Evaluation of CD3 and CD8 T-Cell Immunohistochemistry for Prognostication and Prediction of Benefit From Adjuvant Chemotherapy in Early-Stage Colorectal Cancer Within the QUASAR Trial.

PURPOSE: High densities of tumor infiltrating CD3 and CD8 T-cells are associated with superior prognosis in colorectal cancer (CRC). Their value as predictors of benefit from adjuvant chemotherapy is uncertain. PATIENTS AND METHODS: Tumor tissue from 868 patients in the QUASAR trial (adjuvant fluorouracil/folinic acid v observation in stage II/III CRC) was analyzed by CD3 and CD8 immunohistochemistry. Pathologists, assisted by artificial intelligence, calculated CD3 and CD8 cell densities (cells/mm2) in the core tumor (CT) and invasive margin (IM). Participants were randomly partitioned into training and validation sets. The primary outcome was recurrence-free interval (RFI), 2-year RFI for assessment of biomarker-treatment interactions. Maximum-likelihood methods identified optimal high-risk/low-risk group cutpoints in the training set. Prognostic analyses were repeated in the validation set. RESULTS: In the training set, the recurrence rate in the high-risk group was twice that in the low-risk group for all measures (CD3-CT: rate ratio [RR], 2.00, P = .0008; CD3-IM: 2.38, P < .00001; CD8-CT: 2.17, P = .0001; CD8-IM: 2.13, P = .0001). This was closely replicated in the validation set (RR, 1.96, 1.79, 1.72, 1.72, respectively). In multivariate analyses, prognostic effects were similar in colon and rectal cancers, and in stage II and III disease. Proportional reductions in recurrence with adjuvant chemotherapy were of similar magnitude in the high- and low-recurrence risk groups. Combining information from CD3-IM and CD3-CT (CD3 Score) generated high-, intermediate-, and low-risk groups with numbers needed to treat (NNTs) to prevent one disease recurrence being 11, 21, and 36, respectively. CONCLUSION: Recurrence rates in the high-risk CD3/CD8 groups are twice those in the low-risk groups. Proportional reductions with chemotherapy are similar, allowing NNTs derived in QUASAR to be updated using contemporary, nonrandomized data sets.

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.

SNAP: Supportive non-invasive ventilation for acute chest syndrome prevention for hospitalized children with sickle cell disease: Perspectives of patients, parents, and the healthcare team.

RATIONALE: Acute chest syndrome (ACS) often develops during hospitalizations for sickle cell disease (SCD) vaso-occlusive episodes and may be triggered by a combination of chest wall splinting, opioid use, hypoventilation, and atelectasis. In 2017, Boston Medical Center's general pediatric inpatient unit instituted the novel use of bi-level positive airway pressure (BiPAP) as "supportive non-invasive ventilation for ACS prevention" (SNAP) to prevent ACS and respiratory decompensation. OBJECTIVE: The goals of this qualitative study were to identify perceived benefits, harms, facilitators, and barriers to use of SNAP. METHODS: We conducted semi-structured key informant interviews at three sites with different levels of SNAP implementation (Site 1: extensive implementation; Site 2: limited implementation; Site 3: not yet implemented) regarding experiences with and/or perceptions of SNAP. Interviews and coding were guided by the Promoting Action on Research Implementation in Health Services (PARiHS) framework. RESULTS: Thirty-four participants (physicians, nurses, respiratory therapists, child life specialists, psychologists, youth with SCD, and parents) completed interviews. Major themes included: (i) participants perceive BiPAP as effective at preventing ACS, and for those with medically stable ACS, for preventing respiratory decompensation. (ii) BiPAP use is appropriate on the general pediatric inpatient unit for medically stable patients with SCD. (iii) Improving the patient experience is the most important factor to optimize acceptance of BiPAP by patients and families. CONCLUSION/FUTURE DIRECTIONS: SNAP is perceived as effective and appropriate for hospitalized pediatric patients with SCD. Improving the patient experience is the biggest challenge. These data will inform a future protocol for a multicenter hybrid effectiveness/implementation trial of SNAP.

Benefit-Cost Analysis of the HHS COVID-19 Campaign: April 2021-March 2022.

INTRODUCTION: This study estimated the benefits and costs of the U.S. Department of Health and Human Services' We Can Do This COVID-19 public education campaign (the Campaign) and associated vaccination-related impacts. METHODS: Weekly media market and national Campaign expenditures were used to estimate weekly first-dose vaccinations that would not have occurred absent the Campaign, weekly Campaign-attributed complete vaccinations, and corresponding COVID-19 cases, hospitalizations, and deaths averted. Benefits were valued using estimated morbidity and mortality reductions and associated values of a statistical life and a statistical case. Costs were estimated using Campaign paid media expenditures and corresponding vaccination costs. The net Campaign and vaccination benefit and return on investment were calculated. Analyses were conducted from 2022 to 2024. RESULTS: Between April 2021 and March 2022, an estimated 55.9 million doses of COVID-19 vaccines would not have been administered absent the Campaign. Campaign-attributed vaccinations resulted in 2,576,133 fewer mild COVID-19 cases, 243,979 fewer nonfatal COVID-19 hospitalizations, and 51,675 lives saved from COVID-19. The total Campaign benefit was $740.2 billion, and Campaign and vaccination costs totaled $8.3 billion, with net benefits of approximately $732.0 billion. For every $1 spent, the Campaign and corresponding vaccination costs resulted in benefits of approximately $89.54. CONCLUSIONS: The We Can Do This COVID-19 public education campaign saved more than 50,000 lives and prevented hundreds of thousands of hospitalizations and millions of COVID-19 cases, representing hundreds of billions of dollars in benefits in less than one year. Findings suggest that public education campaigns are a cost-effective approach to reducing COVID-19 morbidity and mortality.

Effects of the Marek's Disease Vaccine on the Performance, Meat Yield, and Incidence of Woody Breast Myopathy in Ross 708 Broilers When Administered Alone or in Conjunction with In ovo and Dietary Supplemental 25-Hydroxycholecalciferol.

The effects of the Marek's disease vaccine (MDV) on the live performance, breast meat yield, and incidence of woody breast myopathy (WBM) of Ross 708 broilers were investigated when administered alone or in conjunction with in ovo and dietary supplemental 25-hydroxycholecalciferol (25OHD3). At 18 d of incubation (doi), four in ovo injection treatments were randomly assigned to live embryonated Ross 708 broiler hatching eggs: (1) non-injected; (2) commercial MDV alone; or MDV containing either (3) 1.2 or (4) 2.4 µg of 25OHD3. An Inovoject multi-egg injector was used to inject a 50 µL solution volume into each egg. The birds were provided a commercial diet that contained 250 IU of cholecalciferol/kg of feed (control) or a commercial diet that was supplemented with an additional 2760 IU of 25OHD3/kg of feed (HyD-diet). In the growout period, 14 male broilers were placed in each of 48 floor pens resulting 6 replicated pens per in ovo x dietary treatment combination. Live performance variable were measured at each dietary phases from 0 to 14, 15 to 28, and 29 to 40 d of age (doa). At 14 and 40 doa, pectoralis major (P. major) and pectoralis minor (P. minor) muscles were determined for one bird within each of the six replicate pens. At 41 doa, WBM incidence was determined. No significant main or interaction effects occurred for WBM among the dietary or in ovo injection treatments. However, in response to in ovo 25OHD3 supplementation, BW and BWG in the 29 to 40 doa period and BWG and FCR in the 0 to 40 doa period improved. In addition, at 40 and 41 doa, breast meat yield increased in response to in ovo and dietary 25OHD3 supplementation. Future research is needed to determine the possible reasons that may have been involved in the aforementioned improvements.

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.

Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality.

Single-cell RNA sequencing (scRNA-seq) technologies are instrumental to improving our understanding of virus-host interactions in cell culture infection studies and complex biological systems because they allow separating the transcriptional signatures of infected versus non-infected bystander cells. A drawback of using biosafety level (BSL) 4 pathogens is that protocols are typically developed without consideration of virus inactivation during the procedure. To ensure complete inactivation of virus-containing samples for downstream analyses, an adaptation of the workflow is needed. Focusing on a commercially available microfluidic partitioning scRNA-seq platform to prepare samples for scRNA-seq, we tested various chemical and physical components of the platform for their ability to inactivate Nipah virus (NiV), a BSL-4 pathogen that belongs to the group of nonsegmented negative-sense RNA viruses. The only step of the standard protocol that led to NiV inactivation was a 5 min incubation at 85 °C. To comply with the more stringent biosafety requirements for BSL-4-derived samples, we included an additional heat step after cDNA synthesis. This step alone was sufficient to inactivate NiV-containing samples, adding to the necessary inactivation redundancy. Importantly, the additional heat step did not affect sample quality or downstream scRNA-seq results.

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.

Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these predictions vary, however, and they do not take into account ligands, covalent modifications or other environmental factors. Here, we evaluate how well AlphaFold predictions can be expected to describe the structure of a protein by comparing predictions directly with experimental crystallographic maps. In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses. We further suggest that it is important to consider the confidence in prediction when interpreting AlphaFold predictions and to carry out experimental structure determination to verify structural details, particularly those that involve interactions not included in the prediction.

The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.

Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Šfor both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Šboth the procedures and their validation break down and do not ensure reliably correct models. This is because in the broad density at lower resolution, critical features such as protein backbone carbonyl O atoms are not just less accurate but are not seen at all, and so peptide orientations are frequently wrongly fitted by 90-180°. This puts both backbone and side chains into the wrong local energy minimum, and they are then worsened rather than improved by further refinement into a valid but incorrect rotamer or Ramachandran region. On the positive side, new tools are being developed to locate this type of pernicious error in PDB depositions, such as CaBLAM, EMRinger, Pperp diagnosis of ribose puckers, and peptide flips in PDB-REDO, while interactive modeling in Coot or ISOLDE can help to fix many of them. Another positive trend is that artificial intelligence predictions such as those made by AlphaFold2 contribute additional evidence from large multiple sequence alignments, and in high-confidence parts they provide quite good starting models for loops, termini or whole domains with otherwise ambiguous density.

Estimating County Level Health Indicators Using Spatial Microsimulation.

Given the importance of understanding health outcomes at fine spatial scales, iterative proportional fitting (IPF), a form of small area estimation, was applied to a fixed number of health-related variables (obesity, overweight, diabetes) taken from regionalized 2019 survey responses (n = 5474) from the Idaho Behavioral Risk Factor Surveillance System (BRFSS). Using associated county-level American Community Survey (ACS) census data, a set of constraints, which included age categorization, race, sex, and education level, were used to create county-level weighting matrices for each variable, for each of the seven (7) Idaho public health districts. Using an optimized modeling construction technique, we identified significant constraints and grouping splits for each variable/region, resulting in estimates that were internally and externally validated. Externally validated model results for the most populated counties showed correlations ranging from .79 to .85, with p values all below .05. Estimates indicated higher levels of obesity and overweight individuals for midsouth and southwestern Idaho counties, with a cluster of higher diabetes estimates in the center of the state (Gooding, Lincoln, Minidoka, and Jerome counties). Alternative external sources for health outcomes aligned extremely well with our estimates, with wider confidence intervals in more rural counties with sparse populations.

Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer.

PURPOSE: High tumor production of the EGFR ligands, amphiregulin (AREG) and epiregulin (EREG), predicted benefit from anti-EGFR therapy for metastatic colorectal cancer (mCRC) in a retrospective analysis of clinical trial data. Here, AREG/EREG IHC was analyzed in a cohort of patients who received anti-EGFR therapy as part of routine care, including key clinical contexts not investigated in the previous analysis. EXPERIMENTAL DESIGN: Patients who received panitumumab or cetuximab ± chemotherapy for treatment of RAS wild-type mCRC at eight UK cancer centers were eligible. Archival formalin-fixed paraffin-embedded tumor tissue was analyzed for AREG and EREG IHC in six regional laboratories using previously developed artificial intelligence technologies. Primary endpoints were progression-free survival (PFS) and overall survival (OS). RESULTS: A total of 494 of 541 patients (91.3%) had adequate tissue for analysis. A total of 45 were excluded after central extended RAS testing, leaving 449 patients in the primary analysis population. After adjustment for additional prognostic factors, high AREG/EREG expression (n = 360; 80.2%) was associated with significantly prolonged PFS [median: 8.5 vs. 4.4 months; HR, 0.73; 95% confidence interval (CI), 0.56-0.95; P = 0.02] and OS [median: 16.4 vs. 8.9 months; HR, 0.66 95% CI, 0.50-0.86; P = 0.002]. The significant OS benefit was maintained among patients with right primary tumor location (PTL), those receiving cetuximab or panitumumab, those with an oxaliplatin- or irinotecan-based chemotherapy backbone, and those with tumor tissue obtained by biopsy or surgical resection. CONCLUSIONS: High tumor AREG/EREG expression was associated with superior survival outcomes from anti-EGFR therapy in mCRC, including in right PTL disease. AREG/EREG IHC assessment could aid therapeutic decisions in routine practice. See related commentary by Randon and Pietrantonio, p. 4021.

Recalled Exposure to COVID-19 Public Education Campaign Advertisements Predicts COVID-19 Vaccine Confidence.

This study examined the relationship between recalled exposure to the We Can Do This COVID-19 Public Education Campaign (the Campaign) and COVID-19 vaccine confidence (the likelihood of vaccination or vaccine uptake) in the general population, including vaccine-hesitant adults (the "Movable Middle"). Analyses used three waves of a triannual, nationally representative panel survey of adults in the U.S. fielded from January to November 2021 (n = 3,446). Proportional odds regression results demonstrated a positive, statistically significant relationship between past 4-month Campaign recall and vaccine confidence, controlling for lagged reports of Campaign recall and vaccine confidence; concurrent and lagged fictional campaign recall; survey wave; and sociodemographics. Results indicated that as one moves from no Campaign recall to infrequent recall, there is a 29% increase in the odds of being in a higher vaccine confidence category. Findings offer evidence of the impact of a COVID-19 public education campaign on increasing vaccine confidence.

The Initial Relationship Between the United States Department of Health and Human Services' Digital COVID-19 Public Education Campaign and Vaccine Uptake: Campaign Effectiveness Evaluation.

BACKGROUND: Over 1 million people in the United States have died of COVID-19. In response to this public health crisis, the US Department of Health and Human Services launched the We Can Do This public education campaign in April 2021 to increase vaccine confidence. The campaign uses a mix of digital, television, print, radio, and out-of-home channels to reach target audiences. However, the impact of this campaign on vaccine uptake has not yet been assessed. OBJECTIVE: We aimed to address this gap by assessing the association between the We Can Do This COVID-19 public education campaign's digital impressions and the likelihood of first-dose COVID-19 vaccination among US adults. METHODS: A nationally representative sample of 3642 adults recruited from a US probability panel was surveyed over 3 waves (wave 1: January to February 2021; wave 2: May to June 2021; and wave 3: September to November 2021) regarding COVID-19 vaccination, vaccine confidence, and sociodemographics. Survey data were merged with weekly paid digital campaign impressions delivered to each respondent's media market (designated market area [DMA]) during that period. The unit of analysis was the survey respondent-broadcast week, with respondents nested by DMA. Data were analyzed using a multilevel logit model with varying intercepts by DMA and time-fixed effects. RESULTS: The We Can Do This digital campaign was successful in encouraging first-dose COVID-19 vaccination. The findings were robust to multiple modeling specifications, with the independent effect of the change in the campaign's digital dose remaining practically unchanged across all models. Increases in DMA-level paid digital campaign impressions in a given week from -30,000 to 30,000 increased the likelihood of first-dose COVID-19 vaccination by 125%. CONCLUSIONS: Results from this study provide initial evidence of the We Can Do This campaign's digital impact on vaccine uptake. The size and length of the Department of Health and Human Services We Can Do This public education campaign make it uniquely situated to examine the impact of a digital campaign on COVID-19 vaccination, which may help inform future vaccine communication efforts and broader public education efforts. These findings suggest that campaign digital dose is positively associated with COVID-19 vaccination uptake among US adults; future research assessing campaign impact on reduced COVID-19-attributed morbidity and mortality and other benefits is recommended. This study indicates that digital channels have played an important role in the COVID-19 pandemic response. Digital outreach may be integral in addressing future pandemics and could even play a role in addressing nonpandemic public health crises.

Accelerating crystal structure determination with iterative AlphaFold prediction.

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold. Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of Cα atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

Personalizing neoadjuvant chemotherapy for locally advanced colon cancer: protocols for the international phase III FOxTROT2 and FOxTROT3 randomized controlled trials.

AIM: FOxTROT1 established a new standard of care for managing locally advanced colon cancer (CC) with neoadjuvant chemotherapy (NAC). Six weeks of neoadjuvant oxaliplatin and fluoropyrimidine (OxFp) chemotherapy was associated with greater 2-year disease-free survival (DFS) when compared with proceeding straight to surgery (STS). There is now a need to refine the use of NAC and identify those most likely to benefit. FOxTROT2 will aim to investigate NAC in older adults and those with frailty. FOxTROT3 will aim to assess whether intensified triplet NAC provides additional benefits over OxFp. METHOD: FOxTROT2 and FOxTROT3 are international, open-label, phase III randomized controlled trials. Eligible patients will be identified by the multidisciplinary team. Patient age, frailty and comorbidities will be considered to guide trial entry. Participants will be randomized 2:1 to the intervention or control arm: 6 weeks of dose-adapted neoadjuvant OxFp versus STS in FOxTROT2 and 6 weeks of neoadjuvant modified oxaliplatin, 5-fluorouracil and irinotecan versus OxFp in FOxTROT3. The primary endpoint in FOxTROT2 is 3-year DFS. In FOxTROT3, tumour regression grade and 3-year DFS are co-primary endpoints. DISCUSSION: FOxTROT2 and FOxTROT3 will establish the FOxTROT platform, a key part of our long-term strategy to develop neoadjuvant treatments for CC. FOxTROT2 will investigate NAC in a population under-represented in FOxTROT1 and wider research. FOxTROT3 will assess whether it is possible to induce greater early tumour responses and whether this translates to superior long-term outcomes. Looking ahead, the FOxTROT platform will facilitate further trial comparisons and extensive translational research to optimize the use of NAC in CC.

Hepatitis of unknown aetiology in children - epidemiological overview of cases reported in Europe, 1 January to 16 June 2022.

Following the report of an excess in paediatric cases of severe acute hepatitis of unknown aetiology by the United Kingdom (UK) on 5 April 2022, 427 cases were reported from 20 countries in the World Health Organization European Region to the European Surveillance System TESSy from 1 January 2022 to 16 June 2022. Here, we analysed demographic, epidemiological, clinical and microbiological data available in TESSy. Of the reported cases, 77.3% were 5 years or younger and 53.5% had a positive test for adenovirus, 10.4% had a positive RT-PCR for SARS-CoV-2 and 10.3% were coinfected with both pathogens. Cases with adenovirus infections were significantly more likely to be admitted to intensive care or high-dependency units (OR = 2.11; 95% CI: 1.18-3.74) and transplanted (OR = 3.36; 95% CI: 1.19-9.55) than cases with a negative test result for adenovirus, but this was no longer observed when looking at this association separately between the UK and other countries. Aetiological studies are needed to ascertain if adenovirus plays a role in this possible emergence of hepatitis cases in children and, if confirmed, the mechanisms that could be involved.

Impact of meningococcal ACWY conjugate vaccines on pharyngeal carriage in adolescents: evidence for herd protection from the UK MenACWY programme.

OBJECTIVE: Serogroup W and Y invasive meningococcal disease increased globally from 2000 onwards. Responding to a rapid increase in serogroup W clonal complex 11 (W:cc11) invasive meningococcal disease, the UK replaced an adolescent booster dose of meningococcal C conjugate vaccine with quadrivalent MenACWY conjugate vaccine in 2015. By 2018, the vaccine coverage in the eligible school cohorts aged 14 to 19 years was 84%. We assessed the impact of the MenACWY vaccination programme on meningococcal carriage. METHODS: An observational study of culture-defined oropharyngeal meningococcal carriage prevalence before and after the start of the MenACWY vaccination programme in UK school students, aged 15 to 19 years, using two cross-sectional studies: 2014 to 2015 "UKMenCar4" and 2018 "Be on the TEAM" (ISRCTN75858406). RESULTS: A total of 10 625 participants preimplementation and 13 438 postimplementation were included. Carriage of genogroups C, W, and Y (combined) decreased from 2.03 to 0.71% (OR 0.34 [95% CI 0.27-0.44], p < 0.001). Carriage of genogroup B meningococci did not change (1.26% vs 1.23% [95% CI 0.77-1.22], p = 0.80) and genogroup C remained rare (n = 7/10 625 vs 17/13 438, p = 0.135). The proportion of serogroup positive isolates (i.e. those expressing capsule) decreased for genogroup W by 53.8% (95% CI -5.0 - 79.8, p = 0.016) and for genogroup Y by 30.1% (95% CI 8.946·3, p = 0.0025). DISCUSSION: The UK MenACWY vaccination programme reduced carriage acquisition of genogroup and serogroup Y and W meningococci and sustained low levels of genogroup C carriage. These data support the use of quadrivalent MenACWY conjugate vaccine for indirect (herd) protection.

The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues.

We have curated a high-quality, "best-parts" reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically acceptable model conformation. The resulting prefiltered data typically contain the entire core of each chain, in quite long continuous fragments. Each reference file is a single protein chain, and the total set of files were selected for low redundancy, high resolution, good MolProbity score, and other chain-level criteria. Then each residue was critically tested for adequate local map quality to firmly support its conformation, which must also be free of serious clashes or covalent-geometry outliers. The resulting Top2018 prefiltered datasets have been released on the Zenodo online web service and are freely available for all uses under a Creative Commons license. Currently, one dataset is residue filtered on main chain plus Cß atoms, and a second dataset is full-residue filtered; each is available at four different sequence-identity levels. Here, we illustrate both statistics and examples that show the beneficial consequences of residue-level filtering. That process is necessary because even the best of structures contain a few highly disordered local regions with poor density and low-confidence conformations that should not be included in reference data. Therefore, the open distribution of these very large, prefiltered reference datasets constitutes a notable advance for structural bioinformatics and the fields that depend upon it.

Atraumatic Medullary Osteonecrosis of the Tibia and Femur Treated With Intraosseous Orthobiologics.

Osteonecrosis (ON) is a painful condition involving bony cell death with resultant architectural collapse. This report discusses the case of a 50-year-old Caucasian female who presented to an outpatient musculoskeletal clinic with severe chronic left knee pain. She had a history of ulcerative colitis and resultant chronic corticosteroid exposure with subsequent development of knee ON. She was treated with an intraosseous autologous bone marrow concentrate (BMC), demineralized bone matrix (DBM), and platelet-rich plasma (PRP) injection. At 11 months post-injection, she demonstrated a significant improvement in pain scores, mobility, activity, and decreased narcotic use. Intraosseous orthobiologic injection for the treatment of knee ON is a promising procedure with a reasonable safety profile that warrants further study as an alternative to surgical intervention.