bluuebunny/crossref_metadata_2025 huggingface dataset:
Reliability and Validity of Visual Estimation of Femoral Head Hypoperfusion on Perfusion MRI in Legg-Calve-Perthes Disease
Authors: Chong David Y. , Schrader Tim , Laine Jennifer C. , Yang Scott , Gilbert Shawn R. , Kim Harry K.W.
Published: August 2021

Background:

Assessing the severity of Legg-Calve-Perthes disease is important for treatment decision-making and determining prognosis. Perfusion magnetic resonance imaging (MRI) scans have improved our ability to assess femoral head hypoperfusion, and the use of an image analysis software called HipVasc (Scottish Rite for Children, Dallas TX) has allowed precise quantification for research purposes. In the clinical setting, using HipVasc software is not practical, and visual estimation is used to assess hypoperfusion. Currently, the reliability of visual estimation is unknown. The purpose of this study was to determine the reliability and validity of visual estimation of hypoperfusion on perfusion MRI and compare the results to measurements obtained with the HipVasc software.

Methods:

Fourteen pediatric orthopaedic surgeons, divided into 4 groups, participated in this study. Each surgeon completed a 30-minute in-person training on HipVasc before proceeding. Stratified by category of severity, 122 MRIs were randomly assigned to 1 of the 4 groups so that each group member measured the same set of ∼30 MRIs. Each surgeon documented their visual estimation of hypoperfusion first, then used HipVasc to measure the hypoperfusion and recorded their results. Interobserver reliability was assessed at the group level by calculating the intraclass correlation coefficient.

Results:

Good correlation and reliability was found between the visual estimate and HipVasc measurements with an overall mean intraclass correlation coefficient of 0.87 and mean Pearson coefficient of 0.90. The mean interobserver reliability of visual estimation was 0.84. Observers had a tendency to overestimate hypoperfusion with visual estimation.

Conclusions:

This study demonstrates the reliability and validity of visual estimation as a clinically applicable method for determining femoral head hypoperfusion. Our study is the first to measure the reliability of visual estimation and HipVasc with a large cohort of clinicians, specifically pediatric orthopaedic surgeons with varied experience in graphical software analysis. We recommend using visual estimation as a clinically applicable method to make treatment decisions, and its accuracy is comparable to HipVasc software analysis.

Level of Evidence:

Level III—diagnostic.
Prospective Evaluation of Tarsal Coalition Excision Show Significant Improvements in Pain and Function
Authors: Mahan Susan T. , Miller Patricia E. , Kasser James R. , Spencer Samantha A.
Published: August 2021

Background:

Excision of pediatric tarsal coalition has been successful in most patients. However, some patients have ongoing pain after coalition excision. This study prospectively assessed patient-based clinical outcomes before and after surgical excision of tarsal coalition, with particular emphasis on comparison to radiologic imaging.

Methods:

We prospectively studied 55 patients who had symptomatic coalition excision for 2 years postoperatively. Patients filled out the modified American Orthopaedic Foot and Ankle Society score, the University of California Los Angeles activity score, and the simple question “does foot pain limit your activity” at 4 different time points: preoperative, 6 months postoperative, 12 months postoperative, and 24 months postoperative. Comparisons were done utilizing patient demographics, imaging parameters, and patient-reported outcomes.

Results:

Compared with preoperative levels, patients showed improvements in all outcome parameters. Patients with calcaneonavicular coalitions showed initial rapid improvement with later slight decline, while patients with talocalcaneal coalitions showed more steady improvement; both were similar at 2 years postoperatively.

Conclusions:

This prospective study demonstrated remarkable clinical improvements after tarsal coalition excision regardless coalition type, though postoperative courses differed between calcaneonavicular and talocalcaneal types. Finally, a subset of patients has ongoing activity limiting foot pain after coalition excision which could not be explained by the data in this study.

Level of Evidence:

Level II—prospective cohort study.
Fracture of the Posteromedial Tubercle of the Talus: Surgical Approach With Case Examples
Authors: Steffensmeier Andrew M. , Matar Robert , Chung David , Dixon Tonya , Laughlin Richard
Published: August 2021

Ten to 21% of talus fractures involve the posteromedial tubercle. A search query of the institutional database was performed for all adult patients that sustained talar fractures over an 8-year period. Fifteen of these patients had isolated fractures of the posteromedial tubercle. Seventy-three percent of the patients had an associated subtalar dislocation; in all of these, the fracture of the posteromedial tubercle was comminuted. Plain radiographs have been shown to lack sensitivity in detecting posterior process fractures, which includes posteromedial and posterolateral tubercles. In this group, 86% had initial plain radiographs that missed the fracture. This paper reviews the posteromedial tubercle fractures and fracture patterns to illustrate surgical strategies and approaches for open reduction and internal fixation. Exposures are described for access to the posteromedial tubercle and strategies for distraction and reduction are described.

Level of Evidence: Diagnostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Arthroscopic Triangular Fibrocartilage Complex Reconstruction Using a Palmaris Longus Tendon Graft
Authors: Abe Shingo , Kataoka Toshiyuki , Suzuki Rie , Yasui Yukihiko , Kuriyama Kohji
Published: August 2021

Patients suffer from persistent ulnar wrist pain and distal radioulnar joint instability because of chronic triangular fibrocartilage complex (TFCC) foveal tear are treated with TFCC reconstruction. We performed an arthroscopic TFCC reconstruction using a palmaris longus tendon graft that provided a minimally invasive procedure. After confirming the TFCC foveal tear and stability between the TFCC remnant and radius, the bone tunnel was made in the ulna from the ulnar shaft to ulnar fovea. The position of the bone tunnel was checked by fluorography and arthroscopy. Curved bendable 18-gauge needles into which 3-0 nylon sutures were inserted in a loop shape were passed through the tunnel from the ulnar side, and both volar-side and dorsal-side TFCC remnants were penetrated. The nylon suture was extracted from the arthroscopic 4/5 portal, and the palmaris longus tendon graft was introduced into the joint. The graft was passed through the TFCC remnant and ulnar bone tunnel from the arthroscopic portal and fixed to the ulna using an interference screw. This procedure was indicated for TFCC foveal tears with intact radial-side TFCC remnants. If the radial-side tear and instability between the TFCC and radius coexist, this technique is contraindicated, and stabilization of both the radial and ulnar sides of the TFCC should be considered. This arthroscopic technique does not violate the distal radioulnar joint capsule, extensor carpi ulnaris tendon, or tendon sheath. In addition, it helps to stabilize the ulnar carpal complex.
Practical Techniques to Ensure Success in Digital Ring Avulsion Injuries
Authors: Gardiner Sonya , Friebel Thessa Rebecca , Bray Juliette , Anadkat Meera , Nikkhah Dariush
Published: August 2021

A ring avulsion results from a longitudinal traction to a digit. We discuss practical microsurgical techniques essential in achieving good functional outcomes in these challenging cases, including aggressive debridement of the affected tissues and vessels, liberal use of vein grafts and arterialized venous flow through flaps when needed, and a meticulous microsurgical technique. We have found that patient selection is key in digit salvage and a good outcome is often achieved with the winning triad of optimal patient factors, surgical factors, and intensive hand therapy. We also include a case performed by our senior author to illustrate what can be achieved.
Reconstruction of Pelvic Exenteration Defect with Free Anterolateral Thigh Flap: A Case Report
Authors: Prasidha Ines , Moisidis Elias , Hsieh Frank
Published: August 2021

The pedicled anterolateral thigh flap, with or without the vastus lateralis muscle, has been described for pelvic exenteration defect reconstruction. However, its use as a free flap for this type of defect is not routinely followed. To reconstruct an extensive pelvic defect in the presence of two ostomies, we describe a free anterolateral thigh flap with deep inferior epigastric pedicles as recipient vessels.
Square-root Palatoplasty: Comparing a Novel Modified-Furlow Double-opposing Z-palatoplasty Technique to Traditional Straight-line Repair
Authors: Tanaka Shoichiro A. , Coombs Demetrius M. , Tuncer Fatma B. , Shikhman Alexander , Keenan Patricia , McNinch Neil L. , Murthy Ananth S.
Published: August 2021

Background:

The purpose of this study was to introduce a modification of the Furlow double-opposing Z-plasty (DOZ)—the square-root palatoplasty (SRP)—and critically evaluate outcomes compared to children who underwent straight-line repair (SLR).

Methods:

A retrospective review was performed of all nonsyndromic children undergoing primary cleft palate closure either by SRP or SLR at our institution between 2009 and 2017. Outcomes of interest included rates/location of oronasal fistula, secondary surgery, speech delay/deficits, resonance, nasal air emission (NAE), articulation errors, and velopharyngeal function. Logistic regression was used to assess for the effect of surgery type on outcomes while controlling for Veau cleft type, age, and gender.

Results:

Seventy-eight patients were included; 46 (59%) underwent SRP, and 32 (41%) underwent SLR. The mean follow-up was 4.07 years. When compared to SLR, children who underwent SRP were less likely to have oronasal fistula [odds ratio (OR) 4.8, P = 0.0159], speech delay/deficits (OR 7.7, P < 0.001), NAE (OR 9.7, P < 0.001), articulation errors (OR 10.2, P < 0.001), or need for secondary speech surgery (OR 13.2, P < 0.0002). Patients who underwent SRP were also more likely to have normal resonance (78.26% versus 43.75%, respectively; P = 0.0043) and good VP function (84.78% versus 56.25%, respectively; P = 0.0094).

Conclusions:

This study describes and evaluates outcomes following a modified-Furlow DOZ technique—the SRP. After adjusting for Veau classification, age, and gender in nonsyndromic children, SRP is associated with significantly less speech delay/deficits, NAE, articulation errors, and need for secondary speech surgery when compared to children who underwent SLR.
Advances in Tissue Expander Technology Enable Early Targeted Intervention in Prepectoral Breast Reconstruction
Authors: Liu Farrah , Henn Dominic , Shrefren Kerry , Momeni Arash
Published: August 2021

Background:

Seroma and infection are among the most common complications after staged prepectoral implant-based reconstruction. Advances in tissue expander technology permit seroma aspiration via an integrated drain port, thus, holding promise for improving clinical outcomes.

Methods:

A prospectively maintained database of patients who had undergone immediate prepectoral breast reconstruction using the Sientra AlloX2 tissue expander was used to determine the rate of postoperative seroma formation, its volume and microbiological spectrum, as well as postoperative complications.

Results:

49 patients (mean age: 49 years, mean body mass index: 24.5 kg/m2) underwent 79 prepectoral breast reconstructions. Seroma was clinically suspected in 26 reconstructions (32.9%) and was easily aspirated in all cases via the integrated drain port. Importantly, periprosthetic fluid was successfully aspirated in 45 reconstructions (57%) without any clinical evidence for seroma, with aspirated cumulative fluid volumes exceeding 10 cm3 in 12 reconstructions. Bacterial cultures from aspirated fluid were positive in six patients (12.2%), of whom two developed clinical signs of infection, at which point targeted antibiotic treatment was initiated.

Conclusions:

Our study demonstrates that routine office-based aspiration of periprosthetic fluid via the integrated drain port of the AlloX2 tissue expander not only permits successful aspiration of periprosthetic fluid but also allows aspirated fluid to be sent for culture, thus, providing a lead-time advantage for initiation of targeted antibiotic therapy in cases of postoperative surgical site infection. Furthermore, our observations indicate that positive bacterial cultures in the absence of clinical signs of infection do not mandate antibiotic therapy.
Contamination Resulting From a Broken 125I Seed During a Brachytherapy Procedure
Authors: Buckley Lesley , Fraser Danielle J. , MacPherson Miller , Foottit Claire
Published: August 2021

Brachytherapy programs within radiation therapy departments are subject to stringent radiation safety requirements in order to ensure the safety of the staff and patients. Training programs often include brachytherapy-specific radiation safety training modules that address the specific risks associated with radioactive sources, emergency procedures, and regulatory requirements specific to the use of radioisotopes. Unlike other uses of radioactive materials, brachytherapy uses sealed sources and therefore under routine operations does not encounter radioactive contaminants. This article presents an unusual clinical situation in which an 125I brachytherapy seed was damaged during routine clinical workflow, resulting in radioactive contamination within the clinical environment. Decisions made at the time of the incident resulted in contamination that spread beyond the initial location. The incident highlighted a shortcoming of the radiation safety program in preparing staff for the possibility of having to deal with unsealed radioactivity. Brachytherapy programs would be strengthened by including training specific to radioactive contamination in their emergency training to equip staff to respond to unexpected damage to the sealed sources.
The Effect of Therapeutic Alliance on Attitudes Toward Psychiatric Medications in Schizophrenia
Authors: Lim Madeline , Li Ziqiang , Xie Huiting , Tan Bhing Leet , Lee Jimmy
Published: August 2021

Purpose/Background

The differential influence of therapeutic alliance with different health care professionals on patients' medication adherence has never been examined.

Methods/Procedures

Ninety-five stable outpatients (91 patients with schizophrenia and 4 patients with schizoaffective disorder) were recruited. Individual, clinical, and medication factors were assessed, along with drug attitude (10-item Drug Attitude Inventory). Comparison on these factors was made between outpatients who identified psychiatrists as the health care professional most involved in their care, as compared with other health care professionals.

Findings/Results

Older age, longer duration of illness, presence of medical comorbidities, lower levels of internalized stigma, higher levels of insight, higher levels of functioning, lesser severity of depressive symptoms, and positive symptoms were found to be significantly associated with greater levels of drug attitude (small to moderate associations). Only therapeutic alliance had a large correlation with drug attitude (ρ = 0.503, P < 0.001). The therapeutic alliance scores between the 2 health care professionals groups are not significantly different. However, participants who have identified psychiatrists as the health care professional that contributed the most to their recovery reported a significantly more positive attitude (μ = 6.18, SD = 3.42) toward psychiatric medication as compared with the other health care professionals group (μ = 3.11, SD = 5.32, P = 0.004). Only 2 factors, the Revised Helping Alliance Questionnaire (β = 0.424, P < 0.001) and Personal and Social Performance scale (β = 0.272, P = 0.006), were statistically significant predictors of drug attitude.

Implications/Conclusions

Therapeutic alliance is found to be the lead factor associated with drug attitude in patients with schizophrenia. Identifying psychiatrists as the health care professional most involved in the patients' recovery can greatly increase patients' drug attitudes. Maintaining individuals' functioning also contributes to drug attitude.
Relational Quality Between the RN and Nursing Assistant
Authors: Campbell Amy Richmond , Kennerly Susan , Swanson Melvin , Forbes Thompson , Anderson Teresa , Scott Elaine S.
Published: August 2021

OBJECTIVE

Nurse (RN) and nursing assistant (NA) relational quality was examined along with associations between relational quality and evaluations of teamwork and communication.

BACKGROUND

RN and NA teams constitute the primary nursing care delivery method, and the quality of their relationship affects system capacity for improving patient outcomes; adverse events are linked to communication and teamwork breakdowns.

METHODS

RN (N = 889) and NA (263) relational quality was examined using a cross-sectional secondary analysis from system assessment with the Agency for Healthcare Research and Quality Hospital Survey on Patient Safety Culture.

RESULTS

RN and NA perceived relational quality indicated significant differences in teamwork and safety grade ratings, with both groups reporting perceived teamwork as high when patient safety grade was low.

CONCLUSIONS

This study supports the benefits of improving the RN-NA teamwork–communication relationship. An enhanced RN-NA relational quality can be used by nurse leaders to optimize patient care delivery outcomes.
SOX6 Expression Is Sensitive for Peritoneal Epithelioid Malignant Mesothelioma, But Not Specific in the Differential Diagnosis With Tubo-ovarian Serous Neoplasia
Authors: Chapel David B. , Hirsch Michelle S.
Published: August 2021

Primary peritoneal malignant mesothelioma (MM) can demonstrate morphologic overlap with low-grade and high-grade tubo-ovarian serous neoplasms; it is also biologically and prognostically distinct from benign mesothelial proliferations. Currently, there is no single biomarker that can definitively distinguish these neoplasms. Sex-determining region Y box 6 (SOX6) immunohistochemistry has been recently described to differentiate pleural epithelioid MM from lung adenocarcinoma, but it has not been evaluated in the peritoneum. SOX6 immunohistochemistry was performed on 43 peritoneal epithelioid MM, 7 peritoneal biphasic MM, 5 well-differentiated papillary mesotheliomas, 5 serous borderline tumors, 29 low-grade serous carcinomas (LGSCs), 20 high-grade serous carcinomas (HGSCs), and 25 cases of peritoneal reactive mesothelial hyperplasia. Quantitative SOX6 expression in epithelioid MM (median, 100% of tumor cells) was significantly greater than in LGSC/serous borderline tumor (median, 90%; P=0.004) and HGSC (median, 45%; P=0.0001). However, when SOX6 is expression is defined as ≥10% of tumor cells, there was no significant difference in the rate of SOX6 positivity between epithelioid MM (41/43, 95%), LGSC (28/29, 97%; P=1.0), and HGSC (17/20, 85%; P=0.16). Quantitative extent of SOX6 expression in epithelioid MM was significantly greater than in biphasic MM (median, 0%; P=0.0001), well-differentiated papillary mesothelioma (median, 20%; P=0.001), and reactive mesothelial hyperplasia (median, 20%; P=0.0001), but not significantly different from flat quiescent mesothelium (median, 90%; P=0.82). SOX6 immunohistochemistry is 95% sensitive for peritoneal epithelioid MM, but is also consistently expressed in LGSC and HGSC, negating its usefulness in this common differential diagnosis. SOX6 also shows variable expression across the spectrum of reactive, benign neoplastic, and malignant mesothelial lesions of the peritoneum, and does not appear to be diagnostically useful in distinguishing benign from malignant mesothelial proliferations.
Dual-Contrast Biphasic Liver Imaging With Iodine and Gadolinium Using Photon-Counting Detector Computed Tomography
Authors: Ren Liqiang , Huber Nathan , Rajendran Kishore , Fletcher Joel G. , McCollough Cynthia H. , Yu Lifeng
Published: August 2021

Purpose

The aims of this study were to develop a single-scan dual-contrast protocol for biphasic liver imaging with 2 intravenous contrast agents (iodine and gadolinium) and to evaluate its effectiveness in an exploratory swine study using a photon-counting detector computed tomography (PCD-CT) system.

Materials and Methods

A dual-contrast CT protocol was developed for PCD-CT to simultaneously acquire 2 phases of liver contrast enhancement, with the late arterial phase enhanced by 1 contrast agent (iodine-based) and the portal venous phase enhanced by the other (gadolinium-based). A gadolinium contrast bolus (gadobutrol: 64 mL, 8 mL/s) and an iodine contrast bolus (iohexol: 40 mL, 5 mL/s) were intravenously injected in the femoral vein of a healthy domestic swine, with the second injection initiated after 17 seconds from the beginning of the first injection; PCD-CT image acquisition was performed 12 seconds after the beginning of the iodine contrast injection. A convolutional neural network (CNN)–based denoising technique was applied to PCD-CT images to overcome the inherent noise magnification issue in iodine/gadolinium decomposition task. Iodine and gadolinium material maps were generated using a 3-material decomposition method in image space. A set of contrast samples (mixed iodine and gadolinium) was attached to the swine belly; quantitative accuracy of material decomposition in these inserts between measured and true concentrations was calculated using root mean square error. An abdominal radiologist qualitatively evaluated the delineation of arterial and venous vasculatures in the swine liver using iodine and gadolinium maps obtained using the dual-contrast PCD-CT protocol.

Results

The iodine and gadolinium samples attached to the swine were quantified with root mean square error values of 0.75 mg/mL for iodine and 0.45 mg/mL for gadolinium from the contrast material maps derived from the denoised PCD-CT images. Hepatic arteries containing iodine and veins containing gadolinium in the swine liver could be clearly visualized. Compared with the original images, better distinctions between 2 liver phases were achieved using CNN denoising, with approximately 60% to 80% noise reduction in contrast material maps acquired with the denoised PCD-CT images compared with the original images.

Conclusions

Simultaneous biphasic liver imaging in a single multienergy PCD-CT acquisition using a dual-contrast (iodine and gadolinium) injection protocol and CNN denoising was demonstrated in a swine study, where the enhanced hepatic arteries (containing iodine) and the enhanced hepatic veins (containing gadolinium) could be clearly visualized and delineated in the swine liver.
Small Brain Lesion Enhancement and Gadolinium Deposition in the Rat Brain
Authors: Violas Xavier , Rasschaert Marlène , Santus Robin , Factor Cécile , Corot Claire , Catoen Sarah , Idée Jean-Marc , Robert Philippe
Published: August 2021

Objectives

The aim of the set of studies was to compare gadopiclenol, a new high relaxivity gadolinium (Gd)–based contrast agent (GBCA) to gadobenate dimeglumine in terms of small brain lesion enhancement and Gd retention, including T1 enhancement in the cerebellum.

Materials and Methods

In a first study, T1 enhancement at 0.1 mmol/kg body weight (bw) of gadopiclenol or gadobenate dimeglumine was evaluated in a small brain lesions rat model at 2.35 T. The 2 GBCAs were injected in an alternated and cross-over manner separated by an interval of 4.4 ± 1.0 hours (minimum, 3.5 hours; maximum, 6.1 hours; n = 6). In a second study, the passage of the GBCAs into cerebrospinal fluid (CSF) was evaluated by measuring the fourth ventricle T1 enhancement in healthy rats at 4.7 T over 23 minutes after a single intravenous (IV) injection of 1.2 mmol/kg bw of gadopiclenol or gadobenate dimeglumine (n = 6/group). In a third study, Gd retention at 1 month was evaluated in healthy rats who had received 20 IV injections of 1 of the 2 GBCAs (0.6 mmol/kg bw) or a similar volume of saline (n = 10/group) over 5 weeks. T1 enhancement of the deep cerebellar nuclei (DCN) was assessed by T1-weighted magnetic resonance imaging at 2.35 T, performed before the injection and thereafter once a week up to 1 month after the last injection. Elemental Gd levels in central nervous system structures, in muscle and in plasma were determined by inductively coupled plasma mass spectrometry (ICP-MS) 1 month after the last injection.

Results

The first study in a small brain lesion rat model showed a ≈2-fold higher number of enhanced voxels in lesions with gadopiclenol compared with gadobenate dimeglumine. T1 enhancement of the fourth ventricle was observed in the first minutes after a single IV injection of gadopiclenol or gadobenate dimeglumine (study 2), resulting, in the case of gadopiclenol, in transient enhancement during the injection period of the repeated administrations study (study 3). In terms of Gd retention, T1 enhancement of the DCN was noted in the gadobenate dimeglumine group during the month after the injection period. No such enhancement of the DCN was observed in the gadopiclenol group. Gadolinium concentrations 1 month after the injection period in the gadopiclenol group were slightly increased in plasma and lower by a factor of 2 to 3 in the CNS structures and muscles, compared with gadobenate dimeglumine.

Conclusions

In the small brain lesion rat model, gadopiclenol provides significantly higher enhancement of brain lesions compared with gadobentate dimeglumine at the same dose. After repeated IV injections, as expected for a macrocyclic GBCA, Gd retention is minimalized in the case of gadopiclenol compared with gadobenate dimeglumine, resulting in no T1 hypersignal in the DCN.
Quantification of Calcium in Peripheral Arteries of the Lower Extremities
Authors: van der Star Simone , de Jong Daan J. , Bleys Ronald L.A.W. , Kuijf Hugo J. , Schilham Arnold , de Jong Pim A. , Kok Madeleine
Published: August 2021

Objectives

The aim of this study was to investigate the interscanner and interscoring platform variability of calcium quantification in peripheral arteries of the lower extremities.

Materials and Methods

Twenty human fresh-frozen legs were scanned using 3 different computed tomography (CT) scanners. The radiation dose (CTDIvol) was kept similar for all scanners. The calcium scores (Agatston and volume scores) were quantified using 4 semiautomatic scoring platforms. Comparative analysis of the calcium scores between scanners and scoring platforms was performed by using the Friedman test; post hoc analysis was performed by using the Wilcoxon signed rank test with Bonferroni correction.

Results

Sixteen legs had calcifications and were used for data analysis. Agatston and volume scores ranged from 12.1 to 6580 Agatston units and 18.2 to 5579 mm3. Calcium scores differed significantly between Philips IQon and Philips Brilliance 64 (Agatston: 19.5% [P = 0.001]; volume: 14.5% [P = 0.001]) and Siemens Somatom Force (Agatston: 18.1% [P = 0.001]; volume: 17.5% [P = 0.001]). The difference between Brilliance 64 and Somatom Force was smaller (Agatston: 5.6% [P = 0.778]; volume: 7.7% [P = 0.003]). With respect to the interscoring platform variability, OsiriX produced significantly different Agatston scores compared with the other 3 scoring platforms (OsiriX vs IntelliSpace: 14.8% [P = 0.001] vs Syngo CaScore: 13.9% [P = 0.001] vs iX viewer: 13.2% [P < 0.001]). For the volume score, the differences between all scoring platforms were small ranging from 2.9% to 4.0%. Post hoc analysis showed a significant difference between OsiriX and IntelliSpace (3.8% [P = 0.001]).

Conclusions

The use of different CT scanners resulted in notably different Agatston and volume scores, whereas the use of different scoring platforms resulted in limited variability especially for the volume score. In conclusion, the variability in calcium quantification was most evident between different CT scanners and for the Agatston score.
Using Lean Six Sigma to Improve First-Case Delays in Pediatric Endoscopy
Authors: Cardini Jeff
Published: August 2021

Pediatric endoscopy is an essential clinical practice used to diagnose and treat gastrointestinal diseases in children. Moreover, pediatric endoscopy programs require a clinically and technically specialized unit organized around performing endoscopic procedures with high levels of training and skill. With the volume of endoscopic procedures steadily rising in large academic medical centers each year, achieving operational efficiency has become critical to running a successful endoscopy program.
Improving Follow-ups With Gastroenterologists Utilizing an Appointment Scheduling Protocol in Inflammatory Bowel Disease
Authors: Choe Monica Y. , VanGraafeiland Brigit , Parian Alyssa
Published: August 2021

Approximately one in four patients with inflammatory bowel disease are readmitted within 90 days. To reduce hospitalizations, regular follow-up appointments with gastroenterologists are essential. However, the mean wait time for gastroenterology clinic appointments significantly exceeded the target goal of 14 days in North America. Based on literature review, we developed and implemented a new appointment scheduling protocol. The inclusion criteria were adult patients with inflammatory bowel disease who were recently hospitalized or newly referred to a gastroenterology clinic. At weeks 0 and 12, wait times were extrapolated from chart review, and patient satisfaction rates were collected via surveys. Patient demographics and outcome data were examined using descriptive statistics. A total of 16 patients were included. Following the intervention, the mean wait time decreased from 40.4 (SD = 31.9) to 21.9 days (SD = 11.4), but the change was statistically insignificant (p = .408). Poor response rates (47%) limited the interpretation of the patient satisfaction data. Despite the small sample size, our project was the first quality improvement initiative that implemented an evidence-based appointment scheduling protocol among adult patients with inflammatory bowel disease. Further studies are warranted with a larger sample size to better evaluate its efficacy in achieving timely outpatient gastroenterology care.
Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout
Authors: Duman Muhammed , Ay Hilal , Altun Soner , Sahin Nevzat , Saticioglu Izzet Burcin
Published: August 2021

Two yellow-pigmented isolates, F-60Tand F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genusFlavobacteriumbased on the results of 16S rRNA gene sequence analysis. Strains F-60Tand F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain ofFlavobacterium crassostreaeLPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genusFlavobacterium. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity based onblast(ANIb) values for strains F-60Tand F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genusFlavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain ofFlavobacterium frigidariumDSM 17623Twhile those values forF. crassostreaeLPB0076Twere obtained as 21.4–21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the nameFlavobacterium muglaensesp. nov. is proposed, with F-60Tas the type strain (=JCM 34196T=KCTC 82256T).
Xanthobacter oligotrophicus sp.nov., isolated from paper mill sewage
Authors: Tikhonova Ekaterina N. , Grouzdev Denis S. , Kravchenko Irina K.
Published: August 2021

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29kT, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5–0.7×1.7–3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C18:1ω7, C19:0cyclo and C16:0. The genomic DNA G+C content was 67.95 mol%. Strain 29kTwas able to grow at 4–37 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 6.5–7.0) and at salinities of 0–0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29kTcould grow chemolithoautotrophically in mineral media under an atmosphere of H2, O2and CO2as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genusXanthobacterwithXanthobacter autotrophicus7cT(99.9% similarity) andXanthobacter viscosus7dT(99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA–DNA hybridization values of 92.7 and 44.9%, respectively, of the 29kTto the genome of the most closely related species,X. autotrophicus7cT, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species,Xanthobacter oligotrophicussp. nov. The type strain is 29kT(=KCTC 72777T=VKM B-3453T).
Characterization of subclinical ZIKV infection in immune-competent guinea pigs and mice
Authors: Westrich Joseph A. , McNulty Erin E. , Edmonds Marisa J. , Nalls Amy V. , Miller Megan R. , Foy Brian D. , Rovnak Joel , Perera Rushika , Mathiason Candace K.
Published: August 2021

An infectious agent’s pathogenic and transmission potential is heavily influenced by early events during the asymptomatic or subclinical phase of disease. During this phase, the presence of infectious agent may be relatively low. An important example of this is Zika virus (ZIKV), which can cross the placenta and infect the foetus, even in mothers with subclinical infections. These subclinical infections represent roughly 80 % of all human infections. Initial ZIKV pathogenesis studies were performed in type I interferon receptor (IFNAR) knockout mice. Blunting the interferon response resulted in robust infectivity, and increased the utility of mice to model ZIKV infections. However, due to the removal of the interferon response, the use of these models impedes full characterization of immune responses to ZIKV-related pathologies. Moreover, IFNAR-deficient models represent severe disease whereas less is known regarding subclinical infections. Investigation of the anti-viral immune response elicited at the maternal-foetal interface is critical to fully understand mechanisms involved in foetal infection, foetal development, and disease processes recognized to occur during subclinical maternal infections. Thus, immunocompetent experimental models that recapitulate natural infections are needed. We have established subclinical intravaginal ZIKV infections in mice and guinea pigs. We found that these infections resulted in: the presence of both ZIKV RNA transcripts and infectious virus in maternal and placental tissues, establishment of foetal infections and ZIKV-mediated CXCL10 expression. These models will aid in discerning the mechanisms of subclinical ZIKV mother-to-offspring transmission, and by extension can be used to investigate other maternal infections that impact foetal development.
scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data
Authors: Khozoie Combiz , Fancy Nurun , Marjaneh Mahdi M. , Murphy Alan E. , Matthews Paul M. , Skene Nathan
Published: August 2021

Advances in single-cell RNA-sequencing technology over the last decade have enabled exponential increases in throughput: datasets with over a million cells are becoming commonplace. The burgeoning scale of data generation, combined with the proliferation of alternative analysis methods, led us to develop the scFlow toolkit and the nf-core/scflow pipeline for reproducible, efficient, and scalable analyses of single-cell and single-nuclei RNA-sequencing data. The scFlow toolkit provides a higher level of abstraction on top of popular single-cell packages within an R ecosystem, while the nf-core/scflow Nextflow pipeline is built within the nf-core framework to enable compute infrastructure-independent deployment across all institutions and research facilities. Here we present our flexible pipeline, which leverages the advantages of containerization and the potential of Cloud computing for easy orchestration and scaling of the analysis of large case/control datasets by even non-expert users. We demonstrate the functionality of the analysis pipeline from sparse-matrix quality control through to insight discovery with examples of analysis of four recently published public datasets and describe the extensibility of scFlow as a modular, open-source tool for single-cell and single nuclei bioinformatic analyses.
Development of a Reproducible Porcine Model of Infected Burn Wounds
Authors: Said Sayf Al-deen , Jatana Samreen , Ponti András K. , Johnson Erin E. , Such Kimberly A. , Zangara Megan T. , Madajka Maria , Papay Francis , McDonald Christine
Published: August 2021

Severe burns are traumatic and physically debilitating injuries with a high rate of mortality. Bacterial infections often complicate burn injuries, which presents unique challenges for wound management and improved patient outcomes. Currently, pigs are used as the gold standard of pre-clinical models to study infected skin wounds due to the similarity between porcine and human skin in terms of structure and immunological response. However, utilizing this large animal model for wound infection studies can be technically challenging and create issues with data reproducibility. We present a detailed protocol for a porcine model of infected burn wounds based on our experience in creating and evaluating partial thickness burn wounds infected with Staphylococcus aureus on six pigs. Wound healing kinetics and bacterial clearance were measured over a period of 27 days in this model. Enumerated are steps to achieve standardized wound creation, bacterial inoculation, and dressing techniques. Systematic evaluation of wound healing and bacterial colonization of the wound bed is also described. Finally, advice on animal housing considerations, efficient bacterial plating procedures, and overcoming common technical challenges is provided. This protocol aims to provide investigators with a step-by-step guide to execute a technically challenging porcine wound infection model in a reproducible manner. Accordingly, this would allow for the design and evaluation of more effective burn infection therapies leading to better strategies for patient care.

Graphical Abstract
Spatially Patterned Bi-electrode Epiretinal Stimulation for Axon Avoidance at Cellular Resolution
Authors: Vilkhu Ramandeep S. , Madugula Sasidhar S. , Grosberg Lauren E. , Gogliettino Alex R. , Hottowy Pawel , Dabrowski Wladyslaw , Sher Alexander , Litke Alan M. , Mitra Subhasish , Chichilnisky E.J.
Published: August 2021

Objective

Epiretinal prostheses are designed to restore vision to people blinded by photoreceptor degenerative diseases by stimulating surviving retinal ganglion cells (RGCs), which carry visual signals to the brain. However, inadvertent stimulation of RGCs at their axons can result in non-focal visual percepts, limiting the quality of artificial vision. Theoretical work has suggested that axon activation can be avoided with current stimulation designed to minimize the second spatial derivative of the induced extracellular voltage along the axon. However, this approach has not been verified experimentally at the resolution of single cells. Approach. In this work, a custom multi-electrode array (512 electrodes, 10 μm diameter, 60 μm pitch) was used to stimulate and record RGCs in macaque retina ex vivo at single-cell, single-spike resolution. RGC activation thresholds resulting from bi-electrode stimulation, which consisted of bipolar currents simultaneously delivered through two electrodes straddling an axon, were compared to activation thresholds from traditional single-electrode stimulation.

Results

On average, across three retinal preparations, the bi-electrode stimulation strategy reduced somatic activation thresholds (∼21%) while increasing axonal activation thresholds (∼14%), thus favoring selective somatic activation. Furthermore, individual examples revealed rescued selective activation of somas that was not possible with any individual electrode. Significance. This work suggests that a bi-electrode epiretinal stimulation strategy can reduce inadvertent axonal activation at cellular resolution, for high-fidelity artificial vision.

Novelty & Significance

The effectiveness of bi-electrode stimulation for enhancing the electrical activation of retinal neurons was tested using high-density multi-electrode recording and stimulation in isolated macaque retina. The results suggest that spatially patterned bi-electrode stimuli reduce unwanted axon activation and thus improve the selectivity of stimulation at cellular resolution. Similar patterns could be implemented in a future high-resolution prosthesis to permit a more faithful replication of normal retinal activity, at the resolution of single-cells and single-spikes, for the treatment of incurable blindness.
STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs
Authors: Balabin Helena , Hoyt Charles Tapley , Birkenbihl Colin , Gyori Benjamin M , Bachman John , Kodamullil Alpha Tom , Plöger Paul G , Hofmann-Apitius Martin , Domingo-Fernández Daniel
Published: August 2021

The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models (KGEMs). However, representations based on a single modality are inherently limited. To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs. This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against two baseline models trained on either one of the modalities (i.e., text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.083. Additionally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications. Finally, the source code and pre-trained STonKGs models are available at https://github.com/stonkgs/stonkgs and https://huggingface.co/stonkgs/stonkgs-150k.
Extreme climatic events but not environmental heterogeneity shape within-population genetic variation in maritime pine
Authors: Archambeau Juliette , Garzón Marta Benito , de Miguel Vega Marina , Brachi Benjamin , Barraquand Frédéric , González-Martínez Santiago C.
Published: August 2021

How evolutionary forces interact to maintain quantitative genetic variation within populations has been a matter of extensive theoretical debates. While mutation and migration increase genetic variation, natural selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e. experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from spatially heterogeneous environments. We used phenotypic measurements of five growth, phenological and functional traits from three clonal common gardens, consisting of 523 clones from 33 populations of maritime pine (Pinus pinasterAiton). Populations from harsher climates (mainly colder areas) showed lower genetic variation for height in the three common gardens. Surprisingly, we did not find any association between within-population genetic variation and environmental heterogeneity or population admixture for any trait. Our results suggest a predominant role of natural selection in driving within-population genetic variation, and therefore indirectly their adaptive potential.
Automated control of odor dynamics for neurophysiology and behavior
Authors: Hernandez-Nunez Luis , Samuel Aravinthan D. T.
Published: August 2021

Animals use their olfactory systems to avoid predators, forage for food, and identify mates. Olfactory systems detect and distinguish odors by responding to the concentration, temporal dynamics, and identities of odorant molecules. Studying the temporal neural processing of odors carried in air has been difficult because of the inherent challenge in precisely controlling odorized airflows over time. Odorized airflows interact with surfaces and other air currents, leading to a complex transformation from the odorized airflow that is desired to the olfactory stimulus that is delivered. Here, we present a method that achieves precise and automated control of the amplitude, baseline, and temporal structure of olfactory stimuli. We use this technique to analyze the temporal processing of olfactory stimuli in the early olfactory circuits and navigational behavior of larval Drosophila. Precise odor control and calcium measurements in the axon terminal of an Olfactory Receptor Neuron (ORN-Or42b) revealed dynamic adaptation properties: as in vertebrate photoreceptor neurons, Or42b-ORNs display simultaneous gain-suppression and speedup of their neural response. Furthermore, we found that ORN sensitivity to changes in odor concentration decreases with odor background, but the sensitivity to odor contrast is invariant – this causes odor-evoked ORN activity to follow the Weber-Fechner Law. Using precise olfactory stimulus control with freely-moving animals, we uncovered correlations between the temporal dynamics of larval navigation motor programs and the neural response dynamics of second-order olfactory neurons. The correspondence between neural and behavioral dynamics highlights the potential of precise odor temporal dynamics control in dissecting the sensorimotor circuits for olfactory behaviors.