Non-invasive stereotactic ablative boost in patients with locally advanced cervical cancer.

INTRODUCTION: The current literature is insufficient to guide care for patients with cervical cancer ineligible for brachytherapy. Stereotactic ablative radiotherapy boost is a clinical necessity for these patients, but highly debated among radiation oncologists. OBJECTIVE: To report toxicity and survival outcomes in a large cohort of patients with locally advanced cervical cancer treated with a non-invasive stereotactic ablative radiotherapy boost instead of brachytherapy METHODS: Patients with locally advanced cervical cancer were entered, between January 2008 and December 2018, who were recommended definitive intent external boost after pelvic radiotherapy to 45-50.4 Gy concurrent with weekly cisplatin and simultaneous/sequential nodal boost up to 55-66 Gy. Simulation CT was facilitated using radio-opaque fiducials, empty rectum, dedicated bladder filling, and whole body vaculoplastic immobilization. Kaplan-Meier survival estimates were used to report local/regional recurrences, distant metastases, cancer-specific survival, and overall survival. RESULTS: A total of 25 patients were analyzed. Median follow-up was 25 months (range 6-54). Patients received stereotactic ablative radiotherapy due to refusal of brachytherapy (9/25, 36%), medical co-morbidities limiting implantation (9/25, 36%), or technical infeasibility (7/25, 28%). Typical fractionation was 24-30 Gy in 4-5 fractions (24/25, 96%). The most common long-term toxicity was grade 1-2 vaginal dryness, discomfort, stenosis, and/or dyspareunia (4/25, 16%). One patient had new post-treatment grade 4 fistula in an area of previous tumor erosion (1/25, 4%). Overall survival, cancer specific survival, loco-regional control, and distant control were 95.5%, 100%, 95.5%, and 89.1%, respectively, at 2 years. CONCLUSION: Further study of stereotactic ablative radiotherapy boost for cervical cancer is needed; a brachytherapy-similar approach portends clinical success with 95.5% overall survival and loco-regional control at 2 years.

The UCSC Archaeal Genome Browser: 2012 update.

The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 archaeal genomes, plus 31 genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available archaeal genomes.

Structural insights into fibrinogen dynamics using amide hydrogen/deuterium exchange mass spectrometry.

We determined the amide hydrogen/deuterium exchange profile of native human fibrinogen under physiologic conditions. After optimization of the quench and proteolysis conditions, more than 1,200 peptides were identified by mass spectrometry, spanning more than 90% of the constituent Aα, Bß, and γ chain amino acid sequences. The compact central and distal globular regions of fibrinogen were well protected from deuterium exchange, with the exception of the unfolded amino-terminal segments of the Aα and Bß chains extending from the central region, and the short γ chain "tail" extending from each distal globular region. The triple-helical coiled-coil regions, which bridge the central region to each distal region, were also well protected with the exception of a moderately fast-exchanging area in the middle of each coiled-coil adjacent to the γ chain carbohydrate attachment site. These dynamic regions appear to provide flexibility to the fibrinogen molecule. The γ chain "out loop" contained within each coiled-coil also exchanged rapidly. The αC domain (Aα 392-610) exchanged rapidly, with the exception of a short segment sandwiched between a conserved disulfide linkage in the N-terminal αC subdomain. This latter finding is consistent with a mostly disordered structure for the αC domain in native fibrinogen. Analysis of the dysfibrinogen Bß 235 Pro/Leu, which exhibits abnormal fibrin structure, revealed enhanced deuterium exchange surrounding the Pro/Leu substitution site as well as in the vicinity of the high affinity calcium binding site and the A knob polymerization pocket within the γC domain. The implication of these changes with respect to fibrin structure is discussed.

Disseminated Miliary and Intestinal Tuberculosis Mimicking Inflammatory Bowel Disease.

The hematogenous dissemination of Mycobacterium tuberculosis (M. tb) is commonly via the pulmonary system. Less commonly, ingestion of M. tb can lead to primary intestinal tuberculosis (TB), often misdiagnosed as inflammatory bowel disease (IBD). In extremely rare cases, the dissemination can involve cardiac infiltration/tuberculoma. One such case involves a 21-year-old man from Guatemala who spoke a rare dialect of Spanish with nonspecific complaints and an abdominal CT scan showing terminal ileum thickening suggestive of Crohn's disease (CD). A colonoscopy revealed ileitis and tissue biopsy showed granulomatous inflammation with a positive acid-fast bacillus (AFB) stain and positive blood cultures isolated for TB. Chest CT angiography (CTA) also revealed miliary nodules and a right atrial mass was confirmed with cardiac MRI. Viral serology revealed chronic hepatitis B virus (HBV) co-infection, but the patient was HIV-negative. Anti-tubercular therapy (ATT) with rifampin, isoniazid, pyrazinamide, and ethambutol (RIPE), in addition to tenofovir, was initiated, followed by a complicated hospital stay including rifampin-induced bone marrow suppression. Ultimately, he was discharged on isoniazid, pyrazinamide, ethambutol, levofloxacin, and entecavir. Intestinal TB can be misdiagnosed as IBD with the administration of steroids, potentially worsening infection. A systemic approach to clinical investigation with a thorough history using medical translators can lead to early diagnosis and treatment of intestinal and disseminated TB.

Surgical repair of distal triceps rupture: a systematic review of outcomes and complications.

Background: Triceps tendon injury is rare and accounts for only 2% of all tendinous injuries. It typically occurs after trauma or physical strain with eccentric loading. Treatment involves surgical repair, commonly with either transosseous bone tunnels or suture anchors. Nonsurgical management is typically reserved for low-demand or high-risk patients, as this is associated with deficits in strength and functional disability. Despite several recent high-quality observational studies that have added to our understanding of outcomes after surgical repair, we are not aware of a systematic review that includes literature published after 2015. In addition, prior reviews did not compare outcomes between different surgical repair methods, particularly transosseous bone tunnel and suture anchor techniques. Methods: This systematic review examines published literature between January 1970 and May 2021 in PubMed, Scopus, and Cochrane databases to further examine reported functional outcomes and compare those outcomes between the two surgical repair methods. Results: Our literature search yielded 309 results, of which only 16 met inclusion criteria. At the latest follow-up, the mean Disabilities of Arm, Shoulder, and Hand score was 4, the mean Quick Disabilities of Arm, Shoulder, and Hand score was 8, the mean Mayo Elbow Performance Score was 92, the mean American Shoulder and Elbow Surgeons-Elbow score was 99, the mean modified American Shoulder and Elbow Surgeons score was 94, the mean Oxford Elbow Score was 43, and the mean isokinetic muscle strength testing was 87%. A very high percentage (95%) of patients reported being satisfied with the repair. Preinjury levels of function were achieved in 92% of patients, and 100% regained at least a score of 4 of 5 for gross muscle strength. Complications occurred in 15% of cases, of which retears accounted for 5%. Subanalysis of cases with reported repair types revealed a significantly higher overall complication rate with transosseous repairs than with suture anchor repairs (18% vs. 8%, P = .008) as well as a higher retear rate in the transosseous repair group (7% vs. 2%, P = .03). Conclusion: Patient-reported outcome measures were favorable for both suture anchor and transosseous tunnel repair methods. Suture anchor repair showed significantly better results with regard to isokinetic strength testing, complication rates, and retear rates. Further study is needed to establish superiority of either technique and cost-efficacy. In light of the evidence supporting greater biomechanical strength and lower clinical rates of failure, surgeons may consider use of a suture anchor technique for repair of distal triceps ruptures.

Influence of Body Mass Index and Gender on Stigmatization of Obesity.

BACKGROUND: Stigmatization and discrimination of people with obesity due to their weight are a common problem that may lead to additional weight gain. This study evaluated the influence of different parameters on the stigmatization of obesity. MATERIAL AND METHODS: Participants of six groups (general population, patients with obesity, medical students, physicians, nurses in training and nurses; n = 490) answered the short-form fat phobia scale (FPS) between August 2016 and July 2017. The influence of body mass index (BMI), gender and other factors on total scores and single adjective pairs was analyzed. RESULTS: A total of 490 participants were evaluated. The total mean FPS rating was 3.5 ± 0.6. FPS was significantly lower (more positive) in participants with obesity (3.2 ± 0.7) compared with participants without obesity (3.5 ± 0.5, p < 0.001). Individuals with obesity and diabetes rated the FPS significantly lower (more positive), whereas age and gender did not have a significant influence. Participants with obesity linked obesity more often with good self-control (p < 0.001), being shapely (p = 0.002), industrious (p < 0.001), attractive (p < 0.001), active (p < 0.001), self-sacrificing (p < 0.001) and having more willpower (p < 0.001) than the participants without obesity. Females rated more positive in shapely versus shapeless (p = 0.038) and attractive versus non-attractive (p < 0.001) than males. CONCLUSIONS: The present study shows that stigmatization of obesity is present in medical professionals as well as the general population. People affected by obesity characterized other people with obesity more positively (e.g. attractive or active), whereas people without obesity linked negative characteristics with obesity. Gender had an influence only on single items of FPS but did not affect overall stigmatization of obesity.

Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons.

von Economo neurons (VENs) are bipolar, spindle-shaped neurons restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear to be selectively vulnerable to neuropsychiatric and neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing of frontoinsula layer 5 identifies a transcriptomically-defined cell cluster that contained VENs, but also fork cells and a subset of pyramidal neurons. Cross-species alignment of this cell cluster with a well-annotated mouse classification shows strong homology to extratelencephalic (ET) excitatory neurons that project to subcerebral targets. This cluster also shows strong homology to a putative ET cluster in human temporal cortex, but with a strikingly specific regional signature. Together these results suggest that VENs are a regionally distinctive type of ET neuron. Additionally, we describe the first patch clamp recordings of VENs from neurosurgically-resected tissue that show distinctive intrinsic membrane properties relative to neighboring pyramidal neurons.

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type.

We describe convergent evidence from transcriptomics, morphology, and physiology for a specialized GABAergic neuron subtype in human cortex. Using unbiased single-nucleus RNA sequencing, we identify ten GABAergic interneuron subtypes with combinatorial gene signatures in human cortical layer 1 and characterize a group of human interneurons with anatomical features never described in rodents, having large 'rosehip'-like axonal boutons and compact arborization. These rosehip cells show an immunohistochemical profile (GAD1+CCK+, CNR1-SST-CALB2-PVALB-) matching a single transcriptomically defined cell type whose specific molecular marker signature is not seen in mouse cortex. Rosehip cells in layer 1 make homotypic gap junctions, predominantly target apical dendritic shafts of layer 3 pyramidal neurons, and inhibit backpropagating pyramidal action potentials in microdomains of the dendritic tuft. These cells are therefore positioned for potent local control of distal dendritic computation in cortical pyramidal neurons.

A Low-Cost Imaging Method for the Temporal and Spatial Colorimetric Detection of Free Amines on Maize Root Surfaces.

Plant root exudates are important mediators in the interactions that occur between plants and microorganisms in the soil, yet much remains to be learned about spatial and temporal variation in their production. This work outlines a method utilizing a novel colorimetric paper to detect spatial and temporal changes in the production of nitrogen-containing compounds on the root surface. While existing methods have made it possible to conduct detailed analysis of root exudate composition, relatively less is known about where in the root system exudates are produced and how this localization changes as the root grows. Furthermore, there is much to learn about how exudate localization and composition varies in response to stress. Root exudates are chemically diverse secretions composed of organic acids, amino acids, proteins, sugars, and other metabolites. The sensor utilized for the method, ninhydrin, is a colorless substance in solution that reacts with free amino groups to form a purple dye. A detection paper was developed by formulating ninhydrin into a print solution that was uniformly deposited onto paper with a commercial ink jet printer. This "ninhydrin paper" was used to analyze the chemical makeup of root surfaces from maize seedlings grown vertically on germination paper. Through contact between the ninhydrin paper and seedling root surfaces, combined with images of both the seedlings and dried ninhydrin papers captured using a standard flatbed scanner, nitrogen-containing substances on the root surface can be localized and concentration of signal estimated for over 2 weeks of development. The method was found to be non-inhibiting to plant growth over the analysis period although damage to root hairs was observed. The method is sensitive in the detection of free amines at concentrations as little as 140 µM. Furthermore, ninhydrin paper is stable, showing consistent color changes up to 2 weeks after printing. This relatively simple, low-cost method could contribute to a better understanding of root exudates and mechanisms used by plants to interact with the complex soil environment during growth and development.

PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX.

Next generation sequencing of the RNA content of single cells or single nuclei (sc/nRNA-seq) has become a powerful approach to understand the cellular complexity and diversity of multicellular organisms and environmental ecosystems. However, the fact that the procedure begins with a relatively small amount of starting material, thereby pushing the limits of the laboratory procedures required, dictates that careful approaches for sample quality control (QC) are essential to reduce the impact of technical noise and sample bias in downstream analysis applications. Here we present a preliminary framework for sample level quality control that is based on the collection of a series of quantitative laboratory and data metrics that are used as features for the construction of QC classification models using random forest machine learning approaches. We've applied this initial framework to a dataset comprised of 2272 single nuclei RNA-seq results and determined that ~79% of samples were of high quality. Removal of the poor quality samples from downstream analysis was found to improve the cell type clustering results. In addition, this approach identified quantitative features related to the proportion of unique or duplicate reads and the proportion of reads remaining after quality trimming as useful features for pass/fail classification. The construction and use of classification models for the identification of poor quality samples provides for an objective and scalable approach to sc/nRNA-seq quality control.

An Extended Polyanion Activation Surface in Insulin Degrading Enzyme.

Insulin degrading enzyme (IDE) is believed to be the major enzyme that metabolizes insulin and has been implicated in the degradation of a number of other bioactive peptides, including amyloid beta peptide (Aß), glucagon, amylin, and atrial natriuretic peptide. IDE is activated toward some substrates by both peptides and polyanions/anions, possibly representing an important control mechanism and a potential therapeutic target. A binding site for the polyanion ATP has previously been defined crystallographically, but mutagenesis studies suggest that other polyanion binding modes likely exist on the same extended surface that forms one wall of the substrate-binding chamber. Here we use a computational approach to define three potential ATP binding sites and mutagenesis and kinetic studies to confirm the relevance of these sites. Mutations were made at four positively charged residues (Arg 429, Arg 431, Arg 847, Lys 898) within the polyanion-binding region, converting them to polar or hydrophobic residues. We find that mutations in all three ATP binding sites strongly decrease the degree of activation by ATP and can lower basal activity and cooperativity. Computational analysis suggests conformational changes that result from polyanion binding as well as from mutating residues involved in polyanion binding. These findings indicate the presence of multiple polyanion binding modes and suggest the anion-binding surface plays an important conformational role in controlling IDE activity.

Assessment of consistency in contouring of normal-tissue anatomic structures.

The purpose of this work is to estimate the uncertainty in the manual contouring of normal anatomical structures. The heart, esophagus, and spinal cord were contoured manually on six sets of computed tomography images by six dosimetrists whose experience ranged from 1 year to over 15 years. To determine the differences between inter- and intraobserver variations, each data set was contoured by one of the dosimetrists five times and once each by the five other dosimetrists. The magnitude of the discrepancies in delineating the contours was assessed. Intradosimetrist contouring discrepancies were as follows: esophagus, average 0.3 cm and maximum 2.9 cm; heart, average 0.5 cm and maximum 7.6 cm; and spinal cord, average 0.1 cm and maximum 0.7 cm. Interdosimetrist contouring discrepancies were as follows: esophagus, average 0.4 cm and maximum 3.1 cm; heart, average 0.7 cm and maximum 8.1 cm; and spinal cord, average 0.2 cm and maximum 0.9 cm. Significant discrepancies can occur when normal anatomic structures are contoured manually. Interdosimetrist discrepancies are typically slightly greater than intradosimetrist discrepancies. The magnitude of the discrepancies does not appear to be correlated to the experience of the dosimetrist.