NeighborNet: improved algorithms and implementation

NeighborNet constructs phylogenetic networks to visualize distance data. It is a popular method used in a wide range of applications. While several studies have investigated its mathematical features, here we focus on computational aspects. The algorithm operates in three steps. We present a new simplified formulation of the first step, which aims at computing a circular ordering. We provide the first technical description of the second step, the estimation of split weights. We review the third step by constructing and drawing the network. Finally, we discuss how the networks might best be interpreted, review related approaches, and present some open questions.

Compression strategies for large-scale electrophysiology data

Objective.With the rapid adoption of high-density electrode arrays for recording neural activity, electrophysiology data volumes within labs and across the field are growing at unprecedented rates. For example, a one-hour recording with a 384-channel Neuropixels probe generates over 80 GB of raw data. These large data volumes carry a high cost, especially if researchers plan to store and analyze their data in the cloud. Thus, there is a pressing need for strategies that can reduce the data footprint of each experiment.Approach.Here, we establish a set of benchmarks for comparing the performance of various compression algorithms on experimental and simulated recordings from Neuropixels 1.0 (NP1) and 2.0 (NP2) probes.Main results.For lossless compression, audio codecs (FLACandWavPack) achieve compression ratios (CRs) 6% higher for NP1 and 10% higher for NP2 than the best general-purpose codecs, at the expense of decompression speed. For lossy compression, theWavPackalgorithm in 'hybrid mode' increases the CR from 3.59 to 7.08 for NP1 and from 2.27 to 7.04 for NP2 (compressed file size of ∼14% for both types of probes), without adverse effects on spike sorting accuracy or spike waveforms.Significance.Along with the tools we have developed to make compression easier to deploy, these results should encourage all electrophysiologists to apply compression as part of their standard analysis workflows.

No increase in adverse events with lateral extra-articular tenodesis augmentation of anterior cruciate ligament reconstruction - Results from the stability randomized trial

OBJECTIVES

Results from the Stability Study suggest that adding a lateral extra-articular tenodesis (LET) to a hamstring tendon autograft reduces the rate of anterior cruciate ligament reconstruction (ACLR) failure in high-risk patients. The purpose of this study is to report adverse events over the 2-year follow-up period and compare groups (ACLR alone vs. ACLR + LET).

METHODS

Stability is a randomized clinical trial comparing hamstring tendon ACLR with and without LET. Patients aged 14-25 years with an ACL deficient knee were included. Patients were followed and adverse events documented (type, actions taken, resolution) with visits at 3, 6, 12, and 24 months postoperatively. Adverse events were categorized as none, minor medical, minor surgical, contralateral ACL rupture, or graft rupture. Patient reported outcome measures (PROMs) collected at each visit included the Knee Injury and Osteoarthritis Outcome Score (KOOS), International Knee Documentation Committee Score (IKDC), and ACL Quality of Life Questionnaire (ACL-QOL).

RESULTS

In total, 618 patients were randomized (mean age 18.9 years, 302 (49%) male). Forty-five patients (7%) suffered graft rupture; 34 (11%) in the ACLR group compared to 11 (4%) in the ACLR + LET group (RRR = 0.67, 95% CI 0.36 to 0.83, p < 0.001). There were no differences in effusion or infection rates between groups. The ACLR + LET group experienced an increased number of hardware removals (10 vs. 4). Overall, the rate of minor medical events (11%), minor surgical events (7%), and ipsilateral or contralateral ACL tears (10%) were low considering the high-risk patient profile. Increasing severity of adverse events was associated with lower PROMs at 24 months post-operative. Patients in the ACLR + LET group reported greater degree of pain at 3 months only. There were no clinically significant differences in range of motion between groups.

CONCLUSIONS

The addition of LET to hamstring tendon autograft ACLR in young patients at high risk of re-injury resulted in a statistically significant reduction in graft rupture. While the addition of LET may increase rates of hardware irritation, there was no significant increase in overall rates of minor medical adverse events, minor surgical events, or overall re-operation rates. The concerns regarding complications associated with a LET did not materialize in this study.

LEVEL OF EVIDENCE

Level I.

Diversities and the Generalized Circumradius

The generalized circumradius of a set of points A ⊆ R d with respect to a convex body K equals the minimum value of λ ≥ 0 such that a translate of λ K contains A. Each choice of K gives a different function on the set of bounded subsets of R d ; we characterize which functions can arise in this way. Our characterization draws on the theory of diversities, a recently introduced generalization of metrics from functions on pairs to functions on finite subsets. We additionally investigate functions which arise by restricting the generalized circumradius to a finite subset of R d . We obtain elegant characterizations in the case that K is a simplex or parallelotope.

Analysis of concordance between microsatellite instability by next generation sequencing (NGS-MSI) and mismatch repair deficiency by immunohistochemistry (IHC-MMR) in >28,000 colorectal tumors

30

Background: The use of immune checkpoint inhibitors (ICI) in MSI-H/MMRd CRC patients has profoundly changed the treatment landscape in the metastatic setting; the most recent NICHE-2 trial showed 100% response rate in MSI-H/MMRd locally advanced CRC patients treated with neoadjuvant ICI, further highlighting the importance of identifying these patients accurately to enhance patient care. Here we report the concordance of NGS-MSI and IHC-MMR from a very large cohort of CRC tumors and study the molecular characteristics and clinical outcomes of these patients. Methods: A total of 28,105 CRC tumors were analyzed by NGS (592 genes, NextSeq or WES, NovaSeq) and IHC. MMRd was defined as complete loss of ≥1 IHC stains (MLH1, MSH2, MSH6, or PMS2) and proficient (MMRp) as any positive staining for all four proteins. MSI status was determined from over 7,000 target microsatellite loci covered by NGS. Central pathology review (CPR) of MMR IHC was done on 73 cases with discordant MMR/MSI results. Real-world overall survival was obtained from insurance claims and calculated from either tissue collection or treatment start to last contact; Kaplan-Meier estimates were calculated for molecularly defined patients. Results: For CRC tumors with NGS and IHC, 28031/28105 were concordant (99.74%), 0.09% were MMRd/MSS, and 0.2% were MMRp/MSI-H. After CPR, 23/24 (96%) of MMRd/MSS cases and 46/49 (94%) of MMRp/MSI-H were confirmed. Of the 46 post-CPR MMRp/MSI-H CRC samples, 52% had ≥1 pathogenic missense mutation in including MLH1/PMS2/MSH2/6 or MLH3, MSH3, PMS1 or POLE. Of the 23 post-CPR MMRd/MSS CRC samples, 38% had MLH1 loss, 91% PMS2 loss, no MSH2 loss and 9% MSH6 loss. When comparing clinical outcomes with concordant MSS/MMRp tumors, concordant MSI-H/MMRd patients had significantly longer OS (HR=1.131 [95% CI: 1.02-1.254], p<0.001) and post-ICI survival (HR= 2.695 [95% CI: 1.932-3.76], p<0.001). Compared to MSS/MMRd tumors (N=21), MSI-H/MMRp (N=29) trends to have longer OS (HR=2.163, [95% CI: 0.939-4.983], p=0.064) and insufficient ICI-treated patients were available for analysis. Conclusions: Here we report from >28,000 CRC tumors that the concordance of IHC-MMR/NGS-MSI is 99.74%. Clinical outcome from a large cohort of patients show NGS is not inferior compared to IHC in identifying patients with MSI-H/MMRd. The additional lens that NGS-MSI offers is of value in identifying CRC patients who may benefit from ICI therapy. [Table: see text]

Dimorphic glioblastoma with glial and epithelioid phenotypes: Clonal evolution and immune selection

Purpose

Epithelioid glioblastoma is an unusual histologic variant of malignant glioma. The present study investigates both the genomic and transcriptomic determinants that may promote the development of this tumor.

Methods

Whole-exome sequencing (WES) and whole-transcriptome sequencing (WTS) were performed on an epithelioid glioblastoma, along with a specific bioinformatic pipeline to generate electronic karyotyping and investigate the tumor immune microenvironment. Microdissected sections containing typical glioblastoma features and epithelioid morphology were analyzed separately using the same methodologies.

Results

An epithelioid glioblastoma, with immunopositivity for GFAP, Olig-2, and ATRX but negative for IDH-1 and p53, was identified. The tumor cell content from microdissection was estimated to be 85-90% for both histologic tumor components. WES revealed that both glioma and epithelioid sections contained identical point mutations in PTEN, RB1, TERT promoter, and TP53. Electronic karyotype analysis also revealed similar chromosomal copy number alterations, but the epithelioid component showed additional abnormalities that were not found in the glioblastoma component. The tumor immune microenvironments were strikingly different and WTS revealed high levels of transcripts from myeloid cells as well as M1 and M2 macrophages in the glioma section, while transcripts from CD4+ lymphocytes and NK cells predominated in the epithelioid section.

Conclusion

Epithelioid glioblastoma may be genomically more unstable and oncogenically more advanced, harboring an increased number of mutations and karyotype abnormalities, compared to typical glioblastomas. The tumor immune microenvironment is also different.

Parsimony and the rank of a flattening matrix

The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for one set A of taxa and columns corresponding to all site patterns for another set B of taxa. Flattenings have been used to prove difficult results relating to phylogenetic invariants and consistency and also form the basis of several methods of phylogenetic inference. We prove that the rank of the flattening equals [Formula: see text], where r is the number of states and [Formula: see text] is the minimum size of a vertex cut separating A from B. When T is binary the rank of the flattening equals [Formula: see text] where [Formula: see text] equals the parsimony length of the binary character separating A and B. We provide a direct proof that requires little more than undergraduate algebra, but note that the formula could also be derived from work by Casanellas and Fernández-Sánchez (2011) on phylogenetic invariants.

Genetic manipulation of Lactobacillus to produce optically pure lactic acid following fermentation using hydrolysed organic fraction of municipal solid waste as a feedstock

Background

Lactic acid for polymer applications must be optically pure to allow the final plastic properties to be controlled. We have isolated a strain of Lactobacillus plantarum capable of utilising a range of carbohydrates and tolerant to high sugar and organic acid concentrations. However, like most Lactobacillus plantarum, this strain produces D- and L-lactic acid. To improve the commercial application of this strain gene editing has been used to ensure only one isoform is produced.

Methods

Using two-step homologous recombination, ldhL was replaced with a truncated version interrupted by a chloramphenicol acetyltransferase resistance marker, then with an unmarked truncated version.

The optical purity shift was quantified biochemically by enzymatic assay and HPLC and fermentation performance compared against the unmodified strain using enzymatically hydrolysed municipal solid waste pulp (MSW sugars) as a feedstock.

Results

The ldhL gene was successfully deleted, leading to a dramatic shift in the optical purity of lactate produced in both synthetic media and MSW sugars. The unmodified strain produced D-lactic acid with an optical purity of 40%, while the mutant achieved 94%. In MSW sugars, the modified strain performed as well as the unmodified control, consuming all available glucose in less than 48 hours with a volumetric productivity of 1.02 g/L/h.

Conclusions

Deletion of ldhL from our strain of Lactobacillus plantarum allowed exclusive production of D-lactic acid from MSW sugars. This provides a laboratory scale demonstration of the production of optically pure lactic acid from renewable sugars for use in the production of biodegradable plastics.

Discrete coalescent trees

In many phylogenetic applications, such as cancer and virus evolution, time trees, evolutionary histories where speciation events are timed, are inferred. Of particular interest are clock-like trees, where all leaves are sampled at the same time and have equal distance to the root. One popular approach to model clock-like trees is coalescent theory, which is used in various tree inference software packages. Methodologically, phylogenetic inference methods require a tree space over which the inference is performed, and the geometry of this space plays an important role in statistical and computational aspects of tree inference algorithms. It has recently been shown that coalescent tree spaces possess a unique geometry, different from that of classical phylogenetic tree spaces. Here we introduce and study a space of discrete coalescent trees. They assume that time is discrete, which is natural in many computational applications. This tree space is a generalisation of the previously studied ranked nearest neighbour interchange space, and is built upon tree-rearrangement operations. We generalise existing results about ranked trees, including an algorithm for computing distances in polynomial time, and in particular provide new results for both the space of discrete coalescent trees and the space of ranked trees. We establish several geometrical properties of these spaces and show how these properties impact various algorithms used in phylogenetic analyses. Our tree space is a discretisation of a previously introduced time tree space, called t-space, and hence our results can be used to approximate solutions to various open problems in t-space.

1463 One Urology Unit’s Experience With Holmium Laser Enucleation Of The Prostate(Holep)

Introduction

Holmium laser enucleation of the prostate (HoLEP) is a minimally invasive procedure for the management of Benign Prostatic Hyperplasia and Bladder Outlet Obstruction. The European Associations of Urologists (EAU) recommend HoLEP should be offered to patients with prostates measuring &gt;30cc or who are anticoagulated

Aim

To review the outcomes of one-unit HoLEP procedures. Comparing the first third of patients to the final third of patients in a 183-patient cohort.

Method

We collected data retrospectively over 44-month period from 183 patients using electronic patient records. Outcomes measured; length of stay (los), length of time for catheter. Length of time of procedure. comparing the 1st 61 patient with the last 61 patients and reviewed rates of complications from HoLEP using the Clavien-Dindo classification

Results

The mean size of prostate was 83cc. 149 (81%) of patients had a LOS of £ 1 day. The mean length of catheter time 3.44 days. Mean length of operating time – 71 minutes. Length of time for the 1st 61 patients was 70.2 minutes compared with 73.1 minutes for last 61 patients. With regards to complications, 8 patient had Grade 3 however 0 patients had grade 4 or 5.

Conclusions

Patients undergo HoLEP procedure with Prostate size in keeping with EAU. This unit has a short length of stay post-op with low complication rate. HoLEP has a short post op catheter time.

Microbial Phylogenetic Context Using Phylogenetic Outlines

Microbial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference genomes. We provide a new interactive graphical tool that addresses this task using Mash sketches to compare against all bacterial and archaeal representative genomes in the Genome Taxonomy Database taxonomy, all within the framework of SplitsTree5. The phylogenetic context of the query sequences is then displayed as a phylogenetic outline, a new type of phylogenetic network that is more general than a phylogenetic tree, but significantly less complex than other types of phylogenetic networks. We propose to use such networks, rather than trees, to represent phylogenetic context, because they can express uncertainty in the placement of taxa, whereas a tree must always commit to a specific branching pattern. We illustrate the new method using a number of draft genomes of different assembly quality.

Questioning COVID-19 Surface Stability and Fomite Spreading in Three Aeromedical Cases: A Case Series

It is well established that coronavirus disease 2019 is primarily transmitted through respiratory droplets, and there is mounting research speculation that it may also be transmitted via fomites. Several studies have shown that the virus can persist on both porous and nonporous surfaces for hours to days, depending upon the material. This article examines three cases of polymerase chain reaction–proven severe acute respiratory syndrome coronavirus 2 infection with several additional individuals meeting CDC close contact criteria. In 1 case, 195 downstream contacts were all tested to prevent a mass outbreak in a deployment posture. Analysis of these contacts yielded only a single positive test, which could be reasonably ascribed to respiratory droplet transmission. While these cases and their contacts ultimately represent a small sample size, we suggest fomite spread may not be a significant means of transmission for severe acute respiratory syndrome coronavirus 2 in real-world operational scenarios.

GHRH secretion from a pancreatic neuroendocrine tumor causing gigantism in a patient with MEN1

SUMMARY

A male patient with a germline mutation in MEN1 presented at the age of 18 with classical features of gigantism. Previously, he had undergone resection of an insulin-secreting pancreatic neuroendocrine tumour (pNET) at the age of 10 years and had subtotal parathyroidectomy due to primary hyperparathyroidism at the age of 15 years. He was found to have significantly elevated serum IGF-1, GH, GHRH and calcitonin levels. Pituitary MRI showed an overall bulky gland with a 3 mm hypoechoic area. Abdominal MRI showed a 27 mm mass in the head of the pancreas and a 6 mm lesion in the tail. Lanreotide-Autogel 120 mg/month reduced GHRH by 45% and IGF-1 by 20%. Following pancreaticoduodenectomy, four NETs were identified with positive GHRH and calcitonin staining and Ki-67 index of 2% in the largest lesion. The pancreas tail lesion was not removed. Post-operatively, GHRH and calcitonin levels were undetectable, IGF-1 levels normalised and GH suppressed normally on glucose challenge. Post-operative fasting glucose and HbA1c levels have remained normal at the last check-up. While adolescent-onset cases of GHRH-secreting pNETs have been described, to the best of our knowledge, this is the first reported case of ectopic GHRH in a paediatric setting leading to gigantism in a patient with MEN1. Our case highlights the importance of distinguishing between pituitary and ectopic causes of gigantism, especially in the setting of MEN1, where paediatric somatotroph adenomas causing gigantism are extremely rare.

LEARNING POINTS

It is important to diagnose gigantism and its underlying cause (pituitary vs ectopic) early in order to prevent further growth and avoid unnecessary pituitary surgery. The most common primary tumour sites in ectopic acromegaly include the lung (53%) and the pancreas (34%) (1): 76% of patients with a pNET secreting GHRH showed a MEN1 mutation (1). Plasma GHRH testing is readily available in international laboratories and can be a useful diagnostic tool in distinguishing between pituitary acromegaly mediated by GH and ectopic acromegaly mediated by GHRH. Positive GHRH immunostaining in the NET tissue confirms the diagnosis. Distinguishing between pituitary (somatotroph) hyperplasia secondary to ectopic GHRH and pituitary adenoma is difficult and requires specialist neuroradiology input and consideration, especially in the MEN1 setting. It is important to note that the vast majority of GHRH-secreting tumours (lung, pancreas, phaeochromocytoma) are expected to be visible on cross-sectional imaging (median diameter 55 mm) (1). Therefore, we suggest that a chest X-ray and an abdominal ultrasound checking the adrenal glands and the pancreas should be included in the routine work-up of newly diagnosed acromegaly patients.

Bayesian Inference of Species Trees using Diffusion Models

We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of data sets containing hundreds or thousands of individuals. The method, which we call Snapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements, and accuracy recovering known model parameters. A reanalysis of soybean SNP data demonstrates that the models implemented in Snapp and Snapper can be difficult to distinguish in practice, a characteristic which we tested with further simulations. We demonstrate the scale of analysis possible using a SNP data set sampled from 399 fresh water turtles in 41 populations. [Bayesian inference; diffusion models; multi-species coalescent; SNP data; species trees; spectral methods.].

Assurance Enzyme Immunoassay for Detection of Enterohemorrhagic Escherichia coli 0157:H7 in Selected Foods: Collaborative Study

Five foods types were analyzed by the Assurance EHEC (Escherichia coli 0157:H7) enzyme immunoassay (EIA) and by the Bacteriological Analytical Manual (BAM) culture method. Each sample of each food type at each inoculation level was simultaneously analyzed by both methods. A total of 21 laboratories representing state and federal government agencies and private industry in the United States and Canada participated. Samples were inoculated with E. coli 0157:H7, except for one lot of poultry that was naturally contaminated. A total of 1304 samples and controls were analyzed and confirmed, of which 473 were positive and 818 were negative by both methods. Thirteen samples were positive by BAM but negative by EIA. Because of the study design, it was not possible for the BAM method to produce false-negative or falsepositive results. The Assurance method for detection of E. coli OI57:H7 in selected foods has been adopted first action by AOAC INTERNATIONAL.

Direct 24-Hour Presumptive Enumeration of Escherichia coli 0157:H7 in Foods Using Hydrophobic Grid Membrane Filter Followed by Serological Confirmation: Collaborative Study

Fifteen laboratories took part in a collaborative study to validate a method for enumerating Escherichia coli 0157:H7. The method is based on use of a hydrophobic grid membrane filter and consists of 24 h presumptive enumeration on SD-39 Agar and serological confirmation to yield a confirmed E. coli 0157:H7 count. Six food products were analyzed: pasteurized apple cider, pasteurized 2% milk, cottage cheese, cooked ground pork, raw ground beef, and frozen whole egg. The test method produced significantly higher confirmed count results than did the reference method for milk, pork, and beef. Test method results were numerically higher than but statistically equivalent to reference method results for cheese, cider, and egg. The test method produced lower repeatability and reproducibility values than did the reference method for most food/inoculation level combinations and values very similar to those of the reference method for the remaining combinations. Overall, 94% of presumptive positive isolates from the test method were confirmed serologically as E. coli 0157:H7, and 98% of these were also biochemically typical of E. coli 0157:H7 (completed test). Corresponding rates for the reference method were 69 and 98%, respectively. On the basis of the results of this collaborative study and the precollaborative study that preceded it, it is recommended that this method be adopted official first action for enumeration of E. coli 0157:H7 in meats, poultry, dairy foods, infant formula, liquid eggs, mayonnaise, and apple cider

Visual Immunoprecipitate Assay (VIP) for Detection of Enterohemorrhagic Escherichia coli (EHEC) 0157:H7 in Selected Foods: Collaborative Study

Five foods representative of a variety of food products were analyzed by the Visual Immunoprecipitate Assay (VIP) and the Bacteriological Analytical Manual (BAM) culture method for the presence of Escherichia coli 0157: H7. A total of 21 laboratories representing state and federal government agencies, as well as private industry, in the United States and Canada participated. Food types were inoculated with strains of E. coli 0157:H7, with the exception of one lot of poultry, which was naturally contaminated. During this study, a total of 1377 samples and controls were analyzed and confirmed, of which 508 were positive and 867 were negative by both methods. Two samples were positive by BAM and negative by VIP. Because of the study design, it was not possible for the BAM method to produce false-negative or false-positive results. The VIP assay for detection of EHEC in selected foods has been adopted first action by AOAC INTERNATIONAL.

Salmonella in Foods: New Enrichment Procedure for TECRA Salmonella Visual Immunoassay Using a Single RV(R10) Only, TT Only, or Dual RV(R10) and TT Selective Enrichment Broths (AOAC Official Method 998.09): Collaborative Study

A collaborative study was conducted to compare a new enrichment procedure for the TECRA® Salmonella Visual Immunoassay (TSVIA) with the reference method given in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (7th Ed.). Three food types (milk powder, pepper, and soy flour) were analyzed in Australia and 3 food types (milk chocolate, dried egg, and raw turkey) were analyzed in the United States. Thirty-eight collaborators participated in the study. The TECRA method was evaluated using both Rappaport-Vassiliadis R10 (RV(R10)) and tetrathionate (TT) broths for selective enrichment. M broth cultures arising from each of the 2 selective enrichment broths were tested in the TSVIA using 2 individual wells, one for each selective broth, and a single well to test the pooled selective enrichment broths. The results for the pooled enrichment broths were reported elsewhere. This study presents the results for the use of single enrichment broths, i.e., RV(R10) only or TT only, with the TSVIA. No significant differences (p &gt; 0.05) were observed for the pairwise comparison of the proportion of positive samples for either RV(R10) or TT used as a single enrichment broth for the TSVIA with that for the reference method.

Modification of Enrichment Protocols for TECRA Listeria Visual Immunoassay Method 995.22: Collaborative Study

A collaborative study was conducted to validate new enrichment methods for the TECRA Listeria Visual Immunoassay (TLVIA). These new methods incorporate a newly formulated medium, TECRA Listeria Enrichment Broth, which does not contain the highly toxic antifungal agent, cycloheximide. The new procedures will provide an alternative to the enrichment procedures described in AOAC Method 995.22. Three food types (raw ground beef, lettuce, and ice cream) were analyzed in the United States, and 2 food types (cooked turkey and cooked fish fillets) were analyzed in Australasia. Thirty collaborators participated in the study, 16 in Australasia and 14 in the United States. With the exception of one batch of ground beef, comparison of the proportion of positive test portions (p ≥ 0.05) showed no significant difference between the TLVIA and the reference method for the 5 foods at 3 inoculation levels. For the one batch of naturally contaminated raw ground beef, the TLVIA gave significantly more confirmed positive results than the reference method.

Dry Rehydratable Film Method for Rapid Enumeration of Coliforms in Foods (3M™ Petrifilm™ Rapid Coliform Count Plate): Collaborative Study

A rehydratable dry-film plating method for coliforms in foods, the 3M™ Petrifilm™ Rapid Coliform Count plate method, was compared with the U.S. Food and Drug Administration's Bacteriological Analytical Manual method for nondairy foods and the American Public Health Association's Standard Methods for the Examination of Dairy Products (SMEDP) method for dairy foods. Six food types, vanilla ice cream, cheddar cheese, fresh refrigerated uncooked pasta, wheat flour, prepared frozen macaroni and cheese, and frozen hash browns, were analyzed for coliforms by 11 collaborating laboratories. For each food product tested, the collaborators received 8 blind samples consisting of a control sample and 3 levels of inoculated sample, each in duplicate. The mean log counts for the methods were comparable. The repeatability and reproducibility variances of the Petrifilm Rapid Coliform Count method at 14 and 24 h were not significantly different from those of the standard methods.

Comparison of the Reveal 20-Hour Method and the BAM Culture Method for the Detection of Escherichia coli O157:H7 in Selected Foods and Environmental Swabs: Collaborative Study

Four different food types along with environmental swabs were analyzed by the Reveal for E. coli O157:H7 test (Reveal) and the Bacteriological Analytical Manual (BAM) culture method for the presence of Escherichia coli O157:H7. Twenty-seven laboratories representing academia and private industry in the United States and Canada participated. Sample types were inoculated with E. coli O157:H7 at 2 different levels. Of the 1095 samples and controls analyzed and confirmed, 459 were positive and 557 were negative by both methods. No statistical differences (p &lt;0.05) were observed between the Reveal and BAM methods.

Reveal 8-Hour Test System for Detection of Escherichia coli O157:H7 in Raw Ground Beef, Raw Beef Cubes, and Iceberg Lettuce Rinse: Collaborative Study

Five different food types were analyzed by the Reveal for E. coli O157:H7 8-Hour Test System (Reveal 8) and either the U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) culture method or the U.S. Department of Agriculture Food Safety Inspection Service (FSIS) culture method for the presence of E. coli O157:H7. A total of 27 laboratories representing academia and private industry in the United States and Canada participated. Food types were inoculated with E. coli O157:H7 at 2 different levels: a high level where predominantly positive results were expected, and a low level where fractional recovery was anticipated. During this study, 1110 samples and controls were analyzed by both the Reveal 8 and by BAM or FSIS by each of the collaborators (2220 samples in total). For each set of samples, 740 were artificially inoculated with E. coli O157:H7, and 370 were uninoculated controls. The Reveal 8 detected 528 presumptive positives of which 487 were confirmed positive by the BAM culture method. In comparison, BAM and FSIS detected 489 of the 740 artificially contaminated samples as positive. In an additional in-house study performed only on chilled and frozen raw ground beef, 240 artificially inoculated samples were analyzed by both the Reveal 8 and by FSIS. The Reveal 8 detected and confirmed 104 samples as positive compared to 79 confirmed positive by FSIS.

Disruption of FOXF2 as a Likely Cause of Absent Uvula in an Egyptian Family

This study investigated the genetic basis of an unusual autosomal dominant phenotype characterized by familial absent uvula, with a short posterior border of the soft palate, abnormal tonsillar pillars, and velopharyngeal insufficiency. Cytogenetic analysis and single-nucleotide polymorphism-based linkage analysis were investigated in a 4-generation family with 8 affected individuals. Whole exome sequencing data were overlaid, and segregation analysis identified a single missense variant, p.Q433P in the FOXF2 transcription factor, that fully segregated with the phenotype. This was found to be in linkage disequilibrium with a small 6p25.3 tandem duplication affecting FOXC1 and GMDS. Notably, the copy number imbalances of this region are commonly associated with pathologies that are not present in this family. Bioinformatic predictions with luciferase reporter studies of the FOXF2 missense variant indicated a negative impact, affecting both protein stability and transcriptional activation. Foxf 2 is expressed in the posterior mouse palate, and knockout animals develop an overt cleft palate. Since mice naturally lack the structural equivalent of the uvula, we demonstrated FOXF2 expression in the developing human uvula. Decipher also records 2 individuals with hypoplastic or bifid uvulae with copy number variants affecting FOXF2. Nevertheless, given cosegregation with the 6p25.3 duplications, we cannot rule out a combined effect of these gains and the missense variant on FOXF2 function, which may account for the rare palate phenotype observed.

Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication

In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.

A Non-Lethal Osteogenesis Imperfecta Type II Mutation

BACKGROUND

We discuss the ethical decision points in a case report that describes a novel COL1A1 mutation associated to Osteogenesis Imperfecta type II, but with a non-lethal outcome.

CASE

A 33-year-old female underwent a 21-week ultrasound that revealed short bowed femurs and humeri with old fractures and bowed tibias and fibulas. Amniotic fluid testing revealed a novel COL1A1 mutation (c.1840G>A; p.Gly614Arg). OI Type II diagnosis was made. A previously reported mutation of the same gene but different locus (c.1840G>C; p.Gly614Arg) led to a lethal form of OI type II. The newborn was delivered via a cesarean delivery and intravenous bisphosphonates (Zaledronic acid) was administered every 3 months. Currently the infant is 22 months old, is growing, with mild bilateral conductive hearing loss.

CONCLUSION

The unexpected clinical outcome should serve as a reminder that phenotypic variability can occur with genetic mutations. Our case shows that the diagnosis of the type of OI should be based not only on clinical findings and genetic investigations but also on the clinical course over time.

The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification

There are two prominent and competing hypotheses that disagree about the effect of competition on diversification processes. The first, the bounded hypothesis, suggests that species diversity is limited (bounded) by competition between species for finite ecological niche space. The second, the unbounded hypothesis, proposes that innovations associated with evolution render competition unimportant over macroevolutionary timescales. Here we use phylogenetically structured niche modelling to show that processes consistent with both of these diversification models drive species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggest a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that can accommodate both bounded and unbounded evolutionary processes.

Association Between Inflammatory Biomarker C-Reactive Protein and Radiotherapy-Induced Early Adverse Skin Reactions in a Multiracial/Ethnic Breast Cancer Population

Purpose This study examined an inflammatory biomarker, high-sensitivity C-reactive protein (hsCRP), in radiotherapy (RT)-induced early adverse skin reactions or toxicities in breast cancer. Patients and Methods Between 2011 and 2013, 1,000 patients with breast cancer who underwent RT were evaluated prospectively for skin toxicities through the National Cancer Institute-funded Wake Forest University Community Clinical Oncology Program Research Base. Pre- and post-RT plasma hsCRP levels and Oncology Nursing Society skin toxicity criteria (0 to 6) were used to assess RT-induced skin toxicities. Multivariable logistic regression analyses were applied to ascertain the associations between hsCRP and RT-induced skin toxicities after adjusting for potential confounders. Results The study comprised 623 white, 280 African American, 64 Asian/Pacific Islander, and 33 other race patients; 24% of the patients were Hispanic, and 47% were obese. Approximately 42% and 15% of patients developed RT-induced grade 3+ and 4+ skin toxicities, respectively. The hsCRP levels differed significantly by race and body mass index but not by ethnicity. In multivariable analysis, grade 4+ skin toxicity was significantly associated with obesity (odds ratio [OR], 2.17; 95% CI, 1.41 to 3.34], post-RT hsCRP ≥ 4.11 mg/L (OR, 1.61; 95% CI, 1.07 to 2.44), and both factors combined (OR, 3.65; 95% CI, 2.18 to 6.14). Above-median post-RT hsCRP (OR, 1.93; 95% CI, 1.03 to 3.63), and change in hsCRP (OR, 2.80; 95% CI, 1.42 to 5.54) were significantly associated with grade 4+ skin toxicity in nonobese patients. Conclusion This large prospective study is the first to our knowledge of hsCRP as an inflammatory biomarker in RT-induced skin toxicities in breast cancer. We demonstrate that nonobese patients with elevated RT-related change in hsCRP levels have a significantly increased risk of grade 4+ skin toxicity. The outcomes may help to predict RT responses and guide decision making.

Exercise to improve functional outcomes in persons with osteoporosis: a systematic review and meta-analysis

Osteoporosis affects many aspects of daily life. The aim of this systematic review was to assess the effects of exercise interventions on functional outcomes in persons with osteoporosis, in comparison with controls.

METHODS

Four databases were searched and yielded 1587 citations. Two reviewers independently determined study eligibility, rated risk of bias, appraised methodological quality of studies, and resolved discordance by consensus.

RESULTS

A total of 28 studies examining 2113 participants met inclusion criteria; 25 studies were suitable for meta-analyses. Four categories of exercise were identified using the ProFaNE taxonomy. After removing studies with high risk of bias and sorting them into intervention sub-types, we were able to sufficiently reduce the heterogeneity. The standardized mean difference (SMD) favored multicomponent exercise for mobility (- 0.56, 95% CI [- 0.81, - 0.32], p = 0.06, I² = 51%); balance (0.50, 95% CI [0.27, 0.74], p = 0.28, I² = 21%); and self-reported measures of functioning (- 0.69, 95% CI [- 1.04, - 0.34], p = 0.02, I² = 61%). Trials were judged at low or unclear risk of selection bias, indicating inadequate reporting and at high risk of performance bias due to lack of participant blinding. The mean methodological quality rating of the studies was 63.5% indicating moderate quality.

CONCLUSIONS

A multicomponent exercise program of high-speed training combined with simulated functional tasks is promising to enhance functional outcomes. Due to substantial clinical heterogeneity of the target groups and specific demands of exercise modes, it is unclear which exercise program is optimal.

Changes in biomechanical risk factors for knee osteoarthritis and their association with 5-year clinically important improvement after limb realignment surgery

OBJECTIVE

To evaluate 5-year outcomes after lower limb realignment and test the hypothesis that surgery-induced changes in selected biomechanical risk factors for medial knee osteoarthritis (OA) are associated with clinically important improvements.

DESIGN

We prospectively evaluated patient-reported outcomes, full-limb standing radiographs and gait biomechanics before, 6 months (surgery-induced change) and 5 years after medial opening wedge high tibial osteotomy (HTO) in 170 patients (46.4 ± 8.9 years, 135 males) with knee OA and varus alignment. Logistic regression tested the associations of 6-month changes in mechanical axis angle and knee adduction moment with achieving an increase of ≥10 points in the Knee injury and Osteoarthritis Outcome Score (KOOS)4 at 5 years, with and without adjusting for covariates. Gait data were also compared to existing data from healthy controls.

RESULTS

Mean 5-year changes (95% confidence interval (CI)) were: KOOS4: +14.2 (10.8, 17.6); mechanical axis angle: +8.21° (7.58, 8.83); knee adduction moment: -1.49 %BW*Ht (-1.35, -1.63). The postoperative knee adduction moments were typically lower than values for healthy controls. When divided into quartiles, although all strata improved significantly, patients with reductions in knee adduction moment of 1.14-1.74 %BW*Ht (neither largest nor smallest changes) had highest 5-year KOOS4 scores. The 6-month change in knee adduction moment (odds ratios (OR) = 0.38; 95% CI: 0.22, 0.67), preoperative KOOS4 (OR = 0.96; 95% CI: 0.94, 0.99) and preoperative medial tibiofemoral narrowing grade (OR = 0.62; 95% CI: 0.37, 1.00) were negatively associated with having a 5-year clinically important improvement (C-statistic = 0.70).

CONCLUSIONS

Substantial improvements in biomechanical risk factors and patient-reported outcomes are observed 5 years after medial opening wedge HTO. The surgery-induced change in load distribution during walking is significantly associated with long-term clinically important improvement.

Can We "Future-Proof" Consensus Trees?

Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when restricted to the original set of taxa. However, if the new trees, restricted to the original set of taxa, were to agree exactly with the earlier trees, then we might hope that their consensus would either agree with or resolve the original consensus tree. In this article, we ask under what conditions consensus methods exist that are "future proof" in this sense. While we show that some methods (e.g., Adams consensus) have this property for specific types of input, we also establish a rather surprising "no-go" theorem: there is no "reasonable" consensus method that satisfies the future-proofing property in general. We then investigate a second notion of "future proofing" for consensus methods, in which trees (rather than taxa) are added, and establish some positive and negative results. We end with some questions for future work.

Meeting report - Intercellular interactions in context: towards a mechanistic understanding of cells in organs

The Company of Biologists held the workshop 'Intercellular interactions in context: towards a mechanistic understanding of cells in organs' at historic Wiston House in West Sussex, UK, 5-8 February 2017. The meeting brought together around 30 scientists from disparate backgrounds - yet with a common interest of how tissue morphogenesis occurs and its dysregulation leads to pathologies - to intensively discuss their latest research, the current state of the field, as well as any challenges for the future. This report summarises the concepts and challenges that arose as key questions for the fields of cell, cancer and developmental biology. By design of the organizers - Andrew Ewald (John Hopkins University, MA), John Wallingford (University of Texas at Austin, TX) and Peter Friedl (Radboud University, Nijmegen, The Netherlands) - the attendee makeup was cross-sectional: both in terms of career stage and scientific background. This intermingling was mirrored in the workshop format; all participants - irrespective of career stage - were given equal speaking and question time, and all early-career researchers also chaired a session, which promoted an atmosphere for discussions that were open, egalitarian and supportive. This was particularly evident in the scheduled 'out-of-the-box' sessions, which provided an avenue for participants to raise ideas and concepts or to discuss specific problems they wanted feedback or clarification on. In the following, rather than act as court reporters and convey chronological accounting of presentations, we present the questions that arose from the workshop and should be posed to the field at large, by discussing the presentations as they relate to these concepts.

Efficient Recycled Algorithms for Quantitative Trait Models on Phylogenies

We present an efficient and flexible method for computing likelihoods for phenotypic traits on a phylogeny. The method does not resort to Monte Carlo computation but instead blends Felsenstein’s discrete character pruning algorithm with methods for numerical quadrature. It is not limited to Gaussian models and adapts readily to model uncertainty in the observed trait values. We demonstrate the framework by developing efficient algorithms for likelihood calculation and ancestral state reconstruction under Wright’s threshold model, applying our methods to a data set of trait data for extrafloral nectaries across a phylogeny of 839 Fabales species.

PD-1 and PD-L1 Expression in Renal Cell Carcinoma with Sarcomatoid Differentiation

Monoclonal antibodies that target the programmed death-1 (PD-1)-programmed death ligand-1 (PD-L1) axis have antitumor activity against multiple cancers. The presence of sarcomatoid differentiation in renal cell carcinoma (RCC) is associated with resistance to targeted therapy and poor responses to IL2 immunotherapy. Given the aggressive nature of RCC with sarcomatoid differentiation and the exclusion of sarcomatoid histology from metastatic RCC clinical trials, less is understood regarding selection of therapies. Here, we characterized the PD-1/PD-L1 axis in RCC with sarcomatoid differentiation. We directly compared two PD-L1 antibodies and found concordance of PD-L1 positivity in 89% of tested RCCs with sarcomatoid differentiation. Coexpression of PD-L1 on neoplastic cells and the presence of PD-1-positive tumor-infiltrating lymphocytes were identified in 50% (13 of 26) of RCCs with sarcomatoid differentiation. In contrast, only 1 of 29 clear cell RCCs (3%) had concurrent expression of PD-L1 and PD-1 (P = 0.002). Our study suggests that RCC with sarcomatoid differentiation may express PD-1/PD-L1 at a higher percentage than RCC without sarcomatoid differentiation, and patients with these tumors may be good candidates for treatment with anti-PD-1/PD-L1 therapies.

Endosymbiotic origin and differential loss of eukaryotic genes

Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.

Phase II double-blind placebo-controlled randomized study of armodafinil for brain radiation-induced fatigue

BACKGROUND

Common acute-term side effects of brain radiotherapy (RT) include fatigue, drowsiness, decreased physical functioning, and decreased quality of life (QOL). We hypothesized that armodafinil (a wakefulness-promoting drug known to reduce fatigue and increase cognitive function in breast cancer patients receiving chemotherapy) would result in reduced fatigue and sleepiness for patients receiving brain RT.

METHODS

A phase II, multi-institutional, placebo-controlled randomized trial assessed feasibility of armodafinil 150 mg/day in participants receiving brain RT, from whom we obtained estimates of variability for fatigue, sleepiness, QOL, cognitive function, and treatment effect.

RESULTS

From September 20, 2010, to October 20, 2012, 54 participants enrolled with 80% retention and 94% self-reported compliance. There were no grade 4-5 toxicities, and the incidence of grade 2-3 toxicities was similar between treatment arms, the most common of which were anxiety and nausea (15%), headaches (19%), and insomnia (20%). There were no statistically significant differences in end-RT or 4 week post-RT outcomes between armodafinil and placebo in any outcomes (Functional Assessment of Chronic Illness Therapy [FACIT]-Fatigue, Brief Fatigue Inventory, Epworth Sleepiness Scale, FACT-Brain, and FACIT-cognitive function). However, in participants with more baseline fatigue, those treated with armodafinil did better than those who received the placebo on the end-RT assessments for several outcomes.

CONCLUSION

Armodafinil 150 mg/day was well tolerated in primary brain tumor patients undergoing RT with good compliance. While there was no overall significant effect on fatigue, those with greater baseline fatigue experienced improved QOL and reduced fatigue when using armodafinil. These data suggest that a prospective, phase III randomized trial is warranted for patients with greater baseline fatigue.

Multiplatform molecular analysis of biomarkers in renal cell carcinoma

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Background: Predictive biomarkers of response to targeted therapy are lacking in renal cell carcinoma (RCC). We evaluated a cohort of RCC patients referred for molecular profiling to identify potentially actionable recurrent molecular aberrations. Methods: 166 consecutive renal cases referred to Caris Life Sciences over 2 yrs were evaluated with central pathology review. Cases were subtyped into clear cell (ccRCC), n=100, papillary (PRCC), n=20, sarcomatoid, n=10, translocation, n=6, medullary, n=4 or unclassified, n=26. 63% of cases were metastatic. Testing included a combination of sequencing (Sanger or next generation sequencing [NGS]), protein expression (immunohistochemistry [IHC]), and/or gene amplification (CISH or FISH). Results: ccRCC had a 52% loss of PTEN, while PRCC had a 21% loss (p value=0.02). 100% of ccRCC with sarcomatoid features (4) showed aberrant expression of PD-L1 and were infiltrated with PD-1+ tumor infiltrating lymphocytes; 100% of 10 non-ccRCC sarcomatoids also had aberrant expression of PD-L1. Loss of PBRM1 expression was observed in 60% of ccRCC. Loss of histone 3 lysine 36 trimethylation (H3K36me3), which is associated with SETD2 mutations, was observed in 30% of ccRCC. TOP2A was overexpressed in ccRCC at 30% and in non-ccRCC at 50%. 100% of ccRCC and PRCC overexpressed EGFR; a single unclassified renal cell carcinoma did not overexpress EGFR. 50% of cases had cMET overexpression, amplification, or mutation. HER2 was not amplified or overexpressed in any RCC; a single rare HER2 mutation (R816H) was found in a collecting duct carcinoma. VHL mutations were identified in 50% of ccRCC tumors. We observed lower rates of TP53 (14%), ATM (6%), and PIK3CA(4% ccRCC, 7% PRCC) mutations compared to other cancers. Conclusions: Multiplatform molecular profiling of renal cell carcinoma identifies potential predictive biomarkers in ccRCC. The documented activity of everolimus in ccRCC (RECORD-1 trial) may be attributable to PIK3CA pathway alterations. RCC with sarcomatoid features may respond to PD1/PD-L1 targeted immunotherapies. The impact of molecular profiling in ccRCC to predict responses to currently available targeted therapy has important implications for trial design and patient selection.