRNA that regulate innate immunity. Polymorphisms of these enzymes are correlated with numerous human diseases, including Alzheimer's, rheumatoid arthritis, and systemic sclerosis. Pharmacological modulation of these immunoregulatory proteins may yield novel immunotherapies and adjuvants. A previous study reported a high-throughput screen (N = 17,952) that discovered a PLD3-selective activator and inhibitor, as well as a nonselective inhibitor, but failed to identify selective modulators of PLD4. However, modulators selective for PLD4 are therapeutically pertinent, since recent reports have shown that regulating this protein has direct implications in cancer and autoimmune diseases. Furthermore, the high expression of PLD4 in dendritic and myeloid cells, in comparison to the broader expression of PLD3, presents the opportunity for a cell-targeted immunotherapy. Here, we describe screening of an expended diversity library (N = 45,760) with an improved platform and report the discovery of one inhibitor and three activators selective for PLD4. Furthermore, kinetic modeling and structural analysis suggest mechanistic differences in the modulation of these hits. These findings further establish the utility of this screening platform and provide a set of chemical scaffolds to guide future small-molecule development for this novel immunoregulator target.

5.
Artigo em Inglês | MEDLINE | ID: mdl-38570291

RESUMO

At present, stock linear distractors are used for internal maxillary distraction osteogenesis. However, the authors' research group has demonstrated, through an in silico analysis, that linear distraction leads to bone deformities and malocclusion, whereas helical distraction can yield ideal outcomes. A system for designing and manufacturing custom helical distractors has recently been developed, and the feasibility of these appliances now needs to be assessed. This study was, therefore, conducted to gain an initial insight into their feasibility. The study had two goals. First, it aimed to demonstrate, in an in vitro model, that the novel system of custom helical distraction can produce appropriate clinical outcomes. The second aim was to compare the performance of custom helical distractors with that of stock devices and hybrid devices (i.e., linear appliances that feature patient-specific footplates). Interpreting the results as trends, this study showed that the system of custom helical distraction resulted in in vitro outcomes that were superior to those obtained with stock and hybrid devices.

6.
Fish Shellfish Immunol ; 150: 109565, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38636740

RESUMO

The jawless vertebrates (agnathans/cyclostomes) are ancestral animals comprising lampreys and hagfishes as the only extant representatives. They possess an alternative adaptive immune system (AIS) that uses leucine-rich repeats (LRR)-based variable lymphocyte receptors (VLRs) instead of the immunoglobulin (Ig)-based antigen receptors of jawed vertebrates (gnathostomes). The different VLR types are expressed on agnathan lymphocytes and functionally resemble gnathostome antigen receptors. In particular, VLRB is functionally similar to the B cell receptor and is expressed and secreted by B-like lymphocytes as VLRB antibodies that bind antigens with high affinity and specificity. The potential repertoire scale of VLR-based antigen receptors is believed to be at least comparable to that of Ig-based systems. VLR proteins inherently possess characteristics that render them excellent candidates for biotechnological development, including tractability to recombinant approaches. In recent years, scientists have explored the biotechnological development and utility of VLRB proteins as alternatives to conventional mammalian antibodies. The VLRB antibody platform represents a non-traditional approach to generating a highly diverse repertoire of unique antibodies. In this review, we first describe some aspects of the biology of the AIS of the jawless vertebrates, which recognizes antigens by means of unique receptors. We then summarize reports on the development of VLRB-based antibodies and their applications, particularly those from the inshore hagfish (Eptatretus burgeri) and their potential uses to address microbial diseases in aquaculture. Hagfish VLRB antibodies (we call Ccombodies) are being developed and improved, while obstacles to the advancement of the VLRB platform are being addressed to utilize VLRBs effectively as tools in immunology. VLRB antibodies for novel antigen targets are expected to emerge to provide new opportunities to tackle various scientific questions. We anticipate a greater interest in the agnathan AIS in general and particularly in the hagfish AIS for greater elucidation of the evolution of adaptive immunity and its applications to address microbial pathogens in farmed aquatic animals and beyond.

7.
Fish Shellfish Immunol ; 149: 109549, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38599365

RESUMO

The study was designed to investigate the effects of replacing fish oil by algal oil and rapeseed oil on histomorphology indices of the intestine, skin and gill, mucosal barrier status and immune-related genes of mucin and antimicrobial peptide (AMP) genes in Atlantic salmon (Salmo salar). For these purposes, Atlantic salmon smolts were fed three different diets. The first was a control diet containing fish oil but no Schizochytrium oil. In the second diet, almost 50 % of the fish oil was replaced with algal oil, and in the third diet, fish oil was replaced entirely with algal oil. The algal oil contained mostly docosahexaenoic acid (DHA) and some eicosapentaenoic acid (EPA). The study lasted for 49 days in freshwater (FW), after which some fish from each diet group were transferred to seawater (SW) for a 48-h challenge test at 33 ppt to test their ability to tolerate high salinity. Samples of skin, gills, and mid intestine [both distal (DI) and anterior (AI) portions of the mid intestine] were collected after the feeding trial in FW and after the SW-challenge test to assess the effects of the diets on the structure and immune functions of the mucosal surfaces. The results showed that the 50 % VMO (Veramaris® algal oil) dietary group had improved intestinal, skin, and gill structures. Principal component analysis (PCA) of the histomorphological parameters demonstrated a significant effect of the algal oil on the intestine, skin, and gills. In particular, the mucosal barrier function of the intestine, skin, and gills was enhanced in the VMO 50 % dietary group after the SW challenge, as evidenced by increased mucous cell density. Immunolabelling of heat shock protein 70 (HSP70) in the intestine (both DI and AI) revealed downregulation of the protein expression in the 50 % VMO group and a corresponding upregulation in the 100 % VMO group compared to 0 % VMO. The reactivity of HSP70 in the epithelial cells was higher after the SW challenge compared to the FW phase. Immune-related genes related to mucosal defense, such as mucin genes [muc2, muc5ac1 (DI), muc5ac1 (AI), muc5ac2, muc5b (skin), and muc5ac1 (gills)], and antimicrobial peptide genes [def3 (DI), def3 (AI), and cath1 (skin)] were significantly upregulated in the 50 % VMO group. PCA of gene expression demonstrated the positive influences on gene regulation in the 50 % VMO dietary group. In conclusion, this study demonstrated the positive effect of substituting 50 % of fish oil with algal oil in the diets of Atlantic salmon. The findings of histomorphometry, mucosal mapping, immunohistochemistry, and immune-related genes connected to mucosal responses all support this conclusion.


Assuntos
Ração Animal , Dieta , Óleo de Brassica napus , Salmo salar , Animais , Salmo salar/imunologia , Dieta/veterinária , Óleo de Brassica napus/química , Ração Animal/análise , Mucosa/imunologia , Óleos de Peixe/administração & dosagem , Pele/imunologia , Pele/efeitos dos fármacos , Estações do Ano , Brânquias/imunologia , Brânquias/efeitos dos fármacos , Intestinos/efeitos dos fármacos , Intestinos/imunologia
8.
Chem Commun (Camb) ; 60(35): 4711-4714, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38596865

RESUMO

Xylazine has emerged as a primary adulterant in fentanyl, exacerbating the complexity of the opioid crisis. Yet, there is no approved drug that can reverse xylazine's pathophysiology. As a prelude to monoclonal antibodies being assessed as a viable therapeutic, a vaccine inquiry was conducted evaluating the immune response in reversing xylazine induced behavior effects.


Assuntos
Haptenos , Xilazina , Xilazina/química , Xilazina/farmacologia , Haptenos/química , Haptenos/imunologia , Animais , Vacinas Conjugadas/química , Vacinas Conjugadas/imunologia , Camundongos
9.
Scand J Rheumatol ; : 1-7, 2024 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-38686835

RESUMO

OBJECTIVE: To evaluate the prevalence and rate of a missed diagnosis of sacroiliitis on abdominal computed tomography (CT) in patients with inflammatory bowel disease (IBD). Factors associated with sacroiliitis were also assessed. METHOD: This retrospective study included 210 patients with IBD (mean age 31.1 years) who underwent abdominal CT. Based on a validated abdominal CT scoring tool, bilateral sacroiliac (SI) joints on abdominal CT in the whole study population were retrospectively reviewed. Subsequently, patients were classified into the 'patients with sacroiliitis' group and the 'patients without sacroiliitis' group. Univariate and multivariate regression analyses were used to clarify the factors associated with sacroiliitis. RESULTS: Sacroiliitis was identified in 26 out of 210 patients (12.4%). However, sacroiliitis was recognized on the primary reading in only five of these 26 patients (19.2%) and was missed on the initial report in the remaining 21 patients (80.8%). Among the 21 patients, 20 (95.2%) were finally diagnosed with axial spondyloarthritis (axSpA). There was a higher prevalence of female sex (p = 0.04), upper gastrointestinal involvement (p = 0.04), and back pain (p < 0.01) in patients with sacroiliitis than in those without sacroiliitis. However, on multivariate analysis, back pain was the only factor associated with sacroiliitis (p = 0.01). CONCLUSION: Physicians should carefully evaluate SI joints on abdominal CT in patients with IBD to enable early detection of sacroiliitis, potentially leading to an early diagnosis of axSpA. In addition, if patients with IBD present with back pain, the possibility of sacroiliitis should be considered.

10.
Viruses ; 16(3)2024 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-38543795

RESUMO

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/epidemiologia , Pandemias , Fluxo de Trabalho , Biologia Computacional
11.
Virulence ; 15(1): 2329568, 2024 12.
Artigo em Inglês | MEDLINE | ID: mdl-38555518

RESUMO

Tilapia Lake Virus (TiLV) is associated with pathological changes in the brain of infected fish, but the mechanisms driving the virus's neuropathogenesis remain poorly characterized. TiLV establishes a persistent infection in the brain of infected fish even when the virus is no longer detectable in the peripheral organs, rendering therapeutic interventions and disease management challenging. Moreover, the persistence of the virus in the brain may pose a risk for viral reinfection and spread and contribute to ongoing tissue damage and neuroinflammatory processes. In this review, we explore TiLV-associated neurological disease. We discuss the possible mechanism(s) used by TiLV to enter the central nervous system (CNS) and examine TiLV-induced neuroinflammation and brain immune responses. Lastly, we discuss future research questions and knowledge gaps to be addressed to significantly advance this field.


Assuntos
Doenças dos Peixes , Infecções por Orthomyxoviridae , Tilápia , Vírus , Animais , Encéfalo/patologia
12.
Disabil Rehabil Assist Technol ; : 1-10, 2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38533741

RESUMO

Brain-computer interfaces (BCI) offer promise to the play of children with significant physical impairments, as BCI technology can enable disabled children to control computer devices, toys, and robots using only their brain signals. However, there is little research on the unique needs of disabled children when it comes to BCI-enabled play. Thus, this paper explored the lived experiences of play for children with significant physical impairments and examined how BCI could potentially be implemented into disabled children's play experiences by applying a social model of childhood disability. Descriptive qualitative methodology was employed by conducting four semi-structured interviews with two children with significant physical impairments and their parents. We found that disabled children's play can be interpreted as passive or active depending on one's definition and perceptions surrounding play. Moreover, disabled children continue to face physical, economic, and technological barriers in their play, as well as play restrictions from physical impairments. We urge that future research should strive to directly hear from disabled children themselves, as their perspectives may differ from their parents' views. Also, future BCI development should strive to incorporate video games, recreational and entertainment applications/platforms, toys and switch-adapted toys, and power wheelchairs to better support the play of children with significant physical impairments.Implications for RehabilitationAssistive technology research should strive to examine the social, infrastructural, and environmental barriers that continue to disable and restrict participation for disabled children and their families through applying a social model of childhood disability and other holistic frameworks that look beyond individual factorsFuture research that examines the needs and lives of disabled children should strive to directly seek the opinions and perspectives of disabled children themselvesBrain-computer interface development should strive to incorporate video games, recreational and entertainment applications/platforms, toys and switch-adapted toys, and power wheelchairs to better support the play of children with significant physical impairments.

13.
Dig Dis Sci ; 69(5): 1808-1825, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38499736

RESUMO

BACKGROUND: Infliximab and vedolizumab are widely used to treat Crohn's disease (CD) and ulcerative colitis (UC). AIMS: This systematic review and network meta-analysis evaluated comparative efficacy of various regimens for intravenous or subcutaneous infliximab and vedolizumab during maintenance treatment in CD and UC. METHODS: Parallel-group randomized controlled trials (RCTs) were identified by a systematic literature review (CRD42022383401) and included if they evaluated therapeutics of interest for maintenance treatment of adults with moderate-to-severe luminal CD or UC and assessed clinical remission between Weeks 30 and 60. Clinical remission rates in CD or UC and mucosal healing rates in UC were analyzed in a Bayesian network meta-analysis model. Endoscopic outcomes in CD were synthesized by proportional meta-analysis. RESULTS: Overall, 13 RCTs were included in the analyses. All vedolizumab studies randomized induction responders to maintenance treatment; infliximab studies used a treat-through design. Subcutaneous infliximab 120 mg every 2 weeks had the highest odds ratio (OR) [95% credible interval] versus placebo for clinical remission during the maintenance phase (CD: 5.90 [1.90-18.2]; UC: 5.45 [1.94-15.3]), with surface under the cumulative ranking curve (SUCRA) values of 0.91 and 0.82, respectively. For mucosal healing in UC, subcutaneous infliximab 120 mg every 2 weeks showed the highest OR (4.90 [1.63-14.1]), with SUCRA value of 0.73, followed by intravenous vedolizumab 300 mg every 4 weeks (SUCRA value, 0.70). Endoscopic outcomes in CD were better with subcutaneous infliximab 120 mg every 2 weeks than intravenous infliximab 5 mg/kg every 8 weeks. CONCLUSIONS: Subcutaneous infliximab showed a favorable efficacy profile for achieving clinical remission and endoscopic outcomes during maintenance treatment in CD or UC.


Assuntos
Anticorpos Monoclonais Humanizados , Fármacos Gastrointestinais , Infliximab , Humanos , Infliximab/administração & dosagem , Infliximab/uso terapêutico , Anticorpos Monoclonais Humanizados/administração & dosagem , Anticorpos Monoclonais Humanizados/uso terapêutico , Injeções Subcutâneas , Fármacos Gastrointestinais/administração & dosagem , Fármacos Gastrointestinais/uso terapêutico , Colite Ulcerativa/tratamento farmacológico , Doença de Crohn/tratamento farmacológico , Administração Intravenosa , Resultado do Tratamento , Adulto , Ensaios Clínicos Controlados Aleatórios como Assunto , Indução de Remissão , Metanálise em Rede , Quimioterapia de Manutenção/métodos
14.
Animals (Basel) ; 14(6)2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38540051

RESUMO

The present study aimed to investigate the effects of Moringa oleifera leaf (MLE) extract-supplemented diets on the growth, feed utilization, hematology, innate immune response, and disease resistance of Nile tilapia against Streptococcus agalactiae Biotype 2. Four hundred and fifty Nile tilapia (32.61 ± 0.2 g/fish) were randomly allocated into fifteen tanks (30 fish/tank). Different concentrations of MLE at 0%, 0.5%, 1%, 1.5%, and 2% were fed to the Nile tilapia for 30 days, and the growth, feed utilization, hematology, and innate immune response of the Nile tilapia were determined. After the feeding trial, the Nile tilapia were challenged with a S. agalactiae Biotype 2 infection, and the relative percentage of survival (RPS) was determined. Results revealed the presence of quercetin, kaempferol, and p-coumaric acid in the MLE extract, exhibiting stronger antimicrobial activity against S. agalactiae Biotype 2. The diets supplemented with the MLE-0.5 group showed a significantly higher growth, feed utilization, hematology, and innate immune response in the Nile tilapia compared to the control and other MLE groups. Additionally, the MLE-0.5 group exhibited a significantly higher RPS of the Nile tilapia against S. agalactiae Biotype 2. Therefore, MLE-0.5 can be employed as an alternative feed supplement in sustainable Nile tilapia farming to protect against S. agalactiae Biotype 2.

16.
Phys Rev Lett ; 132(8): 082501, 2024 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-38457706

RESUMO

The structure and decay of the most neutron-rich beryllium isotope, ^{16}Be, has been investigated following proton knockout from a high-energy ^{17}B beam. Two relatively narrow resonances were observed for the first time, with energies of 0.84(3) and 2.15(5) MeV above the two-neutron decay threshold and widths of 0.32(8) and 0.95(15) MeV, respectively. These were assigned to be the ground (J^{π}=0^{+}) and first excited (2^{+}) state, with E_{x}=1.31(6) MeV. The mass excess of ^{16}Be was thus deduced to be 56.93(13) MeV, some 0.5 MeV more bound than the only previous measurement. Both states were observed to decay by direct two-neutron emission. Calculations incorporating the evolution of the wave function during the decay as a genuine three-body process reproduced the principal characteristics of the neutron-neutron energy spectra for both levels, indicating that the ground state exhibits a strong spatially compact dineutron component, while the 2^{+} level presents a far more diffuse neutron-neutron distribution.

17.
Spinal Cord Ser Cases ; 10(1): 15, 2024 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-38514608

RESUMO

STUDY DESIGN: Anonymous online survey OBJECTIVES: To investigate the priorities, needs and willingness to adopt nerve stimulation devices for managing neurogenic bladder and bowel function in people with spinal cord injury (SCI) living in Australia. SETTING: Online survey of people living with SCI in Australia. METHODS: This anonymous online survey used Qualtrics and was advertised via standard communication channels, such as advocacy groups representing the SCI community in Australia, social media, attending SCI sporting events and by word-of-mouth. RESULTS: Responses from 62 individuals (32% female, 68% male) were included. Bladder emptying through urethra without catheter was the highest priority for bladder function. Reducing time required for bowel routines and constipation were the top priorities regarding bowel function. The highest concern for internal/implanted devices was the 4% chance of device surgical removal, while wearing wires under the clothes was the main concern for external devices. 53% of respondents were willing to trial an implanted nerve stimulation device, while 70% would trial an external device to improve and gain independence in bladder and bowel function. CONCLUSION: The findings of this study highlighted the potential role in which nerve stimulation can have in addressing bladder and bowel dysfunction in people with SCI, and have also identified that there was a need for Australian physiotherapists to evaluate their role in bladder and bowel dysfunction. Results from this study can help guide further research in nerve stimulation devices for bladder and bowel dysfunction in people with SCI. SPONSORSHIP: n/a.


Assuntos
Traumatismos da Medula Espinal , Bexiga Urinária , Humanos , Masculino , Feminino , Defecação , Austrália , Inquéritos e Questionários , Traumatismos da Medula Espinal/complicações
18.
Genome Biol ; 25(1): 60, 2024 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-38409096

RESUMO

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 min. Testing FCS-GX on artificially fragmented genomes demonstrates high sensitivity and specificity for diverse contaminant species. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination, comprising 0.16% of total bases, with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/ or https://doi.org/10.5281/zenodo.10651084 .


Assuntos
Bases de Dados de Ácidos Nucleicos , Genoma , Software
19.
Spinal Cord ; 62(4): 156-163, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38351327

RESUMO

STUDY DESIGN: Longitudinal, qualitative cohort study. OBJECTIVES: To understand how people with newly acquired spinal cord injury (PWS) and their support person (SP) define recovery and successful community reintegration (CR) across the first 12 months post-injury (mpi) and their satisfaction with the rate of recovery and reintegration experienced. SETTING: Academic and Veterans hospitals in Midwest USA. METHODS: In-depth, semi-structured interviews were conducted in two cohorts of PWS and SP during the initial inpatient rehabilitation stay, at 6 mpi, and at 12 mpi. Recordings were transcribed; four authors independently undertook line-by-line coding. The team discussed codes to reach consensus and synthesize into broader themes within the International Classification of Function, Disability, and Health and Transformative frameworks. RESULTS: Data are reported on 23 PWS and 21 SP. PWS and SP are similar in defining recovery as gaining motor function and achieving independence. However, SP more frequently define recovery in terms of maintaining positivity and emotional recovery. At 12 mpi both groups shift to define recovery according to progress. Social roles, being active, and employment are persistent themes of how PWS and SP define successful CR. However, SP also frequently define successful CR as reestablishing identity and emotional adjustment. Veterans with SCI less frequently defined successful CR as employment. CONCLUSIONS: This study is the first to reveal how PWS and SP define recovery and reintegration during the first 12 mpi. Given decreasing lengths of stay, this information can be used to tailor rehabilitation strategies during the critical first year of injury to optimize recovery.


Assuntos
Cuidadores , Traumatismos da Medula Espinal , Humanos , Cuidadores/psicologia , Apoio Social , Estudos de Coortes , Traumatismos da Medula Espinal/reabilitação , Pesquisa Qualitativa
20.
Ann Oncol ; 35(5): 437-447, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38369013

RESUMO

BACKGROUND: Human epidermal growth factor receptor 3 (HER3) is broadly expressed in non-small-cell lung cancer (NSCLC) and is the target of patritumab deruxtecan (HER3-DXd), an antibody-drug conjugate consisting of a HER3 antibody attached to a topoisomerase I inhibitor payload via a tetrapeptide-based cleavable linker. U31402-A-U102 is an ongoing phase I study of HER3-DXd in patients with advanced NSCLC. Patients with epidermal growth factor receptor (EGFR)-mutated NSCLC that progressed after EGFR tyrosine kinase inhibitor (TKI) and platinum-based chemotherapy (PBC) who received HER3-DXd 5.6 mg/kg intravenously once every 3 weeks had a confirmed objective response rate (cORR) of 39%. We present median overall survival (OS) with extended follow-up in a larger population of patients with EGFR-mutated NSCLC and an exploratory analysis in those with acquired genomic alterations potentially associated with resistance to HER3-DXd. PATIENTS AND METHODS: Safety was assessed in patients with EGFR-mutated NSCLC previously treated with EGFR TKI who received HER3-DXd 5.6 mg/kg; efficacy was assessed in those who also had prior PBC. RESULTS: In the safety population (N = 102), median treatment duration was 5.5 (range 0.7-27.5) months. Grade ≥3 adverse events occurred in 76.5% of patients; the overall safety profile was consistent with previous reports. In 78/102 patients who had prior third-generation EGFR TKI and PBC, cORR by blinded independent central review (as per RECIST v1.1) was 41.0% [95% confidence interval (CI) 30.0% to 52.7%], median progression-free survival was 6.4 (95% CI 4.4-10.8) months, and median OS was 16.2 (95% CI 11.2-21.9) months. Patients had diverse mechanisms of EGFR TKI resistance at baseline. At tumor progression, acquired mutations in ERBB3 and TOP1 that might confer resistance to HER3-DXd were identified. CONCLUSIONS: In patients with EGFR-mutated NSCLC after EGFR TKI and PBC, HER3-DXd treatment was associated with a clinically meaningful OS. The tumor biomarker characterization comprised the first description of potential mechanisms of resistance to HER3-DXd therapy.


Assuntos
Anticorpos Monoclonais Humanizados , Carcinoma Pulmonar de Células não Pequenas , Receptores ErbB , Neoplasias Pulmonares , Mutação , Receptor ErbB-3 , Humanos , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/mortalidade , Carcinoma Pulmonar de Células não Pequenas/patologia , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/mortalidade , Neoplasias Pulmonares/patologia , Receptores ErbB/genética , Receptores ErbB/antagonistas & inibidores , Feminino , Receptor ErbB-3/genética , Receptor ErbB-3/antagonistas & inibidores , Pessoa de Meia-Idade , Masculino , Idoso , Adulto , Anticorpos Monoclonais Humanizados/administração & dosagem , Anticorpos Monoclonais Humanizados/uso terapêutico , Anticorpos Monoclonais Humanizados/efeitos adversos , Idoso de 80 Anos ou mais , Camptotecina/análogos & derivados , Camptotecina/uso terapêutico , Camptotecina/administração & dosagem , Anticorpos Monoclonais/uso terapêutico , Anticorpos Monoclonais/administração & dosagem , Anticorpos Monoclonais/efeitos adversos , Anticorpos Amplamente Neutralizantes , Imunoconjugados/uso terapêutico , Imunoconjugados/efeitos adversos , Imunoconjugados/administração & dosagem
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