bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review
Authors: Singh Reema , Kusalik Anthony , Dillon Jo-Anne R 
Published: May 2021

Abstract
Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
Multimodal management of gastroesophageal junction adenocarcinoma: Which type of neoadjuvant treatment?
Authors: Zandirad E , Teixeira-Farinha H , Demartines N , Schäfer M , Mantziari S 
Published: May 2021

Abstract

Objective
The current treatment for locally advanced gastroesophageal junction (GEJ) adenocarcinoma consists of neoadjuvant treatment (NAT) followed by surgery. Preoperative chemotherapy (CT) and radio-chemotherapy (RCT) are both valid options, but comparative data for their efficacy remain scarce. This study aimed to assess the efficacy of RCT and CT to achieve a complete pathologic response (CPR) for locally advanced GEJ adenocarcinoma. Secondary endpoints were R0 resection rates, postoperative complications, long-term survival and recurrence.

Methods
All consecutive patients with locally advanced GEJ adenocarcinoma treated with CT or RCT and oncologic resection from 2009 to 2018 were included. A CPR was defined with the Mandard tumor regression score. Standard statistical tests were used as appropriate. Overall and disease-free survival were compared with the Kaplan Meier method and log-rank test. Multivariate analysis was performed to define independent predictors of CPR, and long-term survival.

Results
Among the 94 patients (84%male, median age 62 years [IQR 9.7]), 67 (71.3%) received preoperative RCT and 27 (28.7%) CT. Patient’s characteristics and pretreatment tumor stages were comparable. Surgical approach was thoracoabdominal Lewis resection in 95.5% RCT and 81.5% CT patients (P = 0.085). CPR was more frequent in the RCT than the CT group (13.4% vs 7.4%, P = 0.009), but R0 resection rates were similar (72.1% vs 66.7%, P = 0.628). There was a trend to higher ypN0 stage in the RCT group (55.2% vs 33.3%; P = 0.057). Postoperatively, RCT patients presented more cardiovascular complications (35.8% vs 11.1%; P = 0.017), although overall morbidity was similar (68.6% vs 62.9%, P = 0.988). 5-year overall survival was comparable (61.1% RCT vs 75.7% CT, P = 0.259), as was 5-year disease-free survival (33.5% RCT vs 22.8% CT, P = 0.763). Isolated loco-regional recurrence occurred in 2.9% RCT vs 3.7% CT patients (P = 0.976). NAT type was not an independent predictor for complete pathologic response nor long-term survival in the multivariate analysis. Median follow-up was 30 months [95%CI 21.3-38.8] for all patients.

Conclusion
Patients with locally advanced GEJ adenocarcinoma demonstrated higher rates of CPR after RCT than CT, and a trend to a better lymph node sterilization, although this did not translate in a significant survival benefit or decreased recurrence rate.
Comparison of robotic-assisted and open Ivor Lewis esophagectomies in 321 patients of a single center: A case-matched analysis
Authors: Neuschütz K J , Fourie L , Däster S , Bolli M , von Flüe M , Steinemann D C , Angehrn F V 
Published: May 2021

Abstract

Objective
We introduced robotic-assisted Ivor Lewis esophagectomies (rob-E) using the da Vinci Xi in Oct. 2015. Prior to that, esophagectomies were performed as open Ivor Lewis (open-E) procedures. Aim of this study is to evaluate the safety of rob-E in comparison to open-E procedures regarding perioperative outcomes.

Methods
Retrospective analysis of prospectively collected data between Feb. 1999 and Dec. 2020. A case-matched analysis, matching open-E to rob-E in a 1:1 manner, was conducted. Cases were matched regarding age, gender, American Society of Anesthesiologists (ASA) score, histological type of tumor, tumor location and stage.

Results
In the study period 321 patients underwent an esophagectomy. 76 received rob-E and 245 open-E. After matching the cases the comparison of preoperative patient and tumor characteristics revealed no differences between the rob-E and open-E group regarding age at time of operation with a median of 69.5 (35-83) respectively 70 (46-88) years (p = 0.900), gender with 84.2% male in both groups (p = 1.000), ASA score with 68.4% ASA 3 or 4 in both groups (p = 1.000), percentage of tumor stage III of 53.9% respectively 57.9% (p = 0.707), and rate of neoadjuvant treatment of 82.9% in rob-E and 81.6% in open-E (p = 1.000). Conversion from rob-E to open-E was never necessary. For rob-E versus open-E no difference was found regarding overall morbidity with 69.7% versus 60.5% (p = 0.307), major morbidity (Clavien-Dindo &gt; = 3b) with 11.8% versus 14.5% (p = 0.811), incidence of anastomotic insufficiency with 7.9% versus 5.3% (p = 0.745), rate of surgical reintervention with 5.3% versus 7.9% (p = 0.745), and mortality with 2.6% versus 3.9% (p = 1.000). Postoperative details showed no difference including a similar duration of hospitalization with a median of 20 (13-62) respectively 18.5 (13-52) days (p = 0.368) and number of harvested lymph nodes with a median of 24.5 (7-59) in rob-E and 23 (2-64) in open-E (p = 0.203).

Conclusion
The introduction of rob-E in our institution was safe, as perioperative morbidity and mortality did not differ from the previously performed open-E. Overall, the incidence of major morbidity and anastomotic insufficiency in rob-E and open-E show a satisfactory rate compared to previous reports in literature. Further studies with a larger cohort of rob-E are planned in order to draw more decisive conclusions.
Prehabilitation in patients undergoing colorectal surgery fails to confer reduction in overall morbidity: Results of a single-center, single-blinded, randomized controlled trial
Authors: Gloor S , Misirlic M , Frei-Lanter C , Herzog P , Müller P , Schäfli-Thurnherr J , Schregel D , Lamdark T , Wyss R , Unger I , Gisi D , Greco N , Mungo G , Wirz M , Raptis D A , Tschuor C , Breitenstein S 
Published: May 2021

Abstract

Objective
Patients undergoing major surgery are prone to a functional decline due to the impairment of muscle, cardiorespiratory and neurological function as a response to surgical stress. Currently, there are solely weak recommendations in the ERAS protocol regarding the role of preoperative physical activity and prehabilitation in patients undergoing colorectal surgery. Studies in heterogenous cohorts showed contradictory results regarding the impact of prehabilitation on the reduction of postoperative complications. This randomized controlled trial assesses the impact of prehabilitation on postoperative complications in patients undergoing colorectal surgery within an ERAS protocol.

Methods
Between July 2016 and June 2019, a single-center, single-blinded , randomized controlled trial designed to test whether physiotherapeutic prehabilitation vs. normal physical activities prior to colorectal surgery may decrease morbidity within a stringent ERAS protocol was carried out. The primary endpoint was postoperative complications assessed by Comprehensive Complications Index (CCI®). Primary and secondary endpoints for both groups were analyzed and compared.

Results
A total of 107 patients (54 in the pERACS and 53 in the control cohort) were included in the study and randomized. Dropout rate was 4.5% (n = 5). Mean age (SD) in the control cohort was 65 (29–86) and 66 (24–90) years in pERACS cohort. The pERACS cohort contained more female patients (40% vs. 55%, p = 0.123) and a higher percentage of colorectal adenocarcinoma (32% vs. 23%, p = 0.384) although not significant. Almost all patients underwent minimally invasive surgery in both cohorts (96% vs 98%, p = 1.000). There was no between-cohort difference in the primary outcome measure 30-day Comprehensive Complications Index (15 [0 – 49] vs. 18 [0 – 43], p = 0.059). Secondary outcome as complications assessed according to Clavien-Dindo, length of hospital stay, reoperation rate and mortality showed no difference between both cohorts.

Conclusion
Routine physiotherapeutic prehabilitation cannot be recommended for patients undergoing colorectal surgery within an ERAS protocol (Grade A recommendation). To eliminate other confounders like geographical difference or difference in surgical technique, further multicenter RCTs are needed.
COVID-19-related abdominal pain is associated with elevated liver transaminases, which could predict poor clinical outcomes
Authors: Balaphas A , Gkoufa K , Colucci N , Perdikis K -C , Gaudet-Blavignac C , Lovis C , Goossens N , Toso C 
Published: May 2021

Abstract

Objective
Abdominal pain and liver injury have been frequently reported during Coronavirus Disease-2019 (COVID-19). In the setting of a systemic infection these features can induce misleading surgical diagnostics. Our aim was to investigate characteristics of abdominal pain in COVID-19 patients and its association with disease severity and liver injury.

Methods
Data of all COVID-19 hospitalized patients over 16 years old were retrieved from the beginning of the epidemic in Switzerland until end of June 2020. Patients admitted exclusively for other pathologies (including surgical abdominal conditions) and/or recovered from COVID-19, and pregnant women were excluded. Abdominal pain was linked to COVID-19 only after evident alternative diagnostic exclusion. Five times the upper limit of transaminases was considered as liver injury.

Results
Among the 1026 patients who fulfill the inclusion/exclusion criteria, 199 (19.4%) exhibited spontaneous abdominal pain and 165 (16.2%) after abdomen palpation. Systematized abdominal pain was most frequently localized in the epigastric (39.8%) and upper right quadrant (23.7%). Considering baseline ALT levels, 7.14% of patients with epigastric pain had pathological ALT value versus 0.29% of patients without symptoms (p = 0.008). When taking the 30days maximal transaminases value, this reached respectively 16.3% versus 2.7% (p &lt; 0.001) and 20% versus 3.8% (p &lt; 0.001) for respectively AST and ALT.
With logistic regression we demonstrated that baseline pathological AST value was associated with hospital mortality and/or admission to intensive/intermediate care unit with an odds ratio of 13.9 (CI 1.5-124.7, p = 0.019).

Conclusion
These results suggest that COVID-19-induced abdominal pain is associated with liver injury which could predict poor evolution of disease.
Extended lymph node resection versus standard resection for pancreatic head and peri-ampullary adenocarcinoma: A systemic review
Authors: Vuille-dit-Bille R N , Staerkle R F , Soll C , Troller R , Muff J , Choudhury R , Holland-Cunz S G , Grochola L F , Samra J , Puhan M , Breitenstein S 
Published: May 2021

Abstract

Objective
For patients with pancreatic and peri-ampullary adenocarcinoma, it has been hypothesized that extended lymphadenectomy may result in higher R0 resection rates and improved survival. As such, the objective of this systematic review was to compare the oncologic outcomes after pancreaticoduodenectomy (PD) with standard lymphadenectomy (SLA) versus PD with extended lymphadenectomy (ELA).

Methods
A Cochrane systematic review was conducted to identify all randomized controlled trials comparing PD with SLA versus PD with ELA for participants with periampullary or pancreatic cancer. The following electronic databases were reviewed: the Cochrane Central Register of Controlled Trials; MEDLINE; PubMed and EMBASE. The methodological quality of the included studies was assessed using the Cochrane risk of bias criteria and the quality of evidence for important outcomes using GRADE. Extended lymphadenectomy included the interaortocaval space, left side of the celiac trunk, and superior mesenteric artery.

Results
Seven randomized controlled trials were included with 843 patients (421 ELA and 422 SLA). No difference in overall survival (1- and 3-years after surgery) was seen between groups. Mortality and morbidity rates (including pancreatic fistula, delayed gastric emptying, and postoperative bleeding) were similar between the two groups. Operative time was significantly longer following extended resection (Mean Difference 50.1 min; 95% CI 19.2 to 81.1 min; P = 0.001). Total amount of blood loss during surgery was significantly increased following extended resection (Mean Difference 137 ml; 95% CI 12 to 263 ml; P = 0.03), as well as transfusion requirements (Mean Difference 0.15 units; 95% CI 0.13 to 0.17 units; P &lt; 0.00001).
More lymph nodes were retrieved during ELA (Mean Difference 11 nodes; 95% CI 7 to 15 nodes; P &lt; 0.00001). Incidence of positive resection margins was not different between groups.

Conclusion
There is no indication for extended lymphadenectomy in pancreatic head resection as a routine procedure.
Long-term effects of laparoscopic sleeve gastrectomy and Roux-Y-gastric bypass on body composition and bone mass density
Authors: Rast S , Bühler J , Beglinger C , Peterli R , Peters T , Gebhart M , Gerspach A C , Wölnerhanssen B K 
Published: May 2021

Abstract

Objective
Currently, the two most common bariatric procedures are laparoscopic sleeve gastrectomy (LSG) and laparoscopic gastric bypass (LRYGB). Long-term data comparing the two interventions in terms of their effect on body composition and bone mass density (BMD) is scarce. The aim of this study was to assess body composition and BMD at least five years after sleeve gastrectomy (LSG) and gastric bypass (LRYGB).

Methods
Bariatric patients at least five years post-surgery (LSG or LRYGB) were recruited and body composition and BMD was measured by means of DEXA. Data from body composition before surgery was included in the analysis. Blood samples were taken for determination of plasma calcium, parathyroid hormone (PTH), Vitamin D3, alkaline phosphatase and C-terminal telopeptide (CTX), and individual risk for osteoporotic fracture assessed by The Fracture Risk Assessment Tool (FRAX) score was calculated. After surgery, all patients received multivitamins, vitamin D3, and zinc. In addition, LRYGB-patients were prescribed calcium.

Results
A total of 142 patients were included, 72 LSG and 70 LRYGB, before surgery: median BMI 43.1 kg/m2, median age 45.5 years, 62.7% females. Follow-up after a median of 6.7 years. For LRYGB, percentage total weight loss (%TWL) at follow up was 26.3%, and for LSG 24.1%, (p = 0.243). LRYGB lead to a slightly lower fat percentage in body composition. At follow-up, 45% of both groups had a T-score at the femoral neck below -1, indicating osteopenia. No clinically relevant difference between the groups in BMD was found.

Conclusion
At 6.7 years post-surgery, no difference in body composition and BMD between LRYGB and LSG was found. Deficiencies and bone loss remain an issue after both interventions and should be monitored.
Incidence and prognostic factors for the development of symptomatic and asymptomatic marginal ulcers after Roux-en-Y gastric bypass procedures
Authors: Süsstrunk J , Wartmann L , Mattiello D , Köstler T , Zingg U 
Published: May 2021

Abstract

Objective
Marginal ulcer (MU) is a serious complication after Roux-en-Y gastric bypass (RYGB) procedures. This study reports the incidence, risk factors and treatment outcomes of symptomatic and incidentally, at routine endoscopy diagnosed, MU.

Methods
All patients undergoing RYGB procedures between 2013 and 2018 at a single center were included. Upper endoscopy was performed in case of symptoms and/or routinely 2 and 5 years postoperatively.

Results
568 patients (83.3% female) underwent RYGB procedure with a median age of 40 years and median initial body mass index of 41 kg/m2. Median time to follow-up was 2.99 years. Routine 2- and 5-year upper endoscopy was performed in 256 (55.3%) and 65 (38.0%) eligible patients, respectively. In 86 (15.1%) patients, MU was diagnosed at a median time of 14.2 months (4.58 – 26.2) postoperatively and 24.4% of patients with MU were asymptomatic. 76.7% of MUs were located on the side of the Roux-limb. 88.4% of MUs were treated conservatively; re-operation was necessary in 10 (11.6%) patients. Smoking and type 2 diabetes mellitus were the only independent risk factors for MU development in multivariate analysis with a hazard ratio of 2.65 and 1.18 (HbA1c per unit &gt;6.0), respectively.

Conclusion
MU is a common complication after gastric bypass surgery with 25% of patients being asymptomatic. Follow-up routine endoscopy is recommended for early MU detection and subsequent accurate therapy, especially in patients with the independent risk factors smoking and type 2 diabetes mellitus.
Distinct fracture characteristics influence decision making and patient management in fragility fractures of the pelvis – an alternative approach for fracture evaluation
Authors: Ramser M , Cadosch D , Vach W , Saxer F , Eckardt H 
Published: May 2021

Abstract

Objective
Pelvic ring fractures in the elderly with osteoporotic bone are often caused by a minor trauma. A separate classification for these fragility fractures of the pelvis (FFP) has been proposed by Rommens. However, at our institution the management algorithm is rather based on patient profile, clinical course and the ability to mobilize than on the fracture category. We aimed to identify fracture characteristics that might better reflect clinical decision making and show an association with outcome.

Methods
Four fracture characteristics were investigated as potential variables: 1. Extent of the dorsal pelvic ring fracture (absent, unilateral, bilateral); 2. Extent of the ventral pelvic ring fracture (absent, unilateral, bilateral); 3. Ventral comminution/dislocation; 4. Presence of a horizontal sacral fracture.
These four characteristics were assessed retrospectively in a series of 548 patients with a CT scan proven FFP. The association of the fracture morphology with the decision to perform surgery, failure of conservative treatment and the length of hospital stay (LOS) was determined.

Results
Three of the four evaluated characteristics showed an independent and significant association with clinical decision making and patient management. In particular the extent of the dorsal fractures was identified as an independent risk factor for the decision to perform surgery with a 7.3-fold increase per category (p &lt; 0.001). The same was observed for the presence of ventral comminution/dislocation (OR = 2.4; p = 0.002). The extent of ventral fractures (OR = 1.5; p = 0.047) was an independent risk factor for a longer LOS in conservatively treated patients.

Conclusion
Three evaluated morphologic aspects of FFPs showed a clear and independent relation to current clinical decision making and patient management at our institution. Importantly, the ventral fracture component has been shown to have major impact on treatment decision and outcome, which has been underestimated in the current FFP classification system.
These four easily distinguishable fracture characteristics have the potential to form the basis of an alternative classification system that matches clinical reality and captures prognostic aspects.
Development of a visual analytics tool for polytrauma patients: Proof of concept for a new assessment tool using a multiple layer sankey diagram in a single-center database
Authors: Niggli C , Pape H -C , Mica L 
Published: May 2021

Abstract

Objective
Early physiological assessment of multiply injured patients is crucial for decision-making and has relied on personal experience of trauma experts. We have developed a new visual analytics tool (Sankey diagram, Watson Trauma Health care tool) that includes known prognostic parameters for polytrauma patients to help guide assessment and treatment decisions for physicians involved in trauma care.

Methods
A prospectively collected trauma database of a single level I trauma center (3655 patients) was used. Inclusion criteria: age &gt; 16 years, an Injury Severity Score (ISS) &gt; 16, and presence of a complete data set in the database. Data collected included admission values of patient age, injury scoring, shock classification, temperature, acid-base and hemostasis parameters. All of these parameters were collected daily as longitudinal parameters. Endpoints of the clinical course we considered were sepsis, SIRS and early in-hospital mortality (&lt;72 hours). A proof of concept of the visualization was developed over a 2-year period in a cooperation between physicians and engineers. Statistically, the most predictive parameters were selected by binary logistic regression and ROC analysis.

Results
A dynamic interactive multi-layer Sankey diagram, based on cohort similarities, was developed in a collaboration between a level I trauma center and IBM, from August 2017 until January 2018. It is a modular tool and allows any user to add a new patient, or work with an existing case. The visualisation used the Data-Driven Documents (D3) interactive visualisation library to create a responsive graphic.

Conclusion
This application summarizes the experience of 3655 polytrauma patients and might serve as a guide for clinical decisions and educative purposes, as well as new scientific questions for the polytrauma patient.
Wide awake local anesthesia no tourniquet (WALANT) – a revolutionary improvement in hand surgery
Authors: Cardell M , Jung F , Zechmann-Müller N , Greminger M , Kern L , Jandali A R 
Published: May 2021

Abstract

Objective
Wide awake local anesthesia no tourniquet (WALANT) hand surgery offers the opportunity to create a bloodless field without using an arm tourniquet. Lidocaine for anesthesia mixed with epinephrine for hemostasis is frequently used without concerns in the hand and finger. This is a major improvement for the patient and the surgeon in terms of patient comfort and having the opportunity to test the hand and finger function intraoperatively. The movement away from tourniquet surgery, which often requires sedation or general anaesthesia is one of the most significant recent advances in hand surgery.

Methods
A subcutaneous infiltration of a mixture (1:100’000) of lidocaine (1%) and epinephrine (buffered 10:1 with 8.4% bicarbonate) is done with a 27 G canula. The mixture is infiltrated wherever surgical dissection, k-wire insertion, or manipulation of fractured bones will occur. The local anesthetic results in an extravascular Bier block. The injection is done slowly from proximal to distal to minimize injection pain. After the last injection a minimum time of 30 minutes should be waited for maximal epinephrine vasoconstriction in the finger.

Results
In the beginning WALANT was only used for small procedures like trigger finger or carpal tunnel release. Meanwhile also major hand surgical procedures like finger fractures, flexor tendon repairs, tendon transfers, arthroscopies, arthroplasties and open triangular fibrocartilage complex (TFCC) repair are performed in WALANT. Even procedures like trapeziectomy have been described using wide awake hand surgery, which involves numbing the joint itself.

Conclusion
The use of WALANT is a proven safe technique that can be used in up to 95% of hand surgical procedures. The benefits for patients and surgeons are obvious. Patients prefer the technique because there are no side effects of opiates or sedation. The anesthetic risk is minimized. Time at hospital is reduced. Patients do not have to suffer tourniquet pain.
Surgeons prefer the technique because of the bloodless surgical field without tourniquet, the possibility of intraoperative testing of stability of prosthesis or fracture stabilization, strength of a tendon repair, the movement and gliding properties in the flexor tendon sheath after repair or testing the tension of tendon transfers. These are probably the reasons for the continuously growing popularity of this technique worldwide.