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1.
CMAJ ; 196(24): E836-E845, 2024 Jul 01.
Article in French | MEDLINE | ID: mdl-38955403

ABSTRACT

CONTEXTE: Les données de surveillance du cancer sont essentielles pour mieux comprendre les lacunes et les progrès réalisés dans la lutte contre le cancer. Nous avons cherché à résumer les répercussions prévues du cancer au Canada en 2024, en effectuant des projections sur les nouveaux cas de cancer et les décès par cancer, par sexe et par province ou territoire, pour tous les âges confondus. MÉTHODES: Nous avons obtenu les données sur les nouveaux cas de cancer (c.-à-d., l'incidence, 1984­2019) et les décès par cancer (c.-à-d., la mortalité, 1984­2020) du Registre canadien du cancer et de la Base canadienne de données de l'état civil ­ Décès, respectivement. Nous avons projeté les chiffres et les taux d'incidence du cancer et de mortalité jusqu'en 2024 pour 23 types de cancer, par sexe et par province ou territoire. Nous avons calculé des taux normalisés selon l'âge au moyen de données de la population type canadienne de 2011. RÉSULTATS: En 2024, les nombres de nouveaux cas de cancer et de décès causés par le cancer devraient atteindre 247 100 et 88 100, respectivement. Le taux d'incidence normalisé selon l'âge (TINA) et le taux de mortalité normalisé selon l'âge (TMNA) devraient diminuer légèrement par rapport aux années précédentes, tant chez les hommes que chez les femmes, avec des taux plus élevés chez les hommes (TINA de 562,2 pour 100 000, et TMNA de 209,6 pour 100 000 chez les hommes; TINA de 495,9 pour 100 000 et TMNA de 152,8 pour 100 000 chez les femmes). Les TINA et les TMNA de plusieurs cancers courants devraient continuer à diminuer (p. ex., cancer du poumon, cancer colorectal et cancer de la prostate), tandis que ceux de plusieurs autres cancers devraient augmenter (p. ex., cancer du foie et des voies biliaires intrahépatiques, cancer du rein, mélanome et lymphome non hodgkinien). INTERPRÉTATION: Bien que l'incidence globale du cancer et la mortalité connexe sont en déclin, il devrait y avoir une augmentation des nouveaux cas et des décès au Canada en 2024, en grande partie en raison de la croissance et du vieillissement de la population. Les efforts en matière de prévention, de dépistage et de traitement ont atténué les répercussions de certains cancers, mais ces projections à court terme soulignent l'effet potentiel du cancer sur les gens et les systèmes de soins de santé au Canada.

2.
Mol Ecol ; : e17448, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38946210

ABSTRACT

Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning.

3.
Sports Med Arthrosc Rev ; 32(2): 75-86, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38978201

ABSTRACT

Cartilage lesions of the knee are a challenging problem, especially for active individuals and athletes who desire a return to high-load activities. They occur both through chronic repetitive loading of the knee joint or through acute traumatic injury and represent a major cause of pain and time lost from sport. They can arise as isolated lesions or in association with concomitant knee pathology. Management of these defects ultimately requires a sound understanding of their pathophysiologic underpinnings to help guide treatment. Team physicians should maintain a high index of suspicion for underlying cartilage lesions in any patient presenting with a knee effusion, whether painful or not. A thorough workup should include a complete history and physical examination. MRI is the most sensitive and specific imaging modality to assess these lesions and can provide intricate detail not only of the structure and composition of cartilage, but also of the surrounding physiological environment in the joint. Treatment of these lesions consists of both conservative or supportive measures, as well as surgical interventions designed to restore or regenerate healthy cartilage. Because of the poor inherent capacity for healing associated with hyaline cartilage, the vast majority of symptomatic lesions will ultimately require surgery. Surgical treatment options range from simple arthroscopic debridement to large osteochondral reconstructions. Operative decision-making is based on numerous patient- and defect-related factors and requires open lines of communication between the athlete, the surgeon, and the rest of the treatment team. Ultimately, a positive outcome is based on the creation of a durable, resistant repair that allows the athlete to return to pain-free sporting activities.


Subject(s)
Athletic Injuries , Cartilage, Articular , Knee Injuries , Magnetic Resonance Imaging , Humans , Cartilage, Articular/injuries , Cartilage, Articular/surgery , Athletic Injuries/surgery , Athletic Injuries/therapy , Athletic Injuries/diagnosis , Knee Injuries/surgery , Arthroscopy/methods , Debridement , Athletes
4.
FASEB J ; 38(13): e23795, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38984928

ABSTRACT

Cystathionine beta-synthase-deficient homocystinuria (HCU) is a life-threatening disorder of sulfur metabolism. HCU can be treated by using betaine to lower tissue and plasma levels of homocysteine (Hcy). Here, we show that mice with severely elevated Hcy and potentially deficient in the folate species tetrahydrofolate (THF) exhibit a very limited response to betaine indicating that THF plays a critical role in treatment efficacy. Analysis of a mouse model of HCU revealed a 10-fold increase in hepatic levels of 5-methyl -THF and a 30-fold accumulation of formiminoglutamic acid, consistent with a paucity of THF. Neither of these metabolite accumulations were reversed or ameliorated by betaine treatment. Hepatic expression of the THF-generating enzyme dihydrofolate reductase (DHFR) was significantly repressed in HCU mice and expression was not increased by betaine treatment but appears to be sensitive to cellular redox status. Expression of the DHFR reaction partner thymidylate synthase was also repressed and metabolomic analysis detected widespread alteration of hepatic histidine and glutamine metabolism. Many individuals with HCU exhibit endothelial dysfunction. DHFR plays a key role in nitric oxide (NO) generation due to its role in regenerating oxidized tetrahydrobiopterin, and we observed a significant decrease in plasma NOx (NO2 + NO3) levels in HCU mice. Additional impairment of NO generation may also come from the HCU-mediated induction of the 20-hydroxyeicosatetraenoic acid generating cytochrome CYP4A. Collectively, our data shows that HCU induces dysfunctional one-carbon metabolism with the potential to both impair betaine treatment and contribute to multiple aspects of pathogenesis in this disease.


Subject(s)
Homocystinuria , Liver , Oxidation-Reduction , Tetrahydrofolate Dehydrogenase , Tetrahydrofolates , Animals , Homocystinuria/metabolism , Homocystinuria/drug therapy , Homocystinuria/genetics , Mice , Tetrahydrofolates/metabolism , Liver/metabolism , Tetrahydrofolate Dehydrogenase/metabolism , Tetrahydrofolate Dehydrogenase/genetics , Betaine/metabolism , Betaine/pharmacology , Homocysteine/metabolism , Mice, Inbred C57BL , Cystathionine beta-Synthase/metabolism , Cystathionine beta-Synthase/genetics , Carbon/metabolism , Male , Folic Acid/metabolism , Female
5.
Microb Genom ; 10(6)2024 Jun.
Article in English | MEDLINE | ID: mdl-38833287

ABSTRACT

It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of short-read depth on polishing performance is not well understood. Here, we introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default and Polypolish-careful commonly introduce false-positive errors at low read depth; (2) most of the benefit of short-read polishing occurs by 25× depth; (3) Polypolish-careful almost never introduces false-positive errors at any depth; and (4) Pypolca-careful is the single most effective polisher. Overall, we recommend the following polishing strategies: Polypolish-careful alone when depth is very low (<5×), Polypolish-careful and Pypolca-careful when depth is low (5-25×), and Polypolish-default and Pypolca-careful when depth is sufficient (>25×).


Subject(s)
Genome, Bacterial , Nanopores , High-Throughput Nucleotide Sequencing/methods , Sequence Analysis, DNA/methods , Nanopore Sequencing/methods , Bacteria/genetics , Bacteria/classification , Software , Genomics/methods
6.
Arthrosc Tech ; 13(5): 102941, 2024 May.
Article in English | MEDLINE | ID: mdl-38835468

ABSTRACT

The acetabular labrum plays a key role in proper biomechanical hip function through creation or maintenance of a suction seal between the femoral head and acetabulum. The suction seal effect has been shown to provide stability within the hip, improve biomechanics, and decrease the chance for long-term development of osteoarthritis by optimizing function and force distribution within the hip. Femoral acetabular impingement syndrome damages the labrum and chondrolabral junction, thus negatively impacting the ability of the labrum to maintain native suction seal. Our technique describes the use of a postless hip arthroscopy table and the on-off traction technique throughout the labral repair, ensuring precise reduction of the labrum and restoration of the suction seal sequentially as anchors are placed.

7.
Article in English | MEDLINE | ID: mdl-38918331

ABSTRACT

PURPOSE OF REVIEW: The management of shoulder instability in throwing athletes remains a challenge given the delicate balance between physiologic shoulder laxity facilitating performance and the inherent need for shoulder stability. This review will discuss the evaluation and management of a throwing athlete with suspected instability with a focus on recent findings and developments. RECENT FINDINGS: The vast majority of throwing athletes with shoulder instability experience subtle microinstability as a result of repetitive microtrauma rather than episodes of gross instability. These athletes may present with arm pain, dead arms or reduced throwing velocity. Recent literature reinforces the fact that there is no "silver bullet" for the management of these athletes and an individualized, tailored approach to treatment is required. While initial nonoperative management remains the hallmark for treatment, the results of rehabilitation protocols are mixed, and some patients will ultimately undergo surgical stabilization. In these cases, it is imperative that the surgeon be judicious with the extent of surgical stabilization as overtightening of the glenohumeral joint is possible, which can adversely affect athlete performance. Managing shoulder instability in throwing athletes requires a thorough understanding of its physiologic and biomechanical underpinnings. Inconsistent results seen with surgical stabilization has led to a focus on nonoperative management for these athletes with surgery reserved for cases that fail to improve non-surgically. Overall, more high quality studies into the management of this challenging condition are warranted.

8.
Arthritis Res Ther ; 26(1): 118, 2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38851726

ABSTRACT

BACKGROUND: Primary osteoarthritis (OA) occurs without identifiable underlying causes such as previous injuries or specific medical conditions. Age is a major contributing factor to OA, and as one ages, various joint tissues undergo gradual change, including degeneration of the articular cartilage, alterations in subchondral bone (SCB) morphology, and inflammation of the synovium. METHODS: We investigated the prevalence of primary OA in aged, genetically diverse UM-HET3 mice. Articular cartilage (AC) integrity and SCB morphology were assessed in 182 knee joints of 22-25 months old mice using the Osteoarthritis Research Society International (OARSI) scoring system and micro-CT, respectively. Additionally, we explored the effects of methylene blue (MB) and mitoquinone (MitoQ), two agents that affect mitochondrial function, on the prevalence and progression of OA during aging. RESULTS: Aged UM-HET3 mice showed a high prevalence of primary OA in both sexes. Significant positive correlations were found between cumulative AC (cAC) scores and synovitis in both sexes, and osteophyte formation in female mice. Ectopic chondrogenesis did not show significant correlations with cAC scores. Significant direct correlations were found between AC scores and inflammatory markers in chondrocytes, including matrix metalloproteinase-13, inducible nitric oxide synthase, and the NLR family pyrin domain containing-3 inflammasome in both sexes, indicating a link between OA severity and inflammation. Additionally, markers of cell cycle arrest, such as p16 and ß-galactosidase, also correlated with AC scores. In male mice, no significant correlations were found between SCB morphology traits and cAC scores, while in female mice, significant correlations were found between cAC scores and tibial SCB plate bone mineral density. Notably, MB and MitoQ treatments influenced the disease's progression in a sex-specific manner. MB treatment significantly reduced cAC scores at the medial knee joint, while MitoQ treatment reduced cAC scores, but these did not reach significance. CONCLUSIONS: Our study provides comprehensive insights into the prevalence and progression of primary OA in aged UM-HET3 mice, highlighting the sex-specific effects of MB and MitoQ treatments. The correlations between AC scores and various pathological factors underscore the multifaceted nature of OA and its association with inflammation and subchondral bone changes.


Subject(s)
Aging , Osteoarthritis , Animals , Male , Female , Mice , Aging/pathology , Aging/genetics , Osteoarthritis/genetics , Osteoarthritis/pathology , Osteoarthritis/metabolism , Cartilage, Articular/pathology , Cartilage, Articular/metabolism , Methylene Blue/pharmacology , Ubiquinone/analogs & derivatives , Ubiquinone/pharmacology , Disease Models, Animal , Disease Progression
9.
Nat Commun ; 15(1): 5387, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38918361

ABSTRACT

Creatine chemical exchange saturation transfer (CrCEST) MRI is an emerging high resolution and noninvasive method for measuring muscle specific oxidative phosphorylation (OXPHOS). However, CrCEST measurements are sensitive to changes in muscle pH, which might confound the measurement and interpretation of creatine recovery time (τCr). Even with the same prescribed exercise stimulus, the extent of acidification and hence its impact on τCr is expected to vary between individuals. To address this issue, a method to measure pH pre- and post-exercise and its impact on CrCEST MRI with high temporal resolution is needed. In this work, we integrate carnosine 1H- magnetic resonance spectroscopy (MRS) and 3D CrCEST to establish "mild" and "moderate/intense" exercise stimuli. We then test the dependence of CrCEST recovery time on pH using different exercise stimuli. This comprehensive metabolic imaging protocol will enable personalized, muscle specific OXPHOS measurements in both healthy aging and myriad other disease states impacting muscle mitochondria.


Subject(s)
Magnetic Resonance Imaging , Muscle, Skeletal , Oxidative Phosphorylation , Proton Magnetic Resonance Spectroscopy , Magnetic Resonance Imaging/methods , Humans , Muscle, Skeletal/metabolism , Muscle, Skeletal/diagnostic imaging , Male , Hydrogen-Ion Concentration , Proton Magnetic Resonance Spectroscopy/methods , Creatine/metabolism , Exercise/physiology , Female , Adult
11.
J Psychopharmacol ; : 2698811241257839, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38888164

ABSTRACT

BACKGROUND: Voter initiatives in Oregon and Colorado authorize legal frameworks for supervised psilocybin services, but no measures monitor safety or outcomes. AIMS: To develop core measures of best practices. METHODS: A three-phase e-Delphi process recruited 36 experts with 5 or more years' experience facilitating psilocybin experiences in various contexts (e.g., ceremonial settings, indigenous practices, clinical trials), or other pertinent psilocybin expertise. Phase I, an on-line survey with qualitative, open-ended text responses, generated potential measures to assess processes, outcomes, and structure reflecting high quality psilocybin services. In Phase II, experts used seven-point Likert scales to rate the importance and feasibility of the Phase I measures. Measures were priority ranked. Qualitative interviews and analysis in Phase III refined top-rated measures. RESULTS: Experts (n = 36; 53% female; 71% white; 56% heterosexual) reported currently providing psilocybin services (64%) for a mean of 15.2 [SD 13.1] years, experience with indigenous psychedelic practices (67%), and/or conducting clinical trials (36%). Thematic analysis of Phase I responses yielded 55 candidate process measures (e.g., preparatory hours with client, total dose of psilocybin administered, documentation of touch/sexual boundaries), outcome measures (e.g., adverse events, well-being, anxiety/depression symptoms), and structure measures (e.g., facilitator training in trauma informed care, referral capacity for medical/psychiatric issues). In Phase II and III, experts prioritized a core set of 11 process, 11 outcome, and 17 structure measures that balanced importance and feasibility. CONCLUSION: Service providers and policy makers should consider standardizing core measures developed in this study to monitor the safety, quality, and outcomes of community-based psilocybin services.

12.
J Prosthet Dent ; 2024 May 03.
Article in English | MEDLINE | ID: mdl-38704320

ABSTRACT

STATEMENT OF PROBLEM: Silicone elastomers are becoming more readily available for additive manufacturing, which may be advantageous for fabricating maxillofacial prostheses. However, the properties of three-dimensionally (3D) printed silicone as compared with conventionally processed silicone have not been well studied. PURPOSE: The purpose of this in vitro study was to compare the dimensional accuracy and surface resolution of additively manufactured with conventional room-temperature vulcanized (RTV) silicones. MATERIAL AND METHODS: A custom aluminum mold was used to generate hand-spatulated specimens (A103 and VerSilTal-50F, n=20). A computer-aided design and computer-aided manufacturing workflow was used to generate additively manufactured specimens (Sil30 and TrueSil, n=20). Digital surface scans of each specimen were recorded; a scan of the mold served as the control. Surface dimensions were measured with a digital metrology software program, while digital overlays were made using a 3D processing software program. The surface resolution of the specimens was assessed by analyzing 4 topographical landmarks (flat surfaces, raised lines, domes, and scribed lines) with a visual qualitative grading scale. The data were analyzed with 1-way analysis of variance, followed by a Student-Newman-Keuls post hoc test (α=.05). RESULTS: The specimens demonstrated statistical differences in trueness and precision (P<.001). The TrueSil specimens showed the largest deviation in measurements of trueness and precision (up to -1.374%). The other specimens yielded percentage mean differences that were more consistently within the range of the American Dental Association International Organization for Standardization standard for elastomers. The manually fabricated specimens yielded more consistently ideal ratings for resolution than did the additively manufactured ones, with the Sil30 specimens receiving the most Charlie (not clinically acceptable) ratings. CONCLUSIONS: Numerical differences between each specimen and the control were considered negligible for maxillofacial applications. Notable discrepancies related to the quality of resolution, wherein the benchtop-manufactured specimens consistently generated better results compared with additively manufactured ones. Other factors, such as resiliency, odor, and cost, posed limitations in justifying the use of silicones in a direct-to-print workflow.

14.
bioRxiv ; 2024 May 14.
Article in English | MEDLINE | ID: mdl-38798522

ABSTRACT

Background: NK cells are being extensively studied as a cell therapy for cancer. Their effector functions are induced by the recognition of ligands on tumor cells and by various cytokines. IL-15 is broadly used to stimulate endogenous and adoptively transferred NK cells in cancer patients. These stimuli activate the membrane protease ADAM17, which then cleaves assorted receptors on the surface of NK cells as a negative feedback loop to limit their activation and function. We have shown that ADAM17 inhibition can enhance IL-15-mediated NK cell proliferation in vitro and in vivo . In this study, we investigated the underlying mechanism of this process. Methods: PBMCs or enriched NK cells from human peripheral blood, either unlabeled or labeled with a cell proliferation dye, were cultured for up to 7 days in the presence of rhIL-15 +/- an ADAM17 function-blocking antibody. Different versions of the antibody were generated; Medi-1 (IgG1), Medi-4 (IgG4), Medi-PGLALA, Medi-F(ab') 2 , and TAB16 (anti-ADAM17 and anti-CD16 bispecific) to modulate CD16A engagement on NK cells. Flow cytometry was used to assess NK cell proliferation and phenotypic markers, immunoblotting to examine CD16A signaling, and IncuCyte-based live cell imaging to measure NK cell anti-tumor activity. Results: The ADAM17 function-blocking mAb Medi-1 markedly increased initial NK cell activation by IL-15. Using different engineered versions of the antibody revealed that the activating Fcγ receptor CD16A, a well-described ADAM17 substrate, was critical for enhancing IL-15 stimulation. Hence, Medi-1 bound to ADAM17 on NK cells can be engaged by CD16A and block its shedding, inducing and prolonging its signaling. This process did not promote evident NK cell fratricide, phagocytosis, or dysfunction. Synergistic activity by Medi-1 and IL-15 enhanced the upregulation of CD137 on CD16A + NK cells and augmented their proliferation in the presence of PBMC accessory cells. Conclusions: Our data reveal for the first time that CD16A and CD137 underpin Medi-1 enhancement of IL-15-driven NK cell activation and proliferation, respectively. The use of Medi-1 represents a novel strategy to enhance IL-15-driven NK cell proliferation, and it may be of therapeutic importance by increasing the anti-tumor activity of NK cells in cancer patients. What is already known on this topic: NK cell therapies are being broadly investigated to treat cancer. NK cell stimulation by IL-15 prolongs their survival in cancer patients. Various stimuli including IL-15 activate ADAM17 in NK cells, a membrane protease that regulates the cell surface density of various receptors as a negative feedback mechanism. What this study adds: Treating NK cells with the ADAM17 function-blocking mAb Medi-1 markedly enhanced their activation and proliferation. Our study reveals that the Fc and Fab regions of Medi-1 function synergistically with IL-15 in NK cell activation. Medi-1 treatment augments the upregulation of CD137 by NK cells, which enhances their proliferation in the presence of PBMC accessory cells. How this study might affect research practice or policy: Our study is of translational importance as Medi-1 treatment in combination with IL-15 could potentially augment the proliferation and function of endogenous or adoptively transferred NK cells in cancer patients.

15.
J Mammal ; 105(3): 490-501, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38812929

ABSTRACT

Among polar bears (Ursus maritimus), only parturient females den for extended periods, emerging from maternal dens in spring after having substantially depleted their energy reserves during a fast that can exceed 8 months. Although den emergence coincides with a period of increasing prey availability, polar bears typically do not depart immediately to hunt, but instead remain at the den for up to a month. This delay suggests that there are likely adaptive advantages to remaining at the den between emergence and departure, but the influence of the timing and duration of this post-emergence period on cub survival has not been evaluated previously. We used temperature and location data from 70 denning bears collared within the Southern Beaufort Sea and Chukchi Sea subpopulations to estimate the phenology of the post-emergence period. We evaluated the influence of various spatial and temporal features on duration of the post-emergence period and evaluated the potential influence of post-emergence duration on litter survival early in the spring following denning. For dens that likely contained viable cubs at emergence (n = 56), mean den emergence occurred on 16 March (SE = 1.4 days) and mean departure on 24 March (SE = 1.6 days), with dates typically occurring later in the Chukchi Sea relative to Southern Beaufort Sea and on land relative to sea ice. Mean duration of the post-emergence period was 7.9 days (SE = 1.4) for bears that were observed with cubs later in the spring, which was over 4 times longer than duration of those observed without cubs (1.9 days). Litter survival in the spring following denning (n = 31 dens) increased from 0.5 to 0.9 when duration of the post-emergence period increased by ~4 days and other variables were held at mean values. Our limited sample size and inability to verify cub presence at emergence suggests that future research is merited to improve our understanding of this relationship. Nonetheless, our results highlight the importance of the post-emergence period in contributing to reproductive success and can assist managers in developing conservation and mitigation strategies in denning areas, which will be increasingly important as human activities expand in the Arctic.

16.
Microb Genom ; 10(5)2024 May.
Article in English | MEDLINE | ID: mdl-38717808

ABSTRACT

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.


Subject(s)
Algorithms , Genome, Bacterial , Software , Plasmids/genetics , Sequence Analysis, DNA/methods , Genomics/methods , High-Throughput Nucleotide Sequencing/methods , Bacteria/genetics , Bacteria/classification
17.
CMAJ ; 196(18): E615-E623, 2024 May 12.
Article in English | MEDLINE | ID: mdl-38740416

ABSTRACT

BACKGROUND: Cancer surveillance data are essential to help understand where gaps exist and progress is being made in cancer control. We sought to summarize the expected impact of cancer in Canada in 2024, with projections of new cancer cases and deaths from cancer by sex and province or territory for all ages combined. METHODS: We obtained data on new cancer cases (i.e., incidence, 1984-2019) and deaths from cancer (i.e., mortality, 1984-2020) from the Canadian Cancer Registry and Canadian Vital Statistics Death Database, respectively. We projected cancer incidence and mortality counts and rates to 2024 for 23 types of cancer, overall, by sex, and by province or territory. We calculated age-standardized rates using data from the 2011 Canadian standard population. RESULTS: In 2024, the number of new cancer cases and deaths from cancer are expected to reach 247 100 and 88 100, respectively. The age-standardized incidence rate (ASIR) and mortality rate (ASMR) are projected to decrease slightly from previous years for both males and females, with higher rates among males (ASIR 562.2 per 100 000 and ASMR 209.6 per 100 000 among males; ASIR 495.9 per 100 000 and ASMR 152.8 per 100 000 among females). The ASIRs and ASMRs of several common cancers are projected to continue to decrease (i.e., lung, colorectal, and prostate cancer), while those of several others are projected to increase (i.e., liver and intrahepatic bile duct cancer, kidney cancer, melanoma, and non-Hodgkin lymphoma). INTERPRETATION: Although the overall incidence of cancer and associated mortality are declining, new cases and deaths in Canada are expected to increase in 2024, largely because of the growing and aging population. Efforts in prevention, screening, and treatment have reduced the impact of some cancers, but these short-term projections highlight the potential effect of cancer on people and health care systems in Canada.


Subject(s)
Neoplasms , Registries , Humans , Canada/epidemiology , Neoplasms/epidemiology , Neoplasms/mortality , Male , Female , Incidence , Sex Distribution , Forecasting , Middle Aged , Aged , Age Distribution , Adult , Mortality/trends
18.
J Pain Res ; 17: 1601-1638, 2024.
Article in English | MEDLINE | ID: mdl-38716038

ABSTRACT

Clinical management of sacroiliac disease has proven challenging from both diagnostic and therapeutic perspectives. Although it is widely regarded as a common source of low back pain, little consensus exists on the appropriate clinical management of sacroiliac joint pain and dysfunction. Understanding the biomechanics, innervation, and function of this complex load bearing joint is critical to formulating appropriate treatment algorithms for SI joint disorders. ASPN has developed this comprehensive practice guideline to serve as a foundational reference on the appropriate management of SI joint disorders utilizing the best available evidence and serve as a foundational guide for the treatment of adult patients in the United States and globally.

19.
Phys Rev Lett ; 132(18): 188301, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38759204

ABSTRACT

While bacterial swarms can exhibit active turbulence in vacant spaces, they naturally inhabit crowded environments. We numerically show that driving disorderly active fluids through porous media enhances Darcy's law. While purely active flows average to zero flux, hybrid active/driven flows display greater drift than purely pressure-driven flows. This enhancement is nonmonotonic with activity, leading to an optimal activity to maximize flow rate. We incorporate the active contribution into an active Darcy's law, which may serve to help understand anomalous transport of swarming in porous media.

20.
Cureus ; 16(4): e58231, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38745794

ABSTRACT

Hypothyroidism is generally considered an autoimmune condition, and typical medical management involves taking levothyroxine (synthetic thyroid hormone) for life. This case report details the results of a mind-body intervention (MBI) called the Neuro-Emotional Technique (NET) used to treat a 28-year-old Caucasian female presenting with symptoms and bloodwork markers associated with two years of hypothyroidism and a long history of stress. The patient's medical doctor provided a diagnosis of hypothyroidism after blood tests showed that thyroid-stimulating hormone (TSH) levels were high at 6.87 mIU/L (where the acceptable range is 0.40-3.50 mIU/L) and free T4 (FT4) levels were low at 8.6 pmol/L (where the acceptable range is 9.0-19.0 pmol/L). Psychometric tests were completed at baseline and after 12 weeks of treatment to evaluate changes in mental health and emotional well-being. The Adverse Childhood Experiences Questionnaire (ACE-Q) revealed a high degree of childhood trauma that may have predisposed to the underlying autoimmune thyroid dysfunction. At the conclusion of the treatment period, serum thyroid-stimulating hormone (TSH) and free T4 were within normal ranges and psychometric indicators normalized. We hypothesize that these changes may be due to the stress-reducing mechanism of NET and outline possible mechanisms via the Psycho-Immune-Neuroendocrine (PINE) network. The PINE network model asserts that chronic stress acts as a potential driver of pathophysiology that can lead to one or more medical and mental health conditions. While further studies with larger sample sizes are required to establish whether these results could be extrapolated to a wider population, the results of this case suggest that it may be pertinent to consider co-management of subclinical hypothyroidism with a relatively quick and cost-effective MBI such as NET.

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