Multidisciplinary approach to the management of renal angiomyolipoma with inferior vena cava thrombus and pulmonary embolism: a case report.

Renal angiomyolipoma (AML) is a benign tumor with rare venous extension. We present a case of a patient with renal AML with inferior vena cava (IVC) tumor thrombus and acute pulmonary embolism (PE). A 34-year-old female presented with chest pain.

Attempted repair of chest wall injury following penetrating injury with surgical stabilization rib and autologous bone graft: A case report.

Rib fractures are one of the most common injuries following blunt trauma. When associated with penetrating trauma, the projectile velocity and immense energy transfer cause significant rib fracture displacement and fragmentation. As a result, these patients are potentially exposed to an even higher risk of complications compared to those seen in more simple rib fractures.

A paradoxical internal hernia at Brolin's anti-obstruction stitch following Roux-en-Y gastric bypass: a case report.

Internal hernias are a rare but morbid complication following Roux-en-Y gastric bypass surgery. The incorporation of Brolin's anti-obstruction stitch has historically demonstrated a significant reduction in the incidence of internal hernias following Roux-en-Y gastric bypass. We present an ironic and unique case of a patient with small bowel herniation into a defect between Brolin's stitch and the stapled closed common enterotomy of the jejunojejunostomy and technical considerations to decrease internal hernias at this site in the future.

Operative technique for a successful laparoscopic en-bloc resection of gastrogastric fistula following roux-en-Y gastric bypass.

Gastrogastric fistulas are rare complications following Roux-en-Y gastric bypass surgery and are characterized by a fistulous connection between the gastric pouch and the remnant stomach. The presentation is often variable and a high-index of suspicion must be maintained for accurate and timely diagnosis. In this case report, we provide a detailed review of the technical steps taken to successfully resect a gastrogastric fistula en-bloc laparoscopically with an unremarkable post-operative course.

Hardware failure for anterior chest wall and costal cartilage injuries: A single-center experience.

Background: Often missed in blunt chest wall injury, costal cartilage injuries can cause chest wall instability, refractory pain, and deformity. Notably, there is only a small amount of evidence regarding hardware performance when applied to costal cartilage. In a prior multicenter study, hardware failure rate was found to be approximately 3% following surgical stabilization of rib fractures (SSRFs) for all fracture locations.

Hepatic sialic acid synthesis modulates glucose homeostasis in both liver and skeletal muscle.

Objective: Sialic acid is a terminal monosaccharide of glycans in glycoproteins and glycolipids, and its derivation from glucose is regulated by the rate-limiting enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE). Although the glycans on key endogenous hepatic proteins governing glucose metabolism are sialylated, how sialic acid synthesis and sialylation in the liver influence glucose homeostasis is unknown. Studies were designed to fill this knowledge gap.

A case report of acute appendicitis complicated by pylephlebitis: medical and surgical management.

Pylephlebitis is a suppurative thrombus of the portal vein and/or its branches secondary to an intra-abdominal infection. Acute appendicitis is the most common cause of emergency operation in general surgery and is typically treated with antibiotics and timely appendectomy with minimal adverse outcomes (Ferris M, Quan S, Kaplan BS, et al. The global incidence of appendicitis: a systematic review of population-based studies.

In- and out-of-hospital outcomes following surgical stabilization of rib fractures in 80 years and older: A single-institution experience.

Background: Surgical stabilization of rib fractures (SSRF) has demonstrated benefit in patients with flail chest and multiple displaced fractures. There is mounting evidence for SSRF following chest wall injury (CWI) for the geriatric trauma population. A recent multi-center retrospective study highlighted a mortality benefit even for those patients aged 80 years and older.

The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process.

There is growing evidence that cytonuclear incompatibilities (i.e. disruption of cytonuclear coadaptation) might contribute to the speciation process.

Multidisciplinary Simulation of Trauma in Pregnancy with Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) Utilization.

Background Studies have demonstrated the use of resuscitative endovascular balloon occlusion catheters of the aorta (REBOA) in the setting of postpartum hemorrhage and traumatic hemorrhagic shock. However, REBOA is infrequently utilized leading to a lack of clinician comfort. This study's aim was to demonstrate the utility of REBOA in a hemorrhaging pregnant trauma patient and improve clinician comfort with the placement of REBOA while emphasizing collaboration between medical specialties.

A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia.

Adiponectin, encoded by ADIPOQ, is an insulin-sensitizing, anti-inflammatory, and renoprotective adipokine that activates receptors with intrinsic ceramidase activity. We identified a family harboring a 10-nucleotide deletion mutation in ADIPOQ that cosegregates with diabetes and end-stage renal disease. This mutation introduces a frameshift in exon 3, resulting in a premature termination codon that disrupts translation of adiponectin's globular domain.

You aren't IMMUNE to the ceramides that accumulate in cardiometabolic disease.

Obesity leads to persistent increases in immune responses that contribute to cardiometabolic pathologies such as diabetes and cardiovascular disease. Pro-inflammatory macrophages infiltrate the expanding fat mass, which leads to increased production of cytokines such as tumor necrosis factor-alpha. Moreover, saturated fatty acids enhance signaling through the toll-like receptors involved in innate immunity.

Reproductive isolation among lineages of Silene nutans (Caryophyllaceae): A potential involvement of plastid-nuclear incompatibilities.

Early stages of speciation in plants might involve genetic incompatibilities between plastid and nuclear genomes, leading to inter-lineage hybrid breakdown due to the disruption between co-adapted plastid and nuclear genes encoding subunits of the same plastid protein complexes. We tested this hypothesis in Silene nutans, a gynodioecious Caryophyllaceae, where four distinct genetic lineages exhibited strong reproductive isolation among each other, resulting in chlorotic or variegated hybrids. By sequencing the whole gene content of the four plastomes through gene capture, and a large part of the nuclear genes encoding plastid subunits from RNAseq data, we searched for non-synonymous substitutions fixed in each lineage on both genomes.

Endoscopic and surgical management of Bouveret's syndrome complicated by gallstone ileus.

Bouveret's syndrome is a rare complication that occurs most commonly in elderly patients with multiple comorbidities. It is secondary to an impacted gallstone causing gastric outlet obstruction from a cholecystoduodenal fistula, and there is no defined standardized management in current literature. A 92-year-old woman presents to our tertiary community hospital with abdominal discomfort concerning for bowel obstruction.

Vaccines are not one size fits all, just like medications: rotavirus vaccine study.

The current global coronavirus disease 2019 pandemic has shown us once again how important vaccination is in controlling and preventing the spread of deadly diseases. Vaccinations are one of the most tried and tested public health measures aimed at the prevention and eventual eradication of various diseases. Many debilitating diseases like polio have been eradicated in countries like India due to effective vaccination strategies.

yacrd and fpa: upstream tools for long-read genome assembly.

Motivation: Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.

Results: We introduce two tools: yacrd for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps.

Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit.

Background: While respiratory viral infections are recognized as a frequent cause of illness in hematopoietic stem cell transplantation (HSCT) recipients, HCoV-OC43 infections have rarely been investigated as healthcare-associated infections in this population.

Objectives: In this report, HCoV-OC43 isolates collected from HSCT patients were retrospectively characterized to identify potential clusters of infection that may stand for a hospital transmission.

Study Design: Whole-genome and S gene sequences were obtained from nasal swabs using next-generation sequencing and phylogenetic trees were constructed.

Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Mitochondrial Genome.

Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions.

Graph analysis of fragmented long-read bacterial genome assemblies.

Motivation: Long-read genome assembly tools are expected to reconstruct bacterial genomes nearly perfectly; however, they still produce fragmented assemblies in some cases. It would be beneficial to understand whether these cases are intrinsically impossible to resolve, or if assemblers are at fault, implying that genomes could be refined or even finished with little to no additional experimental cost.

Results: We propose a set of computational techniques to assist inspection of fragmented bacterial genome assemblies, through careful analysis of assembly graphs.

A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.

Genome sequencing of virus has become a useful tool for better understanding of virus pathogenicity and epidemiological surveillance. Obtaining virus genome sequence directly from clinical samples is still a challenging task due to the low load of virus genetic material compared to the host DNA, and to the difficulty to get an accurate genome assembly. Here we introduce a complete sequencing and analyzing protocol called V-ASAP for Virus Amplicon Sequencing Assembly Pipeline.

Assisted transcriptome reconstruction and splicing orthology.

Background: Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq data identify barely 21 % of the expressed transcripts. While waiting for algorithms and sequencing techniques to improve - as has been strongly suggested in the literature - it is important to evaluate assisted transcriptome prediction; this is the question of how alternative transcription in one species performs as a predictor of protein isoforms in another relatively close species.

ProCARs: Progressive Reconstruction of Ancestral Gene Orders.

Background: In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs).

Retention-error patterns in complex alphanumeric serial-recall tasks.

We propose a new method based on an algorithm usually dedicated to DNA sequence alignment in order to both reliably score short-term memory performance on immediate serial-recall tasks and analyse retention-error patterns. There can be considerable confusion on how performance on immediate serial list recall tasks is scored, especially when the to-be-remembered items are sampled with replacement. We discuss the utility of sequence-alignment algorithms to compare the stimuli to the participants' responses.

Genome dedoubling by DCJ and reversal.

Background: Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant proportion of segmental duplications in Mammals, and the Drosophila species group, to breakpoints in rearrangement events.

Results: In this paper, we introduce and study a combinatorial problem, inspired from the breakpoint-duplication phenomenon, called the Genome Dedoubling Problem.

Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis.

Despite their monophyletic origin, mitochondrial (mt) genomes of plants and animals have developed contrasted evolutionary paths over time. Animal mt genomes are generally small, compact, and exhibit high mutation rates, whereas plant mt genomes exhibit low mutation rates, little compactness, larger sizes, and highly rearranged structures. We present the (nearly) whole sequences of five new mt genomes in the Beta genus: four from Beta vulgaris and one from B.