bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the recall of biomedical named entity recognition with label re-correction and knowledge distillation
Authors: Zhou Huiwei , Liu Zhe , Lang Chengkun , Xu Yibin , Lin Yingyu , Hou Junjie 
Published: June 2021

Abstract
Background
Biomedical named entity recognition is one of the most essential tasks in biomedical information extraction. Previous studies suffer from inadequate annotated datasets, especially the limited knowledge contained in them.

Methods
To remedy the above issue, we propose a novel Biomedical Named Entity Recognition (BioNER) framework with label re-correction and knowledge distillation strategies, which could not only create large and high-quality datasets but also obtain a high-performance recognition model. Our framework is inspired by two points: (1) named entity recognition should be considered from the perspective of both coverage and accuracy; (2) trustable annotations should be yielded by iterative correction. Firstly, for coverage, we annotate chemical and disease entities in a large-scale unlabeled dataset by PubTator to generate a weakly labeled dataset. For accuracy, we then filter it by utilizing multiple knowledge bases to generate another weakly labeled dataset. Next, the two datasets are revised by a label re-correction strategy to construct two high-quality datasets, which are used to train two recognition models, respectively. Finally, we compress the knowledge in the two models into a single recognition model with knowledge distillation.

Results
Experiments on the BioCreative V chemical-disease relation corpus and NCBI Disease corpus show that knowledge from large-scale datasets significantly improves the performance of BioNER, especially the recall of it, leading to new state-of-the-art results.

Conclusions
We propose a framework with label re-correction and knowledge distillation strategies. Comparison results show that the two perspectives of knowledge in the two re-corrected datasets respectively are complementary and both effective for BioNER.
Methodology for comprehensive cell-level analysis of wound healing experiments using deep learning in MATLAB
Authors: Oldenburg Jan , Maletzki Lisa , Strohbach Anne , Bellé Paul , Siewert Stefan , Busch Raila , Felix Stephan B. , Schmitz Klaus-Peter , Stiehm Michael 
Published: June 2021

Abstract
Background
Endothelial healing after deployment of cardiovascular devices is particularly important in the context of clinical outcome. It is therefore of great interest to develop tools for a precise prediction of endothelial growth after injury in the process of implant deployment. For experimental investigation of re-endothelialization in vitro cell migration assays are routinely used. However, semi-automatic analyses of live cell images are often based on gray value distributions and are as such limited by image quality and user dependence. The rise of deep learning algorithms offers promising opportunities for application in medical image analysis. Here, we present an intelligent cell detection (iCD) approach for comprehensive assay analysis to obtain essential characteristics on cell and population scale.

Results
In an in vitro wound healing assay, we compared conventional analysis methods with our iCD approach. Therefore we determined cell density and cell velocity on cell scale and the movement of the cell layer as well as the gap closure between two cell monolayers on population scale. Our data demonstrate that cell density analysis based on deep learning algorithms is superior to an adaptive threshold method regarding robustness against image distortion. In addition, results on cell scale obtained with iCD are in agreement with manually velocity detection, while conventional methods, such as Cell Image Velocimetry (CIV), underestimate cell velocity by a factor of 0.5. Further, we found that iCD analysis of the monolayer movement gave results just as well as manual freehand detection, while conventional methods again shows more frayed leading edge detection compared to manual detection. Analysis of monolayer edge protrusion by ICD also produced results, which are close to manual estimation with an relative error of 11.7%. In comparison, the conventional Canny method gave a relative error of 76.4%.

Conclusion
The results of our experiments indicate that deep learning algorithms such as our iCD have the ability to outperform conventional methods in the field of wound healing analysis. The combined analysis on cell and population scale using iCD is very well suited for timesaving and high quality wound healing analysis enabling the research community to gain detailed understanding of endothelial movement.
Elucidating the multifunctional role of the cell wall components in the maize exploitation
Authors: López-Malvar Ana , Malvar Rosa Ana , Souto Xose Carlos , Gomez Leonardo Dario , Simister Rachael , Encina Antonio , Barros-Rios Jaime , Pereira-Crespo Sonia , Santiago Rogelio 
Published: June 2021

Abstract
Background
Besides the use of maize grain as food and feed, maize stover can be a profitable by-product for cellulosic ethanol production, whereas the whole plant can be used for silage production. However, yield is reduced by pest damages, stem corn borers being one of the most important yield constraints. Overall, cell wall composition is key in determining the quality of maize biomass, as well as pest resistance. This study aims to evaluate the composition of the four cell wall fractions (cellulose, hemicellulose, lignin and hydroxycinnamates) in diverse maize genotypes and to understand how this composition influences the resistance to pests, ethanol capacity and digestibility.

Results
The following results can be highlighted: (i) pests’ resistant materials may show cell walls with low p-coumaric acid and low hemicellulose content; (ii) inbred lines showing cell walls with high cellulose content and high diferulate cross-linking may present higher performance for ethanol production; (iii) and inbreds with enhanced digestibility may have cell walls poor in neutral detergent fibre and diferulates, combined with a lignin polymer composition richer in G subunits.

Conclusions
Results evidence that there is no maize cell wall ideotype among the tested for optimal performance for various uses, and maize plants should be specifically bred for each particular application.
Assessment and management of undifferentiated carcinoma with osteoclastic like giant cells of the pancreas: a case report and revision of literature
Authors: Cavalcanti Elisabetta , Schena Nicolo’ , Serino Grazia , Lantone Giulio , Armentano Raffaele 
Published: June 2021

Abstract
Background
Undifferentiated carcinoma with osteoclast-like giant cells (UCOGCs) is a rare and aggressive non endocrine pancreatic carcinoma characterized by the presence of osteoclastic giant cells mixed with mononuclear cell. Very few cases have been reported in the literature and the histogenesis is controversial as, at the time of diagnosis, the tumor is often of advanced size and stage and it is difficult to pathologically observe its relationship with the pancreatic duct.

Case presentation
We present a case of 65-year-old male patient presenting with abdominal pain, nausea, and weight loss, which was treated with surgical resection. Histological examination revealed an undifferentiated pancreatic carcinoma with osteoclast-like giant cells. The patient underwent to a routine pylorus preserving pancreatoduodenectomy. Actually, the patient was in good performance status and disease-free five months.

Conclusions
Based on the present case and limited previous data, further researches preferably with large cohorts are necessary to clarify the pathogenesis of the neoplasm. However, as show in this case, histopathological and immunohistochemically studies are the gold standard for the diagnosis of UCPOGC. Investigation of the genomic alterations in UPOGCs could help to explain the histologic diversity of variant tumor and could provide a genetic basis for prognosis and treatment.
A comparison of spouse and non-spouse carers of people with dementia: a descriptive analysis of Swedish national survey data
Authors: Johansson Marcus F. , McKee Kevin J. , Dahlberg Lena , Williams Christine L. , Summer Meranius Martina , Hanson Elizabeth , Magnusson Lennart , Ekman Björn , Marmstål Hammar Lena 
Published: June 2021

Abstract
Background
Being an informal carer of a person with dementia (PwD) can have a negative effect on the carer’s health and quality of life, and spouse carers have been found to be especially vulnerable. Yet relatively little is known about the care provided and support received by spouse carers. This study compares spouse carers to other informal carers of PwDs regarding their care provision, the support received and the psychosocial impact of care.

Methods
The study was a cross-sectional questionnaire-based survey of a stratified random sample of the Swedish population aged 18 or over. The questionnaire explored how much care the respondent provided, the support received, and the psychosocial impact of providing care. Of 30,009 people sampled, 11,168 (37.7 %) responded, of whom 330 (2.95 %) were informal carers of a PwD.

Results
In comparison to non-spouse carers, spouse carers provided more care more frequently, did so with less support from family or the local authority, while more frequently experiencing negative impacts on their social life and psychological and physical health. Spouse carers also received more carer support and more frequently experienced a closeness in their relationship with the care-recipient.

Conclusions
Spouse carers of PwD differed from non-spouse carers on virtually all aspects of their care situation. Policy and practice must be more sensitive to how the carer-care-recipient relationship shapes the experience of care, so that support is based on an understanding of the individual carer’s actual needs and preferences rather than on preconceptions drawn from a generalised support model.
Unusual clinical manifestation and challenging serological interpretation of syphilis: insights from a case report
Authors: Magri F. , Donà M. G. , Panetta C. , Pontone M. , Pimpinelli F. , Cameli N. , Cristaudo A. , Zaccarelli M. , Latini A. 
Published: June 2021

Abstract
Background
The clinical manifestations of recent syphilis can be variable, with typical and atypical patterns. Several conditions may cause atypical clinical aspects, including human immunodeficiency virus (HIV) co-infection. Besides the clinical features, co-infections may completely alter syphilis serological tests, causing interpretative difficulties and diagnostic delays. Aim of the work is to describe the difficulties encountered during the diagnostic evaluation of atypical skin manifestations and of the serology for syphilis of an HIV-infected patient who had contracted it several times.

Case presentation
In 2020, a 52-year old HIV-positive bisexual male patient was admitted to our department with a 4-month history of moderately itchy cutaneous lesions localized at his neck, trunk and arms. In 2013, the patient presented with a classic syphilitic roseola of the trunk and a secondary syphilis was diagnosed, with increased levels of rapid plasma reagin (RPR), Treponema pallidum hemagglutination assay (TPHA), anti-Treponema pallidum IgM and IgG Index. A second episode occurred in 2018, as a primary syphilis with multiple ulcerative lesions of the penis, and increased levels of RPR, IgG and IgM. In 2019, a further episode of secondary syphilis was treated with Doxycycline. In 2020, erythematous and papular lesions with vesicular components and urticarial erythema multiforme (EM)-like lesions were present at the neck, trunk and arms. Serological tests and Nucleic Acid Amplification Test (NAAT) for Treponema Pallidum were performed, as well as a cutaneous biopsy with histological and immunohistochemical evaluation of one lesion. NAAT was negative for T. pallidum. Serological test results were discordant with a new syphilis infection, showing only increased levels of RPR and anti-Treponema IgG. The cutaneous biopsy revealed a non specific histological pattern, while the immunohistochemical evaluation with anti-spirochetal antibodies was mandatory for the diagnosis of recent syphilis, showing clusters of rod-shaped elements, some of which with spiral form, focally present at the epidermis and adnexal structures.

Conclusions
Nowadays, syphilis may present with atypical clinical and serological features. Physicians should be aware of these possible alterations and consider syphilis even in case of uncommon clinical aspect and unclear serological tests. Cutaneous biopsy and immunohistochemical exam may be mandatory for the diagnosis.
Risk factors for preeclampsia and eclampsia at a main referral maternity hospital in Freetown, Sierra Leone: a case-control study
Authors: Stitterich N. , Shepherd J. , Koroma M. M. , Theuring S. 
Published: June 2021

Abstract
Background
In the African region, 5.6% of pregnancies are estimated to be complicated by preeclampsia and 2.9% by eclampsia, with almost one in ten maternal deaths being associated with hypertensive disorders. In Sierra Leone, representing one of the countries with the highest maternal mortality rates in the world, 16% of maternal deaths were caused by pregnancy-induced hypertension in 2016. In the light of the high burden of preeclampsia and eclampsia (PrE/E) in Sierra Leone, we aimed at assessing population-based risk factors for PrE/E to offer improved management for women at risk.

Methods
A facility-based, unmatched observational case-control study was conducted in Princess Christian Maternity Hospital (PCMH). PCMH is situated in Freetown and is the only health care facility providing ‘Comprehensive Emergency Obstetric and Neonatal Care services’ throughout the entire country. Cases were defined as pregnant or postpartum women diagnosed with PrE/E, and controls as normotensive postpartum women. Data collection was performed with a questionnaire assessing a wide spectrum of factors influencing pregnant women’s health. Statistical analysis was performed by estimating a binary logistic regression model.

Results
We analyzed data of 672 women, 214 cases and 458 controls. The analysis yielded several independent predictors for PrE/E, including family predisposition for PrE/E (AOR = 2.72, 95% CI: 1.46–5.07), preexisting hypertension (AOR = 3.64, 95% CI: 1.32–10.06), a high mid-upper arm circumflex (AOR = 3.09, 95% CI: 1.83–5.22), presence of urinary tract infection during pregnancy (AOR = 2.02, 95% CI: 1.28–3.19), presence of prolonged diarrhoea during pregnancy (AOR = 2.81, 95% CI: 1.63–4.86), low maternal assets (AOR = 2.56, 95% CI: 1.63–4.02), inadequate fruit intake (AOR = 2.58, 95% CI: 1.64–4.06), well or borehole water as the main source of drinking water (AOR = 2.05, 95% CI: 1.31–3.23) and living close to a waste deposit (AOR = 1.94, 95% CI: 1.15–3.25).

Conclusion
Our findings suggest that systematic assessment of identified PrE/E risk factors, including a family predisposition for PrE/E, preexisting hypertension, or obesity, should be performed early on in ANC, followed by continued close monitoring of first signs and symptoms of PrE/E. Additionally, counseling on nutrition, exercise, and water safety is needed throughout pregnancy as well as education on improved hygiene behavior. Further research on sources of environmental pollution in Freetown is urgently required.
Single nucleotide polymorphisms and the risk of developing a second primary cancer among head and neck cancer patients: a systematic literature review and meta-analysis
Authors: Hoxhaj Ilda , Vukovic Vladimir , Boccia Stefania , Pastorino Roberta 
Published: June 2021

Abstract
Background
Head and Neck Cancer (HNC) survivors are at increased risk of developing a second primary cancer (SPC). Along with the environmental risk factors, genetic factors have been associated with a potential increased susceptibility to SPC development. We aim to identify the Single Nucleotide Polymorphisms (SNPs) that contribute to SPC development among HNC survivors through a systematic review and meta-analysis.

Methods
We searched PubMed, Scopus and ISI Web of Science for eligible studies published in English until January 31st, 2020. We included studies reporting primary data that evaluated the association between SNPs and SPC risk in HNC patients. Data were pooled in a random-effect meta-analyses, when at least two studies on the same SNP evaluated the same genotype model. Heterogeneity was assessed using the χ2-based Q-statistics and the I2 statistics. Quality of the included studies was assessed using the Q-Genie tool.

Results
Twenty-one studies, of moderate to good quality, were included in the systematic review. Fifty-one genes were reported across the included studies to have significant associations with an increased SPC risk. Overall, 81 out of 122 investigated SNPs were significantly associated with the SPC risk. Seven studies were included in the meta-analysis, which showed five SNPs associated with an increased risk of SPC: p21C70T, CT + TT (HR = 1.76; 95% CI: 1.28–2.43); FASLG -844C > T, CT + TT (HR = 1.82; 95% CI: 1.35–2.46), P21 C98A, CA + AA (HR = 1.75; 95% CI: 1.28–2.38); FAS -670A > G (HR = 1.84; 95% CI: 1.28–2.66) and GST-M1, Null genotype (HR = 1.54; 95% CI: 1.13–2.10).

Conclusions
The identified SNPs in our systematic review and meta-analysis might serve as potential markers for identification of patients at high risk of developing SPC after primary HNC.

PROSPERO Registration Number
CRD42019135612.
A clinical study of pegylated recombinant human granulocyte colony stimulating factor (PEG-rhG-CSF) in preventing neutropenia during concurrent chemoradiotherapy of cervical cancer
Authors: Zou Dongling , Guo Mingfang , Zhou Qi 
Published: June 2021

Abstract
Purpose
To evaluate the effectiveness and safety of pegylated recombinant human granulocyte colony stimulating factor (PEG-rhG-CSF) in preventing neutropenia during chemoradiotherapy in patients with cervical cancer.

Methods
From August 2018 to April 2020, 60 patients who were pathologically confirmed as cervical cancer were randomly divided into two groups at a ratio of 2:1: PEG-modified-rhG-CSF experimental group and control group. The primary endpoints were the incidence of grade 3–4 neutropenia. Secondary endpoints included the duration of grade 3–4 neutropenia, the incidence of grade 4 neutropenia, the incidence of febrile neutropenia (FN), delay rate of chemotherapy, prolonged time of chemotherapy, time to complete radiotherapy and safety.

Results
The incidence of grade 3–4 neutropenia in the experimental group was significantly lower than the control group (10% vs. 77.78%, P < 0.001). However, there was no statistical significance between the two groups in the duration of grade 3–4 neutropenia (3.75 days vs. 5.07 days, P = 0.871). The experimental group was better than the control group in the incidence of grade 4 neutropenia, the incidence of FN and delay rate of chemotherapy, and the difference was statistically significant (P < 0.05). Besides, the prolonged time of chemotherapy and the time to complete radiotherapy in the experimental group were less than those in the control group, but the difference was not statistically significant (P > 0.05). The incidence of adverse events in the experimental group and control group were 55.00 and 94.44%, respectively, and the difference was statistically significant (P = 0.003).

Conclusion
PEG-rhG-CSF preventive treatment used in the course of chemoradiotherapy for patients with cervical cancer can reduce the incidence of neutropenia and improve the incidence of delayed chemotherapy cycles.

Trial registration
ClinicalTrials.gov, NCT04542356. Registered 9 September 2020 - Retrospectively registered.
Non-employment and low educational level as risk factors for inequitable treatment and mortality in heart failure: a population-based cohort study of register data
Authors: Ohlsson Anna , Eckerdal Nils , Lindahl Bertil , Hanning Marianne , Westerling Ragnar 
Published: June 2021

Abstract
Background
The risk of heart failure is disproportionately high among the socioeconomically disadvantaged. Furthermore, socioeconomically deprived patients are at risk of inequitable access to heart failure treatment and poor outcomes. Non-employment as a risk factor in this respect has not previously been studied at the level of the individual. The aim of this register-based cohort study was to analyse equity in access to renin-angiotensin system blockers and mortality, by employment status and educational level.

Methods
The study population consisted of Swedish patients aged 20–64 years hospitalised for heart failure in July 2006–December 2010, without a heart failure hospitalisation within one year or more before index hospitalisation and without renin-angiotensin system blocker dispensation in the 6 months preceding index hospitalisation. Non-access to renin-angiotensin system blockers, measured as drug dispensations, was investigated by employment status and educational level through logistic regression. Cox regression models were used to obtain hazard ratios for all-cause death by educational level and employment status. Interaction analysis was used to test whether associations between access to treatment and mortality differed by employment status.

Results
Among the 3874 patients, 1239 (32%) were women. The median age was 57 years. Fifty-three percent were employed. The non-employed patients had more comorbidity and lower access (68%) to renin-angiotensin system blockers compared with the employed (82%). The adjusted odds ratio for non-access to renin-angiotensin system blockers among the non-employed was 1.76. Non-employment was associated with an adjusted hazard ratio of 1.76 for death. Low educational level was associated with a higher death risk. Mortality was highest among the non-employed without access to renin-angiotensin system blockers and the association between access to renin-angiotensin system blockers and survival was slightly weaker in this group.

Conclusions
Non-employment and low educational level were associated with elevated mortality in heart failure. Non-employment was a risk factor for lower access to evidence-based treatment, and among the non-employed access to treatment was associated with a slightly smaller risk reduction than among the employed. The results underscore that clinicians need to be aware of the importance of socioeconomic factors in heart failure care.