Metaphyseal Fixation Using Cones and Sleeves for Severe Proximal Tibial Bone Loss.

BACKGROUND: Tibial bone defects are commonly encountered in revision total knee arthroplasty (rTKA) and can be managed with metaphyseal cones or sleeves. Few studies have directly compared tibial cones and sleeves in rTKA, and none have limited this comparison to the most severe tibial defects. The purpose of this study was to evaluate and compare the outcomes of metaphyseal cones and sleeves for tibial reconstruction in rTKA regarding implant fixation and clinical outcomes. METHODS: A retrospective review was conducted on patients undergoing rTKA in which metaphyseal cones or sleeves were utilized for addressing metaphyseal bone loss (34 cones and 18 sleeves). Tibial bone loss was classified according to the Anderson Orthopaedic Research Institute bone defect classification, with types 2B and 3 being included. Patient-reported outcomes and postoperative complications were collected, and a radiographic evaluation of osseointegration or loosening was performed. RESULTS: There were 52 knees included (34 cones, 18 sleeves), with a median follow-up of 41.0 months. All-cause implant survival was 100% at 2 years and 96% (95% confidence interval: 76 to 99%) at 4 years, with 98% of tibial components demonstrating osseointegration at the final follow-up. During follow-up, there were a total 11 revisions, of which 1 sleeve was revised secondary to implant loosening. Tibial sleeves had a higher risk of revision compared to tibial cones (P < .01), and sleeves fixed with a hybrid technique were more likely to need revision than cones fixed by the same method (P = .01). CONCLUSIONS: Porous metaphyseal tibial cones and tibial metaphyseal sleeves both performed well at a 41-month median follow-up with no difference in aseptic survivorship between the 2 constructs. Both demonstrate high rates of osseointegration, low rates of aseptic failure, and significant improvement in Knee Society Scores in patients with severe tibial defects in rTKA.

Highly Cross-Linked Polyethylene in Patients 50 Years of Age and Younger: A 20-year Follow-Up Analysis.

BACKGROUND: Highly cross-linked polyethylene (HXLPE) has been an excellent bearing for total hip arthroplasty (THA) due to improved wear characteristics compared to conventional materials. Patients 50 years of age or younger are at high risk for wear-related complications of their THA, and few studies have followed these patients who have HXPLE into the third decade. METHODS: In a retrospective review of 88 consecutive THAs performed in 77 patients aged 50 years and younger (mean 41; range, 20 to 50), in which HXLPE was utilized, they were evaluated for their clinical and radiographic results at an average of 20-year follow-up (range, 18 to 24). The current study reports on longer-term follow-up from our previously published series at shorter follow-up times. Patients were categorized by femoral head material: cobalt chrome (n = 14), ceramic (n = 30), and oxidized zirconium (n = 22) and by femoral head size: 26 mm (n = 12), 28 mm (n = 46), and 32 mm (n = 8). Harris Hip Scores were collected preoperatively and at the most recent follow-up. Radiographs were evaluated for linear and volumetric wear, radiolucent lines, and osteolysis. RESULTS: Mean Harris Hip Scores improved from 47.1 (standard deviation [SD] 8.8) preoperatively to 92.0 (SD 7.7) (P < .0001) at 20-year follow-up. There was one hip that was revised for recurrent instability, and no hip demonstrated radiographic evidence of loosening or osteolysis. The mean polyethylene linear wear rate was 0.017 (SD 0.012) mm/y, and the mean polyethylene volumetric wear rate was 3.15 (SD 2.8) mm3/year, with no significant differences based on articulation type or head size. CONCLUSIONS: Total hip arthroplasty with HXLPE in patients ≤ 50 years of age continues to demonstrate excellent long-term clinical and radiographic outcomes with low wear characteristics at 20-year follow-up, regardless of femoral head material or size.

Successful treatment of SARS-CoV-2 in an immunocompromised patient with persistent infection for 245 days: A case report.

Background: Immunocompromised patients receiving B-cell-depleting therapies are at increased risk of persistent SARS-CoV-2 infection, with many experiencing fatal outcomes. We report a successful outcome in a patient with rheumatoid arthritis (RA) on rituximab diagnosed with COVID-19 in July 2020 with persistent infection for over 245 days. Results: The patient received numerous treatment courses for persistent COVID-19 infection, including remdesivir, baricitinib, immunoglobulin and high doses of corticosteroids followed by a prolonged taper due to persistent respiratory symptoms and cryptogenic organizing pneumonia. Her clinical course was complicated by Pseudomonas aeruginosa sinusitis with secondary bacteremia, and cytomegalovirus (CMV) viremia and pneumonitis. SARS-CoV-2 positive RNA samples were extracted from two nasopharyngeal swabs and sequenced using targeted amplicon Next-Generation Sequencing which were analyzed for virus evolution over time. Viral sequencing indicated lineage B.1.585.3 SARS-CoV-2 accumulated Spike protein mutations associated with immune evasion and resistance to therapeutics. Upon slowly decreasing the patient's steroids, she had resolution of her symptoms and had a negative nasopharyngeal SARS-CoV-2 PCR and serum CMV PCR in March 2021. Conclusion: A patient with RA on B-cell depleting therapy developed persistent SARS-CoV-2 infection allowing for virus evolution and had numerous complications, including viral and bacterial co-infections with opportunistic pathogens. Despite intra-host evolution with a more immune evasive SARS-CoV-2 lineage, it was cleared after 245 days with reconstitution of the patient's immune system.

Developing managed aquifer recharge (MAR) to augment irrigation water resources in the sand and gravel (Crag) aquifer of coastal Suffolk, UK.

Managed aquifer recharge (MAR) offers a potential innovative solution for addressing groundwater resource issues, enabling excess surface water to be stored underground for later abstraction. Given its favourable hydrogeological properties, the Pliocene sand and gravel (Crag) aquifer in Suffolk, UK, was selected for a demonstration MAR scheme, with the goal of supplying additional summer irrigation water. The recharge source was a 4.6 km drainage channel that discharges to the River Deben estuary. Trialling the scheme in June 2022, 12,262 m3 of source water were recharged to the aquifer over 12 days via a lagoon and an array of 565 m of buried slotted pipes. Groundwater levels were raised by 0.3 m at the centre of the recharge mound with an approximate radius of 250 m, with no detrimental impact on local water features observed. The source water quality remained stable during the trial with a mean chloride concentration (133 mg L-1) below the regulatory requirement (165 mg L-1). The fraction of recharge water mixing with the groundwater ranged from 69% close to the centre and 5% at the boundary of the recharge mound, leading to a reduction in nitrate-N concentration of 23.6 mg L-1 at the centre of the mound. During July-September 2022, 12,301 m3 of recharge water were abstracted from two, 18 m boreholes to supplement surface irrigation reservoirs during drought conditions. However, the hydraulic conductivity of the Crag aquifer (∼10 m day-1) restricted the yield and thereby reduced the economic viability of the scheme. Construction costs for the MAR system were comparatively low but the high costs of data collection and securing regulatory permits brought the overall capital costs to within 18% of an equivalent surface storage reservoir, demonstrating that market-based mechanisms and more streamlined regulatory processes are required to incentivise similar MAR schemes.

Contrasting water-use strategies revealed by species-specific transpiration dynamics in the Caatinga dry forest.

In forest ecosystems, transpiration (T) patterns are important for quantifying water and carbon fluxes and are major factors in predicting ecosystem change. Seasonal changes in rainfall and soil water content can alter the sensitivity of sap flux density to daily variations in vapor pressure deficit (VPD). This sensitivity is species-specific and is thought to be related to hydraulic strategies. The aim of this work is to better understand how the sap flux density of species with low versus high wood density differ in their sensitivity to VPD and soil water content and how potentially opposing water-use strategies influence T dynamics, and ultimately, correlations to evapotranspiration (ET). We use hysteresis area analysis to quantify the sensitivity of species-specific sap flux density to changes in the VPD, breakpoint-based models to determine the soil water content threshold instigating a T response and multiscalar wavelet coherency to correlate T to ET. We found that low wood density Commiphora leptophloeos (Mart.) Gillett had a more dynamic T pattern, a greater sensitivity to VPD at high soil water content, required a higher soil water content threshold for this sensitivity to be apparent, and had a significant coherency correlation with ET at daily to monthly timescales. This behavior is consistent with a drought avoidance strategy. High wood density Cenostigma pyramidale  (Tul.)  E. Gagnon & G. P. Lewis, conversely, had a more stable T pattern, responded to VPD across a range of soil water content, tolerated a lower soil water content threshold to T, and had a significant coherency correlation with ET at weekly timescales. This behavior is consistent with a drought-tolerant strategy. We build on previous research to show that these species have contrasting water-use strategies that should be considered in large-scale modeling efforts.

Sink-traps are a major source for carbapenemase-producing Enterobacteriaceae transmission.

OBJECTIVE: We studied the extent of carbapenemase-producing Enterobacteriaceae (CPE) sink contamination and transmission to patients in a nonoutbreak setting. METHODS: During 2017-2019, 592 patient-room sinks were sampled in 34 departments. Patient weekly rectal swab CPE surveillance was universally performed. Repeated sink sampling was conducted in 9 departments. Isolates from patients and sinks were characterized using pulsed-field gel electrophoresis (PFGE), and pairs of high resemblance were sequenced by Oxford Nanopore and Illumina. Hybrid assembly was used to fully assemble plasmids, which are shared between paired isolates. RESULTS: In total, 144 (24%) of 592 CPE-contaminated sinks were detected in 25 of 34 departments. Repeated sampling (n = 7,123) revealed that 52%-100% were contaminated at least once during the sampling period. Persistent contamination for >1 year by a dominant strain was common. During the study period, 318 patients acquired CPE. The most common species were Klebsiella pneumoniae, Escherichia coli, and Enterobacter spp. In 127 (40%) patients, a contaminated sink was the suspected source of CPE acquisition. For 20 cases with an identical sink-patient strain, temporal relation suggested sink-to-patient transmission. Hybrid assembly of specific sink-patient isolates revealed that shared plasmids were structurally identical, and SNP differences between shared pairs, along with signatures for potential recombination events, suggests recent sharing of the plasmids. CONCLUSIONS: CPE-contaminated sinks are an important source of transmission to patients. Although traditionally person-to-person transmission has been considered the main route of CPE transmission, these data suggest a change in paradigm that may influence strategies of preventing CPE dissemination.

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.

Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts in which infection was transmitted from one to the other - is using the variation of the pathogen within each single host (within-host variation). However, the role of such variation in transmission is understudied due to a lack of experimental and clinical datasets that capture pathogen diversity in both donor and recipient hosts. In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. In this work we show that, beyond the presence and absence of within-host variants, differences arising in the relative abundance of iSNVs (allelic frequency) can infer transmission pairs more precisely. Our approach further highlights the critical role bottlenecks play in reserving the within-host diversity during transmission.

Woody plant encroachment modifies carbonate bedrock: field evidence for enhanced weathering and permeability.

Little is known about the effects of woody plant encroachment-a recent but pervasive phenomenon-on the hydraulic properties of bedrock substrates. Recent work using stream solute concentrations paired with weathering models suggests that woody plant encroachment accelerates limestone weathering. In this field study, we evaluate this hypothesis by examining bedrock in the Edwards Plateau, an extensive karst landscape in Central Texas. We compared a site that has been heavily encroached by woody plants (mainly Quercus fusiformis and Juniperus ashei), with an adjacent site that has been maintained free of encroachment for the past eight decades. Both sites share the same bedrock, as confirmed by trenching, and originally had very few trees, which enabled us to evaluate how encroachment impacted the evolution of hydraulic properties over a period of no more than 80 years. Using in situ permeability tests in boreholes drilled into the weathered bedrock, we found that the mean saturated hydraulic conductivity of the bedrock was higher-by an order of magnitude-beneath woody plants than in the areas where woody plants have been continuously suppressed. Additionally, woody plant encroachment was associated with greater regolith thickness, greater plant rooting depths, significantly lower rock hardness, and a 24-44% increase in limestone matrix porosity. These findings are strong indicators that woody plant encroachment enhances bedrock weathering, thereby amplifying its permeability-a cycle of mutual reinforcement with the potential for substantial changes within a few decades. Given the importance of shallow bedrock for ecohydrological and biogeochemical processes, the broader impacts of woody plant encroachment on weathering rates and permeability warrant further investigation.

Measurement of Magnetic Cavitation Driven by Heat Flow in a Plasma.

We describe the direct measurement of the expulsion of a magnetic field from a plasma driven by heat flow. Using a laser to heat a column of gas within an applied magnetic field, we isolate Nernst advection and show how it changes the field over a nanosecond timescale. Reconstruction of the magnetic field map from proton radiographs demonstrates that the field is advected by heat flow in advance of the plasma expansion with a velocity v_{N}=(6±2)×10^{5} m/s. Kinetic and extended magnetohydrodynamic simulations agree well in this regime due to the buildup of a magnetic transport barrier.

High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients.

Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic exposures. We integrated drug-microbiome associations to predict clinical outcomes in two validation cohorts on the basis of drug exposures alone, suggesting that this approach can generate biologically and clinically relevant insights into how pharmacological exposures can perturb or preserve microbiota composition. The application of a computational method called PARADIGM to a large dataset of cancer patients' longitudinal fecal specimens and detailed daily medication records reveals associations between drug exposures and the intestinal microbiota that recapitulate in vitro findings and are also predictive of clinical outcomes.

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia.

Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted in high-risk enterobacteria. This indicated a competitive interaction that was validated experimentally. Thus, TaxUMAP can chart comprehensive longitudinal microbiome datasets, enabling insights into microbiome effects on human health.

Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations.

BACKGROUND: The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area. METHODS: We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs. RESULTS: We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5-12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections. CONCLUSIONS: We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5-12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread.

Thicketized oak woodlands reduce groundwater recharge.

Woodlands and pastures across the Post Oak Savannas (POS) in Texas have been undergoing thicketization over the last century via encroachment by understory shrubs such as Yaupon (Ilex decidua, Ilex vomitoria) and expansion of eastern redcedar (Juniperus virginiana). Because a large part of POS overlies the Carrizo-Wilcox (CW) aquifer - the third most important aquifer in Texas, there is a strong incentive to identify opportunities to increase groundwater recharge through land management. The purpose of this research is to evaluate the influence of thicketization of post oak (Quercus stellata) stands on deep drainage (DD) in POS. We achieved this by, a) applying chloride mass balance on soil cores, and b) simultaneously monitoring soil moisture in a woodland pasture setting in POS. Four sites representing different vegetation covers were identified for sampling: 1) a thicketized oak woodland paired with an adjacent open site, 2) a woodland mosaic, 3) a pasture and 4) a pine-oak stand paired with an adjacent open site. A total of 24 soil cores to the depth of 260 cm were collected and (soil) pore water chloride concentrations at multiple depths were measured. Soil moisture was monitored at 21 locations, to the depth of 140-260 cm using a neutron moisture meter. Negligible DD was estimated in the thicketized woodland, whereas most open locations recorded 3-18 cm/year and the woodland mosaic 0-1 cm of DD. Soil moisture data, collected from Jul-2020 to Jun-2021 also suggested higher deep drainage fluxes under open areas - with occurrence of sub-surface saturation only under the open areas and never under the woodlands. These results suggest that the thicketization in oak savannas is substantially reducing groundwater recharge. Given the extent of thicketized oak savannas across United States, this could be impacting water budgets and groundwater recharge rates on regional scales.

X-ray imaging and radiation transport effects on cylindrical implosions.

Magnetization of inertial confinement implosions is a promising means of improving their performance, owing to the potential reduction of energy losses within the target and mitigation of hydrodynamic instabilities. In particular, cylindrical implosions are useful for studying the influence of a magnetic field, thanks to their axial symmetry. Here, we present experimental results from cylindrical implosions on the OMEGA-60 laser using a 40-beam, 14.5 kJ, 1.5 ns drive and an initial seed magnetic field of B0 = 30 T along the axes of the targets, compared with reference results without an imposed B-field. Implosions were characterized using time-resolved x-ray imaging from two orthogonal lines of sight. We found that the data agree well with magnetohydrodynamic simulations, once radiation transport within the imploding plasma is considered. We show that for a correct interpretation of the data in these types of experiments, explicit radiation transport must be taken into account.

Cylindrical implosion platform for the study of highly magnetized plasmas at Laser MegaJoule.

Investigating the potential benefits of the use of magnetic fields in inertial confinement fusion experiments has given rise to experimental platforms like the Magnetized Liner Inertial Fusion approach at the Z-machine (Sandia National Laboratories) or its laser-driven equivalent at OMEGA (Laboratory for Laser Energetics). Implementing these platforms at MegaJoule-scale laser facilities, such as the Laser MegaJoule (LMJ) or the National Ignition Facility (NIF), is crucial to reaching self-sustained nuclear fusion and enlarges the level of magnetization that can be achieved through a higher compression. In this paper, we present a complete design of an experimental platform for magnetized implosions using cylindrical targets at LMJ. A seed magnetic field is generated along the axis of the cylinder using laser-driven coil targets, minimizing debris and increasing diagnostic access compared with pulsed power field generators. We present a comprehensive simulation study of the initial B field generated with these coil targets, as well as two-dimensional extended magnetohydrodynamics simulations showing that a 5 T initial B field is compressed up to 25 kT during the implosion. Under these circumstances, the electrons become magnetized, which severely modifies the plasma conditions at stagnation. In particular, in the hot spot the electron temperature is increased (from 1 keV to 5 keV) while the density is reduced (from 40g/cm^{3} to 7g/cm^{3}). We discuss how these changes can be diagnosed using x-ray imaging and spectroscopy, and particle diagnostics. We propose the simultaneous use of two dopants in the fuel (Ar and Kr) to act as spectroscopic tracers. We show that this introduces an effective spatial resolution in the plasma which permits an unambiguous observation of the B-field effects. Additionally, we present a plan for future experiments of this kind at LMJ.

Contrasting effects of native and exotic vegetation on soil infiltrability in the Sonoran Desert.

Invasion by exotic grasses is transforming drylands across the planet, but the ecohydrological feedbacks of such invasions are not fully understood. For example, in the Sonoran Desert, previous studies have shown that buffelgrass (Cenchrus ciliaris) alters the spatial patterns of soil moisture, leading researchers to hypothesize that such alterations are related to the plants' effects on soil infiltrability. To evaluate this hypothesis, we compared field-saturated hydraulic conductivity (Kfs) in a native shrubland with that in a neighboring savanna extensively dominated by exotic buffelgrass. We measured Kfs during the dormant and growing seasons in both canopy and intercanopy zones. We found that Kfs was generally lower during the dormant season than during the growing season. There were no significant differences between sites during the dormant season, and at both sites, Kfs was 6-7 times higher under shrubs than in the intercanopies. During the growing season, Kfs for the exotic intercanopy was comparable to that for shrub cluster edges (140 mm h-1) and was more than twice that for the native intercanopy. Both shrubs and buffelgrass improved Kfs by reducing soil bulk density (thus increasing porosity). Additionally, surface roughness in the exotic intercanopy was nearly 3 times higher than in the native intercanopy. The combination of greater surface roughness and higher infiltration rates during the growing season most likely alters hydrological connectivity in savannas invaded by exotic grasses such as buffelgrass. By capturing portions of the runoff generated in the intercanopy, these grasses reduce runon into shrub patches, with potentially substantial impacts on native vegetation dynamics and stability.

Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.

BACKGROUND: Throughout the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff as well as from the outside community, complicating our ability to resolve transmission chains in order to inform hospital infection control policy. Here we show how the incorporation of sequences from public genomic databases aided genomic surveillance early in the pandemic when circulating viral diversity was limited. METHODS: We sequenced a subset of discarded, diagnostic SARS-CoV-2 isolates between March and May 2020 from Boston Medical Center HCWs and combined this data set with publicly available sequences from the surrounding community deposited in GISAID with the goal of inferring specific transmission routes. RESULTS: Contextualizing our data with publicly available sequences reveals that 73% (95% confidence interval, 63%-84%) of coronavirus disease 2019 cases in HCWs are likely novel introductions rather than nosocomial spread. CONCLUSIONS: We argue that introductions of SARS-CoV-2 into the hospital environment are frequent and that expanding public genomic surveillance can better aid infection control when determining routes of transmission.

Post-operative opioid analgesic prescribing patterns in gynecologic oncology patients following the implementation of a statewide -prescription monitoring and reporting system.

OBJECTIVE: To analyze the effect of the Connecticut Prescription Monitoring and Reporting System (CPMRS) on the number of opioid tablets prescribed to gynecologic oncology patients post-operatively. DESIGN/PARTICIPANTS: This was a retrospective chart review of patients who received surgery for suspicious masses, premalignant, or malignant conditions of uterus, tubes, ovaries, or cervix. Charts were divided into two groups before and after the implementation of an updated prescription monitoring system in July 2016. Quantitative data were collected on the number of opioids prescribed from hospital discharge summaries. Qualitative data included prescription and/or -recommendation of nonopioid analgesics and type of procedure (open versus minimally invasive). Demographic information included age, ethnicity, and insurance coverage. OUTCOMES: We identified a statistically significant, 50 percent decrease in opioid tablets in the After July 2016 group (n = 226) compared with the Before July 2016 group (n = 136) (p < 0.001). As anticipated, fewer opioid tablets were prescribed following minimally invasive procedures compared to open cases (p = 0.007). On examining nonopioid analgesic data, we found more patients received a prescription for nonopioid analgesics in the After July 2016 group compared with the Before July 2016 group (p < 0.001). CONCLUSION: This study confirms a decrease in opioid tablets prescribed to post-operative gynecologic oncology patients since July 2016. This difference cannot be attributed to the implementation of the CPMRS alone, but chronologically relates to updated requirements. Additionally, our results re-emphasize that minimally invasive surgery has a reduced number of prescribed opioids. A multi-institutional study is required with more patients to detail the factors involved in further decreasing opioid prescribing.

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.

Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (Rt) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the Rt of these variants were up to 50% larger than that of other variants. We then use phylogeography to show that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of Alpha were larger than those resulting from Iota introductions. By monitoring the dynamics of individual variants throughout our study period, we demonstrate the importance of routine surveillance in the response to COVID-19.