bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a prototype machine learning tool to semi-automate data extraction for systematic literature reviews
Authors: Panayi Antonia , Ward Katherine , Benhadji-Schaff Amir , Ibanez-Lopez A Santiago , Xia Andrew , Barzilay Regina 
Published: October 2023

Abstract
Background
Evidence-based medicine requires synthesis of research through rigorous and time-intensive systematic literature reviews (SLRs), with significant resource expenditure for data extraction from scientific publications. Machine learning may enable the timely completion of SLRs and reduce errors by automating data identification and extraction.

Methods
We evaluated the use of machine learning to extract data from publications related to SLRs in oncology (SLR 1) and Fabry disease (SLR 2). SLR 1 predominantly contained interventional studies and SLR 2 observational studies.
Predefined key terms and data were manually annotated to train and test bidirectional encoder representations from transformers (BERT) and bidirectional long-short-term memory machine learning models. Using human annotation as a reference, we assessed the ability of the models to identify biomedical terms of interest (entities) and their relations. We also pretrained BERT on a corpus of 100,000 open access clinical publications and/or enhanced context-dependent entity classification with a conditional random field (CRF) model.
Performance was measured using the F1 score, a metric that combines precision and recall. We defined successful matches as partial overlap of entities of the same type.

Results
For entity recognition, the pretrained BERT+CRF model had the best performance, with an F1 score of 73% in SLR 1 and 70% in SLR 2. Entity types identified with the highest accuracy were metrics for progression-free survival (SLR 1, F1 score 88%) or for patient age (SLR 2, F1 score 82%). Treatment arm dosage was identified less successfully (F1 scores 60% [SLR 1] and 49% [SLR 2]). The best-performing model for relation extraction, pretrained BERT relation classification, exhibited F1 scores higher than 90% in cases with at least 80 relation examples for a pair of related entity types.

Conclusions
The performance of BERT is enhanced by pretraining with biomedical literature and by combining with a CRF model. With refinement, machine learning may assist with manual data extraction for SLRs.
Epigenomic signature of major congenital heart defects in newborns with Down syndrome
Authors: Mouat Julia S. , Li Shaobo , Myint Swe Swe , Laufer Benjamin I. , Lupo Philip J. , Schraw Jeremy M. , Woodhouse John P. , de Smith Adam J. , LaSalle Janine M. 
Published: October 2023

Abstract
Background
Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS), but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs.

Methods
We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: (1) 45 DS-CHD (27 female, 18 male) and (2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD versus DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell-type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS versus typical development (TD) WGBS NDBS samples.

Results
We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS versus TD samples.

Conclusions
A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.
Assessment of the mind-body connection: preliminary psychometric evidence for a new self-report questionnaire
Authors: Van Bael Kristen , Ball Michelle , Scarfo Jessica , Suleyman Emra 
Published: October 2023

Abstract
Objectives
While interoceptive self-report scales provide a foundation for measuring the mind-body connection, they variably consider other important factors that could influence interpretations of internal bodily sensations and perceptions related to mind-body integration. The proposed Body-Mind Connection Questionnaire (BMCQ) aimed to operationalise the notion that this construct involves three major components: (a) Interoceptive Attention, (b) Sensation-Emotion Articulation, and (c) Body-Mind Values.

Methods
Following panel review and piloting with the target population, the developed BMCQ was evaluated in 316 participants (189 identifying as female) aged 18-50 (MAge=30.78), alongside established self-report measures of interoceptive sensibility, body awareness, sensory processing sensitivity, and alexithymia. We examined the BMCQ factor structure through exploratory factor analysis and analysed convergent and discriminant validity.

Results
Exploratory factor analysis supported three scales of the BMCQ, which explained 54.03% of variance. Factor loadings (>0.44) and reliability indices (0.74 to 0.85) were acceptable. Inter-scale correlations suggested that the scales are distinct but related (rs=0.38 to 0.59). BMCQ scales were supported by convergent (r=0.33 to 0.67) and discriminant evidence (rs=0.01 to 0.39, p range n.s. to <.05).

Conclusions
Preliminary psychometric properties indicate that the BMCQ is multidimensional and consists of three constructs that differentially relate to theoretically associated measures. Interoceptive Attention, Sensation-Emotion Articulation, and Body-Mind Values may serve as a basis for efficiently assessing the mind-body connection more holistically, which could be useful for developing interventions aimed at enhancing mind-body integration.
De novo synthesis of nervonic acid and optimization of metabolic regulation by Yarrowia lipolytica
Authors: Zhao Xin-Ru , Chen Xin-Liang , Yang Jing-Lin , Gao Qi , Shi Jiang-Ting , Hua Qiang , Wei Liu-Jing 
Published: October 2023

AbstractNervonic acid, a natural fatty acid compound and also a core component of nerve fibers and nerve cells, has been widely used to prevent and treat related diseases of the brain nervous system. At present, fatty acids and their derivatives are mainly obtained by natural extraction or chemical synthesis which are limited by natural resources and production costs. In this study, the de novo synthetic pathway of nervonic acid was constructed in Yarrowia lipolytica by means of synthetic biology, and the yield of nervonic acid was further improved by metabolic engineering and fermentation optimization. Specially, heterologous elongases and desaturases derived from different organism were successfully expressed and evaluated for their potential for the production of nervonic acid in Y. lipolytica. Meanwhile, we overexpressed the genes involved in the lipid metabolism to increase the nervonic acid titer to 111.6 mg/L. In addition, the potential of adding oil as auxiliary carbon sources for nervonic acid production by the engineered Y. lipolytica was analyzed. The results indicated that supplementation with colleseed oil as an auxiliary carbon source can be beneficial for the nervonic acid productivity, which led to the highest concentration of 185.0 mg/L in this work. To summarize, this study describes that the Y. lipolytica can be used as a promising platform for the production of nervonic acid and other very long-chain fatty acids.
Graphical Abstract
Identification of fragmented cranial remains excavated from a site adjoining Ajnala well: a forensic anthropological case report
Authors: Sehrawat J. S. , Rai Niraj 
Published: October 2023

Abstract
Background
Mankind have suffered several unexpected disasters, heinous crimes, and brutalities, resulting into large number of unknown skeletal remains to be identified and repatriated to their relatives.

Case presentation
One such incident of mass killing of 282 Indian-origin soldiers by the colonial rulers in 1857 was reported from Ajnala (India) in early 2014. The damaged cranial fragments belonging to two individuals were retrieved from the vicinity of Ajnala mass-burial site later in 2014. In present study, the retrieved cranial elements were examined forensic anthropologically to assess whether their affinity is akin to the slain Ajnala sepoys or to the deceased who were buried prior to or later than it. The morphological and molecular analyses of these remains affirmed their affiliation to the mutiny sepoys of 1857 killed at Ajnala.

Conclusions
The forensic anthropological and molecular examinations of cranial fragments found that these remains belonged to the individuals killed in the Ajnala incident. The multidisciplinary approach applied for identification of the badly damaged, fragmented, and commingled human remains helped in their presumptive identification.
Aparecium: understanding and detecting scam behaviors on Ethereum via biased random walk
Authors: Yan Chuyi , Zhang Chen , Shen Meng , Li Ning , Liu Jinhao , Qi Yinhao , Lu Zhigang , Liu Yuling 
Published: October 2023

AbstractEthereum’s high attention, rich business, certain anonymity, and untraceability have attracted a group of attackers. Cybercrime on it has become increasingly rampant, among which scam behavior is convenient, cryptic, antagonistic and resulting in large economic losses. So we consider the scam behavior on Ethereum and investigate it at the node interaction level. Based on the life cycle and risk identification points we found, we propose an automatic detection model named Aparecium. First, a graph generation method which focus on the scam life cycle is adopted to mitigate the sparsity of the scam behaviors. Second, the life cycle patterns are delicate modeled because of the crypticity and antagonism of Ethereum scam behaviors. Conducting experiments in the wild Ethereum datasets, we prove Aparecium is effective which the precision, recall and F1-score achieve at 0.977, 0.957 and 0.967 respectively.
The role of miRNA-29b1, MMP-2, MMP-9 mRNAs, and proteins in early diagnosis of HCC
Authors: Abdel-Tawab Marwa Sayed , Fouad Hanan , Khalil Doaa Mahmoud , Shaaban Saeed , Nafady Shaymaa , Moawad Hanan Hosni , Mostafa Heba Ahmed , Abdel-Salam Soha Mahmoud , Elazeem Naglaa Adly Abd , Mohamed Alaa A. 
Published: October 2023

AbstractBackgroundHepatocellular carcinoma (HCC) is a common, serious malignancy with a dismal prognosis. As HCC is frequently missed in its early stages, non-invasive early detection is urgently needed. The purpose of this study was to evaluate the possible utility of circulating miRNA-29b1, matrix metalloproteinases (MMPs)-2 and -9 mRNAs, and proteins as diagnostic and predictive biomarkers for HCC.Subjects and methodsThis study included 92 subjects, including 52 patients with HCC at various stages and grades and 40 healthy subjects as controls. RT-PCR was used to detect circulating miRNA-29b1, MMPs-2, and 9 mRNAs, while ELISA was used to detect AFP, MMPs-2, and 9 proteins in the participants’ blood.ResultsWhen HCC patients were compared to controls, there were significant increases in the levels of MMPs-2, 9 mRNAs, and proteins, and a significant drop in the levels of miRNA-29b1. There were no significant variations in the levels of miRNA-29b1, mRNAs, and MMP-2 and -9 proteins in advanced HCC. There were negative associations between miRNA-29b1 and MMPs-2, 9 mRNAs, and proteins, implying overlapping molecular microRNA-mediated mechanisms that control MMPs that should be investigated further in the future. The levels of miRNA-29b1, MMPs-2, 9 mRNAs, and proteins indicated significant sensitivity and specificity in the early identification of HCC.ConclusionMMP-2, 9 mRNAs, and proteins may be employed as diagnostic but not prognostic biomarkers in HCC. miRNA-29b1 may play a protective role in HCC. An overlapping molecular microRNA-29b1-mediated pathway that may control MMPs-2 and 9 requires further experimental investigation in the future.
Stem cell therapy in sensorineural hearing loss: a systematic review
Authors: Mady Ossama Mustafa , Ezzat Waleed Farag , Askoura Anas Mohamed , Elbadawy Gamal Mohamed Gamal 
Published: October 2023

Abstract
Background
Damage to the inner ear or cochlear nerve results in sensorineural hearing loss (SNHL), which is typically persistent deafness. SNHL can range in severity from mild to profound. The shape of the audiogram is used to categorise it as high-frequency hearing loss, low-frequency, flat, peaked, or notched. Pure tone audiometry can be used to diagnose SNHL.

Objective
To summarise the recent updates in the usage of stem cells in sensory neural hearing loss (SNHL).

Methods
Published studies about using stem cell therapy in ENT practice through comprehensive PubMed, EKG, and Google Scholar search (from 2010 to 2022). Including studies in English, experimental studies, and studies that discuss the application of regenerative medicine in SNHL.

Results
Progenitor stem cells may be employed to repair damaged cells and restore sensorineural hearing function, according to 36 of the publications. The majority of these articles—about 90%—discussed animal model-based experimental investigations; the remaining 10% were clinical trials.

Conclusion
The application of stem cells in the treatment of SNHL will be a significant step in the future since it will change the way that patients are now treated in the hopes of regaining their hearing. The application to the clinical setting is still in its early stage, although a number of encouraging researches illustrate how progenitor stem cells differentiate into sensorineural cells.
FRI042 Worsening Shortness Of Breath After A Mild Case Of Covid-19
Authors: Qureshi Khurrum , Krause Terry S , Vidlock Kathryn 
Published: October 2023

Abstract
Disclosure: K. Qureshi: None. T.S. Krause: None. K. Vidlock: None.
This case demonstrates a complication of COVID 19 that may be more common than we know and overlooked. A 34-year-old female presents to the Emergency Department with worsening shortness of breath and tachycardia for 3 days. Her symptoms are worse with ambulation. She feels dizzy and lightheaded. The patient had COVID-19 about two weeks ago and received monoclonal antibodies. The patient has a history of “drenching” night sweats and unintentional weight loss. She denies fever and cough. The patient is eating and drinking normally with no abdominal pain, nausea, or rash. No changes in bowel movements. The patient’s past medical history consists of ADHD, Anxiety, Neuropathy, and Insomnia. The patient takes Adderall, amitriptyline (ELAVIL), fluocinonide (LIDEX). The patient’s family history consists of an aunt who has autoimmune disease and a maternal grandfather who has Non-Hodgkin's Lymphoma. She works as a medical assistant in a family medicine clinic. Patient underwent a CTA which displayed a new anterior mediastinal mass measuring 4.6 x 2.6 x 3.2 cm which was not shown on a previous CT scan 11 months prior. She was referred to a thoracic surgeon for mediastinoscopy, which couldn’t be performed due to location not adjacent to trachea. A PET scan showed mildly FDG-avid soft tissue density in the anterior mediastinum. Four months later, the patient had a CT scan which showed a modest decrease in size measuring 2.1 x 2.5 cm. The thymus is important in maturation of T cells and is replaced with fat through aging. The thymus plays an important immunological role in defending against pathogens and cancer by maturing and releasing T cells. Thymic hyperplasia is a response that has been displayed in autoimmune diseases such as Myasthenia Gravis. Thymic rebound hyperplasia is seen more often in children, typically after chemotherapy treatment but not seen in adults. Rebound hyperplasia occurs less often with viral illness. There have been a limited number of cases seen with COVID-19. An observational study of 87 participants suggested that rebound thymic hyperplasia may be a positive predictive factor due to the benefit of T-cell lymphocyte production. The presence of thymic hyperplasia on CT scan in COVID patients correlated with a better prognosis in a retrospective study of 325 COVID patients that had a CT scan. This patient will require repeated imaging and follow up. The long-term consequences of this finding are unknown and this patient has a history of night sweats which preceded the COVID course.
Presentation: Friday, June 16, 2023
SAT154 Insulin Autoimmune Syndrome In The Setting Of Metastatic Colon Cancer: Case Report
Authors: Bernal Maria , Suarez Janine , Tuna Kubra M , Amer Farah , Lamas Marcos 
Published: October 2023

Abstract
Disclosure: M. Bernal: None. J. Suarez: None. K.M. Tuna: None. F. Amer: None. M. Lamas: None.
Insulin Autoinmune Syndrome is a rare cause of hypoglycemia. Its incidence is higher among Asians, Japanese patients. Also known as Hirata’s disease, it is characterized by the presence of a hyperinsulinemic state, hypoglycemia, elevated insulin antibodies titers without prior exposure to exogenous insulin, and no pathological abnormalities of the pancreatic islets cells. Some commonly used drugs and viruses have been identified as triggers. We present the case of 65-year-old male Caucasian patient who presented with recurrent episodes of hypoglycemia, that started after surgical resection of a metastatic liver lesion, in the context of metastatic colon cancer. During the workup, it was confirmed that patient had hyperinsulinemia, hypoglycemia, and positive auto-insulin antibodies without previous exposure to exogenous insulin and no imaging findings suggestive of a pancreatic abnormality. The relevance of this case is not only related to the rarity of this entity in the Western World, but also the possibility of being associated with a paraneoplastic syndrome in the setting of metastatic colon cancer, which to the best our knowledge, has not yet been described in the literature as a possible trigger of Insulin Autoimmune Syndrome.
Presentation: Saturday, June 17, 2023
FRI276 KNDy-Neuron Kisspeptin Is Dispensable For Feeding Behavior, But Critical For Energy Expenditure Leading To Metabolic Dysfunction In Female Mice
Authors: Nandankar Nimisha , Ganesh Harshini , Negron Ariel L , Al-Samerria Sarmed , Levine Jon E , Radovick Sally 
Published: October 2023

Abstract
Disclosure: N. Nandankar: None. H. Ganesh: None. A.L. Negron: None. S. Al-Samerria: None. J.E. Levine: None. S. Radovick: None.
Hypothalamic kisspeptin (Kiss1) is a critical master regulator of the hypothalamic-pituitary-gonadal axis responsible for reproductive development and function. Kiss1, originating from KNDy neurons in the arcuate nucleus (ARC) of the hypothalamus, is implicated in having a dual role in both reproductive and metabolic functions. Using KNDy neuron-specific Kiss1 KO mice (Pdyn-Cre/Kissfl/fl or KO), we explored the role of Kiss1 from KNDy neurons in peripheral metabolism without dietary intervention. Here, we report that KO females have significantly greater body weight, fat mass, and glucose intolerance vs. control females. Interestingly, these parameters did not differ between KO male mice and controls. To determine whether this phenotype was due to dysregulated feeding behavior (i.e., hyperphagia) in KO mice, we tracked daily food consumption in adult mice for 3 weeks. We found no significant differences in food intake between genotypes of either sex. We used the Comprehensive Laboratory Animal Monitoring System (CLAMS, Columbus Instruments) to analyze energy expenditure in our mouse model. Data from the CLAMS experiments revealed reduced energy expenditure in KO females vs. control females, whereas there was no difference in energy expenditure between KO males and control males. Specifically, the respiratory exchange ratio (RER) was not significantly different in KO females vs. control females, indicating that both groups utilize both carbohydrates and fats as their primary energy source. However, heat expenditure was significantly lower in KO females (20.27 ± 2.29 kcal/kg/hr vs. 14.02 ± 1.18 kcal/kg/hr, WT vs. KO, p &lt; 0.0001, 2-way ANOVA, n = 6-7) during the active dark phase, suggesting a decreased energy expenditure. This data suggests that the obesity and impaired glucose tolerance in females lacking Kiss1 from KNDy neurons is likely due to lower energy expenditure (with the expended energy derived from both carbohydrates and fats), rather than hyperphagic behavior.
Presentation: Friday, June 16, 2023