bluuebunny/crossref_metadata_2025_split huggingface dataset:
COFFEE: consensus single cell-type specific inference for gene regulatory networks
Authors: K Lodi Musaddiq , Chernikov Anna , Ghosh Preetam 
Published: September 2024

Abstract
The inference of gene regulatory networks (GRNs) is crucial to understanding the regulatory mechanisms that govern biological processes. GRNs may be represented as edges in a graph, and hence, it have been inferred computationally for scRNA-seq data. A wisdom of crowds approach to integrate edges from several GRNs to create one composite GRN has demonstrated improved performance when compared with individual algorithm implementations on bulk RNA-seq and microarray data. In an effort to extend this approach to scRNA-seq data, we present COFFEE (COnsensus single cell-type speciFic inFerence for gEnE regulatory networks), a Borda voting-based consensus algorithm that integrates information from 10 established GRN inference methods. We conclude that COFFEE has improved performance across synthetic, curated, and experimental datasets when compared with baseline methods. Additionally, we show that a modified version of COFFEE can be leveraged to improve performance on newer cell-type specific GRN inference methods. Overall, our results demonstrate that consensus-based methods with pertinent modifications continue to be valuable for GRN inference at the single cell level. While COFFEE is benchmarked on 10 algorithms, it is a flexible strategy that can incorporate any set of GRN inference algorithms according to user preference. A Python implementation of COFFEE may be found on GitHub: https://github.com/lodimk2/coffee
Summary statistics knockoffs inference with family-wise error rate control
Authors: Yu Catherine Xinrui , Gu Jiaqi , Chen Zhaomeng , He Zihuai 
Published: September 2024

Abstract
Testing multiple hypotheses of conditional independence with provable error rate control is a fundamental problem with various applications. To infer conditional independence with family-wise error rate (FWER) control when only summary statistics of marginal dependence are accessible, we adopt GhostKnockoff to directly generate knockoff copies of summary statistics and propose a new filter to select features conditionally dependent on the response. In addition, we develop a computationally efficient algorithm to greatly reduce the computational cost of knockoff copies generation without sacrificing power and FWER control. Experiments on simulated data and a real dataset of Alzheimer’s disease genetics demonstrate the advantage of the proposed method over existing alternatives in both statistical power and computational efficiency.
Design of cyborg proteins by loop region replacement with oligo(ethylene glycol): exploring suitable mutations for cyborg protein construction using machine learning
Authors: Yospanya Wijak , Matsumura Akari , Imasato Yukihiro , Itou Tomoyuki , Aoki Yusuke , Nakazawa Hikaru , Matsui Takashi , Yokoyama Takeshi , Ui Mihoko , Umetsu Mitsuo , Nagatoishi Satoru , Tsumoto Kouhei , Tanaka Yoshikazu , Kinbara Kazushi 
Published: September 2024

Abstract
We synthesized a “cyborg protein,” wherein a synthetic molecule partially substitutes the main peptide chain by linking 2 protein domains with a synthetic oligomer. Green fluorescent protein (GFP) served as the model for constructing the cyborg proteins. We prepared circularly permuted GFP (cpGFP) with new termini between β10 and β11, where the original N- and C-termini were linked by a cleavable peptide loop. The cyborg GFP was constructed from cpGFP by linking the β10 and β11 with oligo(ethylene glycol) (OEG) using maleimide–cysteine couplings, followed by the enzymatic cleavage of the N- and C-termini linking loop by thrombin. With the help of machine learning, we were able to obtain the cpGFP mutants that significantly alter the fluorescence intensity (53% increase) by thrombin treatment, which splits cpGFP into 2 fragments (fragmented GFP), and by heat shock. When the cyborg GFP was constructed using this mutant, the fluorescence intensity increased by 13% after heat treatment, similar to cpGFP (33% increase), and the behavior was significantly different from that of the fragmented GFP. This result suggests the possibility that the OEG chain in the cyborg protein plays a similar role to the peptide in the main chain of the protein.
Neural network potential calculations for melamine adsorption onto Pt (111) compared with density functional theory
Authors: Tada Kohei 
Published: September 2024

Abstract
The investigation of Pt-adsorbed melamine is important in elucidating the effect of molecular decoration on the enhancement of catalytic performance for fuel cells, and is an interesting system in which covalent stabilization between the surface and the molecule competes with resonance destabilization by the coordination. The present work discusses whether graph neural network potentials can predict the adsorption structure with the competition. The most stable structure predicted by preferred potential was consistent with that by density functional theory but underestimated resonance destabilization.
Lipid and Glucose Profiles in Pregnant Women With Human Immunodeficiency Virus (HIV) on Tenofovir-based Antiretroviral Therapy
Authors: Eke Ahizechukwu C , Brummel Sean S , Aliyu Muktar H , Stranix-Chibanda Lynda , Eleje George U , Ezebialu Ifeanyichukwu U , Korutaro Violet , Wabwire Deo , Matubu Allen , Mbengeranwa Tapiwa , Chakhtoura Nahida , Chinula Lameck , McCarthy Katie , Knowles Kevin , Krotje Chelsea , Linton Macrae F , Dooley Kelly E , Sax Paul E , Brown Todd , Lockman Shahin 
Published: September 2024

Abstract

Background
Tenofovir alafenamide (TAF)-based antiretroviral therapy (ART) regimens have been associated with adverse changes in lipid and glucose profiles compared with tenofovir disoproxil fumarate (TDF)-based ART, but data in pregnancy are limited. We evaluated metabolic markers in pregnant women with human immunodeficiency virus (HIV) after starting TAF- versus TDF-based ART.

Methods
We analyzed data within the IMPAACT 2010/VESTED trial, which demonstrated better pregnancy outcomes in pregnant women randomized to initiate TAF/Emtricitabine/Dolutegravir (TAF/FTC + DTG; n = 217) or TDF/FTC + DTG (n = 215). We measured non-fasting plasma concentrations of glucose, total-cholesterol, low-density lipoprotein-cholesterol (LDL-C), high-density lipoprotein-cholesterol (HDL-C), lipoprotein (a), and triglycerides from samples collected 8 weeks after enrollment. We employed linear regression models to estimate by-arm mean differences.

Results
In total, 219 participants enrolled in the DTG arms in Zimbabwe and Uganda: 109 in the TAF/FTC + DTG and 110 in the TDF/FTC + DTG arms. At study entry, mean gestational age was 22.6 weeks, median HIV-1 RNA was 711 copies/mL, and mean age was 25.8 years. By 8 weeks, mean total cholesterol was 12 mg/dL higher in women randomized to TAF/ FTC + DTG versus TDF/FTC + DTG (95% confidence interval [CI]: 3.8, 21.1). Pregnant women in the TAF/FTC + DTG arm had higher mean LDL-C (7.1 mg/dL, 95% CI: .2, 14.0), triglycerides (12.3 mg/dL, 95% CI: 1.8, 22.7), lipoprotein (a) (7.3 mg/dL, 95% CI: 1.1, 13.6), and lower mean HDL-C (2.8 mg/dL, 95% CI: .1, 5.6) compared to the TDF/FTC + DTG arm.

Conclusions
Pregnant women randomized to start TAF/FTC + DTG had higher lipids than those randomized to TDF/FTC + DTG within 8 weeks of ART initiation. However, lipid levels were within normal reference ranges.
An attempt to generate panoramic radiographs including jaw cysts using StyleGAN3
Authors: Fukuda Motoki , Kotaki Shinya , Nozawa Michihito , Tsuji Kaname , Watanabe Masahiro , Akiyama Hironori , Ariji Yoshiko 
Published: September 2024

Abstract

Objectives
The purpose of this study was to generate radiographs including dentigerous cysts by applying the latest generative adversarial network (GAN; StyleGAN3) to panoramic radiography.

Methods
A total of 459 cystic lesions were selected, and 409 images were randomly assigned as training data and 50 images as test data. StyleGAN3 training was performed for 500 000 images. Fifty generated images were objectively evaluated by comparing them with 50 real images according to four metrics: Fréchet inception distance (FID), kernel inception distance (KID), precision and recall, and inception score (IS). A subjective evaluation of the generated images was performed by three specialists who compared them with the real images in a visual Turing test.

Results
The results of the metrics were as follows: FID, 199.28; KID, 0.14; precision, 0.0047; recall, 0.00; and IS, 2.48. The overall results of the visual Turing test were 82.3%. No significant difference was found in the human scoring of root resorption.

Conclusions
The images generated by StyleGAN3 were of such high quality that specialists could not distinguish them from the real images.
265. INITIAL RESULTS FROM RESOLVE, A PHASE 1B DOSE-ESCALATION STUDY OF EP-104GI (EXTENDED-RELEASE FLUTICASONE PROPIONATE INTRA-ESOPHAGEAL INJECTION) FOR EOSINOPHILIC ESOPHAGITIS
Authors: Helliwell James , Malone Amanda , Bredenoord Arjan J , Nguyen Nam , Ko Hin Hin , Dobek Christine , Peck Vik , Dellon Evan S 
Published: September 2024

Abstract

Background
Eosinophilic esophagitis (EoE) is a chronic, immune-mediated disease characterized by inflammation, influx of eosinophils and esophageal remodeling. Therapy for EoE includes swallowed/topical corticosteroids, dupilumab, and dietary elimination; but these are not always effective.
EP-104GI is an extended-release fluticasone propionate (FP) intra-esophageal injection being developed as a novel treatment for EoE. EP-104GI consists of coated FP crystals that release locally via diffusion at a pre-defined rate to reduce peak concentrations and prolong therapeutic window.
RESOLVE (NCT05608681) is a Phase 1b, multicenter, open-label, dose-escalation study to evaluate the safety, tolerability, pharmacokinetics, and efficacy of EP-104GI in patients with EoE.

Methods
The conservative starting dose of EP-104GI consisted of 1 mg injected at each of 4 sites in 4 quadrants over two ‘rings’ in the esophagus. Dose escalations increase the dose per site and/or number of sites; the second cohort received 1 mg at each of 8 sites.
After a single administration of EP-104GI, participants are assessed for up to 24 weeks including adverse events (AEs) and laboratory tests. Efficacy assessments include histological endpoints and patient-reported symptom outcomes including the Straumann Dysphagia Index (SDI). Esophageal biopsies are collected at baseline, Week 4 and Week 12.

Results
All subjects demonstrated decreased symptom scores compared to baseline, with generally greater responses at the higher EP-104GI dose in Cohort 2 (Fig 1). Histologically, all Cohort 2 patients showed decreases in EoEHSS scores with 2/3 having ≈50% decrease in total grade score and ≈35% decrease in total stage score at Week 4, also, eosinophil counts were reduced by ≈35% at Week 4 and ≈40% at Week 12.
Findings from Cohorts 1 and 2 of the ongoing trial include mild-moderate treatment-emergent AEs, the majority occurring on the day of treatment. No AEs were related to EP-104GI.

Conclusions
The initial results presented here indicate that the novel diffusion-based localized delivery of FP via EP-104GI injection into the esophagus is feasible and safe in patients with EoE and could avoid the side-effects typically associated with swallowed/topical corticosteroids. Efficacy data from the doses studied, although limited at this point, suggest a dose-response relationship with symptom outcomes and also show histologic improvements. These findings support the potential for an interval of at least 6 months between inter-esophageal injections, which may be further extended at the higher doses to be investigated in this study. Recruitment is ongoing.
266. NSQIP 5-FACTOR MODIFIED FRAILTY INDEX PREDICTS MORBIDITY BUT NOT MORTALITY AFTER ESOPHAGECTOMY
Authors: Qu Linda Chang , Vogt Kelly , Malthaner Richard 
Published: September 2024

Abstract

Background
Frailty is a source of morbidity in esophagectomy patients. To aid clinical decision making, it is important to determine if the simplified 5-factor modified frailty index (mFI-5) retains the same associations between frailty and adverse outcomes as its 11-factor predecessor.

Methods
Patients undergoing esophagectomy for esophageal cancer or dysplasia from 2016-2018 were identified using National Surgical Quality Improvement Program (NSQIP). The mFI-5 was used to determine association between frailty and post-esophagectomy morbidity and mortality.

Results
In total, 2,567 patients were included. No patients had a mFI-5 score higher than 3/5 and the score distribution was wide: mFI0 = 1103 (43%), mFI1 = 982 (38.3%), mFI2 = 435 (16.9%), mFI3 = 47 (1.8%). Clavien-Dindo grade IV complications increased with mFI score: mFI0 (11.2%), mFI1 (15.6%), mFI2 (19.8%), mFI3 (25.5%), as did mortality: mFI0 (1.9%), mFI1 (3%), mFI2 (3.4%), mFI3 (4.3%). Multivariate logistic regression analyses controlling for age, sex, body mass index, American Society of Anesthesiology classification, operative duration, emergency surgery status, and neoadjuvant therapy status showed increasing frailty score was associated with Clavien-Dindo grade IV complications (p=0.01), but not mortality (p=0.13).

Conclusions
The mFI-5 is associated with morbidity but not mortality in patients who have undergone esophagectomy for esophageal cancer. Compared to the mFI-11, the mFI-5 may not be nuanced enough in the assessment of frailty specific to this patient population.
273. PERIOPERATIVE BLOOD TRANSFUSIONS AND SURVIVAL IN GASTROESOPHAGEAL CANCERS – A SWEDISH POPULATION-BASED STUDY
Authors: Edholm David , Lagergren Jesper , Hedberg Jakob , Rouvelas Ioannis , Johansson Jan , Lindblad Mats , Linder Gustav 
Published: September 2024

Abstract

Background
Blood transfusions have been associated with decreased long-term survival in cancer patients, possibly due to immunological factors. This cohort study aimed to investigate associations, if any, between perioperative transfusions and survival in gastroesophageal cancer patients.

Methods
A population-based cohort study was conducted based on the National Registry for Esophageal and Gastric cancer (NREV), which harbors clinical data including given transfusions. All patients resected for esophageal or gastric cancer in Sweden, between 2017 and 2022, were included and their survival was acquired from the Swedish Cause of Death Registry. Multivariable Cox regression was used to calculate hazard ratios (HR) with 95% confidence intervals (CI), adjusted for confounders (age, American Society of Anesthesiologist class, access of surgery and pathological TNM stage)

Results
Of 1,368 patients, 227 patients (17%) received perioperative transfusions. Transfusion was associated with an increased risk of all-cause mortality within 3 years of surgery (HR 1.48 95% CI 1.17-1.91). Kaplan-Meier curves depicted worse crude survival in patients having received peroperative transfusion (Figure 1).
To exclude the effects of surgery-related postoperative complications on short-term mortality, a sensitivity analysis was performed, excluding patients who died within 30 days of resection, and found that the impact of transfusions on survival remained.

Conclusion
Perioperative blood transfusions might have a negative impact on survival in patients who undergo gastroesophageal cancer surgery.
274. ROBOTIC REVISIONAL HIATAL HERNIA REPAIR (R-RHR): DOES IT MAKE SENSE?
Authors: Vicente Christian Jose Herrero , Font Arantxa Clavell , Martín Ms Marta Viciano , Savall Elisenda Garsot 
Published: September 2024

Abstract

Background
The gastroesophageal reflux disease (GERD) is increasing among our population and Nissen Fundoplication still remains as the most widely performed technique. The robotic approach to the hiatal hernia repair has been proven to be safe and feasible.
Precision and comfort seem to be some reasons that it makes, at least, comparable to the laparoscopic approach.
Revisional hiatal hernia is a challenging situation to the operator due the adhesions and fibrosis of the tissues so our concern is that the best technology available is needed.

Methods
From June 2019 to November 2023 our division performed 14 cases of Robotic Revisional Hiatal Hernia Repair (R-RHR). Demographic items such as Gender, Age, Body Mass Index (BMI), Previous surgery, Time from first surgery and Postoperative outcomes as Operation Time, Length of stay (LOS), Mesh use, Complications and Readmissions were recorded.

Results
10 women and 4 men were recruited. In all cases the DaVinci robotic platform X and Xi (Intuitive) was used. Mean age resulted in 63.5 years old (sd 12.25). Mean BMI was 26.97 (sd 3.52). In 71.4% cases the Previous HH Surgery was Nissen Fundoplication. 49.3 months was the mean time from the first surgery to the revisional procedure.
163.5 (sd 83.7) minutes was the mean operation time. Mean Lenght Of Stay resulted in 3.4 days (sd 1.4). There were no conversions to the laparoscopic approach. In 5 patients (35.8%) a mesh was placed.
Pleural effusion was the only postoperative complication reported (1/14) and it was managed non-operatively. No other complications were recorded and mortality rate was 0.

Conclusions
To the authors knowledge, this is Spain’s largest Robotic - Revisional Hiatal Hernia Repair (R- RHR) series. The results lead us to conclude that the robotic approach, even the complexity of the surgery, is safe and feasible in trained teams with similar outcomes from the primary surgery that are published.
276. AI NAVIGATION SURGERY FOR ESOPHAGEAL CANCER
Authors: Takeuchi Masashi , Kawakubo Hirofumi , Furube Tasuku , Nakao Atsushi , Hisaoka Kazuhiko , Matsuda Satoru , Kitagawa Yuko 
Published: September 2024

Abstract
With recent technological innovations, artificial intelligence (AI) has begun to be used not only in endoscopic diagnosis and pathology diagnosis but also in the field of surgery. AI enables objective and consistent recognition and evaluation, making it suitable for surgical assistance in surgical operations as well as for the evaluation of surgical techniques and learning curves. First, an AI-assisted surgical procedure recognition system for robotic esophagectomy was developed. By focusing on surgical procedures, the system automatically recognizes surgical procedures with 84% accuracy using AI. In particular, more than 90% of accuracy was obtained in the phase for Left RLN lymph node dissection and Post-dissection to completion of surgery. In addition, as intraoperative navigation, a system for automatic recognition of critical organs such as the recurrent laryngeal nerve, trachea, and subclavian artery was developed, and its recognition accuracy is gradually improving, enabling organ recognition in real time. Currently, with data from more than 100 cases, the system is able to predict Intersection over Union (IoU) with an accuracy of 0.3-0.4.
Similar developments are underway in other areas, such as automatic recognition of the surgical process in robotic distal gastrectomy, and a surgical difficulty prediction system is being built using this technology. This system is expected to make it possible to automatically determine the degree of difficulty of surgery during the operation, leading to the decision to change the surgical team during the operation and the prediction of the operation completion time. These technologies can be useful not only for intraoperative navigation, but also surgical education and postoperative care. Using them, young surgeons have the opportunity to dive into authentic scenarios and acquire practical experience safely, bypassing the dangers inherent in real-life surgeries. Through the use of AI-powered interactive simulations, they can deeply grasp surgical methods, establishing the groundwork of crucial practical abilities needed for performing successful operations.
In the future, we intend to verify the external validity of these systems using data from multiple facilities, and further work on the development of a surgical support system that transcends fields, with the aim of obtaining regulatory approval as a medical device. In addition to the potential clinical applications of the systems under development, we would like to discuss the current status and future of AI-based surgical support systems in the surgical field.
277. FLUORESCENCE-GUIDED ANASTOMOSIS DURING SINGLE-PORT VATS IVOR LEWIS ESOPHAGECTOMY
Authors: Rajan Shiv , Kumar Vijay 
Published: September 2024

Abstract

Background
Minimally Invasive Esophagectomy (MIE) is the standard approach for esophageal cancer. The thoracic part is performed using multiple ports during video or robotic approach with CO2 inflation of 8-10 mmHg. There are recent publications of successful lung & thymic surgeries utilizing single port. This video describes our technique for performing ICG-guided intrathoracic anastomosis during single-port Ivor Lewis (IL) esophagectomy.

Methods
The surgery was performed on a 58-year-old male patient with Siwert type 1 adenocarcinoma (cT3, N0 M0). The patient underwent 4 cycles of neoadjuvant FLOT chemotherapy following a Multidisciplinary tumour board decision. Single-port Ivor Lewis (IL) esophagectomy was planned after three weeks of last cycle.

Results
Following the laparoscopic abdominal phase with extracorporeal gastric conduit formation and feeding jejunostomy, the patient was placed in a semiprone position. The thoracic phase was performed through single-port (4 cm in the 6th intercostal) VATS without CO2. The intrathoracic anastomosis was performed with a linear stapler in side-to-side manner under 1.5 ml indocyanine green (ICG) guidance. Thoracic phase time was 65 minutes. There were no intraoperative and postoperative complications. The pain score was three without opioid use. The patient was allowed orally on day five and discharged home on the eighth postoperative day.

Conclusion
Single port VATS IL MIE is a quick and safe surgical technique. Optics, instrumentations and surgical stapler maneuvering through a single port require a learning curve but are not difficult in our experience. A larger cohort and long-term follow-up are necessary for wider utilization of this approach.
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