CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny.

BACKGROUND: The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield new insights not revealed with a single modality. For example, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) simultaneously profiles the RNA transcriptome and the surface protein expression. The surface protein markers in CITE-Seq can be used to identify cell populations similar to the iterative filtration process in flow cytometry, also called "gating", and is an essential step for downstream analyses and data interpretation. While several packages allow users to interactively gate cells, they often do not process multi-omic sequencing datasets and may require writing redundant code to specify gate boundaries. To streamline the gating process, we developed CITEViz which allows users to interactively gate cells in Seurat-processed CITE-Seq data. CITEViz can also visualize basic quality control (QC) metrics allowing for a rapid and holistic evaluation of CITE-Seq data. RESULTS: We applied CITEViz to a peripheral blood mononuclear cell CITE-Seq dataset and gated for several major blood cell populations (CD14 monocytes, CD4 T cells, CD8 T cells, NK cells, B cells, and platelets) using canonical surface protein markers. The visualization features of CITEViz were used to investigate cellular heterogeneity in CD14 and CD16-expressing monocytes and to detect differential numbers of detected antibodies per patient donor. These results highlight the utility of CITEViz to enable the robust classification of single cell populations. CONCLUSIONS: CITEViz is an R-Shiny app that standardizes the gating workflow in CITE-Seq data for efficient classification of cell populations. Its secondary function is to generate basic feature plots and QC figures specific to multi-omic data. The user interface and internal workflow of CITEViz uniquely work together to produce an organized workflow and sensible data structures for easy data retrieval. This package leverages the strengths of biologists and computational scientists to assess and analyze multi-omic single-cell datasets. In conclusion, CITEViz streamlines the flow cytometry gating workflow in CITE-Seq data to help facilitate novel hypothesis generation.

Predicting the Strength of Cohesive and Adhesive Interparticle Interactions for Dry Powder Inhalation Blends of Terbutaline Sulfate with α-Lactose Monohydrate.

Grid-based systematic search methods are used to investigate molecule-molecule, molecule-surface, and surface-surface contributions to interparticle interactions in order to identify the crystal faces that most strongly affect particle behavior during powder blend formulation and delivery processes. The model system comprises terbutaline sulfate (TBS) as an active pharmaceutical ingredient (API) and α-form lactose monohydrate (LMH). A combination of systematic molecular modeling and X-ray computed tomography (XCT) is used to determine not only the adhesive and cohesive interparticle energies but, also the agglomeration behavior during manufacturing and de-agglomeration behavior during delivery after inhalation. This is achieved through a detailed examination of the balance between the adhesive and cohesive energies with the XCT results confirming the blend segregation tendencies, through the particle-particle de-agglomeration process. The results reveal that the cohesive interaction energies of TBS-TBS are higher than the adhesive energies between TBS and LMH, but that the cohesive energies of LMH-LMH are the smallest between molecule and molecule, molecule and surface, and surface and surface. This shows how systematic grid-search molecular modeling along with XCT can guide the digital formulation design of inhalation powders in order to achieve optimum aerosolization and efficacy for inhaled medicines. This will lead to faster pharmaceutical design with less variability, higher quality, and enhanced performance.

Novel Role of Dehydrated Human Amnion/Chorion Membrane in Healing of Denuded Ureter in Robot-Assisted Excision of Endometriosis.

Ureteral injury is an uncommon but potentially morbid complication following any open or endoscopic pelvic procedure. Gynecologic surgeries alone make up 50 percent of nonurologic ureteral injuries leading to prolonged hospital stays, secondary interventions, and potential loss of renal function. The use of AmnioFix ® a processed dehydrated, immunologically privileged cellular amniotic membrane allograft has been well established in urologic and gynecologic procedures. These allografts contain human extracellular matrix components, growth factors, and cytokines that mediate inflammation and facilitate would healing. We report the first application of AmnioFix on a denuded ureter during a case of robotic-assisted excision of endometriosis. We include a literature review and discussion on the management outcomes of iatrogenic injury to the ureters.

Robot-Assisted Laparoscopic Adrenalectomy for Rare Myxoid Adrenocortical Carcinoma.

BACKGROUND: Surgical resection remains the standard treatment for adrenocortical carcinoma. Higher rates of local and peritoneal recurrence have been reported with the laparoscopic approach compared to open resection, although the evidence is limited. A dilemma occurs when tumors appear benign in nature, measure >5 cm, or when patients request a minimally invasive surgical approach. We describe the first reported case to date of successful robot-assisted laparoscopic adrenalectomy for myxoid variant adrenocortical carcinoma. CASE PRESENTATION: A 38 year old female presented with a large 8.0 cm enhancing left adrenal mass concerning for pheochromocytoma, given refractory hypertension and symptoms of palpitations and headaches. Functional work up was negative. The patient underwent robot-assisted laparoscopic left adrenalectomy after appropriate alpha and beta blockade. Histological sections demonstrated a cortical neoplasm with prominent myxoid changes consistent with myxoid adrenocortical carcinoma. The patient's symptoms resolved and serial imaging demonstrated no recurrence three and nine months, post-operatively. CONCLUSION: Myxoid adrenocortical carcinoma is a rare and aggressive entity best managed with surgical resection. Though open resection for invasive adrenal cancer remains the gold standard, minimally invasive approaches are being increasingly used, whether deliberately or not. We describe the first reported robot-assisted laparoscopic adrenalectomy for invasive myxoid adrenocortical carcinoma.

Laparoscopic augmentation cystoplasty: a comparison between native ileum and small intestinal submucosa in the porcine model.

OBJECTIVES: To determine the feasibility of laparoscopic augmentation cystoplasty (LAC) in the porcine model and to compare LAC using standard bowel vs a small intestinal submucosa (SIS) allograft. MATERIALS AND METHODS: Fourteen female pigs underwent LAC; six had standard ileal AC and eight AC with SIS. All the pigs had limited cystometrogram studies before surgery to determine bladder capacity. At 6 weeks after surgery the pigs were anaesthetized, the bladder capacities were re-assessed and then the pigs were killed; the bladders were harvested and examined histologically. RESULTS: In all, 12 of 14 pigs completed the 6-week survival period; two pigs from the SIS group died from urinary ascites secondary to anastomotic leaks at the cystoplasty site. There were no complications in the ileal augmentation group. The operative duration was similar in both groups. The bladder capacities increased significantly in both groups, although more reliably in the native ileum group. In two pigs in the SIS group there was no increase in bladder capacity. CONCLUSIONS: LAC is feasible in the porcine model and results in a significant increase in bladder capacity. AC using SIS does not appear to increase bladder capacity as reliably as native ileum, and has a higher complication rate.

Spontaneous dissolution of a guaifenesin stone.

Guaifenesin is a commonly used expectorant whose use may lead to the occasional formation of guaifenesin urinary stones. We herein describe a patient who was taking 2400 mg Guaifenesin per day as part of his treatment for asthma. He had a past history of a guaifenesin stone removed ureteroscopically. His current presentation was with a 9 mm by 6 mm stone in the upper left ureter, seen on CT scan, and treated initially with a ureteral stent and hydration. After 3 weeks, the stone had disappeared, as confirmed by repeat CT scan. The genesis and treatment of guaifenesin stones is discussed.

Technique for ensuring negative surgical margins during laparoscopic partial nephrectomy.

BACKGROUND AND PURPOSE: Obtaining a negative surgical margin during laparoscopic partial nephrectomy (LPN) is paramount to optimizing the oncologic efficacy of the procedure. Limitations of laparoscopy hinder the ability to extrapolate the intraparenchymal tumor extension from the exophytic portion. We developed a technique wherein ultrasound-confirmed needle localization of the deep tumor margin prior to tumor extirpation ensured negative surgical margins. MATERIALS AND METHODS: Our technique was developed and initially tested using an agar-based ultrasound phantom designed to mimic 2-cm exophytic renal tumors. Needle placement was imaged with ultrasonography and subsequently correlated with findings on sectioning of the tumor mimic. Laparoscopic extirpation of the tumor mimic following needle placement was carried out in a pelvic trainer. The technique has subsequently been incorporated into our LPN technique in four patients. RESULTS: Ultrasound-confirmed needle localization of intraparenchymal tumor extension was feasible and reproducible in an ultrasound phantom. Ultrasound findings correlated with gross findings. Needle placement prior to tumor resection helped to ensure negative surgical margins when applied in the pelvic trainer and when used in three patients. In the remaining patient, improper needle placement resulted in a grossly positive deep margin. CONCLUSION: Ultrasound-confirmed needle placement effectively and reproducibly marks the deep margin of small renal tumors in a mimic as well as in vivo. Our needle technique eliminates the guesswork and unreliability associated with mental visualization and extrapolation of tumor extent during LPN.

A novel technique to prevent inadvertent sheath migration.

Inadvertent trocar-sheath migration is annoying to the surgeon and may result in serious visceral injury. Herein is described a novel technique to prevent such migration. A 0.25-in. Penrose drain is wrapped around the trocar-sheath unit as a collar to prevent sheath migration.