bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of daily versus weekly service of infectious diseases consultation on hospital antimicrobial consumption: a retrospective study
Authors: Cona Andrea , Gazzola Lidia , Viganò Ottavia , Bini Teresa , Marchetti Giulia Carla , Monforte Antonella d'Arminio 
Published: October 2020

Abstract
Background: To verify whether a daily service of Infectious Diseases consultation (ID-cons) is more effective than a weekly service in reducing antibiotic (ATB) consumption without worsening of clinical outcomes. Methods: Two-year observational analysis of the ID-cons provided in a hospital setting in Milan, Italy. ID-cons resulted in: start-of-ATB; no-ATB; confirmation; modification-of-ATB. The impact of a weekly (September 1, 2016 - August 31, 2017) versus a daily (September 1, 2017 – September 30, 2018) service of ID-cons was evaluated in terms of: time-from-admission-to-first-ID-cons, type of ATB-intervention and number-of-ID-cons per 100 bed-days (bd). Primary outcomes: reduction of hospital ATB consumption overall and by department and classes expressed as Defined Daily Dose (DDD)/100bd (by Wilcoxon test for paired data). Secondary outcomes: overall and sepsis-related in-hospital annual mortality rates (as death/patient’s admissions). Results: Overall 2552 ID-cons in 1111 patients (mean, 2.3 ID-cons per patient) were performed (18.6% weekly vs 81.4% daily). No differences in patient characteristics were observed. In the daily-service, compared to the weekly-service, patients were seen by the ID-consultant earlier (time-from-admission-to-ID-cons: 6 days (IQR 2-13) vs 10 days (IQR 6-19), p<0.001) and ATB was more often started by the ID-consultant (Start-of-ATB: 11.6% vs 8%, p=0.02), rather than treating physicians. After switching to daily-service, the number-of-ID-cons increased from 0.4/100bd to 1.5/100bd (p=0.01), with the greatest increase in the emergency department (1.5/100bd vs 6.7/100bd, p<0.001). Total ATB consumption decreased from 64 to 60 DDD/100bd. As for the number-of-cons, the consumption of ATB decreased mainly in the emergency area. According to ATB classes, glycopeptides consumption was reduced from 3.1 to 2.1 DDD/100bd (p=0.02) while carbapenem use decreased from 3.7 to 3.1 DDD/100bd (p=0.07). No changes in overall mortality (5.2% vs 5.2%) and sepsis-related mortality (19.3% vs 20.9%; p=0.7) were observed among the two time-period. Conclusions: Daily-ID-cons resulted in a more comprehensive management of the infected patient by the ID-consultant, especially in the emergency area where we also observed the highest rate of reduction of ATB-usage. No change in mortality was observed.
Development of a Fuzzy Model for Differentiating Peanut Plant from Broadleaf Weeds Using Image Features
Authors: Bakhshipour Adel , Zareiforoush Hemad 
Published: October 2020

Abstract
A combination of decision tree (DT) and fuzzy logic techniques was used to develop a fuzzy model for differentiating peanut plant from weeds. Color features and wavelet-based texture features were extracted from images of peanut plant and its three common weeds. Two feature selection techniques namely Principal Component Analysis (PCA) and Correlation-based Feature Selection (CFS) were applied on input dataset and three Decision Trees (DTs) including J48, Random Tree (RT), and Reduced Error Pruning (REP) were used to distinguish between different plants. In all cases, the best overall classification accuracies were achieved when CFS-selected features were used as input data. The obtained accuracies of J48-CFS, REP-CFS, and RT-CFS trees for classification of the four plant categories namely peanut plant, Velvetleaf, False daisy, and Nicandra, were 80.83%, 80.00% and 79.17% respectively. Along with these almost low accuracies, the structures of the decision trees were complex making them unsuitable for developing a fuzzy inference system. The classifiers were also used for differentiating peanut plant from the group of weeds. The overall accuracies on training and testing datasets were respectively 95.56% and 93.75% for J48-CFS; 92.78% and 91.67% for REP-CFS; and 93.33% and 92.59% for RT-CFS DTs. The results showed that the J48-CFS and REP-CFS were the most appropriate models to set the membership functions and rules of the fuzzy classifier system. Based on the results, it can be concluded that the developed DT-based fuzzy logic model can be used effectively to discriminate weeds from peanut plant in the form of machine vision-based cultivating systems.
Combination of phenotype and polygenic risk score in breast cancer risk evaluation in the Spanish population: A case –control study
Authors: Trivino juan , Ceba A , Rubio-Solsona E , Serra D , Sanchez-Guiu I , Ribas G , Rosa R , Cabo M , Bernad L , Pita G , Gonzalez-Neira A , Legarda G , Diaz JL , García-Vigara A , Martínez-Aspas A , Escrig M , Bermejo B , Eroles P , Ibáñez J , Salas D , Julve A , Cano A , Lluch A , Miñambres R , Benitez Javier 
Published: October 2020

Abstract
Background: In recent years, the identification of genetic and phenotypic biomarkers of cancer for prevention, early diagnosis and patient stratification has been a main objective of research in the field. Different multivariable models that use biomarkers have been proposed for the evaluation of individual risk of developing breast cancer. Methods: This is a case control study based on a population-based cohort. We describe and evaluate a multivariable model that incorporates 92 Single-nucleotide polymorphisms (SNPs) and five different phenotypic variables and which was employed in a Spanish population of 642 healthy women and 455 breast cancer patients. Results: Our model allowed us to stratify two groups: high and low risk of developing breast cancer. The 9th decile included 1% of controls vs 9% of cases, with an odds ratio (OR) of 12.9 and a p-value of 3.43E-07. The first decile presented an inverse proportion: 1% of cases and 9% of controls, with an OR of 0.097 and a p-value of 1.86E-08. Conclusions: These results indicate the capacity of our multivariable model to stratify women according to their risk of developing breast cancer. The major limitation of our analysis is the small cohort size. However, despite the limitations, the results of our analysis provide proof of concept in a poorly studied population, and opens up the possibility of using this method in the routine screening of the Spanish population.
Does chemotherapy or radiotherapy affect the postoperative complication in patients who underwent immediate breast reconstruction with tissue expander?
Authors: Jung Sung Mi , Jeon Byung-Joon , Woo Jinsun , Ryu Jai Min , Lee Se Kyung , Chae Byung-Joo , Yu Jonghan , Kim Seok Won , Nam Seok Jin , Bang Sa Ik , Mun Goo-Hyun , Pyon Jai-Kyong , Lee Jeong Eon 
Published: October 2020

Abstract
Background: Immediate breast reconstruction with tissue expander in patients who were expected to receive adjuvant therapy, such as chemotherapy or radiotherapy, has been a topic of debate. Postoperative complications from tissue expander procedures can delay the timing of adjuvant treatment and subsequently increase the probability of recurrence. The purpose of this study was to identify the impact of chemotherapy and radiotherapy on postoperative complications in patients who underwent immediate reconstruction (IR) using tissue expander.Methods: We conducted a retrospective study of 1,081 breast cancer patients who underwent mastectomy and IR using tissue expander insertion between 2012 and 2017 in Samsung Medical Center. The patients were divided into two groups based on complications (complication group vs. no complication group). Complication group was regarded to have surgical removal or conservative treatment based on clinical findings such as infection, capsular contracture, seroma, hematoma, rupture, malposition, tissue viability, or cosmetic problem. The complication group had 59 patients (5.5%) and the no complication group had 1,022 patients (94.5%). Results: In univariate analysis, adjuvant radiotherapy and adjuvant chemotherapy were significantly associated with postoperative complications. In multivariate analysis, however, only higher pathologic N stage was significantly associated with postoperative complications (p < 0.001). Chemotherapy (p = 0.775) or radiotherapy (p = 0.825) were not risk factors for postoperative complications.Conclusions: IR with tissue expander after mastectomy may be a treatment option even when the patients are expected to receive adjuvant chemotherapy or radiotherapy. These results will aid patients who are concerned about the complications of IR caused by chemotherapy or radiotherapy determine whether or not to have IR.
Gap-analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians
Authors: Paz Guy , Rinkevich Baruch 
Published: October 2020

Abstract
BackgroundAll-inclusive DNA barcoding libraries in the storage and analysis platform of the BOLD (Barcode of Life Data) system are essential for the study of the marine biodiversity and are pertinent for regulatory purposes, including ecosystem monitoring and assessment, such as in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). Here we investigate knowledge gaps in the lists of DNA barcoded organisms within two inventories, Cnidaria (Anthozoa and Hydrozoa) and Ascidiacea from the reference libraries of the European Register of Marine Species (ERMS) dataset (402 ascidians and 1200 cnidarian species). ERMS records were checked species by species, against publicly available sequence information and other data stored in BOLD system. As the available COI barcode data adequately covers just a small fraction of the ERMS reference library, it is of importance to employ quality control on existing data, to close the knowledge gaps and purge errors off BOLD. ResultsResults revealed that just 22.9% and 29.2% of the listed ascidians and cnidarians species, respectively, are BOLD barcodes of which, 58.4% and 52.3% of the seemingly barcoded species, respectively, were noted to have complete BOLD pages. Thus, only 11.44% of the tunicate and 17.07% of the cnidarian data in the ERMS lists are of high quality. Deep analyses revealed seven common types of gaps in the list of the barcoded species in addition to a wide range of discrepancies and misidentifications, discordances and errors primarily in the GenBank mined data as with the BINs assignments, among others. ConclusionsGap knowledge in barcoding of important taxonomic marine groups exist and in addition, quality management elements (quality assurance and quality control) were not employed when using the list for national monitoring projects, for regulatory compliance purposes and other purposes. Even though BOLD is the most trustable DNA barcoding reference library, worldwide projects of DNA barcoding are needed to close these gaps of mistakes, verifications, missing data and unreliable sequencing labs. Tight quality control and quality assurance is important to close the knowledge gaps of Barcoding of the European recommended ERMS reference library.
Left atrial functional assessment and mortality in patients with severe aortic stenosis with sinus rhythm
Authors: Ferreira João , Gonçalves Valdirene , Marques-Alves Patrícia , Martins Rui , Monteiro Sílvia , Teixeira Rogério , Gonçalves Lino 
Published: October 2020

Abstract
Background: Aortic valve stenosis (AS) is the most common primary valvular heart disease leading to surgical or percutaneous aortic valve replacement (AVR) in Europe and its prevalence keeps growing. While other risk factors in severe AS are well documented, little is known about the prognostic value of left atrial (LA) function in AS. Our aim is to clarify the relationship between LA function measured at severe AS diagnosis (evaluated by means of volumetric assessment) and all-cause mortality during follow-up.

Methods: We retrospectively evaluated patients diagnosed with severe AS for the first time at our echocardiography laboratory. We evaluated LA reservoir, conduit and pump function by measuring LA volumes at different timings of cardiac cycle. Treatment strategy was decided according to heart team consensus and patient decision. We divided patients into groups according to terciles of LA reservoir, conduit and pump function. Primary outcome was defined by the occurrence of all-cause mortality during follow-up.

Results: A total of 408 patients were included in the analysis, with a median follow-up time of 45 months (interquartile range 54 months). 57.9% of patients underwent AVR and 44.9% of patients registered the primary outcome during follow-up. Left atrial emptying fraction (LAEF) was the best LA functional parameter and the best overall parameter in discriminating primary outcome (AUC 0.845, 95%CI 0.81-0.88, P <0.001). After adjustment for clinical, demographic and echocardiographic variables, cumulative survival of patients with LAEF <37% and LAEF 37 to 53% relative to patients with LAEF ≥54% remained significantly lower (HR 13.91, 95%CI 6.20-31.19, P <0.001 and HR 3.40, 95%CI 1.57-7.37, P =0.002, respectively). After adjustment for AVR, excess risk of LAEF <37% and LAEF 37 to 53% relative to LAEF ≥54% remained significant (HR 11.71, 95%CI 5.20-26.40, P <0.001 and HR 3.59, 95%CI 1.65-7.78, P =0.001, respectively).

Conclusions: In patients with a first diagnosis of severe AS, LA function, evaluated by means of volumetric assessment, is an independent predictor of all-cause mortality and a more potent predictor of death compared to classical severity parameters. These data can be useful to identify high-risk patients who might benefit of AVR.
Effectiveness of the Close Collaboration with Parents intervention on parent-infant closeness in hospital
Authors: He Felix , Axelin Anna , Ahlqvist-Björkroth Sari , Raiskila Simo , Löyttyniemi Eliisa , Lehtonen Liisa 
Published: October 2020

Abstract
Background: Parent-infant closeness during hospital care of newborns has many benefits for both infants and parents. We developed an educational intervention for neonatal staff, Close Collaboration with Parents, to increase parent-infant closeness during hospital care. The aim of this study was to evaluate the effectiveness of the intervention on parent-infant closeness in nine hospitals in Finland. Methods: Parents of hospitalized infants were recruited in the hospitals during 3-month periods before and after the Close Collaboration with Parents intervention. The data were collected using daily Closeness diaries. Mothers and fathers separately filled in the time they spent in the hospital and the time of skin-to-skin contact with their infant during each hospital care day until discharge. Statistical analyses were done using a linear model with covariates. Results: Diaries were kept before and after the intervention by a total of 170 and 129 mothers and 126 and 84 fathers, respectively. Either parent was present on average 453 minutes per day before the intervention and 620 minutes after the intervention in the neonatal unit. In the adjusted model, the increase was 99 minutes per day (p=0.0007). The infants were in skin-to-skin contact on average 76 minutes per day before the intervention and 114 minutes after the intervention. In the adjusted model, skin-to-skin contact increased by 24 minutes per day (p=0.0405). Conclusion: The Close Collaboration with Parents intervention increased parents’ presence and skin-to-skin contact in nine hospitals. This study suggests that parent-infant closeness may be one mediating factor explaining benefits of parenting interventions.
Choroidal vessel density in unilateral hyperopic amblyopia using en-face optical coherence tomography
Authors: Araki Syunsuke , Miki Atsushi , Goto Katsutoshi , Yamashita Tsutomu , Yoneda Tsuyoshi , Fujiwara Atsushi , Haruishi Kazuko , Ieki Yoshiaki , Kiryu Junichi , Maehara Goro , Yaoeda Kiyoshi 
Published: October 2020

Abstract
Background Structural changes of the choroid, such as choroidal thickening, have been indicated in amblyopic eyes with hyperopic anisometropia as compared to fellow or healthy eyes. The purpose of the present study was to investigate choroidal vascular density (CVD) in children with unilateral hyperopic amblyopia.Methods This study included 88 eyes of 44 patients with unilateral amblyopia due to hyperopic anisometropia with or without strabismus and 29 eyes of 29 age-matched normal controls. The CVD of Haller's layer was quantified from en-face images constructed by 3-dimensional swept-source optical coherence tomography images flattened relative to Bruch's membrane. The analysis area was a 3×3-mm square of macula after magnification correction. Relationships between CVD and other parameters [best-corrected visual acuity (BCVA), refractive error and subfoveal choroidal thickness (SFCT)] were investigated, and CVDs were compared between amblyopic, fellow, and normal control eyes.Results Mean CVD was 59.11 ± 0.66% in amblyopic eyes, 59.23 ± 0.81% in fellow eyes, and 59.29 ± 0.74% in normal control eyes. CVD showed a significant positive relationship with SFCT (p=0.004), but no relationships with other parameters. No significant differences in CVD were evident among amblyopic, fellow, and normal control eyes after adjusting for SFCT (p=0.502).Conclusions CVD was unrelated to BCVA, and CVD did not differ significantly among amblyopic, fellow and normal control eyes. These results suggest that the local CVD of Haller's layer is unaffected in unilateral hyperopic amblyopic eyes.
Repeatability of two semi-automatic artificial intelligence approaches for tumor segmentation in PET
Authors: Pfaehler Elisabeth , Mesotten Liesbet , Kramer Gem , Thomeer Michiel , Vanhove Karolien , de Jong Johan , Adriaensens Peter , Hoekstra Otto S. , Boellaard Ronald 
Published: October 2020

Abstract
Background: Positron Emission Tomography (PET) is routinely used for cancer staging and treatment follow up. Metabolic active tumor volume (MATV) as well as total MATV (TMATV - including primary tumor, lymph nodes and metastasis) and/or total lesion glycolysis (TLG) derived from PET images have been identified as prognostic factor or for the evaluation of treatment efficacy in cancer patients. To this end, a segmentation approach with high precision and repeatability is important. However, the implementation of a repeatable and accurate segmentation algorithm remains an ongoing challenge. Methods: In this study, we compare two semi-automatic artificial intelligence (AI) based segmentation methods with conventional semi-automatic segmentation approaches in terms of repeatability. One segmentation approach is based on a textural feature (TF) segmentation approach designed for accurate and repeatable segmentation of primary tumors and metastasis. Moreover, a Convolutional Neural Network (CNN) is trained. The algorithms are trained, validated and tested using a lung cancer PET dataset. The segmentation accuracy of both segmentation approaches is compared using the Jaccard Coefficient (JC). Additionally, the approaches are externally tested on a fully independent test-retest dataset. The repeatability of the methods is compared with those of two majority vote (MV2, MV3) approaches, 41%SUVMAX, and a SUV>4 segmentation (SUV4). Repeatability is assessed with test-retest coefficients (TRT%) and intraclass correlation coefficient (ICC). An ICC>0.9 was regarded as representing excellent repeatability.Results: The accuracy of the segmentations with the reference segmentation was good (JC median TF: 0.7, CNN: 0.73) Both segmentation approaches outperformed most other conventional segmentation methods in terms of test-retest coefficient (TRT% mean: TF: 13.0%, CNN: 13.9%, MV2: 14.1%, MV3: 28.1%, 41%SUVMAX: 28.1%, SUV4: 18.1% ) and ICC (TF: 0.98, MV2: 0.97, CNN: 0.99, MV3: 0.73, SUV4: 0.81, and 41%SUVMAX: 0.68).Conclusion: The semi-automatic AI based segmentation approaches used in this study provided better repeatability than conventional segmentation approaches. Moreover, both algorithms lead to accurate segmentations for both primary tumors as well as metastasis and are therefore good candidates for PET tumor segmentation.
COVID-19 Lung CT Image Segmentation Using Deep Learning Methods: UNET Vs. SegNET
Authors: Saood Adnan , Hatem Iyad 
Published: October 2020

Abstract
Background: Currently, there is an urgent need for efficient tools to assess the diagnosis of COVID-19patients. In this paper, we present feasible solutions for detecting and labeling infected tissues on CT lungimages of such patients. Two structurally-different deep learning techniques, SegNet and UNET, areinvestigated for semantically segmenting infected tissue regions in CT lung images.Methods: We propose to use two known deep learning networks, SegNet and UNET, for image tissueclassification. SegNet is characterized as as scene segmentation network and UNET as a medical segmentationtool. Both networks were exploited as binary segmentors to discriminate between infected and healthy lungtissue, also as multi-class segmentors to learn the infection type on the lung. Each network is trained usingseventy-two data images, validated on ten images, and tested against the left eighteen images. Severalstatistical scores are calculated for the results and tabulated accordingly.Results: The results show the superior ability of SegNet in classifying infected/non-infected tissues comparedto the other methods (with 0:95 mean accuracy), while the UNET shows better results as a multi-classsegmentor (with 0:91 mean accuracy).Conclusion: Semantically segmenting CT scan images of COVID-19 patients is a crucial goal because it wouldnot only assist in disease diagnosis, also help in quantifying the severity of the illness, and hence, prioritize thepopulation treatment accordingly. We propose computer-based techniques that prove to be reliable asdetectors for infected tissue in lung CT scans. The availability of such a method in today’s pandemic wouldhelp automate, prioritize, fasten, and broaden the treatment of COVID-19 patients globally.
Boerhaave Syndrome Due to Excessive Alcohol Consumption: Two Case Reports
Authors: Haba Yuichiro , Yano Shungo , Akizuki Hikaru , Hashimoto Takashi , Naito Toshio , Hashiguchi Naoyuki 
Published: October 2020

Abstract
Background: Spontaneous esophageal rupture, or Boerhaave syndrome, is a fatal disorder caused by an elevated esophageal pressure owing to forceful vomiting. Patients with Boerhaave syndrome often present with chest pain, dyspnea, and shock. We report on two patients of Boerhaave syndrome with different severities that was triggered by excessive alcohol consumption and was diagnosed immediately in the emergency room.Case presentation: The patient in case 1 complained of severe chest pain and nausea and vomited on arrival at the hospital. He was subsequently diagnosed with Boerhaave syndrome coupled with mediastinitis using computed tomography (CT) and esophagogram. An emergency operation was successfully performed, in which a 3-cm tear was found on the left-posterior wall of the distal esophagus. The patient subsequently had anastomotic leakage but was discharged 41 days later. The patient in case 2 complained of severe chest pain, nausea, vomiting, and hematemesis on arrival. He was suggested of having Boerhaave syndrome without mediastinitis on CT. The symptoms gradually disappeared after conservative treatment. Upper gastrointestinal endoscopy performed on the ninth day revealed a scar on the left wall of the distal esophagus. The patient was discharged 11 days later. In addition to the varying severity between the cases, the patient in case 2 was initially considered to have Mallory–Weiss syndrome.Conclusion: Owing to similar histories and symptoms, Boerhaave syndrome and Mallory–Weiss syndrome must be accurately distinguished by emergency clinicians. CT can be a useful modality to detect any severity of Boerhaave syndrome and also offers the possibility to distinguish Boerhaave syndrome from Mallory–Weiss syndrome.