OrthoPhyl - Streamlining large scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.

There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification, but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use-cases: E. coli/Shigella, Brucella/Ochrobactrum, and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

Strong association between reduction of late-stage cancers and reduction of cancer-specific mortality in meta-regression of randomized screening trials across multiple cancer types.

BACKGROUND: Late-stage cancer incidence has been proposed as an early surrogate for mortality in randomized controlled trials (RCTs) of cancer screening; however, its validity has not been systematically evaluated across screening RCTs of different cancers. METHODS: We conducted a meta-regression analysis of cancer screening RCTs that reported both late-stage cancer incidence and cancer mortality. Based on a systematic literature review, we included 33 RCTs of screening programs targeting seven cancer types, including lung (n = 12), colorectal (n = 8), breast (n = 5), and prostate (n = 4), among others. We regressed the relative reduction of cancer mortality on the relative reduction of late-stage cancer incidence, inversely weighted for each RCT by the variance of estimated mortality reduction. RESULTS: Across cancer types, the relative reduction of late-stage cancer incidence was linearly associated with the relative reduction of cancer mortality. Specifically, we observed this association for lung (R2 = 0.79 and 0.996 in three recent large trials), breast (R2 = 0.94), prostate (R2 = 0.98), and colorectal cancer (R2 = 0.75 for stage III/IV cancers and 0.93 for stage IV cancers). Trials with a 20% or greater reduction in late-stage cancers were more likely to achieve a significant reduction in cancer mortality. Our results also showed that no reduction of late-stage cancer incidence was associated with no or minimal reduction in cancer mortality. CONCLUSIONS: Meta-regression of historical screening RCTs showed a strong linear association between reductions in late-stage cancer incidence and cancer mortality.

Ongoing Cooperative Engagement Facilitates Agile Pandemic and Outbreak Response: Lessons Learned Through Cooperative Engagement Between Uganda and the United States.

Pathogens threaten human lives and disrupt economies around the world. This has been clearly illustrated by the current COVID-19 pandemic and outbreaks in livestock and food crops. To manage pathogen emergence and spread, cooperative engagement programs develop and strengthen biosafety, biosecurity, and biosurveillance capabilities among local researchers to detect pathogens. In this case study, we describe the efforts of a collaboration between the Los Alamos National Laboratory and the Uganda Virus Research Institute, the primary viral diagnostic laboratory in Uganda, to implement and ensure the sustainability of sequencing for biosurveillance. We describe the process of establishing this capability along with the lessons learned from both sides of the partnership to inform future cooperative engagement efforts in low- and middle-income countries. We found that by strengthening sequencing capabilities at the Uganda Virus Research Institute before the COVID-19 pandemic, the institute was able to successfully sequence SARS-CoV-2 samples and provide data to the scientific community. We highlight the need to strengthen and sustain capabilities through in-country training, collaborative research projects, and trust.

Seroprevalence of Brucella spp. and Rift Valley fever virus among slaughterhouse workers in Isiolo County, northern Kenya.

Brucella spp. and Rift Valley fever virus (RVFV) are classified as priority zoonotic agents in Kenya, based on their public health and socioeconomic impact on the country. Data on the pathogen-specific and co-exposure levels is scarce due to limited active surveillance. This study investigated seroprevalence and co-exposure of Brucella spp. and RVFV and associated risk factors among slaughterhouse workers in Isiolo County, northern Kenya. A cross-sectional serosurvey was done in all 19 slaughterhouses in Isiolo County, enrolling 378 participants into the study. The overall seroprevalences for Brucella spp. and RVFV were 40.2% (95% CI: 35.2-45.4) and 18.3% (95% CI: 14.5-22.5), respectively while 10.3% (95% CI 7.4%-13.8%) of individuals were positive for antibodies against both Brucella spp. and RVFV. Virus neutralisation tests (VNT) confirmed anti-RVFV antibodies in 85% of ELISA-positive samples. Our seroprevalence results were comparable to community-level seroprevalences previously reported in the area. Since most of the study participants were not from livestock-keeping households, our findings attribute most of the detected infections to occupational exposure. The high exposure levels indicate slaughterhouse workers are the most at-risk population and there is need for infection, prevention, and control programs among this high-risk group. This is the first VNT confirmation of virus-neutralising antibodies among slaughterhouse workers in Isiolo County and corroborates reports of the area being a high-risk RVFV area as occasioned by previously reported outbreaks. This necessitates sensitization campaigns to enhance awareness of the risks involved and appropriate mitigation measures.

If You're Not Confused, You're Not Paying Attention: Ochrobactrum Is Not Brucella.

Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.

Identification and distribution of pathogens coinfecting with Brucella spp., Coxiella burnetii and Rift Valley fever virus in humans, livestock and wildlife.

Zoonotic diseases, such as brucellosis, Q fever and Rift Valley fever (RVF) caused by Brucella spp., Coxiella burnetii and RVF virus, respectively, can have devastating effects on human, livestock, and wildlife health and cause economic hardship due to morbidity and mortality in livestock. Coinfection with multiple pathogens can lead to more severe disease outcomes and altered transmission dynamics. These three pathogens can alter host immune responses likely leading to increased morbidity, mortality and pathogen transmission during coinfection. Developing countries, such as those commonly afflicted by outbreaks of brucellosis, Q fever and RVF, have high disease burden and thus common coinfections. A literature survey provided information on case reports and studies investigating coinfections involving the three focal diseases. Fifty five studies were collected demonstrating coinfections of Brucella spp., C. burnetii or RVFV with 50 different pathogens, of which 64% were zoonotic. While the literature search criteria involved 'coinfection', only 24/55 studies showed coinfections with direct pathogen detection methods (microbiology, PCR and antigen test), while the rest only reported detection of antibodies against multiple pathogens, which only indicate a history of co-exposure, not concurrent infection. These studies lack the ability to test whether coinfection leads to changes in morbidity, mortality or transmission dynamics. We describe considerations and methods for identifying ongoing coinfections to address this critical blind spot in disease risk management.

Flight system morphology and minimum flight temperature in North American cicadas (Insecta: Hemiptera: Cicadidae).

Thermal responses in cicadas have been studied for many years. The minimum flight temperature (MFT) does not show the same relationship to habitat and behavior as other thermal responses. We measured live mass, wing length, wingspan, wing area and wing loading in an attempt to correlate these morphological parameters to the MFT. We analyzed both intraspecific (in Magicicada cassinii (Fisher, 1852)) and interspecific relationships of the wing morphology and the ability of the cicadas to fly in a large number of North American cicada taxa (n=119). A total of 109 species and 10 subspecies from 17 genera, six tribes, and three subfamilies including all major North American habitats were studied. Analyses show that wing morphology (wing length, wingspan, wing area and wing loading) scales to body size as predicted by geometric similarity (all P<0.0001) for all species and wing area and wing loading (both P<0.0001) in M. cassinii. Mass (P=0.0105), wing length (P=0.0006), wingspan (P=0.0006), wing area (P=0.0055), and wing loading (P=0.0455) all demonstrate a significant correlation to MFT between species, as would be predicted by aerodynamic theory, but not within species. However, the low correlation coefficients suggest the flight system has minimal influence on the MFT of cicadas. Specific physiological adaptations appear to be responsible for the between species variability in MFT rather than being the result of modifications to the flight system morphology.

Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants.

Experimental evolution (serial passage) of Friend virus complex (FVC) in mice demonstrates phenotypic adaptation to specific host major histocompatibility complex (MHC) genotypes. These evolved viral lines show increased fitness and virulence in their host-genotype-of-passage, but display fitness and virulence tradeoffs when infecting unfamiliar host MHC genotypes. Here, we deep sequence these viral lines in an attempt to discover the genetic basis of FVC adaptation. The principal prediction for genotype-specific adaptation is that unique mutations would rise to high frequency in viral lines adapted to each host MHC genotype. This prediction was not supported by our sequencing data as most observed high-frequency variants were present in each of our independently evolved viral lines. However, using a multi-variate approach to measure divergence between viral populations, we show that populations of replicate evolved viral lines from the same MHC congenic mouse strain were more similar to one another than to lines derived from different MHC congenic mouse strains, suggesting that MHC genotype does predictably act on viral evolution in our model. Sequence analysis also revealed rampant recombination with endogenous murine leukemia virus sequences (EnMuLVs) that are encoded within the BALB/c mouse genome. The highest frequency variants in all six lines contained a 12 bp insertion from a recombinant EnMuLV source, suggesting such recombinants were either being favored by selection or were contained in a recombinational hotspot. Interestingly, they did not reach fixation, as if they are low fitness. The amount of background mutations linked to FVC/EnMuLV variable sites indicated that FVC/EnMuLV recombinants had not reached mutation selection equilibrium and thus, that EnMuLV sequences are likely continuously introgressing into the replicating viral population. These discoveries raise the question: is the expression of EnMuLV sequences in mouse splenocytes that permit recombination with exogenous FVC a pathogen or host adaptation?

How Cooperative Engagement Programs Strengthen Sequencing Capabilities for Biosurveillance and Outbreak Response.

The threat of emerging and re-emerging infectious diseases continues to be a challenge to public and global health security. Cooperative biological engagement programs act to build partnerships and collaborations between scientists and health professionals to strengthen capabilities in biosurveillance. Biosurveillance is the systematic process of detecting, reporting, and responding to especially dangerous pathogens and pathogens of pandemic potential before they become outbreaks, epidemics, and pandemics. One important tool in biosurveillance is next generation sequencing. Expensive sequencing machines, reagents, and supplies make it difficult for countries to adopt this technology. Cooperative engagement programs help by providing funding for technical assistance to strengthen sequencing capabilities. Through workshops and training, countries are able to learn sequencing and bioinformatics, and implement these tools in their biosurveillance programs. Cooperative programs have an important role in building and sustaining collaborations among institutions and countries. One of the most important pieces in fostering these collaborations is trust. Trust provides the confidence that a successful collaboration will benefit all parties involved. With sequencing, this enables the sharing of pathogen samples and sequences. Obtaining global sequencing data helps to identify unknown etiological agents, track pathogen evolution and infer transmission networks throughout the duration of a pandemic. Having sequencing technology in place for biosurveillance generates the capacity to provide real-time data to understand and respond to pandemics. We highlight the need for these programs to continue to strengthen sequencing in biosurveillance. By working together to strengthen sequencing capabilities, trust can be formed, benefitting global health in the face of biological threats.

Raman spectroscopy and machine learning for biomedical applications: Alzheimer's disease diagnosis based on the analysis of cerebrospinal fluid.

Current Alzheimer's disease (AD) diagnostics is based on clinical assessments, imaging and neuropsychological tests that are efficient only at advanced stages of the disease. Early diagnosis of AD will provide decisive opportunities for preventive treatment and development of disease-modifying drugs. Cerebrospinal fluid (CSF) is in direct contact with the human brain, where the deadly pathological process of the disease occurs. As such, the CSF biochemical composition reflects specific changes associated with the disease and is therefore the most promising body fluid for AD diagnostic test development. Here, we describe a new method to diagnose AD based on CSF via near infrared (NIR) Raman spectroscopy in combination with machine learning analysis. Raman spectroscopy is capable of probing the entire biochemical composition of a biological fluid at once. It has great potential to detect small changes specific to AD, even at the earliest stages of pathogenesis. NIR Raman spectra were measured of CSF samples acquired from 21 patients diagnosed with AD and 16 healthy control (HC) subjects. Artificial neural networks (ANN) and support vector machine discriminant analysis (SVM-DA) statistical methods were used for differentiation purposes, with the most successful results allowing for the differentiation of AD and HC subjects with 84% sensitivity and specificity. Our classification models show high discriminative power, suggesting the method has a great potential for AD diagnostics. The reported Raman spectroscopic examination of CSF can complement current clinical tests, making early AD detection fast, accurate, and inexpensive. While this study shows promise using a small sample set, further method validation on a larger scale is required to indicate the true strength of the approach.

Incidence and Early Course of Retinopathy of Prematurity.

In the Multicenter Trial of Cryotherapy for Retinopathy of Prematurity (ROP), 4099 infants weighing less than 1251 g at birth underwent sequential ophthalmic examinations, beginning at age 4 to 6 weeks, to monitor the incidence and course of ROP. Overall, 65.8% of the infants developed ROP to some degree; 81.6% for infants of less than 1000 g birth weight. As expected, ROP incidence and severity were higher in lower birth weight and gestational age categories. Black infants appeared less susceptible to ROP, of all severity categories, than nonblack infants. The timing of retinal vascular events correlated more closely with postconceptional age than with postnatal age, implicating the level of maturity more than postnatal environmental influences in governing the timing of these vascular events. These results include the current incidence of various severity stages of ROP found in the United States and provide new. insight into the development of ROP.

Utility of 99mTc-Sestamibi SPECT/CT in the Early Localization of Metastatic Parathyroid Carcinoma.

Parathyroid carcinoma is very rare, with only a few documented cases. Hence, metastatic lesions are infrequently documented on scintigraphic imaging. We present a case of a 63-year-old female presenting with elevated serum levels of ionized calcium and parathyroid hormone (PTH) who was referred to our department for a parathyroid scan with SPECT/CT. Parathyroid scintigraphy showed a focus of increased 99mTc-sestamibi uptake corresponding to a solid mass with calcification in the inferior pole of the right thyroid lobe; tracer retention was noted on delayed images. Incidentally, focal uptake was also seen in a soft tissue mass on the 7th right rib. The patient soon underwent total thyroidectomy, with biopsy revealing parathyroid carcinoma on the right lobe. A bone scan done 7 months after surgery confirmed the presence of metastatic bone disease. The concomitant detection of intrathyroidal and extrathyroidal sestamibi-avid masses on parathyroid scintigraphy should increase clinical suspicion of a metastatic process from parathyroid carcinoma.

Mortarmen's Knee: Adult-Onset Tibial Tubercle Exostoses in 2 Infantrymen.

Two 20-year-old male patients presented together to a multidisciplinary primary care sports medicine clinic with reports of focal swelling and pain at the left anterior knee just distal to the patella. Both patients enlisted together, chose the same occupational specialty, and trained together, resulting in similar exposure to training loads. Following examination, radiographic imaging was ordered for both patients. Radiographs of both patients revealed exostosis and fragmentation, with multiple ossicles of the tibial tubercle. J Orthop Sports Phys Ther 2018;48(6):510. doi:10.2519/jospt.2018.8005.

Gut microbiota utilize immunoglobulin A for mucosal colonization.

The immune system responds vigorously to microbial infection while permitting lifelong colonization by the microbiome. Mechanisms that facilitate the establishment and stability of the gut microbiota remain poorly described. We found that a regulatory system in the prominent human commensal Bacteroides fragilis modulates its surface architecture to invite binding of immunoglobulin A (IgA) in mice. Specific immune recognition facilitated bacterial adherence to cultured intestinal epithelial cells and intimate association with the gut mucosal surface in vivo. The IgA response was required for B. fragilis (and other commensal species) to occupy a defined mucosal niche that mediates stable colonization of the gut through exclusion of exogenous competitors. Therefore, in addition to its role in pathogen clearance, we propose that IgA responses can be co-opted by the microbiome to engender robust host-microbial symbiosis.

The Aerobic and Cognitive Exercise Study (ACES) for Community-Dwelling Older Adults With or At-Risk for Mild Cognitive Impairment (MCI): Neuropsychological, Neurobiological and Neuroimaging Outcomes of a Randomized Clinical Trial.

Prior research has found that cognitive benefits of physical exercise and brain health in older adults may be enhanced when mental exercise is interactive simultaneously, as in exergaming. It is unclear whether the cognitive benefit can be maximized by increasing the degree of mental challenge during exercise. This randomized clinical trial (RCT), the Aerobic and Cognitive Exercise Study (ACES) sought to replicate and extend prior findings of added cognitive benefit from exergaming to those with or at risk for mild cognitive impairment (MCI). ACES compares the effects of 6 months of an exer-tour (virtual reality bike rides) with the effects of a more effortful exer-score (pedaling through a videogame to score points). Fourteen community-dwelling older adults meeting screening criteria for MCI (sMCI) were adherent to their assigned exercise for 6 months. The primary outcome was executive function, while secondary outcomes included memory and everyday cognitive function. Exer-tour and exer-score yielded significant moderate effects on executive function (Stroop A/C; d's = 0.51 and 0.47); there was no significant interaction effect. However, after 3 months the exer-tour revealed a significant and moderate effect, while exer-score showed little impact, as did a game-only condition. Both exer-tour and exer-score conditions also resulted in significant improvements in verbal memory. Effects appear to generalize to self-reported everyday cognitive function. Pilot data, including salivary biomarkers and structural MRI, were gathered at baseline and 6 months; exercise dose was associated with increased BDNF as well as increased gray matter volume in the PFC and ACC. Improvement in memory was associated with an increase in the DLPFC. Improved executive function was associated with increased expression of exosomal miRNA-9. Interactive physical and cognitive exercise (both high and low mental challenge) yielded similarly significant cognitive benefit for adherent sMCI exercisers over 6 months. A larger RCT is needed to confirm these findings. Further innovation and clinical trial data are needed to develop accessible, yet engaging and effective interventions to combat cognitive decline for the growing MCI population. ClinicalTrials.gov ID: NCT02237560.

A NOVEL, REMOVABLE, CERROBEND, BEAM-BLOCKING DEVICE FOR RADIATION THERAPY OF THE CANINE HEAD AND NECK: PILOT STUDY.

Radiation therapy of the head and neck can result in mucositis and other acute affects in the oral cavity. This prospective pilot study evaluated a novel, intraoral, beam-blocking device for use during imaging and therapeutic procedures. The beam-blocking device was made from a metal alloy inserted into a coated frozen dessert mold (Popsicle® Mold, Cost Plus World Market, Oakland, CA). The device was designed so that it could be inserted into an outer shell, which in turn allowed it to be placed or removed depending on the need due to beam configuration. A Farmer type ionization chamber and virtual water phantom were used to assess effects of field size on transmission. Six large breed cadaver dogs, donated by the owner after death, were recruited for the study. Delivered dose at the dorsal and ventral surfaces of the device, with and without the alloy block in place, were measured using radiochromic film. It was determined that transmission was field size dependent with larger field sizes leading to decreased attenuation of the beam, likely secondary to scatter. The mean and median transmission on the ventral surface without the beam-blocking device was 0.94 [range 0.94-0.96]. The mean and median transmission with the beam-blocking device was 0.52 [range 0.50-0.57]. The mean and median increase in dose due to backscatter on the dorsal surface of the beam-blocking device was 0.04 [range 0.02-0.04]. Findings indicated that this novel device can help attenuate radiation dose ventral to the block in dogs, with minimal backscatter.

Anti-Ri-associated paraneoplastic brainstem cerebellar syndrome with coexisting limbic encephalitis in a patient with mixed large cell neuroendocrine lung carcinoma.

Paraneoplastic neurologic syndromes (PNS) can be the first manifestations of occult malignancies. If left untreated, PNS often lead to significant morbidity and mortality. Anti-Ri (anti-neuronal nuclear antibody type 2 [ANNA-2]) autoantibodies are commonly associated with breast and small cell lung cancers. Cases of anti-Ri paraneoplastic cerebellar degeneration are reported, but few describe severe nausea and coexisting limbic encephalitis as the major presenting features. We report a 75-year-old woman with medically-intractable emesis, encephalopathy, diplopia, vertigo, and gait ataxia for 3 months. Examination revealed rotary nystagmus, ocular skew deviation, limb dysmetria, and gait ataxia. After two courses of intravenous immunoglobulin, there was minimal improvement. Anti-Ri antibodies were positive in serum only. CT scan identified a 2.0 cm left lung mass, and histopathology revealed large cell neuroendocrine carcinoma with admixed adenocarcinoma non-small cell lung carcinoma (NCSLC). Though the patient achieved nearly complete clinical recovery after tumor resection, anti-Ri levels remained high at 20 months post-resection. To our knowledge this is the first report of a paraneoplastic brainstem cerebellar syndrome with coexisting limbic encephalitis involving anti-Ri positivity and associated mixed neuroendocrine/NSCLC of the lung with marked improvement after tumor resection.

Raman spectroscopy of blood serum for Alzheimer's disease diagnostics: specificity relative to other types of dementia.

The key moment for efficiently and accurately diagnosing dementia occurs during the early stages. This is particularly true for Alzheimer's disease (AD). In this proof-of-concept study, we applied near infrared (NIR) Raman microspectroscopy of blood serum together with advanced multivariate statistics for the selective identification of AD. We analyzed data from 20 AD patients, 18 patients with other neurodegenerative dementias (OD) and 10 healthy control (HC) subjects. NIR Raman microspectroscopy differentiated patients with more than 95% sensitivity and specificity. We demonstrated the high discriminative power of artificial neural network (ANN) classification models, thus revealing the high potential of this developed methodology for the differential diagnosis of AD. Raman spectroscopic, blood-based tests may aid clinical assessments for the effective and accurate differential diagnosis of AD, decrease the labor, time and cost of diagnosis, and be useful for screening patient populations for AD development and progression. Multivariate data analysis of blood serum Raman spectra allows for the differentiation between patients with Alzheimer's disease, other types of dementia and healthy individuals.