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Background: Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome., Findings: Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding., Conclusions: The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

Background: The American Academy of Neurology (AAN) does not recommend routine use of prophylactic antiepileptic drugs (pAEDs) in patients with newly diagnosed brain tumors. If used in the perioperative setting, discontinuation is suggested after the first postoperative week. It is unclear whether such recommendations are followed. Our objective was to compare our perioperative and long-term pAED use in glioma patients with AAN practice parameters., Methods: Retrospective chart review was performed on 578 glioma patients from 2006 to 2013. Seizures and AED use were assessed at surgery, 3 months postoperatively and death, last visit or 16 months postoperatively. Patients were divided into three groups at surgery: seizure-free with pAED, seizure-free without pAED, and seizure patients. Long-term pAED use was defined as continued use at 3 months postsurgery without seizures. pAEDs efficacy, factors influencing its use, and survival were examined., Results: Out of 578 patients identified, 330 (57.1%) were seizure-naïve preoperatively. There were no significant differences in age, histology, tumor location or resection status between seizure-free populations with and without prophylaxis. Of 330 seizure-naïve patients, 205 (62.1%) received pAEDs at surgery. Ninety-six (46.9%) of those patients were still on pAEDs 3 months postsurgery (median use = 58 days). Rate of long-term prophylaxis use decreased by 13.5% over 6 years (70.3% in 2006; 56.8% in 2012). Phenytoin was preferred in 2006 (98.2%) with increasing use of levetiracetam over 6 years (44.6% in 2012). The only predictive factor for pAED use was complete resection ( P = .0069). First seizure prevalence was similar in both seizure-free populations ( P = .91). The seizure population had more men ( P = .007), younger patients ( P < .0001), lower-grade gliomas ( P = .0003) and survived longer ( P = .001) compared with seizure-free populations., Conclusions: In our center, long-term prophylactic AED use is high, deviating from current AAN Guidelines. Corrective measures are warranted.

Endogenous circulating digoxin-like immunoreactive factors (DLIF) are known to cross-react with antibodies to digoxin and to inhibit Na+/K(+)-transporting ATPase (Na+K+ATPase; EC 3.6.1.37). Moreover, increasing the immunoassay temperature from 4 to 37 degrees C markedly decreases DLIF from human cord serum. We tested several compounds, including hormonal steroids, bile salts, lipids, and methionine-enkephalin, for their ability to cross-react with two commercially available 125I digoxin RIAs, to inhibit porcine Na+K+ATPase, and to see whether they present the same incubation temperature dependence as human cord serum. Except for methionine-enkephalin, all compounds were inhibitors of Na+K+ATPase in the range of 1-10 mmol/L. Progesterone exhibited the highest cross-reactivity in the two RIAs. The apparent digoxin immunoreactivity for the majority of the cross-reacting steroids, bile salts, and linoleic acid was markedly decreased by increasing the incubation temperature from 4 to 37 degrees C, whereas estriol, pregnanediol, and nonspecific compounds (e.g., ethanol, human serum albumin) did not appear to be temperature-sensitive. Both lysophosphatidyl lipids gave an increased apparent digoxin concentration with increasing incubation temperature. Our data suggest that numerous weakly cross-reactive compounds can parallel the response of human cord serum. However, the temperature-dependent effect could be an additional criterion for identifying DLIF.