De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, ...we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9 d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100 kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV = 30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.
Maternal pregnancy nutrition influences fetal growth. Evidence is limited, however, on the relationship of maternal diet during pregnancy and lactation on infant postnatal growth and adiposity. Our ...purpose was to examine associations between maternal diet quality during pregnancy and lactation with offspring growth and body composition from birth to six months. Maternal diet quality was serially assessed in pregnancy and at one and three months postpartum, using the Healthy Eating Index⁻2015 in a cohort of 354 fully breastfeeding mother⁻infant dyads. Infant length-for-age (LAZ), weight-for-age (WAZ), and weight-for-length (WLZ) Z-scores were assessed at birth, one, three, and six months. Infant body fat percent (BF%), fat mass (FM), and fat-free mass (FFM) were measured at six months using dual-energy X-ray absorptiometry. Higher maternal diet quality from pregnancy through three months postpartum was associated with lower infant WLZ from birth to six months (
= 0.02) and BF% at six months (
≤ 0.05). Higher maternal diet quality at one and three months postpartum was also associated with lower infant FM at six months (
< 0.01). In summary, maternal diet quality during pregnancy and lactation was inversely associated with infant relative weight and adiposity in early postnatal life. Additional research is needed to explore whether associations persist across the life course.
Full breastfeeding (FBF) is promoted as effective for losing pregnancy weight during the postpartum period. This study evaluated whether longer FBF is associated with lower maternal postpartum weight ...retention (PPWR) as compared to a shorter FBF duration. The MILK (Mothers and Infants Linked for Healthy Growth) study is an ongoing prospective cohort of 370 mother-infant dyads, all of whom fully breastfed their infants for at least 1 month. Breastfeeding status was subsequently self-reported by mothers at 3 and 6 months postpartum. Maternal PPWR was calculated as maternal weight measured at 1, 3, and 6 months postpartum minus maternal prepregnancy weight. Using linear mixed effects models, by 6 months postpartum, adjusted means ± standard errors for weight retention among mothers who fully breastfed for 1-3 (3.40 ± 1.16 kg), 3-6 (1.41 ± 0.69 kg), and ≥6 months (0.97 ± 0.32 kg) were estimated. Compared to mothers who reported FBF for 1-3 months, those who reported FBF for 3-6 months and ≥6 months both had lower PPWR over the period from 1 to 6 months postpartum (
= 0.04 and
< 0.01, respectively). However, PPWR from 3 to 6 months was not significantly different among those who reported FBF for 3-6 versus ≥6 months (
> 0.05). Interventions to promote FBF past 3 months may increase the likelihood of postpartum return to prepregnancy weight.
How predictable are life trajectories? We investigated this question with a scientific mass collaboration using the common task method; 160 teams built predictive models for six life outcomes using ...data from the Fragile Families and Child Wellbeing Study, a high-quality birth cohort study. Despite using a rich dataset and applying machine-learning methods optimized for prediction, the best predictions were not very accurate and were only slightly better than those from a simple benchmark model. Within each outcome, prediction error was strongly associated with the family being predicted and weakly associated with the technique used to generate the prediction. Overall, these results suggest practical limits to the predictability of life outcomes in some settings and illustrate the value of mass collaborations in the social sciences.
Abstract
To determine effects of dam parity on perinatal nutrient availability in beef cattle, data and samples were collected from 18 primiparous and 35 multiparous spring-calving Sim-Angus dams and ...their calves. Time to stand was recorded and neonatal vigor assessed. Jugular blood was collected from a subset of calves at 0 (post-standing and pre-suckling) 6, 12, 24, 48, and 72 h of age, and blood chemistry panels were completed. Expelled placentas were dissected, dried, and weighed. Prepartum maternal circulating glucose, non-esterified fatty acids (NEFA), triglycerides, and urea N were analyzed. All statistical models included the fixed effect of dam parity, and calf sex (when P ≤ 0.25) was included for calf and placental variables. Effects of sampling hour, and parity × hour were included for calf metabolites over time using repeated measures. Multiparous dams had greater body weight prepartum (P < 0.001) but similar (P = 0.25) body condition score. Maternal circulating urea N and triglycerides were greater (P ≤ 0.05) in multiparous dams pre-calving. Calves born to primiparous dams weighed 10% less (P ≤ 0.04) at birth with smaller (P ≤ 0.01) heart and abdominal girths. Cotyledonary, intercotyledonary, and total placental masses were less (P ≤ 0.05) for primiparous dams. Dam parity did not affect (P ≥ 0.58) calf time to stand, vigor score at 10 min, or rectal temperature. Serum glucose was greater (P = 0.03) at 0 h but less (P ≤ 0.04) at all other hours in calves from primiparous dams. Calves from primiparous dams had greater (P ≤ 0.02) serum NEFA at 6, 12, and 24 h although plasma triglycerides were greater (P < 0.001) at 6 h. Calves from primiparous dams had greater (P ≤ 0.04) serum urea N at 12 h and creatinine at 12 and 24 h. Plasma insulin was greater (P ≤ 0.04) in calves from multiparous dams at 12, 48, and 72 h, but parity did not affect (P ≥ 0.18) serum total protein or plasma cortisol. Serum aspartate aminotransferase was greater (P ≤ 0.04) at 6 and 24 h, creatine kinase was greater at 24 h, and gamma-glutamyl transpeptidase was less (P ≤ 0.04) at 6, 12, and 24 h, for calves from primiparous dams. Calves born to primiparous dams had greater (P ≤ 0.02) total bilirubin and direct bilirubin at 12 and 24 h. Data indicate that calves born to first-parity heifers had decreased perinatal nutrient availability, resulting in reduced fetal and placental growth, as well as greater energy reserve mobilization and metabolic indicators of stress as neonates.
Calves born to first-parity heifers had altered nutrient availability during both the prenatal and neonatal periods. Primiparous dams gave birth to calves that were smaller at birth, with smaller placentas, but had greater energy reserve mobilization and metabolic indicators of stress as neonates.
Lay Summary
Approximately two-thirds of beef calf deaths prior to weaning occur within the first 3 wk after birth. The goal to have heifers produce their first calf by 2 yr of age likely contributes to factors that limit nutrients available for fetuses and calves immediately after birth. However, little is known about differences in heifers (first parity) and cows (later parities) regarding factors affecting calf resilience, such as fetal growth and calf metabolism shortly after birth. Our data show that calves born to first-parity heifers had altered nutrient availability, demonstrated through smaller placentas, lower birth weights, and altered metabolites in early life. Although calves had similar vigor and ability to maintain body temperature, calves born to first-parity heifers had to mobilize more energy and had lower insulin during the first 3 d post-birth. Calves born to first-parity heifers had greater indicators of stress during the first 72 h of life not associated with calving difficulties. Overall, these effects may have increased morbidity and mortality of calves born to first-parity heifers if they were in a less intensively-managed system. Better understanding of challenges faced by calves born to first-parity dams provides opportunities for their improved management.
Objective
Report clinical outcomes of dogs with surgically excised mast cell tumors (MCT) and soft tissue sarcomas (STS).
Study design
Prospective clinical study.
Sample population
Fifty‐three dogs ...with 52 MCT (50 low grade, 2 high grade) and 19 STS (12 grade I, 6 grade II, 1 grade III).
Methods
All dogs were examined at 3, 6, 12, 18, and 24 months postoperatively, with cytologic or histopathologic evaluation of suspected local recurrences. Dogs euthanized because of study tumor‐related causes underwent necropsy.
Results
Median intraoperative margins were 20 mm and 30 mm wide for MCT and STS, respectively, with 1 fascial plane resected en bloc. The narrowest histologic tumor‐free margins measured <1 mm in 21 of 52 (40%) MCT and 7 of 19 (37%) STS. All dogs were followed for 24 months. Two of 50 (4%) low‐grade MCT were diagnosed, with local recurrence 181 and 265 days postoperatively. Two of 36 (6%) dogs with low‐grade MCT developed visceral metastasis 181 and 730 days postoperatively. One of 2 dogs with high‐grade MCT developed local recurrence 115 days postoperatively. No local recurrence or metastasis was diagnosed after excision of 19 STS.
Conclusion
Local recurrence rates among predominantly low‐ to intermediate‐grade MCT and STS were low, despite a high prevalence of histologic tumor‐free margins <1 mm. Surgical recommendations for high‐grade tumors cannot be extrapolated from this population.
Clinical significance
Surgeons should seek to achieve microscopically complete excision for MCT and STS while minimizing patient morbidity and considering limitations of histopathology in predicting outcomes.
The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. ...Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.
Biologic therapies targeting tumor necrosis factor (TNF)‐alpha have become a mainstay in the management of a number of autoimmune diseases. We report a series of adverse skin eruptions in six ...patients (four females, two males, age: 21–58 years, mean: 39) receiving 4 months to 10 years (mean 3.1 years) of anti‐TNF‐alpha therapies (infliximab, n = 4; adalimumab, n = 1 or etanercept, n = 1). The following drug‐associated diagnoses were made in eight skin biopsies performed at Massachusetts General Hospital between 3/2007 and 10/2010: pustular folliculitis, psoriasis, interface dermatitis, neutrophilic eccrine hidradenitis, Sweet's syndrome, lupus, vasculitis and palmoplantar pustulosis. The descriptions of neutrophilic eccrine hidradenitis‐like and Sweet's‐like hypersensitivity eruptions induced by anti‐TNF‐alpha therapies are the first such cases described in the literature. Each cutaneous eruption improved or resolved with switching to a different TNF‐alpha inhibitor, discontinuation of the anti‐TNF‐alpha agent, and/or topical or systemic steroids. There was a clear chronologic relationship with, and clinical remission upon withdrawal or steroid suppression of the anti‐TNF‐alpha agents. The mechanism for such diverse cutaneous eruptions among this class of medications remains poorly understood. The cutaneous adverse reaction profile of TNF‐alpha inhibitors is broad and should be considered in the histopathologic differential in this clinical setting.
Hawryluk EB, Linskey KR, Duncan LM, Nazarian RM. Broad range of adverse cutaneous eruptions in patients on TNF‐alpha antagonists.
To examine Hedgehog signaling in cutaneous fibrosing disorders for which effective approved therapies are lacking, expand our knowledge of pathophysiology, and explore the rationale for targeted ...inhibition.
Stain intensity and percentage of cells staining for Sonic hedgehog (Shh), Indian hedgehog (Ihh), Patched (Ptch), glycogen synthase kinase 3 β (GSK3-β), β-catenin, and Snail were evaluated in human skin biopsy specimens of keloid, hypertrophic scar (Hscar), scleroderma, nephrogenic systemic fibrosis (NSF), scar, and normal skin using a tissue microarray.
Ihh, but not Shh, was detected in a significantly larger proportion of cells for all case types. Ptch, GSK3-β, and β-catenin showed a gradient of expression: highest in NSF and keloid; moderate in normal skin, scar, and Hscar; and lowest in scleroderma. Snail expression was binary: low in normal skin but high in all fibrosing conditions studied.
Differential overexpression of Hedgehog and Snail in cutaneous fibrosing disorders demonstrates a role for targeted inhibition. Ptch, GSK3-β, and β-catenin can help differentiate scleroderma from NSF in histologically subtle cases. Differences in expression between keloid and hypertrophic scar support the concept that they are pathophysiologically distinct disorders. Our findings implicate Snail as a target for the prevention of fibrogenesis or fibrosis progression and may offer a means to assess response to therapy.
Basaloid squamous cell carcinoma (bSCC) is an uncommon variant of squamous cell carcinoma, which may overlap histologically with basal cell carcinoma with squamous metaplasia (BCCm).
To aid in the ...differentiation of these neoplasms using immunohistochemical staining because of the worse prognosis associated with bSCC.
Using immunohistochemical techniques, we investigated BerEp4, cytokeratin 17 (CK17), and cytokeratin 14 (CK14) protein expression in 25 cases of bSCC (8 cutaneous 32%, 12 aerodigestive tract 48%, and 5 lymph node metastases 20%) and 43 cases of BCCm (39 cutaneous 91%, and 4 metastases 9%). An immunoreactivity score was assigned using the percentage of tumor cells staining and the pattern of expression. Interobserver agreement for 2 independent pathologists was assessed using a κ coefficient.
The mean percentage of staining was significantly higher in BCCm, compared with bSCC (BerEp4, P = .006; CK17, P < .001; CK14, P < .001; unpaired t test), with 58% of BCCm cases (25 of 43) displaying diffuse staining for all markers, and nearly all (98%; 42 of 43) displaying diffuse staining for CK17 and CK14. In contrast, no bSCC cases (0%) displayed diffuse staining for all 3 markers, and only 8% (2 of 25) displayed diffuse staining for CK17 and CK14. High interobserver agreement was determined.
BerEp4 alone is unreliable for differentiation between BCCm and bSCC, and the addition of either CK14 or CK17 will augment the sensitivity and negative predictive value of BerEp4 staining in BCCm and bSCC diagnosis.
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