SASpector: analysis of missing genomic regions in draft genomes of prokaryotes.

Summary: Missing regions in short-read assemblies of prokaryote genomes are often attributed to biases in sequencing technologies and to repetitive elements, the former resulting in low sequencing coverage of certain loci and the latter to unresolved loops in the de novo assembly graph. We developed SASpector, a command-line tool that compares short-read assemblies (draft genomes) to their corresponding closed assemblies and extracts missing regions to analyze them at the sequence and functional level. SASpector allows to benchmark the need for resolved genomes, can be integrated into pipelines to control the quality of assemblies, and could be used for comparative investigations of missingness in assemblies for which both short-read and long-read data are available in the public databases.

A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog.

Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the anish nteric irme atalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes.

COVID-19 and physical activity in sedentary individuals: differences in metabolic, cardiovascular, and respiratory responses during aerobic exercise performed with and without a surgical face masks.

Background: The Coronavirus-19 (COVID-19) impairs metabolic, cardiovascular, and pulmonary functions in human metabolism, and wearing face masks is recommended for the prevention of contracting or exposing others to cardio-respiratory infections. Since the effect of wearing a surgical face mask (SFM) on cardiopulmonary exercise capacity has not been systematically reported we aimed to determine the effects of wearing SFM during an incremental walking test on metabolic, cardiovascular, and pulmonary gas exchange responses in sedentary individuals.

Methods: The evaluations were performed using a repeated measures study design.

Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study.

In vertebrates, the mineralocorticoid receptor (MR) is a steroid-activated nuclear receptor (NR) that plays essential roles in water-electrolyte balance and blood pressure homeostasis. It belongs to the group of oxo-steroidian NRs, together with the glucocorticoid (GR), progesterone (PR), and androgen (AR) receptors. Classically, these oxo-steroidian NRs homodimerize and bind to specific genomic sequences to activate gene expression.

Printed Graphene Derivative Circuits as Passive Electrical Filters.

The objective of this study is to inkjet print resistor-capacitor () low pass electrical filters, using a novel water-based cellulose graphene ink, and compare the voltage-frequency and transient behavior to equivalent circuits constructed from discrete passive components. The synthesized non-toxic graphene-carboxymethyl cellulose (G-CMC) ink is deposited on mechanically flexible polyimide substrates using a customized printer that dispenses functionalized aqueous solutions. The design of the printed first-order and second-order low-pass filters incorporate resistive traces and interdigitated capacitors.

Diagnostic microRNA markers for screening sporadic human colon cancer and active ulcerative colitis in stool and tissue.

By routinely and systematically being able to perform quantitative stem-loop reverse transcriptase followed by TaqMan PCR expression analysis on stool and tissue samples using fifteen human (Homo sapiens, hsa) micro(mi)RNA genes selected by careful analysis of the peer-reviewed literature, we were able to monitor changes at various stages of CRC, allowing for reliable diagnostic screening of colon cancer particularly at the early, pre-malignant stages, and for difficult-to-treat active ulcerative colitis (UC). Although the expression of some of the miRNA genes tested in tissue showed less variability in CRC or UC patients than in stool, the stool by itself appears well-suited to screening. A miRNA approach using stool samples promises to offer more sensitivity and specificity than currently used screening genomic, methylomic or proteomic methods for colon cancer.

Standardization for transcriptomic molecular markers to screen human colon cancer.

Establishing test performance criteria for a transcriptomic colon cancer marker approach must be carried out in a standardized fashion in order tso ensure that the test will perform the same way in any laboratory, anywhere. Condition of sample preservation and shipping prior to total RNA extraction is critical, and we recommend preserving stool samples in an appropriate preservative and shipping them in cold packs so as to keep stools at 4 degrees C. It is not necessary to isolate colonocytes to obtain adequate RNA for testing.

Transcriptomic molecular markers for screening human colon cancer in stool and tissue.

There is a need for sensitive and specific diagnostic molecular markers that can be used to monitor early patterns of gene expression in non-invasive exfoliated colonocytes shed in the stool, and in situ in adenoma-carcinoma epithelium of the colon. RNA-based detection methods are more comprehensive than either DNA-, protein- or methylation-based screening methods. By routinely and systematically being able to perform quantitative gene expression studies on these samples using less than ten colon cancer genes selected by the enormous resources of the National Cancer Institute's Cancer Genome Anatomy Project, we were able to monitor changes at various stages in the neoplastic process, allowing for reliable diagnostic screening of colon cancer particularly at the early, pre-malignant stages.

Improved methods for extracting RNA from exfoliated human colonocytes in stool and RT-PCR analysis.

In order to diagnose colon cancer at an earlier, more localized stage, there is a need to develop diagnostic markers (genes) which can detect early patterns of gene expression in exfoliated colonocytes shed in the stool during routine screening for this disease. An RNA-based detection is more pertinent than either a DNA-based or a protein-based method as a screening procedure, but it has not been widely used as a cancer screen because of the difficulty of handling and stabilizing the RNA molecule. We describe a method that permits extraction of intact nondegraded total RNA from human colonocytes in stool and from normal and malignant colon tissues (which were employed for comparison with stool).

Suppression of nocturnal acid secretion with famotidine accelerates gastric ulcer healing.

Although nocturnal acid secretion has been emphasized in the pathophysiology and treatment of duodenal ulcer, its importance in gastric ulcer disease has been questioned. To explore this area, this multicenter U.S.

Absence of luminal intrinsic factor after gastric bypass surgery for morbid obesity.

Abnormally low serum cobalamin levels (less than 180 pg/ml) have been observed in 154 of 429 patients (36%) at an average of 22 months (range 3-64 months) after gastric bypass surgery for morbid obesity. Twenty-four patients underwent a Schilling test and retrograde endoscopy of the bypassed gastric segment to determine the presence of intrinsic factor (IF) in gastric aspirates and in mucosal biopsies at 22 +/- 4 months after surgery. Five patients had a normal cobalamin level (405 +/- 44 pg/ml), and gastric juice intrinsic factor was present in three of them (11 +/- 7 ng/ml).

Gastric ulcer healing after laser treatment in dogs.

Endoscopic laser photocoagulation of ulcers is increasingly used to produce hemostasis in patients who are actively bleeding or in patients with stigmata of recent hemorrhage. Little information is available describing ulcer healing rates after laser treatments. The aim of this study was to compare the healing rates of gastric ulcers treated with laser energy (Nd:YAG) with untreated ulcers in dogs.

Intraoperative video panendoscopy for diagnosing sites of chronic intestinal bleeding.

Intraoperative video panendoscopy was performed in 14 patients with chronic, recurrent gastrointestinal bleeding. All of the study patients had undergone extensive and expensive diagnostic testing including multiple radiographic contrast studies of the gastrointestinal tract, upper and lower endoscopy, nuclear bleeding scans, and selective mesenteric angiography without definition of the bleeding source. Intraoperative video panendoscopy, employing a segmental advance and look technique, allowed visualization and transillumination of the entire gut and identified mucosal disease in 13 patients (93 percent).

Multicenter trial of sucralfate suspension for the treatment of reflux esophagitis.

The efficacy of sucralfate suspension in the treatment of reflux esophagitis was assessed in a multicenter, randomized, double-blind, placebo-controlled trial. Sixty-eight patients with symptomatic and endoscopic esophagitis received either sucralfate suspension (n = 31) or liquid placebo (n = 37) for eight weeks. The two groups were comparable at entry with the exception that despite randomization, a disproportionately high number of patients with esophageal ulcers were assigned to receive sucralfate.

Gastric bypass.

The success of gastric bypass probably depends on factors other than merely the restrictive size of the gastric pouch and outlet. Postoperative dumping and a mild degree of malabsorption derived from the redirection of intestinal contents contribute to long-term success. Thus, gastric bypass combines some elements of both malabsorptive and gastric restrictive procedures.

Histologic and endoscopic studies before and after gastric bypass surgery.

The purposes of this study were to establish a standardized multiparameter analysis system for histologic grading of gastritis and to compare histologic changes with endoscopic findings in the proximal and distal bypassed stomach in obese patients undergoing gastric bypass surgery. Three groups, comprising a total of 91 patients, were studied: a preoperative group (34 patients), a postoperative group at one year (33 patients), and a postoperative group at two years (24 patients). the biopsy specimens from the proximal and distal bypassed stomach were compared in all groups.

Effects of oral potassium supplements on upper gastrointestinal mucosa: multicenter clinical comparison of three formulations and placebo.

In a carefully controlled multicenter investigation of the effects of oral potassium chloride (KCl) supplements on the gastrointestinal mucosa, 120 healthy men with no endoscopically apparent gastrointestinal lesions were confined to a research ward for 18 days. By random assignment, they were given 60 mEq/day (20 mEq TID) of KCl as either a microencapsulated gelatin capsule, a wax/polymer matrix tablet, or a powder-in-liquid formulation or a placebo capsule for two weeks. All subjects were given glycopyrrolate concomitantly to delay gastric emptying.

Lidocaine inhibition of esophageal peristalsis and lower esophageal sphincter pressure in baboons.

Intravenous lidocaine was infused at 0.82 ml/min in a concentration of 1.2 mg/ml (2.

Retrograde endoscopy of the bypassed stomach segment after gastric bypass surgery: unexpected lesions.

Surgical measures for the treatment of morbid obesity include gastric bypass of the stomach and duodenum. We endoscopically evaluated the bypassed segments in 51 patients three to 24 months after a standard gastric bypass procedure. Retrograde endoscopy was successful in 33 of the patients (65%).

The bypassed stomach.

Retrograde duodenogastroscopy solves the problem of postoperative evaluation of the gastric bypass patient. The stomach may be bypassed to treat morbid obesity, but it no longer need be inaccessible. Endoscopic gastritis is rare in the proximal gastric pouch but common in the distal gastric segment and may be related to the presence of bile.

The Greenville gastric bypass. Progress report at 3 years.

Two hundred and ten morbidly obese patients underwent a standardized gastric bypass procedure between February 1980 and November 1983. We conclude, based on 100% follow-up, that the operation is safe (operative mortality--1%, significant complications--10%) and effective (reoperation rate--4%). Only one patient failed to lose more than 25% of preoperative weight.