bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms
Authors: Cox Andrew , Park Chanhee , Koduru Prasad , Wilson Kathleen , Weinberg Olga , Chen Weina , García Rolando , Kim Daehwan 
Published: December 2021

Abstract

Motivation
Algorithms for classifying chromosomes, like convolutional deep neural networks (CNNs), show promise to augment cytogeneticists’ workflows; however, a critical limitation is their inability to accurately classify various structural chromosomal abnormalities. In hematopathology, recurrent structural cytogenetic abnormalities herald diagnostic, prognostic and therapeutic implications, but are laborious for expert cytogeneticists to identify. Non-recurrent cytogenetic abnormalities also occur frequently cancerous cells. Here, we demonstrate the feasibility of using CNNs to accurately classify many recurrent cytogenetic abnormalities while being able to reliably detect non-recurrent, spurious abnormal chromosomes, as well as provide insights into dataset assembly, model selection and training methodology that improve overall generalizability and performance for chromosome classification.

Results
Our top-performing model achieved a mean weighted F1 score of 96.86% on the validation set and 94.03% on the test set. Gradient class activation maps indicated that our model learned biologically meaningful feature maps, reinforcing the clinical utility of our proposed approach. Altogether, this work: proposes a new dataset framework for training chromosome classifiers for use in a clinical environment, reveals that residual CNNs and cyclical learning rates confer superior performance, and demonstrates the feasibility of using this approach to automatically screen for many recurrent cytogenetic abnormalities while adeptly classifying non-recurrent abnormal chromosomes.

Availability and implementation
Software is freely available at https://github.com/DaehwanKimLab/Chromosome-ReAd. The data underlying this article cannot be shared publicly due to it being protected patient information.

Supplementary information
Supplementary data are available at Bioinformatics online.
A network-based drug repurposing method via non-negative matrix factorization
Authors: Sadeghi Shaghayegh , Lu Jianguo , Ngom Alioune 
Published: December 2021

Abstract

Motivation
Drug repurposing is a potential alternative to the traditional drug discovery process. Drug repurposing can be formulated as a recommender system that recommends novel indications for available drugs based on known drug-disease associations. This article presents a method based on non-negative matrix factorization (NMF-DR) to predict the drug-related candidate disease indications. This work proposes a recommender system-based method for drug repurposing to predict novel drug indications by integrating drug and diseases related data sources. For this purpose, this framework first integrates two types of disease similarities, the associations between drugs and diseases, and the various similarities between drugs from different views to make a heterogeneous drug–disease interaction network. Then, an improved non-negative matrix factorization-based method is proposed to complete the drug–disease adjacency matrix with predicted scores for unknown drug–disease pairs.

Results
The comprehensive experimental results show that NMF-DR achieves superior prediction performance when compared with several existing methods for drug–disease association prediction.

Availability and implementation
The program is available at https://github.com/sshaghayeghs/NMF-DR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Lipid signatures reflect the function of the murine primary placentation
Authors: Lee Jong Geol , Kim Globinna , Park Seul Gi , Yon Jung-Min , Yeom Jeonghun , Song Ha Eun , Cheong Seung-A , Lim Joon Seo , Sung Young Hoon , Kim Kyunggon , Yoo Hyun Ju , Hong Eui-Ju , Nam Ki-Hoan , Seong Je Kyung , Kim Chong Jai , Nam Sang-Yoon , Baek In-Jeoung 
Published: December 2021

Abstract

The placenta regulates maternal-fetal communication, and its defect leads to significant pregnancy complications. The maternal and embryonic circulations are primitively connected in early placentation, but the function of the placenta during this developmentally essential period is relatively unknown. We thus performed a comparative proteomic analysis of the placenta before and after primary placentation and found that the metabolism and transport of lipids were characteristically activated in this period. The placental fatty acid (FA) carriers in specific placental compartments were upregulated according to gestational age, and metabolomic analysis also showed that the placental transport of FAs increased in a time-dependent manner. Further analysis of two mutant mice models with embryonic lethality revealed that lipid-related signatures could reflect the functional state of the placenta. Our findings highlight the importance of the nutrient transport function of the primary placenta in the early gestational period and the role of lipids in embryonic development.

Summary Sentence
The placenta is activated characteristically in terms of lipid transport during primary placentation, and the lipid-related signatures closely reflect the functional state of the placenta.
P001 IS PROPHYLACTIC MESH IS ROUTINELY REQUIRED FOR STOMA CONSTRUCTION? IDENTIFICATION OF THE ‘TARGET GROUP’
Authors: Hassan Ahmed , Toh Wei , Ayathamattam James , Thomas Zachary , Ryska Ondrej 
Published: December 2021

Abstract

Background
Evidence to support routine prophylactic mesh insertion during stoma construction is conflicting. The PREVENT randomised controlled trial (RCT) suggested lower incidence of parastomal hernia (PSH) with prophylactic mesh but with no quality of life or cost benefit. Another two RCTs has shown no prophylactic benefit (STOMAMESH & STOMA-const). Although European Hernia guidelines recommends routine prophylactic mesh in end-colostomy, NICE guidelines suggest mesh on individual basis not routinely.

Aim
To identify the group with higher risk to develop a symptomatic PSH when prophylactic mesh should be considered

Material and Methods
A single center retrospective review of all stoma formed. Younger patient than 18 years and patients who had less than 6 months’ follow-up were excluded. Development of PSH was confirmed by radiological evidence or direct intra-operative visualization

Results
194 patients between January 2015 till December 2019 were included with mean follow-up of 15.7±13.5 months where 91 patients developed PSH. On multivariate analysis, older age (&gt;65) (OR 2.3, 95% CI 1.08 – 4.99, p 0.03) and Obesity (OR 5.8, 95% CI 2.53 – 13.57, p 0.00) were risk factors of developing PSH. Among the PSH group, 28 were symptomatic (31%). Symptomatic subgroup had higher ASA (ASA &gt;2) than asymptomatic subgroup (50% Vs 27%, p 0.05)

Conclusions
Obese patients older than 65 years are at increased risk of PSH. IF their ASA &gt;2 this PSH is likely to become symptomatic. This is the group who should benefit the most from prophylactic measures including mesh insertion and should be targeted for future trials
P007 COMPLETE FASCIAL CLOSURE IN LARGE HERNIAS AFTER LIVER TRANSPLANT USING BOTOX
Authors: Powelson John , Yeap Yar Luan , O'Brien Daniel , Fridell Jonathan , Wolfe John 
Published: December 2021

Abstract

Aim
Hernias after liver transplant (HaLT), being transverse, preclude mechanical muscle release for fascial advancement. However, even with large HaLT, complete fascial closure is possible following Botox muscle release.

Material and Methods
A retrospective review included 31 consecutive large primary HaLT repairs between 2017 and 2021. Patients were immunosuppressed, with BMI=33+/-5. Fascial defects were 13+/-5cm (range 7.5-28cm) transversely and 11+/-3cm (range 5-17cm) vertically. Botox was administered 29+/-3days preoperatively. After extensive myofascial mobilization, mesh was inserted intraperitoneally and covered with omental flap alone or with posterior components, followed by fascial closure, progressive tension sutures and drains.

Results
Operative time was 235+/-69min (range 111-418min), with no enterotomy or blood transfusion. Complete fascial closure was achieved in all. No mortality or abdominal compartment syndrome occurred. Two patients had long ICU stays (135 and 75days, aspiration and caecal necrosis), but were discharged with intact repairs, off dialysis and sound mentally. Other patients had a postoperative hospital stay of 5.8+/-2.2days (range 3-13days). Mean follow-up was 48+/-28.3 months (range 1-84 months). One patient with a mainly left sided repair developed a hernia on the right, beyond the mesh edge. No other recurrence or mesh infection occurred. One wound required open abscess drainage. Two seromas were aspirated.

Conclusions
Abdominal wall reconstruction with complete fascial closure is possible following abdominal muscle release with Botox, even in large HaLT. However, these immunosuppressed patients with multiple comorbidities may develop significant medical complications. One recurrence along the mesh edge suggests the need for complete incision mesh coverage, not just hernia coverage.
P011 THE EARLY OUTCOMES OF ABDOMINAL WALL RECONSTRUCTION WITH POLYVINYLIDENE (PVDF) MESH IN THE INFECTED SETTING: A CASE-CONTROL SERIES
Authors: Birolini Claudio , Tanaka Eduardo , Miranda Jocielle , Murakami Abel , Utiyama Edivaldo 
Published: December 2021

Abstract

Aim
The use of synthetic mesh to repair infected defects of the abdominal wall remains controversial. PVDF mesh was introduced in 2002 as an alternative to polypropylene, with the advantages of improved biostability, lowered bending stiffness, and minimum tissue response. This study aimed to evaluate the short-term outcomes of using PVDF mesh to treat infected abdominal wall defects in the elective setting.

Material and Methods
A prospective clinical trial started in 2016 and designed to evaluate the short and mid-term outcomes of 38 patients submitted to abdominal wall reconstruction in the setting of active mesh infection and/or enteric fistulas (AI) when compared to a group of 38 patients submitted to clean ventral hernia repairs (CC). Patients were submitted to single-staged repairs, using onlay PVDF mesh reinforcement to treat their defects.

Results
Groups had comparable demographic characteristics. The AI group had more previous abdominal operations and a longer operative and anesthesia time. At 30-days, surgical site occurrences were observed in 18 (47.4%) AI vs. 17 (44.7%) CC; surgical site infection occurred in 4 (10.4%) AI vs. 6 (15.8%) CC, and a higher number of procedural interventions were required in the CC group, 15.8% AI vs. 28.9% CC. At 6-months follow-up, no chronic infections or hernia recurrences were observed in both groups.

Conclusions
The use of PVDF mesh in the infected setting presented very favorable results with a low incidence of wound infection.
P016 A COMPARATIVE STUDY BETWEEN ROBOTIC AND LAPAROSCOPIC VENTRAL AND INCISIONAL HERNIA REPAIR WITH THE ETEP - TAR TECHNIQUE
Authors: Archontovasilis Fotis , Tselios Ioannis 
Published: December 2021

Abstract

Aim
The aim of this study is to present a single centre’s experience in Robotic and Laparoscopic eTEP TAR technique in ventral and incisional hernia repair. Additionally, the purpose of this study is to compare these Robotic and Laparoscopic techniques in terms of feasibility, efficacy, safety, advantages and disadvantages.

Material and Methods
This is a case-series comparative study of patients with M1-M5 / W3 ventral and incisional hernia that underwent Robotic or Laparoscopic eTEP-TAR repair in a single institution. Patients’ characteristics were reviewed and perioperative outcomes were extracted. All patients were followed-up at the outpatient surgical unit. Intraoperative and postoperative parameters were analyzed.

Results
35 patients (19 males) with a mean age of 57 years underwent Robotic eTEP-TAR (21 patients) and Laparoscopic eTEP-TAR (14 patients) repair of M1-M3/W3 ventral (12 patients) and M2-M5/W3 incisional hernia. There were 3 conversions to open repair in the Robotic group (Rg) and 1 for the Laparoscopic group (Lg). The mean operative time in Rg was 345 minutes, while in Lg was 320 min. All patients were discharged between the first and fifth postoperative day. No major complications or recurrences were revealed during a mean postoperative follow-up time of 26 months.

Conclusions
Both techniques are feasible, reproducible, and safe, with no major differences in operative time, recurrence and complications rate. Nevertheless, these techniques are highly demanding procedures that should be performed by experienced hernia surgeons, in well-organized centers of excellence in hernia surgery.
P018 COLLABORATIVE APPROACH FOR SIMULTANEOUS REPAIR OF COMPLEX INCISIONAL HERNIA AND STOMA REVERSAL
Authors: Olona Carles , Caro Aleidis , Casanova Raquel , Espina Beatriz , Vadillo Jordi , Sales Ricard , Jorba Rosa 
Published: December 2021

Abstract

Aim
The simultaneous repair of incisional hernias (IH) and the reconstruction of the intestinal transit may pose a challenge for many surgeons. Collaboration between units specialized in abdominal wall and colorectal surgery can favor simultaneous treatment.
We present our experience in the collaboration between specialized units for the simultaneous treatment of complex incisional hernias and ostomy closure.

Material and Methods
Descriptive study of patients undergoing simultaneous surgery of complex IH repair and intestinal transit reconstruction in the period 2018.2021.
All interventions were performed electively and with the collaboration of surgeons experts in abdominal wall and colorectal surgery. Demographic variables, hernias characteristics, surgical techniques, postoperative evolution, morbidity and mortality are recorded

Results
16 patients are included. 8 with ileostomy, 3 lateral colostomies and 5 end colostomies . All the patients presented IH of the middle laparotomy and 12 had stomal hernias associated. The mean diameters of the IH were 16.2cm longitudinal and 11cm transverse. Intestinal transit was reconstructed in 15 cases (94%) and incisional hernia repair in 100%. Component separation was required in 75% of cases (8 posterior and 4 anterior).
Morbidity in the first postoperative month was 18%, requiring 2 reoperations (12%). At the end of the mean follow-up of 10.8 months, 81% of the cases did not present complications.

Conclusions
The collaboration between specialist allows the use of advanced techniques in the simultaneous reconstruction of the abdominal wall and intestinal transit, with good clinical results and patient quality of life.
P051 NATIONAL TRENDS IN VOLUME, COSTS, AND PATIENT RISK PROFILE OF INPATIENTS UNDERGOING INCISIONAL HERNIA REPAIR IN RELATION TO ABDOMINAL SURGERY
Authors: Rios-Diaz Arturo , Morris Martin , Christopher Adrienne , Patel Viren , Broach Robyn , Hsu Jesse , Fischer John 
Published: December 2021

Abstract

Aim
We describe trends in inpatient burden by volume, cost, and patient risk profiles of incisional hernia repair (IHR) as compared to other abdominal surgery (AS) procedures in the United States.

Material and Methods
Patients undergoing AS were identified using the National Inpatient Sample (2008-2018) by ICD-9/ICD-10 codes. National weighted procedure rates and hospital costs were ascertained and plotted using sampling weights and normalized per 1,000,000 people. Regression models allowed identification of statistical significance of trends and prediction of mean differences in rates, costs and patient characteristics.

Results
Over 38,000,000 AS discharges were identified, averaging 3.5 million annually, with over 1,200,000 discharges following IHR (3.1% of all AS). The difference between AS and IHR significantly decreased over time from 12,702 procedures per million (PPM) to 9,039 PPM. Open and laparoscopic AS down-trended (46.2% and 20.8%, respectively), whereas robotic AS up-trended (95.2% [all p &lt; 0.01]). Open IHR down-trended (60.9%) and laparoscopic IHR up-trended (83.6%, [both p &lt; 0.01]). Robotic IHR increased by 99.5% (p = 0.17). Average annual national charges for AS and IHR were $183.8 and $6.6 billion, respectively. Costs increased by 20.3% for AS and 25.6% for IHR. Patients undergoing IHR were 45-64 years old (46%), female (63.1%), White (68.1%), publicly insured (55.1%), with moderate loss of function (43.2%) and ≥2 comorbidities (43.3%).

Conclusions
IH continues to carry a significant societal and healthcare burden. With AS decreasing and IHR remaining stable from 2008 to 2018, the percentage of patients developing IH after AS has increased, as well as cost per IHR, critically underscoring the need to adopt and implement risk reduction and hernia prevention.
P063 COMPARATIVE ANALYSIS OF INCISIONAL HERNIA REPAIRS WITH MESH IN SUBLAY AND ONLAY POSITION: PROSPECTIVE SERIES
Authors: Amador Sara , Gómez Montserrat Juvany , Martin Aurora Aldeano , Palomino Arantzazu Rada , Valentini Mauro , Alonso Xavier Mira 
Published: December 2021

Abstract

Aim
Sublay mesh placement in incisional hernia repair (IH) does not seem to show lower surgical site infection (SSI) or recurrence than onlay placement, according to a recent review. Our aim was to analyze both techniques in an abdominal wall department.

Material and Methods
Prospective data collection of all IHs for four years. Results were analyzed at one month and during follow-up. The characteristics of IH, operative time, incidence of SSI and recurrence was compared by groups depending on location of the mesh in sublay (SM) or onlay (OM).

Results
“The surface area of the hernial defect was greater in the SM group (216±338 vs 68±84cm2; P = 0.002), as well as longer surgical time (131±91 vs 70±54 min; P &lt; 0.001). A higher number of hematoma was diagnosed in the SM (OR 1.39; CI95% 1.21-1.60; P = 0.18) in 88 operations. No differences were observed in the incidence of SSI between the groups (27.7 vs 21.7%; P = 0.78). 74 patients completed a mean follow-up of 11.4 months, any difference in IH recurrence appeared (5.8 vs 9.1%; P = 0.63) in SM group vs OM group, respectively.

Conclusions
A SM repair is performed in IHs with large defects, which entails a longer surgical time and the appearance of hematoma, although no statistically significant differences in the rate of SSI or IH recurrence was observed between SM and OM repair.
P080 ROUTINE ELECTIVE ILIOHYPOGASTRIC NEURECTOMY IN LICHTENSTEIN INGUINAL HERNIA REPAIR
Authors: Mitura Kryspin 
Published: December 2021

Abstract

Aim
Chronic postherniorraphy pain occurs in 8-25% of patients undergoing groin hernioplasty with mesh insertion. The most common cause for inguinodynia is neuropathy resulting from nerve damage or entrapment during mesh fixation. With wide mesh insertion there is often a conflict between upper prosthesis margin and an iliohypogastric nerve. The aim of this study is to present a routine elective iliohypogastric neurectomy in Lichtenstein groin hernia repair for prevention of chronic inguinodynia.

Material and Methods
Between 2018 and 2020, 398 patients were admitted for open inguinal hernia repair. 218 patients underwent a Lichtenstein repair with transection of iliohypogastric nerve before implantation of 10x14 polypropylene mesh (IH group). In the control group of 180 patients all nerves were spared (C group). Follow-up was conducted on 1 POD,1 month, and 1 year after surgery.

Results
1 month after a surgery a pain was reported in 24 (11%) patients in IH group (2.9% severe; 8.1% moderate; 89% no pain), and 48 (26.7%) patients in C group (3.9% severe; 22.8% moderate; 73.3% no pain). 1 year after a surgery a persistent pain was reported in 1 (0.4%) patient in IH group, and in 5 (2.8%) patients in C group. An incidence of inguinodynia was significantly lower after iliohypogastric neurectomy (0.5% vs. 2.8%; p &lt; 0.001).

Conclusions
Routine neurectomy of iliohypogastric nerve appears to be an effective technique in chronic inguinodynia after open mech repair for inguinal hernias. Iliohypogastric nerve resection allows to place a flat synthetic mesh with wide coverage of myopectineal orifice with no need for additional mesh trimming.
P081 CHRONIC GROIN PAIN IN SPORTSMEN. EVIDENCE-BASED IN EXPERIENCE
Authors: Santilli Osvaldo , Santilli Hernán , Scaravonati Rodolfo , Nardelli Nicolás , Etchepare Hernán 
Published: December 2021

Abstract

Aim
The main objective of this study is to describe and analyze the assessment and treatment of chronic groin pain (CGP) based on the experience collected in 20 years.

Material and Methods
Descriptive, observational, and retrospective study. It is a multidisciplinary team formed by surgeons, physiotherapists, orthopedists, and imaging specialists. That had developed an assessment, diagnosis, and treatment algorithm for (CGP), which have been implemented for more than 20 years. Follow-up included a record of clinical examination findings, clinical entities diagnosed, ultrasound findings, physiotherapy treatment, operation notes, and postoperative recovery, time to return to sporting activity, and complications.

Results
In the period between August 2000 and August 2020, we assessed 9996 patients with CGP. (91%) men and (9%) women with a mean age of 30 (SD: 11.21).
The most frequently practiced sports were: football (43%), rugby (25%), tennis (12%).
The most frequent clinical entities registered were tendinopathies (69%): iliopsoas-pectineus- related (36%) and adductor-related (33%). Tendinopathy sports rehabilitation treatment: (95.7%) presented total recovery in 45 days; 260 patients (4.3%)intra-tissue percutaneous electrolysis was used with favorable recovery. Only 16 patients required tenotomies
The ultrasound has been used to detect signs of adductor tendinopathy (92%) and sportsman hernia, but has low sensitivity in iliopsoas-pectineus tendinopathy (21%).

Conclusions
The algorithm used has proven to be safe and successful.
Tendinopathies and Sportsman's hernia are the most common causes of chronic groin pain in sportsmen, presenting together in 82% of the cases.
TAPP hernioplasty repair, followed by physical rehabilitation offered excellent results to treat sportsman hernia.
P083 PARASTOMAL HERNIA REPAIR - EXPERIENCES WITH THE MODIFIED RETROMUSCULAR SUGARBAKER TECHNIQUE
Authors: Gröger Christian , Kundel Lena , Adam Ulrich , Riediger Hartwig 
Published: December 2021

Abstract

Aim
Parastomal hernias are complex findings with a high recurrence rate. Various methods were described for surgical repair. A new method for the treatment of parastomal hernias with extraperitoneal mesh placement was published in 2016 (Pauli et al.). Recently, open retromuscular repair has been shown to be safe, effective and durable (Beffa et al. 2017). Still, there are concerns regarding mesh related complications (Tastaldi et al. 2017).

Material and Methods
All patients who underwent an open or laparoscopic modified retromuscular Sugarbaker parastomal hernia repair at our institution were identified. We describe the patient characteristics, operative details, perioperative results and the follow-up.

Results
Between January 2018 to May 2021 14 patients received surgical repair for parastomal hernia at our institution. Eight of these patients received retromuscular extraperitoneal mesh placement (4 open, 4 laparoscopic) in the aforementioned technique. The median age was 72 years (65 – 85) and the median BMI was 31 kg/m² (26 – 34). Six patients had a urostomy and two had a colostomy. One patient had a recurrent parastomal hernia after previous intraabdominal mesh repair. The median operating time was 223 minutes (144 – 425). Median Mesh size was 300 cm² (225 – 750). Two minor complications (Clavien-Dindo Classification Grade II) demanding pharmacological treatment. The median hospital stay was 8 days (4 – 17). Median follow up was 17 month (range 1 – 26). Recurrence rate was 25 %.

Conclusions
The modified retromuscular sugerbaker technique seems to be safe and feasible as shown by our data. Due to the extraperitoneal mesh position, we see fundamental methodological advantages. Further studies are necessary for long-term results.