Genome-centric view of carbon processing in thawing permafrost.

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

Mass Participation and Tournament Event Management for the Team Physician: A Consensus Statement (2022 Update).

ABSTRACT: Mass participation events include endurance events (e.g., marathon, triathlon) and/or competitive tournaments (e.g., baseball, tennis, football (soccer) tournaments). Event management requires medical administrative and participant care planning. Medical management provides safety advice and care at the event that accounts for large numbers of participants, anticipated injury and illness, variable environment, repeated games or matches, and mixed age groups of varying athletic ability. This document does not pertain to the care of the spectator.

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.

Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees. The speed and accuracy of GraftM was benchmarked with in silico and in vitro mock communities using taxonomic markers, and was found to have higher accuracy at the family level with a processing time 2.0-3.7× faster than currently available software. Exploration of a wetland metagenome using 16S rRNA- and methyl-coenzyme M reductase (McrA)-specific gpkgs revealed taxonomic and functional shifts across a depth gradient. Analysis of the NCBI nr database using the McrA gpkg allowed the detection of novel sequences belonging to phylum-level lineages. A growing collection of gpkgs is available online (https://github.com/geronimp/graftM_gpkgs), where curated packages can be uploaded and exchanged.

Comprehensive Case-Based Review of Knee Ligament Injuries.

The management of knee ligament injuries continues to evolve, and much debate persists over the timing of surgery, repair versus reconstruction, surgical technique, postoperative rehabilitation, graft selection, and fixation. Surgeons should be aware of updates on the best management strategies of knee ligament injuries in 2018 and understand the important history and physical examination findings of the knee with ligamentous injury; the anterior cruciate ligament; the role of the anterolateral ligament and lateral extra-articular tenodesis; combined anterior cruciate ligament and medial collateral ligament injuries; the posterior cruciate ligament; medial collateral ligament repair versus reconstruction; posterolateral corner repair versus reconstruction; the role of coronal plane osteotomies, including high tibial osteotomy and distal femoral osteotomy; the role of sagittal plane osteotomies, including anterior closing wedge osteotomy and anterior opening wedge osteotomy; the initial management of the multiligament-injured knee; and five keys to avoiding complications in the multiligament-injured knee. The best available evidence and sample case presentations help guide surgical decision making and improve patient outcomes.

OrfM: a fast open reading frame predictor for metagenomic data.

UNLABELLED: Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However, the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here, we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools ('GetOrf' and 'Translate') but is four-five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at http://github.com/wwood/OrfM or through GNU Guix under the LGPL 3+ license. OrfM is implemented in C and supported on GNU/Linux and OSX. CONTACTS: b.woodcroft@uq.edu.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMMA-titania floating macrospheres for the photocatalytic remediation of agro-pharmaceutical wastewater.

Antibiotics such as tetracycline are used on a large scale in agriculture, and can become concentrated in wastewater lagoons that are used in conjunction with confined animal feeding operations. Solar-illuminated titanium dioxide can be used to photocatalytically degrade aqueous tetracycline, but its application in a lagoon environment requires that the photocatalyst be supported on a macroscopic support material to prevent loss of the nanoscale photocatalyst into the environment. In this work, titanium dioxide was deposited within a porous poly(methyl methacrylate) film on the surface of floating 7.0 cm diameter acrylic spheres. Six of these floating spheres removed over 96% of the tetracycline in 3.5 L of 60 mg/L tetracycline in natural pond water during 24 hours of solar illumination. The durability of these spheres under long-term solar exposure was also investigated along with the amount of photocatalyst lost from the sphere surface during use. These macroscale floating composite spheres provide a new method for removing tetracycline from wastewater lagoons with minimal risk of being displaced in the environment due to the large size of the spheres.

Part I: An anatomic-based tunnel in the fibular head for posterolateral corner reconstruction using magnetic resonance imaging.

PURPOSE: Currently, there are no studies that clearly define a method for the placement of the fibular tunnel between the fibular collateral ligament (FCL) and popliteofibular ligament (PFL) insertions when performing an anatomic-based posterolateral corner reconstruction. The purpose of this study was to use magnetic resonance-based anatomic landmarks to describe the orientation of a fibular tunnel between the FCL and PFL insertions. METHODS: Magnetic resonance imaging (MRI) of 105 patients with normal posterolateral corner knee anatomy was identified by a musculoskeletal radiologist, and the FCL and popliteofibular insertions were labelled. Three experienced providers independently evaluated the images. In the axial plane, the Cobb angle of a fibular tunnel from the FCL to the popliteofibular insertion was measured using the tibial tubercle as a reference. In the sagittal plane, the same tunnel was measured in reference to the lateral tibial plateau. RESULTS: In the axial plane, the average Cobb angle for an anatomic-based fibular tunnel was 48.1° ± 10.7° (ICC(2,1) = 0.76, p < 0.01) externally rotated to the tibial tubercle. In the sagittal plane, the average Cobb angle for an anatomic-based fibular tunnel was 59.8° ± 11.9° (ICC(2,1) = 0.81, p < 0.01) cranial, referenced from the lateral tibial plateau. The average length of the fibular tunnel was 2.0 ± 0.4 cm (ICC(2,1) = 0.78, p < 0.01), at the point of the fibular insertion. The distance from the midpoint of the fibular tunnel to the posterolateral wall of the fibular head was 0.8 ± 0.2 cm (ICC(2,1) = 0.63, p < 0.01). CONCLUSIONS: The results of this study suggest that MRI can be used to identify the orientation between the FCL and PFL insertions to create an anatomic-based fibular tunnel, which is 50° externally rotated from the tibial tubercle in the axial plane and placed in a cranial direction of 60° relative to the lateral joint line. The clinical relevance of this study is that this information may aid surgeons in placing a fibular tunnel connecting the FCL and PFL insertions. LEVEL OF EVIDENCE: IV.

Accuracy and reliability of determining the isometric point of the knee for multiligament knee reconstruction.

PURPOSE: To compare the accuracy and reliability of the anatomic and radiographic techniques for identifying the isometric point of the knee. METHODS: Only four specimens were used; however, eight experienced multiligament knee injury surgeons were recruited to address this limitation. Surgeons estimated the isometric point (EIP) on the medial and lateral sides using an anatomic and radiographic method. The x and y coordinates of the EIP were compared to the true isometric point (TIP). T-tests and interclass correlation coefficients (ICC) were performed to determine the accuracy and reliability between the methods. RESULTS: There was no difference in placement of the EIP on the medial side of the knee in the anterior/posterior (x; p = n.s.) and superior/inferior direction (y; p = n.s). The EIP was anterior (p = 0.001) to the TIP with the radiographic method on the lateral side and approached significance (p = 0.05) in the superior/inferior direction. The ICC (95% CI) for identifying the EIP on the medial side in the anterior/posterior direction using the anatomic method was 0.64 (0.28-0.96) and 0.11 (-0.06 to 0.77) in the superior/inferior direction. Using the radiographic method, the ICC in the anterior/posterior and superior/inferior direction was 0.49 (0.14-0.94) and 0.15 (-0.47 to 0.81), respectively. On the lateral side, the ICC for the anatomic method was 0.84 (0.56-0.99) in the anterior/posterior direction and 0.36 (0.05-0.90) in the superior/inferior direction. Using the radiographic method, the ICC in the anterior/posterior and superior/inferior direction was 0.61 (0.26-0.96) and 0.89 (0.67-0.99), respectively. CONCLUSIONS: There was no difference in accuracy on the medial side of the knee. On the lateral side, the anatomic method was more accurate in the anterior/posterior direction. Reliability was greater in the anterior/posterior direction on both sides of the knee. Surgeons were most likely to place the isometric point anterior and superior to the TIP on both the medial and lateral sides of the knee with either method which has the potential to cause graft lengthening. This should be taken into consideration during reconstruction/repair of the MCL/PMC and LCL/PLC.

Mass Participation and Tournament Event Management for the Team Physician: A Consensus Statement (2022 Update).

ABSTRACT: Mass participation events include endurance events (e.g., marathon, triathlon) and/or competitive tournaments (e.g., baseball, tennis, football (soccer) tournaments). Event management requires medical administrative and participant care planning. Medical management provides safety advice and care at the event that accounts for large numbers of participants, anticipated injury and illness, variable environment, repeated games or matches, and mixed age groups of varying athletic ability. This document does not pertain to the care of the spectator.

Aseptically processed and chemically sterilized BTB allografts for anterior cruciate ligament reconstruction: a prospective randomized study.

PURPOSE: To compare the clinical outcomes of bone-patellar tendon-bone (BTB) allografts processed via a novel sterilization system with the traditional aseptically processed BTB allografts for anterior cruciate ligament (ACL) reconstruction. METHODS: A total of 67 patients undergoing ACL reconstruction at 6 independent investigation sites were randomized into one of two intervention groups, BioCleanse-sterilized or aseptic BTB allografts. Inclusion criteria included an acute, isolated, unilateral ACL tear, and exclusion criteria included prior ACL injury, multi-ligament reconstruction, and signs of degenerative joint disease. Post-op examiners and patients were blinded to graft type. Patients were evaluated at 6, 12, and 24 months. Clinical outcomes were compared using the IKDC, a KT-1000 knee arthrometer, level of effusion, and ranges of motion (ROM). RESULTS: After randomization, 24 patients received aseptic BTB allografts and 43 patients received BioCleanse-sterilized allografts. Significant improvement in IKDC scores (P < 0.0001) as well as KT-1000 results (P < 0.0001) was noted over the 24-month period for both groups. IKDC or KT-1000 results were not significantly different between groups at any time point. Active flexion ROM significantly improved from pre-op to 24-month follow-up (P < 0.0001) with no difference between groups at any time point. Active extension ROM did not differ significantly between the two groups. CONCLUSIONS: These results indicate that the sterilization process, BioCleanse, did not demonstrate a statistical difference in clinical outcomes for the BTB allograft at 2 years. The BioCleanse process may provide surgeons with allografts clinically similar to aseptically processed allograft tissue with the benefit of addressing donor-to-recipient disease. LEVEL OF EVIDENCE: II.

Draft genome sequence of two "Candidatus Intestinicoccus colisanans" strains isolated from faeces of healthy humans.

OBJECTIVES: In order to provide a better insight into the functional capacity of the human gut microbiome, we isolated a novel bacterium, "Candidatus Intestinicoccus colisanans" gen. nov. sp. nov., and performed whole genome sequencing. This study will provide new insights into the functional potential of this bacterium and its role in modulating host health and well-being. We expect that this data resource will be useful in providing additional insight into the diversity and functional potential of the human microbiome. DATA DESCRIPTION: Here, we report the first draft genome sequences of "Candidatus Intestinicoccus colisanans" strains MH27-1 and MH27-2, recovered from faeces collected from healthy human donors. The genomes were sequenced using short-read Illumina technology and whole-genome-based comparisons and phylogenomics reconstruction indicate that "Candidatus Intestinicoccus colisanans" represents a novel genus and species within the family Acutalibacteraceae. Both genomes were estimated to be > 98% completed and to range in size from 2.9 to 3.3 Mb with a G + C content of approximately 51%. The gene repertoire of "Candidatus Intestinicoccus colisanans" indicate it is likely a saccharolytic gut bacterium.

Initial evaluation of the acute and chronic multiple ligament injured knee.

Multiple ligament injuries of the knee are rare, and severe injuries are often present following a knee dislocation. Appropriate initial evaluation and management is of critical importance for maximizing the potential outcome and avoiding disastrous consequences associated with these difficult injuries. While many of these injuries present acutely in an emergency department or clinic, presentation on a delayed basis is not uncommon. Injuries can present in a variety of situations, such as an isolated knee injury in an athlete or as part of a multisystem-injured trauma patient. In this publication, we review the etiology, classification, and comprehensive initial evaluation of the acute and chronic multiple-ligament injured knee.

Correlating MRI findings with disability in syndesmotic sprains of NFL players.

BACKGROUND: Syndesmotic sprains may be a significant source of missed playing time, especially in football players. Advanced imaging is frequently used to confirm the clinical diagnosis. Our purpose was to evaluate the prognostic ability of MRI in predicting time of disability. METHODS: Training room records from 1993 to 2007 for three National Football League teams were reviewed. Forty-three players were diagnosed with syndesmotic ankle injuries and underwent radiographs and magnetic resonance imaging. A blinded musculoskeletal radiologist interpreted all images. Players with fractures were excluded. RESULTS: Thirty-six professional football players were included in the final analysis. Twenty-three players had a positive squeeze test which was correlated with increased missed practices (p = 0.012) and increased missed games (p ≤ 0.01). The average number of games missed was 3.3 (range, 0 to 20) and the average number of practices missed was 16.7 (range, 0 to 114). Four players had isolated injury to the anterior tibio-fibular ligament (AITFL) (MRI Grade I). Five players had injury to the AITFL and interosseous ligament (MRI Grade II). Twenty-four players sustained injury to the AITFL, interosseous ligament, and posterior inferior tibio-fibular ligament (MRI Grade III). Three players had Grade III injuries with additional injury to the deltoid ligament (MRI Grade IV). Increasing grade of injury was positively correlated with increased number of missed games (p = 0.033) and missed practices (p = 0.002). CONCLUSION: MRI can be useful to help delineate the injury pattern and associated injuries, and may be useful in predicting time of disability using a grading system. Positive squeeze test can also be useful to determine prognosis.

Autograft versus allograft: an economic cost comparison of anterior cruciate ligament reconstruction.

PURPOSE: The purpose of this study was to compare the costs associated with anterior cruciate ligament (ACL) reconstruction with either bone-patellar tendon-bone (BPTB) autograft or BPTB allograft. METHODS: Surgical costs are reported, including supply costs, based on invoice costs per item used per procedure, and personnel costs calculated as cost per minute. All operations were performed at an ambulatory surgery center between March 2005 and March 2006. A total of 160 patients underwent primary ACL reconstruction with either BPTB autograft (n = 106) or BPTB allograft (n = 54). Procedure cost data were retrieved from a financial management database and divided into various categories for comparison of the 2 groups. Payment data were provided by the surgery center's billing office. RESULTS: The total mean cost per case was $4,147 ± $943 in the allograft group compared with $3,154 ± $704 in the autograft group; this was statistically significant (P < .001). The mean operating room time was 12 minutes greater in autograft cases (P = .006). Supply costs comprised a mean of 58.7% of total expenses in the autograft group and 72.2% in the allograft group. CONCLUSIONS: Allograft reconstruction of the ACL was significantly more expensive than autograft reconstruction. LEVEL OF EVIDENCE: Level II, economic analysis.

Management of complex knee ligament injuries.

The ideal management of the dislocated knee remains controversial. These injuries often can be elusive; a significant number of dislocated knees spontaneously reduce and appear relatively benign on routine radiographs. A high index of suspicion, based on the mechanism of injury, soft-tissue assessment of the limb, and the level of knee instability should alert the physician to the possibility of a dislocated knee. Early recognition and appropriate neurovascular assessment is paramount to the successful treatment of these complex injuries. Controversies exist regarding surgical versus nonsurgical management, early versus delayed surgery, the use of allograft versus autograft tissue, the decision to repair versus reconstruct torn ligamentous structures, and the type of reconstruction technique and postoperative rehabilitation program. To achieve optimal patient care, it is important to be aware of the current evaluation and treatment strategies for complex knee ligament injuries, including modern anatomic reconstruction techniques. Current recommendations include measurement of the ankle-brachial indices in each patient, early surgical management, the use of autograft or allograft tissue, reconstruction as opposed to repair alone of the fibular collateral ligament/posterolateral corner structures, reconstruction of the anterior and posterior cruciate ligaments, and repair and/or reconstruction of the medial collateral ligament/posteromedial corner depending on the injury pattern and the quality of tissue.

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.

BACKGROUND: Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters. RESULTS: Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively. CONCLUSIONS: Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.

Critical evaluation of faecal microbiome preservation using metagenomic analysis.

The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.

Diagnosis and management of knee dislocations.

An acute knee dislocation is an uncommon injury, with a high rate of associated vascular and neurologic injuries as well as potentially limb-threatening complications. High-energy trauma is the most common cause of an acute knee dislocation, although lower-energy injuries, such as those sustained during athletic competition, are increasing in incidence. Injuries to the popliteal artery and common peroneal nerve are relatively common, requiring a high index of suspicion and complete neurovascular examination in a timely fashion. All cases of suspected knee dislocation should have an ankle-brachial index performed, reserving arteriography for those with an abnormal finding. Initial management consists of closed reduction, if possible, and application of a hinged brace or external fixator. Definitive management remains an area of controversy, although anatomic surgical repair or reconstruction is favored by most surgeons to help optimize knee function. Most patients treated for a knee dislocation can expect to return to their daily activities, but with less predictable returns to sporting activities.

How Canada's Black Hockey League Shaped the Sport and the Path to Our Arrival in the NHL Today.

Willie O'Ree, known as the "Jackie Robinson of hockey," was the first Black player in the National Hockey League (NHL), debuting with the Boston Bruins in 1958. From the moment the Canadian-born player stepped onto the ice, he changed the notion of hockey as a "White sport," and he has dedicated his career to making it more accessible, including working with the NHL Diversity Task Force initiative Hockey Is For Everyone (HIFE). HIFE supports nonprofit hockey programs around the country and gives kids from all backgrounds the opportunity to try out their skills on the ice. Since 1994, Willie O'Ree has introduced 50,000 children across North America to the sport. Nonetheless, in the NHL today, only approximately 5% of the players (43 of >700) are players of color. However, several aspects of hockey's history, and innovations in the game, can be traced back to communities of color. Established in 1895, the Black Hockey League (BHL) of the Maritimes in Canada grew out of local churches in small towns such as Africville, Nova Scotia. By the beginning of the 20th century, the BHL had grown from a 3-team league to include newly formed teams across the region. The league had its own championship at a time when Black players were not allowed to play for the Stanley Cup. The BHL was at its height between 1890 and 1930, with hundreds of players, 12 teams, and as many as 1,200 spectators. Unfortunately, the Canadian government did not provide equitable resources, and churches alone could not maintain these small Black communities. As the NHL developed, focus shifted away from regional leagues. In 2018, Willie O'Ree was inducted into the NHL Hall of Fame. Although he may have broken the color barrier in 1958, hockey is still a predominantly White sport, and society continues to grapple with systematic racism. NHL players have formed an independent group, the Hockey Diversity Alliance, to work to make the game more socioeconomically inclusive and to help eradicate racism and intolerance.

Controversies in the treatment of knee dislocations and multiligament reconstruction.

A systematic approach to evaluation and treatment is needed for the patient with knee dislocation. There is a paucity of high-level evidence on which to base treatment decisions. Reported controversies related to the treatment of the multiligament-injured knee include the selective use of arteriography for vascular assessment, serial physical examination with the ankle-brachial index, acute surgical treatment of all damaged structures, the selective application of preoperative and postoperative joint-spanning external fixation, arthroscopic reconstruction of the anterior cruciate ligament and posterior cruciate ligament, simultaneous open reconstruction with repair of the posterolateral corner, reconstruction and/or repair of the posteromedial corner, and the use of allograft tissue.