bluuebunny/crossref_metadata_2025 huggingface dataset:
Pediatric ERCP in the Setting of Acute Pancreatitis: A Secondary Analysis of an International Multicenter Cohort Study
Authors: Trocchia Carolena , Khalaf Racha , Amankwah Ernest , Ruan Wenly , Fishman Douglas S. , Barth Bradley A. , Liu Quin Y. , Giefer Matthew , Kim Kyung Mo , Martinez Mercedes , Dall’oglio Luigi , Torroni Filippo , De Angelis Paola , Faraci Simona , Bitton Sam , Werlin Steven L. , Dua Kulwinder , Gugig Roberto , Huang Clifton , Mamula Petar , Quiros J. Antonio , Zheng Yuhua , Piester Travis , Grover Amit , Fox Victor L. , Wilsey Michael , Troendle David M.
Published: March 2023

Previous studies have demonstrated the safety of performing endoscopic retrograde cholangiopancreatography (ERCP) in the pediatric population; however, few have addressed the outcomes of children undergoing ERCP during acute pancreatitis (AP). We hypothesize that ERCP performed in the setting of AP can be executed with similar technical success and adverse event profiles to those in pediatric patients without pancreatitis. Using the Pediatric ERCP Database Initiative, a multi-national and multi-institutional prospectively collected dataset, we analyzed 1124 ERCPs. One hundred and ninety-four (17%) of these procedures were performed in the setting of AP. There were no difference in the procedure success rate, procedure time, cannulation time, fluoroscopy time, or American Society of Anesthesiology class despite patients with AP having higher American Society of Gastrointestinal Endoscopy grading difficulty scores. This study suggests that ERCP can be safely and efficiently performed in pediatric patients with AP when appropriately indicated.
Patient Empowerment in Cancer Care
Authors: Kim Soo Hyun , Choe Yu Hyeon , Kim Da Hye
Published: March 2023

Background

Patient empowerment is receiving increasing attention in cancer care, and its relevance has led to a growing body of literature. Empowerment-related evidence, however, has not been comprehensively reviewed.

Objective

The purpose of this scoping review was to summarize the available evidence on patient empowerment in cancer care. Specifically, we examined how patient empowerment has been defined and measured and what we have learned.

Methods

We searched 6 databases (MEDLINE, PubMed, CINAHL, EMBASE, Cochrane Library, and PsycINFO), adapting key search terms (eg, “neoplasm,” “empowerment”) to each. Extracted data included author, publication year, country of data collection, main study purpose, study design, sampling method, setting, cancer trajectory, definition of empowerment and its source, measurement of empowerment, correlates, intervention (if applicable), and major results.

Results

Of the 2987 articles we initially identified, we included 64 studies (18 quantitative, 9 qualitative, 9 psychometric validation, 8 mixed methods, 6 reviews, and 14 others). Across designs, randomized controlled trials were the most frequent. A comprehensive summary by study designs was provided.

Conclusions

The review highlights the importance of defining the empowerment concept, which is generally vague. There is a paucity of research on examining the relationship between empowerment and its related concepts. More nonexperimental studies (eg, cross-sectional, longitudinal, case-control studies) are required.

Implications for Practice

Nurses are in an optimal position to engage in the process of empowerment, leading to its benefits. To achieve the best outcomes, nurses need to clarify the definition, select an appropriate measurement, and be trained in empowerment strategies.
The Effect of the Breast Cancer Risk Reduction Program on Women With High Breast Cancer Risk in Terms of Their Participation in Screening and Their Health Beliefs and Behavior
Authors: Ozcelik Habibe , Gozum Sebahat
Published: March 2023

Background

First-degree biological relatives of individuals with breast cancer have a higher risk of breast cancer.

Objective

The purpose of this study was to create a protocol for evaluating the effect of the Breast Cancer Risk Reduction Program (BrCaRRP) on the participation of women at risk in screening and on their health beliefs and risk reduction behaviors.

Methods

The research was planned as a single-site, single-blind randomized controlled experimental study with a parallel group. Participants will be assigned to intervention and control groups using the Stratified Permuted Block Randomization method. The BrCaRRP will be applied to the intervention group within the theoretical framework of the Health Belief Model and the Health Promotion Model. The BrCaRRP is a 12-week program that encompasses 6 meetings, the first being face-to-face and the others via phone. Multidisciplinary experts calculated the content validity index of BrCaRRP as being 0.954 (high); its weighted kappa statistic is 0.70 (high).

Results

The difference in the likelihood of participation in breast cancer screening between the BrCaRRP and control groups will be evaluated after the interventions. Findings will be presented in terms of our hypotheses.

Conclusions

The BrCaRRP is a nurse-led program based on the Health Belief Model and the Health Promotion Model. The BrCaRRP has high content validity and interrater reliability.

Implications for Practice

This protocol can be tested as an intervention in a randomized controlled study.
“The Lasso Suture: Ex vivo testing of an alternative to the high-tension deep dermal stitch”
Authors: Ross Colton J. , Miyake Bradley A. , Marsh Henry R. , Bryant Parker R. , Lee Chung-Hao , Barreiro Guilherme C.
Published: March 2023

Wound dehiscence is generally under-reported, with an estimated >4% occurrence rate in plastic surgery and can be an indicator of increased mortality or remission. In this work, we developed the Lasso suture as a stronger alternative to the current standard patterns that is also faster to perform than the standard “high-tension” wound repair method. To examine this, we dissected caprine skin specimens (SI, VM, HM, DDR, n=10; Lasso, n=9) to create full thickness skin wounds for suture repair using our Lasso technique and four traditional methods: simple interrupted (SI), vertical mattress (VM), horizontal mattress (HM), and deep dermal with running intradermal (DDR). We then conducted uniaxial failure testing to quantify the suture rupture stresses/strains. We also measured the suture operating time with medical students/residents (PGY or MS programs) performing wound repair (10 cm wide, 2 cm deep, 2-0 polydioxanone sutures) on soft-fixed human cadaver skin. Our developed Lasso stitch demonstrated a larger first suture rupture stress compared to all other patterns (p<0.001): 2.46 ± 0.27 MPa vs. SI, 0.69 ± 0.14 MPa; VM, 0.68 ±0.13 MPa; HM, 0.50 ±0.10 MPa; DDR, 1.17 ±0.28 MPa. The Lasso suture was also 28% faster to perform than the gold-standard DDR (264±21s vs. 349±25 s, p=0.027). In summary, we showed that the Lasso has superior mechanical properties compared to all the other studied (traditional) sutures and that the new technique can be performed faster than the current gold-standard (DDR stitch) used for high-tension wounds. Future animal and in-clinic studies will be helpful to confirm our findings in this proof-of-concept study.
Secondary Surgery after Lower Extremity Free Flap Reconstruction.
Authors: Wong Frankie K. , Christensen Joani M. , Meulendijks Mara Z. , Iskhakov David , Ahn Leah , Fruge Seth , Cetrulo Curtis L. , Helliwell Lydia A. , Winograd Jonathan M. , Valerio Ian L. , Eberlin Kyle R.
Published: March 2023

Background:

Microsurgical free tissue transfer may be the only reconstructive option for lower extremity limb salvage. However, the functional and aesthetic results following free tissue transfer after initial salvage may be suboptimal, thus requiring secondary surgeries to facilitate definitive wound healing and/or refinement.

Methods:

A multi-institutional retrospective cohort study was performed including patients who underwent lower extremity free tissue transfer from January 2002 to December 2020. Our primary outcome variable was the presence of secondary surgery after free tissue transfer for lower extremity reconstruction. Independent variables (wound etiology, flap, donor type, recipient, co-morbidities, etc.) were collected. Secondary surgery was categorized as (1) procedures for definitive wound closure and (2) refinement procedures. Multivariable logistic regression was performed to determine which variables were independently associated with the outcome.

Results:

Four-hundred-and-twenty free tissue transfers for lower extremity reconstruction were identified. Secondary surgery was performed in over half (57%) of the patients. Presence of diabetes (OR: 2.0, p: 0.01, 95% CI: 1.2-3.5) and use of a latissimus dorsi donor (OR: 2.4, p: 0.037, 95% CI: 1.1-5.4) were predictors of wound closure procedures. Fasciocutaneous (OR 3.6, p: <0.001, 95% CI 1.8-7.2) and myocutaneous (OR: 3.0, p=0.005, 95% CI 1.5-9.9) flaps were predictors of refinement procedures when compared to muscle-only flaps with skin grafts.

Conclusions:

The majority of lower extremity free tissue reconstructions required secondary procedures to provide definitive wound closure and/or refinement. Overall, this study provides predictors of secondary surgery that will help formulate patients’ expectations of lower extremity limb salvage.
Preventing Postoperative Urinary Retention (POUR) in Patients Undergoing Elective Lumbar Surgery: A Quality Improvement Project
Authors: Jasinski Jacob , Tong Doris , Yoon Elise , Claus Chad , Lytle Evan , Houseman Clifford , Bono Peter , Soo Teck M.
Published: March 2023

Background and Objectives:

Postoperative urinary retention (POUR) is associated with significant morbidity. Our institution's POUR rate was elevated among patients undergoing elective lumbar spinal surgery. We sought to demonstrate that our quality improvement (QI) intervention would significantly lower our POUR rate and length of stay (LOS).

Methods:

A resident-led QI intervention was implemented from October 2017 to 2018 on 422 patients in an academically affiliated community teaching hospital. This consisted of standardized intraoperative indwelling catheter utilization, postoperative catheterization protocol, prophylactic tamsulosin, and early ambulation after surgery. Baseline data on 277 patients were collected retrospectively from October 2015 to September 2016. Primary outcomes were POUR and LOS. The focus, analyze, develop, execute, and evaluate (FADE) model was used. Multivariable analyses were used. P value <.05 was considered significant.

Results:

We analyzed 699 patients (277 pre-intervention vs 422 post-intervention). The POUR rate (6.9% vs 2.6%, Δ confidence interval [CI] 1.15-8.08, P = .007) and mean LOS (2.94 ± 1.87 days vs 2.56 ± 2.2 days, Δ CI 0.066-0.68, P = .017) were significantly improved following our intervention. Logistic regression demonstrated that the intervention was independently associated with significantly decreased odds for developing POUR (odds ratio [OR] = 0.38, CI 0.17-0.83, P = .015). Diabetes (OR = 2.25, CI 1.03-4.92, P = .04) and longer surgery duration (OR = 1.006, CI 1.002-1.01, P = .002) were independently associated with increased odds of developing POUR.

Conclusions:

After implementing our POUR QI project for patients undergoing elective lumbar spine surgery, the institutional POUR rate significantly decreased by 4.3% (62% reduction) and LOS, by 0.37 days. We demonstrated that a standardized POUR care bundle was independently associated with a significant decrease in the odds of developing POUR.
Cutis Laxa and the Value of Rhytidectomy: 4 Patients and Years of Follow-Up
Authors: Li Wuyan , Wang Tailing , Wang Jiaqi
Published: March 2023

The modalities of the esthetic treatment of cutis laxa (CL) patients have rarely been discussed. Here, the authors present 4 CL rhytidectomy cases. The surgery method was designed based on the traditional full-incision face-lift technique combined with lamellar superficial musculoaponeurotic system flap elevation and plication. Temporal, buccal, mandibular, and cervical regions were targeted. The shortest follow-up was 30 months, and the longest was 72. The results were assessed by subjective satisfaction and third-party photo evaluation. The subjective satisfaction was graded into worse than preoperation, no improvement, slight improvement, moderate improvement, and obvious improvement. The satisfaction rate was the sum of moderate and obvious improvement. Eighteen uncorrelated professionals participated in the third-party photo evaluation, in which the preoperative and follow-up photos were presented, and frontal, temporal, mid-face (including jowl), and cervical (including mandibular line) regions were evaluated as improved or nonimproved. The outcome of the subjective satisfaction was graded as no improvement (2/12, 16.7%), slight improvement (3/12, 25%), moderate improvement (4/12, 33.3%), and obvious improvement (3/12, 25%). The satisfaction rate was 58.3%, most investigators denied the frontal and temporal region improvement, 60% observed mid-face improvement, and 80% noticed cervical improvement. Most patients and their parents had positive attitudes towards the treatment results; however, the full expectation was not achieved. The cervical region maintained the best improvement after our treatment and the mid-face ranked second. This surgery method conduces to the esthetic requirement of CL patients; however, skin laxity remains a challenge.
Perioperative Comparison Between Open Cranial Vault Remodeling and Distraction Osteogenesis for Unilateral Lambdoid Craniosynostosis
Authors: Belza Caitlyn C. , Modi Rishi N. , Kamel George N. , McKee Ryan M. , Carbullido Mary K. , Kim Erinn , Gosman Amanda A.
Published: March 2023

There are multiple treatment options for unilateral lambdoid craniosynostosis (ULS) including open posterior cranial vault remodeling (OCVR) and distraction osteogenesis (DO). There is a paucity of data comparing these techniques in the treatment of ULS. This study compared the perioperative characteristics of these interventions for patients with ULS. An IRB-approved chart review was performed from January 1999 to November 2018 at a single institution. Inclusion criteria included the diagnosis of ULS, treatment with either OCVR or DO using a posterior rotational flap technique, and a minimum 1-year follow-up. Seventeen patients met the inclusion criteria (12 OCVR and 5 DO). Patients in each cohort were found to have a similar distribution in sex, age at the time of surgery, synostosis laterality, weight, and length of follow-up. There was no significant difference in mean estimated blood loss/kg, surgical time, or transfusion requirements between cohorts. Distraction osteogenesis patients had a longer mean hospital length of stay (3.4 +/− 0.6 d versus 2.0 +/− 0.6 d, P = 0.0004). All patients were admitted to the surgical ward postoperatively. In the OCVR cohort, complications included 1 dural tear, 1 surgical site infection, and 2 reoperations. In the DO cohort, 1 patient had a distraction site infection, treated with antibiotics. There was no significant difference in estimated blood loss, volume of blood transfusion, or surgical time between OCVR and DO. Patients who underwent OCVR had a higher incidence of postoperative complications and the need for reoperation. This data provides insight into the perioperative differences between OCVR and DO in patients with ULS.
Morphological and Metrical Relationships Between Sphenoid Sinus and Sella Turcica: Possible Applications in Transnasal Transsphenoidal Surgery
Authors: Lazzeroni Matteo , Accorona Remo , Capaccio Pasquale , Pignataro Lorenzo , Cellina Michaela Iva , Gibelli Daniele Maria , Sforza Chiarella
Published: March 2023

Introduction:

Transsphenoidal surgeries imply the risk of intraoperative lesions to the neurovascular structures surrounding the sphenoid sinus (SS). Aim of the present study is to assess the metrical and morphologic relationships existing between SS and sella turcica (ST).

Materials and Methods:

Two hundred computed tomography-scans of patients were selected. For each patient volumes of SS were calculated from their 3-dimensional models segmented through ITK-SNAP program. Variants of SS in pneumatisation and sellar diameters [antero-posterior (AP) diameter, depth, and length] were evaluated on each computed tomography-scan. Correlations among different measurements were assessed through Spearman test (P<0.01), whereas associations between sellar parameters and presence of pneumatisation variants were assessed through Mann-Whitney test (P<0.01).

Results:

In males, pneumatization of the greater wings was related to smaller AP diameter (P<0.01) and depth of ST (P<0.01), whereas in females lower values of depth were found in patients with pneumatization of the pterygoid processes (P<0.01). In both sexes, a positive correlation was found between AP diameter and, respectively, length and depth of ST (P<0.01), together with a negative correlation between volume of SS and depth of ST (P<0.01). Lastly, in females a positive correlation was found between age and, respectively, length and depth of ST (P<0.01).

Conclusions:

The present study highlighted new metrical and morphologic relationships between volume and pneumatisation of SS and diameters of ST. Knowledge of these correlations allows to understand more clearly, in the preoperative setting, the surgical working space. Further studies are needed, especially for what concerns the relationship between sellar measurements and age in females.
The ‘Invisible Lazy-T’ Procedure for Correction of Medial Ectropion
Authors: Uemura Kazuhisa , Okuda Katsuya , Ueno Kazuki , Kumegawa Shinji , Wada Yoshitaka , Asamura Shinichi
Published: March 2023

No accepted standard for the correction of medial ectropion has been established. The most critical part of the surgical treatment for medial ectropion is the tightening of both horizontal and vertical laxity. To correct this ectropion, we have applied a combination procedure which includes tightening of the conjunctiva and the eyelid retractors (posterior lamellae) and the lateral tarsal strip procedure. Our imitation of the ‘Lazy-T’, a surgical operation performed on the medial ectropion, is tentatively named ‘Invisible Lazy-T’. It is a versatile technique with a less visible scar than alternative techniques because skin incision is made along the crease line of the ‘the crow’s feet’. Results suggest a satisfactory solution to this problem and with better outcomes than by other techniques. We propose this novel combination technique is the best strategy for the medial ectropion, and it does not require specialized surgical skill, so ectropion can be managed by craniofacial surgeons.
Precise Coronoidectomy and Zygomatic Arch Reduction for Unilateral Hyperplasia of the Coronoid Process (Jacob’s Disease) via Computer-aided Design and Manufacture
Authors: Zhao Hanjiang , Xin Pengfei , Wu Dandan , Zhang Jianfei
Published: March 2023

Jacob disease is the new formation of a pseudo-joint between both of enlarged coronoid process and even zygomatic arch. A 23-year-old female patient with facial asymmetry and limited mouth opening was reported. Computed tomography images showed the classic symptom of Jacob disease with a mushroom-shaped tumor mass from the coronoid process a pseudoarthrosis joint with zygomatic arch. Coronoidectomy and zygomatic arch reduction were planned to operate based on computer-aided design/computer-aided manufacturing. During the actual operation, the excision of coronoid process and reconstruction of zygomatic arch were all navigated by 3-dimensional-printed surgical templates as designed through an intraoral approach. As a result, the enlarged coronoid process was smoothly removed without sequela and mouth opening along with facial symmetry were successfully improved. The authors suggested that computer-aided design/computer-aided manufacturing should be considered as an auxiliary technique to shorten operation time and enhance surgical accuracy.
Current Outcome after Surgery for Type A Aortic Dissection
Authors: Biancari Fausto , Juvonen Tatu , Fiore Antonio , Perrotti Andrea , Hervé Amélie , Touma Joseph , Pettinari Matteo , Peterss Sven , Buech Joscha , Dell’Aquila Angelo M. , Wisniewski Konrad , Rukosujew Andreas , Demal Till , Conradi Lenard , Pol Marek , Kacer Petr , Onorati Francesco , Rossetti Cecilia , Vendramin Igor , Piani Daniela , Rinaldi Mauro , Ferrante Luisa , Quintana Eduard , Pruna-Guillen Robert , Rodriguez Lega Javier , Pinto Angel G. , Acharya Metesh , El-Dean Zein , Field Mark , Harky Amer , Nappi Francesco , Gerelli Sebastien , Di Perna Dario , Gatti Giuseppe , Mazzaro Enzo , Rosato Stefano , Raivio Peter , Jormalainen Mikko , Mariscalco Giovanni
Published: March 2023

Objective:

The aim of this study was to evaluate the outcomes of different surgical strategies for acute Stanford type A aortic dissection (TAAD).

Summary Background Data:

The optimal extent of aortic resection during surgery for acute TAAD is controversial.

Methods:

This is a multicenter, retrospective cohort study of patients who underwent surgery for acute TAAD at 18 European hospitals.

Results:

Out of 3902 consecutive patients, 689 (17.7%) died during the index hospitalization. Among 2855 patients who survived 3 months after surgery, 10-year observed survival was 65.3%, while country-adjusted, age-adjusted, and sex-adjusted expected survival was 81.3%, yielding a relative survival of 80.4%. Among 558 propensity score-matched pairs, total aortic arch replacement increased the risk of in-hospital (21.0% vs. 14.9%, P=0.008) and 10-year mortality (47.1% vs. 40.1%, P=0.001), without decreasing the incidence of distal aortic reoperation (10-year: 8.9% vs. 7.4%, P=0.690) compared with ascending aortic replacement. Among 933 propensity score-matched pairs, in-hospital mortality (18.5% vs. 18.0%, P=0.765), late mortality (at 10-year: 44.6% vs. 41.9%, P=0.824), and cumulative incidence of proximal aortic reoperation (at 10-year: 4.4% vs. 5.9%, P=0.190) after aortic root replacement was comparable to supracoronary aortic replacement.

Conclusions:

Replacement of the aortic root and aortic arch did not decrease the risk of aortic reoperation in patients with TAAD and should be performed only in the presence of local aortic injury or aneurysm. The relative survival of TAAD patients is poor and suggests that the causes underlying aortic dissection may also impact late mortality despite surgical repair of the dissected aorta.
The Thresholds of Caprini Score Associated With Increased Risk of Venous Thromboembolism Across Different Specialties
Authors: Lobastov Kirill , Urbanek Thomasz , Stepanov Eugeniy , Lal Brajesh K. , Marangoni Jim , Krauss Eugene S. , Cronin MaryAnne , Dengler Nancy , Segal Ayal , Welch Harold J. , Gianesini Sergio , Chen Xiaolan , Caprini Joseph A.
Published: March 2023

Objective:

Estimation of the specific thresholds of the Caprini risk score (CRS) that are associated with the increased incidence of venous thromboembolism (VTE) across different specialties, including identifying the highest level of risk.

Background:

Accurate risk assessment remains an important but often challenging aspect of VTE prophylaxis. One well-established risk assessment model is CRS, which has been validated in thousands of patients from many different medical and surgical specialties.

Methods:

A search of MEDLINE and the Cochrane Library was performed in March 2022. Manuscripts that reported on (1) patients admitted to medical or surgical departments and (2) had their VTE risk assessed by CRS and (3) reported on the correlation between the score and VTE incidence, were included in the analysis.

Results:

A total of 4562 references were identified, and the full text of 202 papers was assessed for eligibility. The correlation between CRS and VTE incidence was reported in 68 studies that enrolled 4,207,895 patients. In all specialties, a significant increase in VTE incidence was observed in patients with a CRS of ≥5. In most specialties thresholds of ≥7, ≥9, and ≥11 to 12 were associated with dramatically increased incidences of VTE. In COVID-19, cancer, trauma, vascular, general, head and neck, and thoracic surgery patients with ≥9 and ≥11 to 12 scores the VTE incidence was extremely high (ranging from 13% to 47%).

Conclusion:

The Caprini score is being used increasingly to predict VTE in many medical and surgical specialties. In most cases, the VTE risk for individual patients increases dramatically at a threshold CRS of 7 to 11.
The Enterococcus secretome inhibits the growth of Mycobacterium tuberculosis complex mycobacteria.
Authors: ACHACHE Wafaa , MEGE Jean Louis , FELLAG Mustapha , DRANCOURT Michel
Published: March 2023

Abstract
Enterococcus mundtii (E. mundtii), a commensal intestinal bacterium, was demonstrated to inhibit the growth of some Mycobacterium tuberculosis (M. tuberculosis) complex (MTC) species that cause tuberculosis in humans and mammals. To further expand this preliminary observation, we cross-investigated five E. mundtii strains and seven MTC strains representative of four MTC species using a standardized quantitative agar well diffusion assay. All five E. mundtii strains, calibrated at 3.109 colony forming units/mL, inhibited the growth of all M. tuberculosis strains with various susceptibility profiles, but no inhibition was observed with lower inoculums. Further, 9 Enterococcus species freeze-dried cell-free culture supernatants (CFCS) including Enterococcus avium, Enterococcus devriesei, Enterococcus durans, Enterococcus dispar, Enterococcus hirae, Enterococcuscasseliflavus, Enterococcus faecalis, Enterococcus faecium, and E. mundtii, inhibited the growth of M. tuberculosis, Mycobacterium africanum (M. africanum), Mycobacterium bovis (M. bovis) and Mycobacterium canettii (M. canettii), the most susceptible MTC species (inhibition diameter 25 ±1 mm), proportionally to CFCS protein concentrations. Data reported here indicated that the Enterococcus secretome inhibits growth of main MTC species of medical interest, which broadens previously reported data. In the gut, the Enterococcus secretome may modulate the expression of tuberculosis, exhibiting an anti-tuberculosis effect, with some protective roles in human and animal health.
Retinal Disease Early Detection using Deep Learning on Ultra-wide-field Fundus Images
Authors: Nguyen Toan Duc , Jung Kyunghee , Bui Phuoc-Nguyen , Pham Van-Nguyen , Bum Junghyun , Le Duc-Tai , Kim Seongho , Song Su Jeong , Choo Hyunseung
Published: March 2023

Ultra-wide-field Fundus Imaging captures the main components of a patient’s eyes such as optic dics, fovea and macula, providing doctors with a profound and precise observation, allowing diagnosis of diseases with appropriate treatment. In this study, we exploit and compare deep learning models to detect eye disease using Ultra-wide-field Fundus Images. To fulfil this, a fully-automated system is brought about which pre-process and amplify 4697 images using cutting-edge computer vision techniques with deep neural networks. These neural networks are state-of-the-art methods in modern artificial intelligence system combined with transfer learning to learn the best representation of medical images. Overall, our system is composed of 3 main steps: data augmentation, data pre-processing and classification. Our system demonstrates that ResNet152 achieved the best results amongst the models, with the area under the curve (AUC) score of 96.47% (95% confidence interval (CI), 0.931-0.974). Furthermore, we visualise the prediction of the model with the corresponding confidence score and provide the heatmaps which show the focal point focused by the models, where the lesion exists in the eye because of damage. In order to help the ophthalmologists in their assessment, our system is an essential tool to speed up the process as it can automate diagnosing procedures and giving detailed predictions without human interference. Through this work, we show that Ultra-wide-field Images are feasible and applicable to be used with deep learning.
Sophisticated Prediction of Carotid-Plaque Vulnerability by Nanocluster Sensitized High-resolution Vessel-Wall-Imaging Profile in Rabbit Atherosclerotic Model
Authors: Gong Yan , Wu Menglin , Fu Dingwei , Guo Yu , Lu Xiudi , Zou Ying , Zhang Xiang , Zhu Jinxia , Zhang Xianchang , Li Xue , Xia Shuang
Published: March 2023

OBJECTIVE

To innovatively developed a macrophage-target nanoparticle based contrast-enhanced high-resolution magnetic resonance vessel wall imaging (HR-VWI) strategy to characterize the plaques’ vulnerable features on rabbits.

BACKGROUND

Lacking of sensitive and specific image-marker of HR-VWI leads this technique depending upon the plaque morphological characteristics. Nanoparticle-based contrast agents modified with targeting ligands allow amplifying MR signals of the interested components. The key to successful translation is the requirement that conducting studies in larger animals to provide reasonable diagnostic readouts.

METHODS

The HR-VWI enhanced with macrophage-targeted PP1-Au@GSH@Gd (GdMG) nanoclusters (NCs) and the conventional Gadovist were utilized for the plaque vulnerability evaluation by a systematic histogram analysis in atherosclerosis (AS) rabbit model.

RESULTS

Due to the compelling targeting capacity of GdMG NCs to foamy macrophages, the contrast-to-noise ratio (CNR) from pre-injection baseline dramatically raised from 6.50 to 36.91 (p< 0.001), with an increment of 1.39-fold higher than that of the Gadovist approach. Spearman’ s correlation test confirmed that the coefficient of variation (CV) derived from the histogram analysis based on GdMG NCs HR-VWI was indeed positively linearly correlated with pathology vulnerability index (VIP) significantly (p< 0.05) with adjusted R2= 0.775. Finally, mathematic formulas with histogram-derived parameters as variables were fitted to quantitatively calculate the histogram vulnerability index (VIH) with the strength of the adjusted R2= 0.952 (p< 0.001), and Area under the curve (AUC) of 0.875 (p< 0.001) to realize thein vivoand quantitative calculation of the plaque vulnerability.

CONCLUSION

Profiting from the splendid inflammation targeted capacity and excellent MRI performance of GdMG NCs, as well as the highly quantitative characteristics of histogram analysis, we disclosed that our established imaging protocol was able to identify the plaques’ vulnerability index that were comparable to pathological examinations in both retrospective and prospective experiments.
An efficient error correction and accurate assembly tool for noisy long reads
Authors: Hu Jiang , Wang Zhuo , Sun Zongyi , Hu Benxia , Ayoola Adeola Oluwakemi , Liang Fan , Li Jingjing , Sandoval José R. , Cooper David N. , Ye Kai , Ruan Jue , Xiao Chuan-Le , Wang De-Peng , Wu Dong-Dong , Wang Sheng
Published: March 2023

Long read sequencing data, particularly those derived from the Oxford Nanopore (ONT) sequencing platform, tend to exhibit a high error rate. Here, we present NextDenovo, a highly efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. NextDenovo can rapidly correct reads; these corrected reads contain fewer errors than other comparable tools and are characterized by fewer chimeric alignments. We applied NextDenovo to the assembly of high quality reference genomes of 35 diverse humans from across the world using ONT Nanopore long read sequencing data. Based on thesede novogenome assemblies, we were able to identify the landscape of segmental duplications and gene copy number variation in the modern human population. The use of the NextDenovo program should pave the way for population-scale long-read assembly, thereby facilitating the construction of human pan-genomes, using Nanopore long read sequencing data.
Unravelling bird nest arthropod community structure using metabarcoding
Authors: Levesque-Beaudin Valerie , Steinke Dirk , Böcker Mieke , Thalinger Bettina
Published: March 2023

Bird nests are fascinating microcosms harboring a wide range of arthropods parasitizing the nesting birds or feeding on prey remains, feces, and the nest material. Studies of these communities have been entirely based on emergence traps which collect live organisms out of the nests. The analysis of nest contents and environmental DNA (eDNA) via metabarcoding could expand our knowledge and identify prey, exuviae, and other animal remains in bird nests.

Here, we investigated the potential of arthropod remains, nest dust, and feathers to better describe taxonomic diversity accumulated in 20 bird nests collected in Guelph (Canada). We used subsampling strategies and tested two extraction approaches to investigate the distribution of DNA in nests, account for low-quality DNA, and the presence of inhibitory substances.

In total, 103 taxa were detected via metabarcoding. Arthropod remains delivered the highest number of taxa (n=67), followed by nest dust (n=29). Extractions with the PowerSoil kit outperformed DNeasy extractions coupled with PowerClean Pro inhibitor removal. The subsamples of the same nest showed 5.5% and 47.1% taxonomic overlap for arthropod remains and PowerSoil extracted nest dust, respectively, indicating a heterogeneous eDNA distribution in nests. Most detected species were either feeding in the nest, i.e., herbivorous / predatory, or bird food. We also detected molecular traces of 25 bird species, whose feathers were likely used as nest material.

Consequently, the metabarcoding of bird nest materials provides a more complete picture of nest communities, which can enable future studies on functional diversity and better comparisons between nesting species.
Arabidopsis calmodulin-like proteins CML13 and CML14 interact with proteins that have IQ domains
Authors: Teresinski Howard J. , Hau Bryan , Symonds Kyle , Kilburn Ryan , Munro Kim A. , Doner Nathan M. , Mullen Robert , Li Vivian H. , Snedden Wayne A.
Published: March 2023

In response to Ca2+signals, the evolutionarily-conserved Ca2+sensor calmodulin (CaM) regulates protein targets via direct interaction. Plants possess many CaM-like (CML) proteins, but their binding partners and functions are mostly unknown. Here, using Arabidopsis CML13 as ‘bait’ in a yeast two-hybrid screen, we isolated putative targets from three, unrelated protein families, namely, IQD proteins, calmodulin-binding transcriptional activators (CAMTAs), and myosins, all of which possess tandem isoleucine-glutamine (IQ) structural domains. Using the split-luciferase complementation assayin plantaand the yeast 2-hybrid system, CML13 and CML14 showed a preference for interaction with tandem over single IQ domains. Relative to CaM, CML13 and CML14 displayed weaker signals when tested with the non-IQ, CaM-binding domain of glutamate decarboxylase or the single IQ domains of CNGC20 (cyclic-nucleotide gated channel-20) or IQM1 (IQ motif protein1). We examined IQD14 as a representative tandem IQ-protein and found that only CaM, CML13, and CML14 interacted with IQD14 among 12 CaM/CMLs tested. CaM, CML13, and CML14 boundin vitroto IQD14 in the presence or absence of Ca2+. Binding affinities were in the nM range and were higher when two tandem IQ domains from IQD14 were present. Green fluorescent protein-tagged versions of CaM, CML13, and CML14 localized to both the cytosol and nucleus in plant cells but were partially relocalized to the microtubules when co-expressed with IQD14 tagged with mCherry. These and other data are discussed in the context of possible roles for these CMLs in gene regulation via CAMTAs and cytoskeletal activity via myosins and IQD proteins.
Transcription factor GLK2 regulates key steps of anthocyanin biosynthesis to antagonize photo-oxidative stress during greening of Arabidopsis seedlings
Authors: Zeng Xiyu , Ye Luhuan , Zhang Rui , Wang Peng
Published: March 2023

The greening of young seedling is light induced but vulnerable to photo-oxidative stress at the same time, due to the immature status of chloroplasts. Accumulation of anthocyanin is a protective response to high light, by absorbing excess energy and serving as antioxidant. In this work with Arabidopsis, we found that GARP family transcription factors GOLDEN2-LIKE 2 (GLK2), as a key regulator to chloroplast development, also plays an intensive role in regulating anthocyanin biosynthesis during seedling de-etiolation, especially under high light stress. We demonstrate that GLK2 positively regulates anthocyanin biosynthesis by directly activating the transcription of anthocyanin late biosynthetic genes (LBGs) as well asTRANSPARENT TESTA GLABRA 1(TTG1) gene, which encodes a key component of the regulatory MYB–bHLH–WDR (MBW) complex (which also activates LBGs). Our data further show that GLK2 and MBW each could activate the expression ofDFRgene (key LBG) independently, via distinct promoter regions. We therefore propose a multifaceted involvement of GLK2 in anthocyanin biosynthesis as an important protective measure for developing chloroplasts, against excessive light exposure during seedling photomorphogenesis.
Stabilization of Interdomain Interactions in G protein αiSubunits Determines GαiSubtype Signaling Specificity
Authors: Lefevre Tyler J. , Wei Wenyuan , Mukhaleva Elizaveta , Venkata Sai Pranathi Meda , Chandan Naincy R. , Abraham Saji , Li Yong , Dessauer Carmen W. , Vaidehi Nagarajan , Smrcka Alan V.
Published: March 2023

Highly homologous members of the Gαifamily, Gαi1-3, have distinct tissue distributions and physiological functions, yet the functional properties of these proteins with respect to GDP/GTP binding and regulation of adenylate cyclase are very similar. We recently identified PDZ-RhoGEF (PRG) as a novel Gαi1effector, however, it is poorly activated by Gαi2. Here, in a proteomic proximity labeling screen we observed a strong preference for Gαi1relative to Gαi2with respect to engagement of a broad range of potential targets. We investigated the mechanistic basis for this selectivity using PRG as a representative target. Substitution of either the helical domain (HD) from Gαi1into Gαi2or substitution of a single amino acid, A230 in Gαi2to the corresponding D in Gαi1, largely rescues PRG activation and interactions with other Gαitargets. Molecular dynamics simulations combined with Bayesian network models revealed that in the GTP bound state, dynamic separation at the HD-Ras-like domain (RLD) interface is prevalent in Gαi2relative to Gαi1and that mutation of A230s4h3.3to D in Gαi2stabilizes HD-RLD interactions through formation of an ionic interaction with R145HD.11in the HD. These interactions in turn modify the conformation of Switch III. These data support a model where D229s4h3.3in Gαi1interacts with R144HD.11stabilizes a network of interactions between HD and RLD to promote protein target recognition. The corresponding A230 in Gαi2is unable to form the “ionic lock” to stabilize this network leading to an overall lower efficacy with respect to target interactions. This study reveals distinct mechanistic properties that could underly differential biological and physiological consequences of activation of Gαi1or Gαi2by GPCRs.
Generating high quality reference genomes from field collected specimens by optimizing preservation
Authors: Minich Jeremiah J , Moore Malia L , Allsing Nicholas A , Murray Emily R , Tran Loi , Michael Todd P
Published: March 2023

Sample preservation challenges efforts to generate high-quality reference genomes or pangenomes for all 2 million+ plant and animal species. Here we show 95% ethanol protects against degradation for fish blood (22°C, ≤6 weeks) and plant tissue (4°C, ≤3 weeks). Using Nanopore, we assemble high quality reference genomes from three fish and two plant species (contig N50: 6.5-13.8Mb; BUSCO completeness: 94.4-99.2%; QV: 43.8 forM. esculenta).
Efferocytosis-Induced Lactate Enables the Proliferation of Pro-Resolving Macrophages to Mediate Tissue Repair
Authors: Ngai David , Schilperoort Maaike , Tabas Ira
Published: March 2023

The clearance of apoptotic cells (ACs) by macrophages (efferocytosis) promotes tissue repair by preventing necrosis and inflammation and by activating pro-resolving pathways, including continual efferocytosis. A key resolution processin vivois efferocytosis-induced macrophage proliferation (EIMP), in which AC-derived nucleotides trigger Myc-mediated macrophage proliferation, thereby increasing the pool of efferocytosis-competent macrophages. Here we show that EIMP requires a second input that is integrated with cellular metabolism, notably, efferocytosis-induced lactate production. While the AC-nucleotide pathway leads to induction ofMycmRNA, lactate signaling is required for the stabilization of Myc protein and subsequent macrophage proliferation. Lactate, via GPR132 and protein kinase A, activates AMP kinase, which increases the NAD+:NADH ratio. This upstream pathway then activates the NAD+-dependent protein deacetylase, SIRT1, which deacetylates Myc to promote its stabilization. Inhibition or silencing of any step along this pathway prevents the increase in Myc protein and proliferation in efferocytosing macrophages despite the presence of the AC-nucleotide/MycmRNA pathway. To test importancein vivo, we transplanted mice with bone marrow cells in which the lactate biosynthetic enzyme lactate dehydrogenase A (LDHA) was knocked down. We then subjected these mice and control bone marrow-transplanted mice to dexamethasone-induced thymocyte apoptosis, a model of high-AC burden. The thymi of the LDHA-knockdown cohort showed reduced macrophage Myc protein expression and proliferation, impaired AC clearance, and increased tissue necrosis. Thus, efferocytosis-induced macrophage proliferation, which is a key process in tissue resolution, requires inputs from two independent efferocytosis-induced processes: a signaling pathway induced by AC-derived nucleotides and a cellular metabolism pathway involving lactate production. These findings illustrate how seemingly distinct pathways in efferocytosing macrophages are integrated to carry out a key process in tissue resolution.
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Authors: Curion Fabiola , Rich-Griffin Charlotte , Agarwal Devika , Ouologuem Sarah , Thomas Tom , Theis Fabian J. , Dendrou Calliope A.
Published: March 2023

Single-cell multiomic analysis of the epigenome, transcriptome and proteome allows for comprehensive characterisation of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets presents a challenge given a paucity of approaches for systematic, joint evaluation of different modalities. Here, we present Panpipes, a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
Itaconate promotes the differentiation of murine stress erythroid progenitors by increasing Nrf2 activity
Authors: Ruan Baiye , Chen Yuanting , Trimidal Sara , Koo Imhoi , Cai Jingwei , Mcguigan John , Hall Molly A. , Patterson Andrew D. , Prabhu K. Sandeep , Paulson Robert F.
Published: March 2023

Steady state erythropoiesis produces new erythrocytes at a constant rate to replace senescent erythrocytes removed in the spleen and liver. Inflammation caused by infection or tissue damage skews bone marrow hematopoiesis, increasing myelopoiesis at the expense of steady state erythropoiesis. To compensate for the loss of production, stress erythropoiesis is induced. Stress erythropoiesis is highly conserved between mouse and human but utilizes a different strategy than steady state erythropoiesis. Inflammatory signals promote the proliferation of immature stress erythroid progenitors (SEPS), which in response to erythropoietin and other signals transition to stress erythroid progenitors committed to differentiation. Here we show that TNFα dependent signaling increases ROS in SEPs during the proliferation stage, however, blocking ROS production impairs their later differentiation. In addition to TNFα, nitric oxide dependent signaling drives the proliferation of stress erythroid progenitors and production of nitric oxide must be decreased so that the progenitor cells can differentiate. As progenitor cells transition to differentiation, increased production of the anti-inflammatory metabolite itaconate activates Nfe2l2 or Nrf2, which inhibits Nos2 expression, leading to decreased nitric oxide production. Mutation of Irg1, the enzyme that catalyzes the production of itaconate, causes a delayed recovery from inflammatory anemia induced by heat killedBrucella abortus. Loss of itaconate-dependent activation of Nrf2 is rescued in vivo by IL-10, which leads to activation of Nrf2 and differentiation. These data show that the differentiation of stress erythroid progenitors relies on a switch to an anti-inflammatory metabolism and increased expression of pro-resolving cytokines.

Key points

1.

The transition to differentiation of stress erythroid progenitors requires anti-inflammatory signals.

2.

The anti-inflammatory metabolite itaconate and IL-10 increase Nrf2 activity to promote the differentiation of stress erythroid progenitors.
Co-evolution of ion channels and neurotoxins in cnidarians leads to diversification of ion channel genes
Authors: Guruacharya Anuj
Published: March 2023

Understanding the diversity of ion channels in cnidarians may shed light on the origin and evolution of early nervous systems. It is hypothesized that cnidarian neurotoxins led to the evolution of diverse ion channel proteins in cnidarians. I tested this hypothesis by investigating several evolutionary factors of both cnidarian neurotoxins and their target ion channels. I examined homologs of 250 cnidarian toxins, 75 ion channel genes, and 70 housekeeping genes from 37 transcriptomes/genomes of cnidarian species. Analysis on the presence or absence of genes by species, selection analysis, and evolutionary rate analysis were performed on the homologs of neurotoxin and ion channel proteins. I found evidence of positive selection, correlation between the number of homologous gene families, and difference in the evolutionary rates among the gene families. I have shown for the first time that neurotoxins may have coevolved with the ion channels in cnidarians. This is consistent with an evolutionary arms race between ion channels and neurotoxins leading to extensive diversity of ion channel genes found in cnidarians.