Metabolic immaturity of newborns and breast milk bile acid metabolites are the central determinants of heightened neonatal vulnerability to norovirus diarrhea

Noroviruses are the leading global cause of acute gastroenteritis, responsible for 685 million annual cases. While all age groups are susceptible to noroviruses, children are vulnerable to more severe infections than adults, underscored by 200 million pediatric cases and up to 200,000 deaths in children annually. Understanding the basis for the increased vulnerability of young hosts is critical to developing effective treatments. The pathogenic outcome of any enteric virus infection is governed by a complex interplay between the virus, intestinal microbiota, and host immune factors. A central mediator in these complex relationships are host- and microbiota-derived metabolites. Noroviruses bind a specific class of metabolites, bile acids, which are produced by the host and then modified by commensal bacterial enzymes. Paradoxically, bile acids can have both proviral and antiviral roles during norovirus infections. Considering these opposing effects, the microbiota-regulated balance of the bile acid pool may be a key determinant of the pathogenic outcome of a norovirus infection. The bile acid pool in newborns is unique due to immaturity of host metabolic pathways and developing gut microbiota, which could underlie the vulnerability of these hosts to severe norovirus infections. Supporting this concept, we demonstrate herein that microbiota and their bile acid metabolites protect from severe norovirus diarrhea whereas host-derived bile acids promote disease. Remarkably, we also report that maternal bile acid metabolism determines neonatal susceptibility to norovirus diarrhea during breastfeeding by delivering proviral bile acids to the newborn. Finally, directed targeting of maternal and neonatal bile acid metabolism can protect the neonatal host from norovirus disease. Altogether, these data support the conclusion that metabolic immaturity in newborns and ingestion of proviral maternal metabolites in breast milk are the central determinants of heightened neonatal vulnerability to norovirus disease.

Western diet influences on microbiome and carcinogenesis

The intestinal microbiota composition and associated bioactivities are sensitive to various modifier cues such as stress, inflammation, age, life-style and nutrition, which in turn are associated with susceptibility to developing cancer. Among these modifiers, diet has been shown to influence both microbiota composition as well as being an important source of microbial-derived compounds impacting the immunological, neurological and hormonal systems. Thus, it is necessary to take a holistic view when considering effect of diet on health and diseases. In this review, we focus on the interplay between western diet, the microbiota and cancer development by dissecting key components of the diet and leveraging data from human interventions and pre-clinical studies to better understand this relationship. We highlight key progress as well as stressing limitations in this field of research.

Gut Microbiota Dysbiosis Associated with Persistent Fatigue in Hematopoietic Cell Transplantation Survivors

Fatigue is one of the most prevalent and distressing complications among hematopoietic stem cell transplantation (HCT) survivors, negatively affecting physical, social, and emotional domains of quality of life. Chronic systemic inflammation has been linked to alterations in nervous system activity and initiation of distressing symptoms, such as fatigue. Damage to gut mucosa due to alteration in gut microbiota (GM) composition and microbial translocation has been shown to increase systemic proinflammatory cytokines. The aim of this study was to evaluate the relationship between fatigue and GM by measuring the differences in GM composition in HCT survivors with and without persistent fatigue. This cross-sectional study included 30 adults who underwent HCT for a hematologic disease and were at least 1 year post-HCT. Patients with chronic graft-versus-host disease were excluded. Fatigue severity was assessed by the Brief Fatigue Inventory (BFI). Based on the BFI score, patients were grouped into 2 categories: 0 to 3 (without fatigue) and ≥4 (with fatigue). The V1 to V3 region of the 16S rRNA gene from fecal specimens was sequenced using the Illumina MiSeq. Sequencing reads were processed, denoised, and replicated, chimeras were filtered, amplicon sequence variants (ASVs) were generated, and taxonomy was assigned using DADA2. Beta diversity analysis through principal coordinate analysis was generated using the Bray-Curtis dissimilarity matrix, and the difference was tested using linear model with generalized least squares in R. An alpha diversity analysis was performed using Chao1. Linear discriminant analysis effect size (LEfSe) was used to find markers that differ between the 2 groups. Based on the BFI results, patients were categorized into 2 cohorts: with fatigue (n = 14) and without fatigue (n = 16). The 2 cohorts were similar in terms of demographics, disease, and transplant characteristics. Based on the GM analysis, there was a significant difference in GM composition (beta diversity) between the 2 cohorts (P = .001). Alpha diversity (richness) was also significantly lower in survivors with fatigue (P =.002). LEfSe analysis identified 46 discriminative features (P < .05; linear discriminant analysis score >2) whose relative abundance varied significantly among individuals with fatigue and those without fatigue. Ten ASVs were associated with the patients with fatigue, and 36 ASVs were associated with those without fatigue. Several ASVs enriched in survivors with fatigue included organisms such as Klebsiella and Enterococcus, which have been implicated in inflammatory bowel diseases. The ASVs enriched in the cohort without fatigue were members of the Ruminococcaceae family (Oscillospira spp) and the Lachnospiraceae family (Fusicatenibacter and Coprococcus spp), which are known to have the ability to ferment complex plant carbohydrates. These findings show an association between GM composition and fatigue and suggest a microbial contribution to clinically significant fatigue post-HCT, which may guide the development of new approaches to treating fatigue based on manipulation of the GM.

Development of an algorithm using natural language processing to identify metastatic breast cancer patients from clinical notes

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Background: Determination of the metastatic status of a patient is important for outcomes research and candidacy for clinical trials. Structured data in EMR may not always capture the metastatic status, and it is useful to extract it automatically from physician notes. Contextual understanding of the notes is important to resolve issues such as a) local vs distal metastasis b) statements involving family history of metastasis or physician instructing the patient to look for certain signs of metastasis c) text indicating suspicion of metastasis or absence of metastasis d) indirect utterances, e.g. cancer has spread to the bone. e) corrections to previous findings. Methods: We used a set of 20138 breast cancer patients from Concerto HealthAI real world oncology dataset that includes data from CancerLinQ Discovery to build & validate the set of NLP algorithms. 5300 sentences from 1500 patients were annotated & algorithms manually validated by data abstractors for 500 patients. The algorithms developed were the following: 1) Classification of a sentence into 3 classes: Distal/Local metastasis, Suspicious & Other 2) Classification of a sentence into 2 classes: Distal or Local 3) Classification of a patient into 2 classes: Distal metastasis or not distal metastasis 4) Multi label classification for detecting sites of metastasis. Sentence level algorithms were built using Deep Learning and patient level aggregation of sentence level prediction was done using ML approaches including temporal features. Pretrained ULMFiT model was fine-tuned with Concerto HealthAI’s corpus for sentence classification tasks. Results: At a sentence level, we obtained an accuracy of 0.85 for the distal/local vs suspicious vs irrelevant model and 0.97 for the distal vs not distal metastasis model. Our patient level metrics are shown in the table. The classes used for sites of metastasis are Brain, Bone, Lung, Liver, Distant Lymph nodes & Unknown sites. Subset accuracy (mean fraction of labels which match ) of 0.93 was obtained on the hold out test set at patient level. Conclusions: Metastatic status & site of metastasis can be reliably extracted automatically from clinical notes using deep learning techniques. This information will be valuable for clinical trial matching, outcomes research and other applications. [Table: see text]

Intestinal microbiota enhances pancreatic carcinogenesis in preclinical models

Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the United States yet data are scant regarding host factors influencing pancreatic carcinogenesis. Increasing evidence support the role of the host microbiota in carcinogenesis but its role in PDAC is not well established. Herein, we report that antibiotic-mediated microbial depletion of KrasG12D/PTENlox/+ mice showed a decreased proportion of poorly differentiated tumors compared to microbiota-intact KrasG12D/PTENlox/+ mice. Subsequent 16S rRNA PCR showed that ~50% of KrasG12D/PTENlox/+ mice with PDAC harbored intrapancreatic bacteria. To determine if a similar observation in humans correlates with presence of PDAC, benign and malignant human pancreatic surgical specimens demonstrated a microbiota by 16S bacterial sequencing and culture confirmation. However, the microbial composition did not differentiate PDAC from non-PDAC tissue. Furthermore, murine pancreas did not naturally acquire a pancreatic microbiota, as germ-free mice transferred to specific pathogen-free housing failed to acquire intrapancreatic bacteria over time, which was not augmented by a murine model of colitis. Finally, antibiotic-mediated microbial depletion of Nod-SCID mice, compared to microbiota-intact, showed increased time to PDAC xenograft formation, smaller tumors, and attenuated growth. Interestingly, both xenograft cohorts were devoid of intratumoral bacteria by 16S rRNA PCR, suggesting that intrapancreatic/intratumoral microbiota is not the sole driver of PDAC acceleration. Xenografts from microbiota-intact mice demonstrated innate immune suppression by immunohistochemistry and differential regulation of oncogenic pathways as determined by RNA sequencing. Our work supports a long-distance role of the intestinal microbiota on PDAC progression and opens new research avenues regarding pancreatic carcinogenesis.

Linking bone development on the caudal aspect of the distal phalanx with lameness during life

Claw horn disruption lesions (CHDL; sole hemorrhage, sole ulcer, and white line disease) cause a large proportion of lameness in dairy cattle, yet their etiopathogenesis remains poorly understood. Untreated CHDL may be associated with damage to the internal anatomy of the foot, including to the caudal aspect of the distal phalanx upon which bone developments have been reported with age and with sole ulcers at slaughter. The primary aim of this study was to assess whether bone development was associated with poor locomotion and occurrence of CHDL during a cow's life. A retrospective cohort study imaged 282 hind claws from 72 Holstein-Friesian dairy cows culled from a research herd using X-ray micro-computed tomography (μ-CT; resolution: 0.11mm). Four measures of bone development were taken from the caudal aspect of each distal phalanx, in caudal, ventral, and dorsal directions, and combined within each claw. Cow-level variables were constructed to quantify the average bone development on all hind feet (BD-Ave) and bone development on the most severely affected claw (BD-Max). Weekly locomotion scores (1-5 scale) were available from first calving. The variables BD-Ave and BD-Max were used as outcomes in linear regression models; the explanatory variables included locomotion score during life, age, binary variables denoting lifetime occurrence of CHDL and of infectious causes of lameness, and other cow variables. Both BD-Max and BD-Ave increased with age, CHDL occurrence, and an increasing proportion of locomotion scores at which a cow was lame (score 4 or 5). The models estimated that BD-Max would be 9.8mm (SE 3.9) greater in cows that had been lame at >50% of scores within the 12mo before slaughter (compared with cows that had been assigned no lame scores during the same period), or 7.0mm (SE 2.2) greater if the cow had been treated for a CHDL during life (compared with cows that had not). Additionally, histology demonstrated that new bone development was osteoma, also termed "exostosis." Age explained much of the variation in bone development. The association between bone development and locomotion score during life is a novel finding, and bone development appears specific to CHDL. Bone development on the most severely affected foot was the best explained outcome and would seem most likely to influence locomotion score. To stop irreparable anatomical damage within the foot, early identification of CHDL and effective treatment could be critical.

Claw length recommendations for dairy cow foot trimming

The aim was to describe variation in length of the dorsal hoof wall in contact with the dermis for cows on a single farm, and hence, derive minimum appropriate claw lengths for routine foot trimming. The hind feet of 68 Holstein-Friesian dairy cows were collected post mortem, and the internal structures were visualised using x-ray µCT. The internal distance from the proximal limit of the wall horn to the distal tip of the dermis was measured from cross-sectional sagittal images. A constant was added to allow for a minimum sole thickness of 5 mm and an average wall thickness of 8 mm. Data were evaluated using descriptive statistics and two-level linear regression models with claw nested within cow. Based on 219 claws, the recommended dorsal wall length from the proximal limit of hoof horn was up to 90 mm for 96 per cent of claws, and the median value was 83 mm. Dorsal wall length increased by 1 mm per year of age, yet 85 per cent of the null model variance remained unexplained. Overtrimming can have severe consequences; the authors propose that the minimum recommended claw length stated in training materials for all Holstein-Friesian cows should be increased to 90 mm.

Development of a risk-ranking framework to evaluate potential high-threat microorganisms, toxins, and chemicals in food

Through a cooperative agreement with the U.S. Food and Drug Administration, the Institute of Food Technologists developed a risk-ranking framework prototype to enable comparison of microbiological and chemical hazards in foods and to assist policy makers, risk managers, risk analysts, and others in determining the relative public health impact of specific hazard-food combinations. The prototype is a bottom-up system based on assumptions that incorporate expert opinion/insight with a number of exposure and hazard-related risk criteria variables, which are propagated forward with food intake data to produce risk-ranking determinations. The prototype produces a semi-quantitative comparative assessment of food safety hazards and the impacts of hazard control measures. For a specific hazard-food combination the prototype can produce a single metric: a final risk value expressed as annual pseudo-disability adjusted life years (pDALY). The pDALY is a harmonization of the very different dose-response relationships observed for chemicals and microbes. The prototype was developed on 2 platforms, a web-based user interface and an Analytica(R) model (Lumina Decision Systems, Los Gatos, Calif., U.S.A.). Comprising visual basic language, the web-based platform facilitates data input and allows use concurrently from multiple locations. The Analytica model facilitates visualization of the logic flow, interrelationship of input and output variables, and calculations/algorithms comprising the prototype. A variety of sortable risk-ranking reports and summary information can be generated for hazard-food pairs, showing hazard and dose-response assumptions and data, per capita consumption by population group, and annual p-DALY.

Patient-reported Outcomes in End-of-Life Research in Pediatric Oncology

OBJECTIVE

The purpose of this review of published literature was to identify the number and focus of empirically based papers that included research methods used to directly solicit patient-reported outcomes (PRO) from pediatric oncology patients at end of life.

METHODS

Key terms including "pediatric or child and oncology or cancer and end of life or palliative or hospice or dying" were used with five data bases (PubMed, Ovid, Cochrane, PsycInfo & PsycArticles, and CINAHL) for English language literature published between January, 2001 and June, 2006. All retrieved documents were independently reviewed by a panel of six (nurses, physicians, and one psychologist) with backgrounds in pediatric oncology.

RESULTS

Thirty-five publications were identified but nine (25.7%) were eliminated from the analysis as they did not meet inclusion criteria. Of the remaining 26, four (15.4%) included patient-reported outcomes, six (23.1%) included parent only-reported outcomes, and five (19.2%) included staff only-reported outcomes. Nine (34.6%) were retrospective medical record reviews. Two (7.7%) included parent and record review data or parent and physician reports.

CONCLUSIONS

Empirically-based end-of-life publications in pediatric oncology are relatively few in number and nearly 85% of completed studies do not include PRO.

Histological findings of a choroidal neovascular membrane removed at the time of macular translocation in a patient previously treated with intravitreal bevacizumab treatment (Avastin)

AIM

To report the findings in a patient treated by repeated intravitreal bevacizumab (Avastin) injections, followed by macular relocation and excision of subfoveal choroidal neovascular membrane (CNV).

METHODS

Histopathological evaluation of the CNV specimen, including immunohistochemical assessment.

RESULTS

During surgical excision, the CNV seemed to be avascular and its underlying bed did not bleed. Histopathological examination revealed that the CNV comprised avascular fibrous subretinal tissue containing fibroblastic retinal pigment epithelial (RPE) cells, fragments of irregular thickened Bruch's membrane and fibrotic choroidal tissue containing some medium-sized vessels but no choriocapillaris.

CONCLUSIONS

The development of an RPE tear during the course of Avastin treatment may reflect contraction of the avascular subretinal tissue, whereas the lack of capillaries in both choroidal and subretinal components may be caused by the increased access of Avastin to the choriocapillaris in the presence of the RPE tear.

The effect of feeding tall fescue seed infected by Acremonium coenophialum on pregnancy and parturition in female rats

1. Female Sprague-Dawley rats (Rattus norvegicus) were randomly assigned to various dietary treatments containing: (1) 100% Purina rodent chow, ad libitum; (2) same as 1, but restricted to daily intake of 7; (3) 50% rodent chow (w/w) and 50% endophyte-free tall fescue (Festuca arundinacea) seed; (4) same as 3, but restricted to intake of 5; (5) 50% rodent chow, 25% endophyte-free tall fescue seed and 25% endophyte-infected (Acremonium coenophialum) tall fescue seed; (6) 50% rodent chow, 12.5% endophyte-free and 37.5% endophyte-infected tall fescue seed; and (7) 50% rodent chow and 50% endophyte infected tall fescue seed. 2. Average daily feed intakes and average daily weight gains decreased with higher levels of endophyte infected seed. 3. Frequency of litter production was affected by all endophyte-infected containing diets. 4. Conception was reduced only in dietary treatment (7). 5. Litter weights, number of pups per litter and weight per pup were proportionally reduced as higher levels of infected seed were incorporated in the ingested diets.

The effect of feeding endophyte infected tall fescue seed on reproductive performance in female rats

Female Sprague-Dawley rats (Rattus norvegicus) were randomly assigned to diets containing mixtures of rat chow and tall fescue (Festuca arundinacea) seed with 0, 5, 10, 20 and 40% infection levels of Acremonium coenophialum to assess the effect of the diets on the reproductive potential of rats. Rats fed 40% infected seed had decreased body weight, decreased mean percent body weight of uteri, failed to maintain normal estrous cycles and were unable to become pregnant. Animals fed a diet of 20% infected fescue seed had extended estrous cycles. There were no significant differences among the 0, 5 and 10% dietary treatments.