A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'.

Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation gives breeders, researchers, and growers information about cultivar specific traits such as fruit quality and disease resistance, and informs strategies to enhance postharvest storage. Here we present a haplotype-phased, chromosomal level genome of Malus domestica, 'WA 38', a new apple cultivar released to market in 2017 as Cosmic Crisp®. Using both short and long read sequencing data with a k-mer based approach, chromosomes originating from each parent were assembled and segregated. This is the first pome fruit genome fully phased into parental haplotypes in which chromosomes from each parent are identified and separated into their unique, respective haplomes. The two haplome assemblies, 'Honeycrisp' originated HapA and 'Enterprise' originated HapB, are about 650 Megabases each, and both have a BUSCO score of 98.7% complete. A total of 53,028 and 54,235 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to 'Gala', 'Honeycrisp', and other relevant cultivars highlighting major differences in genome structure and gene family circumscription. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that includes 'WA 38' (Washington State University), 'd'Anjou' pear (Auburn University), and many more. To ensure transparency, reproducibility, and applicability for any genome project, our genome assembly and annotation workflow is recorded in detail and shared under a public GitLab repository. All software is containerized, offering a simple implementation of the workflow.

Selection on standing genetic variation mediates convergent evolution in extremophile fish.

Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.

Pyogenic brain abscess associated with an incidental pulmonary arteriovenous malformation.

Pulmonary arteriovenous malformations (PAVMs) are rare and often asymptomatic vascular anomalies that can be associated with serious neurological consequences due to right-to-left shunting. We report a case of a woman in her 80s without substantial medical history who presented with a headache, weakness and personality changes, and was found to have a pyogenic brain abscess requiring emergent neurosurgical evacuation. The abscess grew oral flora, suspected to have reached the brain via an incidentally discovered PAVM. With drainage and antibiotics, the patient achieved a full recovery and the PAVM was embolised. To our knowledge, this is the oldest presentation of a PAVM-associated brain abscess in the published literature. Older patients may present without the typical signs and symptoms of a given illness, which complicates accurate diagnosis and treatment. Primary care physicians can help facilitate timely care and positive clinical outcomes.

Favorable response to second-line atezolizumab and bevacizumab following progression on nivolumab in advanced hepatocellular carcinoma: A case report demonstrating that anti-VEGF therapy overcomes resistance to checkpoint inhibition.

RATIONALE: Advanced hepatocellular carcinoma (HCC) remains a deadly disease in part due to decades of limited therapeutic options. With recent advances in our understanding of the tumor biology, several promising treatment strategies involving targeted and immunotherapies have emerged. However, enhancing their modest efficacy in HCC and other gastrointestinal malignancies is essential to improving survival. PATIENT CONCERNS: A man in his late 50s with a history of type 2 diabetes mellitus and morbid obesity initially presented with progressive abdominal pain and anorexia prompting an abdominal computed tomography scan that revealed a large solitary liver mass with extensive local involvement. DIAGNOSES: Although there were features consistent with a primary gastric tumor on subsequent endoscopic evaluation leading to early diagnostic uncertainty, his clinical picture, including a dominant liver mass, immunohistochemical staining profile, and significantly elevated alpha fetoprotein ultimately favored HCC. INTERVENTIONS: The patient received palliative systemic therapy with infusional fluorouracil for a presumed gastric primary, however restaging scans after 3 cycles demonstrated disease progression. The consensus from a multidisciplinary discussion was that his pathology was more consistent with primary HCC. He was subsequently started on nivolumab with a partial response, although after 5 months, he progressed prompting initiation of second-line atezolizumab and bevacizumab with a favorable response. OUTCOMES: The addition of atezolizumab and bevacizumab led to a sustained biochemical and radiographic response that appeared to overcome the resistance to nivolumab monotherapy. Aside from several mild immune-related adverse effects, his quality of life has greatly improved and he has tolerated treatment well to date. LESSONS: Our findings suggest that vascular endothelial growth factor inhibition can overcome resistance to checkpoint inhibition in advanced HCC by resulting in a unique synergy that has never before been described in patients. The biological rationale for this response is likely attributable to the immunomodulatory effects of antiangiogenic agents, promoting an immunostimulatory microenvironment that can be exploited by immune checkpoint inhibitors for more effective antitumor activity. Given the considerable benefit patients may derive following progression on first-line treatment, it is important to consider this strategic combination of therapies which can ultimately lead to improved patient outcomes.

A Quality Initiative for Reducing Postoperative Hypothermia for Neonatal Intensive Care Unit Surgical Patients.

INTRODUCTION: The association between hypothermia in the neonatal intensive care unit (NICU) patients and morbidity and mortality is well described. Neonates are at higher risk of perioperative hypothermia when compared to older children. Previous studies showed that quality improvement tools reduced postoperative hypothermia in NICU patients, but none showed sustained improvement at incidence rates of <10%. As a single institution, we aimed to reduce the percentage of postoperative temperatures < 36°C in NICU patients from 10% to 6% over 6 months and sustain for 6 months. METHODS: An interdisciplinary team created a key driver diagram and implemented interventions, including monthly reporting of postoperative hypothermia incidence to the anesthesiologists, individual feedback sessions with the anesthesiologists, use of a perioperative checklist, and continuous axillary temperature monitoring of the infant throughout the perioperative period. Data were collected retrospectively using a chart review of electronic medical records. The primary outcome was the percentage of hypothermic patients (T < 36°C) based on the first postoperative temperature taken in the NICU. We tracked this measure using a statistical control chart and evaluated it using Plan-Do-Study-Act cycles. RESULTS: From February 1, 2016 to May 30, 2018, data were collected for 554 patients (pre-intervention: 242 and post-intervention: 312). The percentage of surgical patients who returned to the NICU hypothermic decreased from 9.7% to 2.5% (P < 0.002)-a change sustained for greater than 12 months. CONCLUSIONS: Quality improvement tools are useful in reducing postoperative hypothermia in NICU surgical patients and in maintaining these results.

Regional sequence expansion or collapse in heterozygous genome assemblies.

High levels of heterozygosity present a unique genome assembly challenge and can adversely impact downstream analyses, yet is common in sequencing datasets obtained from non-model organisms. Here we show that by re-assembling a heterozygous dataset with variant parameters and different assembly algorithms, we are able to generate assemblies whose protein annotations are statistically enriched for specific gene ontology categories. While total assembly length was not significantly affected by assembly methodologies tested, the assemblies generated varied widely in fragmentation level and we show local assembly collapse or expansion underlying the enrichment or depletion of specific protein functional groups. We show that these statistically significant deviations in gene ontology groups can occur in seemingly high-quality assemblies, and result from difficult-to-detect local sequence expansion or contractions. Given the unpredictable interplay between assembly algorithm, parameter, and biological sequence data heterozygosity, we highlight the need for better measures of assembly quality than N50 value, including methods for assessing local expansion and collapse.