bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing natural language processing representations of coded disease sequences for prediction in electronic health records
Authors: Beaney Thomas , Jha Sneha , Alaa Asem , Smith Alexander , Clarke Jonathan , Woodcock Thomas , Majeed Azeem , Aylin Paul , Barahona Mauricio 
Published: May 2024

Abstract

Objective
Natural language processing (NLP) algorithms are increasingly being applied to obtain unsupervised representations of electronic health record (EHR) data, but their comparative performance at predicting clinical endpoints remains unclear. Our objective was to compare the performance of unsupervised representations of sequences of disease codes generated by bag-of-words versus sequence-based NLP algorithms at predicting clinically relevant outcomes.

Materials and Methods
This cohort study used primary care EHRs from 6 286 233 people with Multiple Long-Term Conditions in England. For each patient, an unsupervised vector representation of their time-ordered sequences of diseases was generated using 2 input strategies (212 disease categories versus 9462 diagnostic codes) and different NLP algorithms (Latent Dirichlet Allocation, doc2vec, and 2 transformer models designed for EHRs). We also developed a transformer architecture, named EHR-BERT, incorporating sociodemographic information. We compared the performance of each of these representations (without fine-tuning) as inputs into a logistic classifier to predict 1-year mortality, healthcare use, and new disease diagnosis.

Results
Patient representations generated by sequence-based algorithms performed consistently better than bag-of-words methods in predicting clinical endpoints, with the highest performance for EHR-BERT across all tasks, although the absolute improvement was small. Representations generated using disease categories perform similarly to those using diagnostic codes as inputs, suggesting models can equally manage smaller or larger vocabularies for prediction of these outcomes.

Discussion and Conclusion
Patient representations produced by sequence-based NLP algorithms from sequences of disease codes demonstrate improved predictive content for patient outcomes compared with representations generated by co-occurrence-based algorithms. This suggests transformer models may be useful for generating multi-purpose representations, even without fine-tuning.
Streamlining social media information retrieval for public health research with deep learning
Authors: Hua Yining , Wu Jiageng , Lin Shixu , Li Minghui , Zhang Yujie , Foer Dinah , Wang Siwen , Zhou Peilin , Yang Jie , Zhou Li 
Published: May 2024

Abstract

Objective
Social media-based public health research is crucial for epidemic surveillance, but most studies identify relevant corpora with keyword-matching. This study develops a system to streamline the process of curating colloquial medical dictionaries. We demonstrate the pipeline by curating a Unified Medical Language System (UMLS)-colloquial symptom dictionary from COVID-19-related tweets as proof of concept.

Methods
COVID-19-related tweets from February 1, 2020, to April 30, 2022 were used. The pipeline includes three modules: a named entity recognition module to detect symptoms in tweets; an entity normalization module to aggregate detected entities; and a mapping module that iteratively maps entities to Unified Medical Language System concepts. A random 500 entity samples were drawn from the final dictionary for accuracy validation. Additionally, we conducted a symptom frequency distribution analysis to compare our dictionary to a pre-defined lexicon from previous research.

Results
We identified 498 480 unique symptom entity expressions from the tweets. Pre-processing reduces the number to 18 226. The final dictionary contains 38 175 unique expressions of symptoms that can be mapped to 966 UMLS concepts (accuracy = 95%). Symptom distribution analysis found that our dictionary detects more symptoms and is effective at identifying psychiatric disorders like anxiety and depression, often missed by pre-defined lexicons.

Conclusions
This study advances public health research by implementing a novel, systematic pipeline for curating symptom lexicons from social media data. The final lexicon's high accuracy, validated by medical professionals, underscores the potential of this methodology to reliably interpret, and categorize vast amounts of unstructured social media data into actionable medical insights across diverse linguistic and regional landscapes.
Mosquitoes harvested from rice fields as alternative protein ingredient in broiler feed: insights from the first pilot study
Authors: Tsafrakidou Panagiota , Papoti Vasiliki T , Giannakakis Efstathios , Christaki Androniki , Miaoulis Michael , Oppert Brenda , Cohnstaedt Lee W , Arsi Komala , Donoghue Annie M , Vergos Evangelos , Chaskopoulou Alexandra , Zinoviadou Kyriaki 
Published: May 2024

AbstractGlobal population continuous growth and increasing consumers’ demands for protein-rich diets have posed sustainability challenges for traditional livestock feed sources. Consequently, exploring alternative and sustainable protein sources has become imperative to address the environmental burden and resource limitations associated with conventional ingredients. With respect to food security assurance, insects have emerged as a promising solution due to their exceptional nutritional profile, rapid reproduction rates, and low environmental impact. In the present pilot study, 10% of a soybean meal-based diet was replaced by adult mosquitoes harvested from rice fields. The objective was to assess the effect of this partial substitution on meat quality aspects and consumer acceptance. A total of 40 Cobb hybrid broiler chickens were randomly placed in a control and a mosquito-fed group. The study was conducted for 42 days and carcass physicochemical, nutritional, and microbiological characteristics, as well as sensory attributes were evaluated. Overall, results regarding quality attributes were comparable between the control and the treatment group. The organoleptic evaluation showed that the thighs from the mosquito-fed group had the highest overall consumer acceptance. These outcomes indicate that mosquitoes could be successfully used as a protein source for broiler feed without compromising the quality and acceptability of the meat.
Clinical characteristics and prognosis of patients with incidentally discovered chest wall sarcoma compared with those of symptomatic patients
Authors: Iwatsu Jun , Yoshida Shinichirou , Watanuki Munenori , Hitachi Shin , Oguro Sota , Watanabe Mika , Aizawa Toshimi 
Published: May 2024

Abstract

Objective
Sarcomas of the bone and soft tissues are detected after the onset of pain, detectable mass and related symptoms in the absence of a standardized screening examination. However, primary chest wall sarcomas can be incidentally detected upon chest X-ray or computed tomography. Previous studies of incidental primary chest wall sarcomas lack prognosis and disease-specific clinical data. This study aimed to investigate the prognoses of patients with incidental chest wall sarcomas and compare them with those of symptomatic patients.

Methods
This study included 18 patients diagnosed with primary chest wall sarcoma between 2010 and 2023. Patient information such as age, sex, tumour diameter, tumour location, symptoms, treatment, time to treatment initiation, pathological diagnosis and outcome were retrospectively analysed.

Results
Among the 18 patients, the sarcomas were incidentally detected in five by chest X-ray and computed tomography in three and two patients, respectively. The pathological diagnoses of the patients were Ewing sarcoma, Chondrosarcoma grade 1, grade 2, periosteal osteosarcoma and malignant peripheral nerve sheath tumour. The patients had no symptoms at the first visit to our hospital, and no lesions in other organs were detected at the time of the initial examination. At the final follow-up, the patients remained disease-free after radical treatment. The tumour sizes of the five patients were significantly smaller than those of patients with symptoms (P = 0.003).

Conclusions
The incidental detection of chest wall sarcomas and consequent early detection and treatment of tumours improves patient prognosis relative to that of symptomatically diagnosed patients.
Cecal volvulus secondary to mesodiverticular band
Authors: Blum Brice , Grimes Arthur D , Carroll Hannah L , Stettler Gregory R 
Published: May 2024

Abstract
Meckel’s diverticula are one of the most common gastrointestinal anomalies, yet mesodiverticular bands are rare. The treatment of these bands commonly requires surgery. A healthy patient in his 20s presented to the emergency department with a 1 day history of acute onset abdominal pain. Computed tomography imaging was consistent with volvulus of the large intestine. In the operating room, the patient was noted to have a band between the ileal mesentery and tip of a Meckel’s diverticulum, consistent with a mesodivertiular band, through which cecum had volvulized. The patient underwent resection. The patient recovered without major complications. Mesodiverticular bands are rare, but may present as hemoperitoneum, small bowel obstruction, or volvulus. Pre-operative diagnosis of a mesodiverticular band is often difficult and they are most commonly diagnosed intraoperatively. Treatment should include surgery and may include simple lysis of the band, bowel resection, or more extensive resection if other pathology is present.
A rare posterior mediastinal mass: chordoma
Authors: Willatt Lily Frances Stocking , Wollheim Martina Henrietta , Ehrsam Jonas Peter , Bode-Lesniewska Beata , Woernle Christoph , Schoeb Othmar , Inci Ilhan 
Published: May 2024

Abstract
A 72-year-old female presented with 2 years of pro-gradient pain in the upper thoracic spine radiating to the left arm and leg. MRI revealed a 2.7 × 2.0 × 12 cm paravertebral mass at T2/T3, extending into the foraminal and epidural nerves with extensive dural sac contact in the left hemithorax. The removed tumour was surprisingly soft for a schwannoma or chordoma. However, after the surgery, histopathology revealed the presence of brachyury protein (T-box transcription factor T), which is characteristic of a chordoma. While chordomas are extremely rare, it is important that they are kept in mind for the differential diagnosis of a posterior mediastinal mass. Successful treatment can only be achieved through a complete en bloc resection. This can often be complex due to their location along the spine. This case report aims to highlight the features and treatment of this rare disease.
Parameterization of manipulative media discourse: possibilities and problems of automatic diagnosis
Authors: Shakenova Maigul , Tashimkhanova Dybys , Shaikova Gulvira , Ospanova Ulzhan , Popovich Olga 
Published: May 2024

Abstract
The issue of quantitative measurement and automatic processing is a significant problem in determining the markers of the manipulative potential of media texts, since linguistic indicators are the basis of machine parameterization. The purpose of the research is to analyse the possibilities of the main language parameters of the manipulativeness of media discourse, which can be identified using machine learning. To achieve the research goals, the following methods were used: system, content analysis, computer modelling, and comparative. The results of the article determined that such language indicators as use of the subjunctive mood of verbs, capital letters, high frequency of use of the ‘not’ particle, punctuation marks, questions, or exclamations of a rhetorical nature, use of quotation marks for the purpose of irony, double negative sentences, use of the word ‘no’, and verbal structures calling to action act as computer classification parameters. In order to cover the above purpose, PYTHON software was implemented that allowed texts to be analysed and visualized in algorithmic and lexical-vocabulary ways. In addition, it was determined that by integrating the PYTHON tool, it became possible to use language transformation markers that formed linguistic patterns in the analysed text. The list of parameters for diagnosing manipulative texts is non-exhaustive, which emphasizes the possibility of machine measurement of the manipulative component of mass media discourse.
Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics
Authors: Hirsch Pascal , Molano Leidy-Alejandra G , Engel Annika , Zentgraf Jens , Rahmann Sven , Hannig Matthias , Müller Rolf , Kern Fabian , Keller Andreas , Schmartz Georges P 
Published: May 2024

Abstract
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the analysis of large sequencing data and are now widely used to annotate metagenomic data. We make use of k-mer counting techniques for efficient and accurate compositional analysis of microbiota from whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual preprocessing or complete data exchange. It handles diverse sequencing platforms, including short single-end, paired-end, and long read technologies. Our sketch-based workflow significantly reduces the data volume transferred from the user to the server (up to 99.59% size reduction) to subsequently perform taxonomic profiling with enhanced efficiency and privacy. Mibianto offers functionality beyond k-mer quantification; it supports advanced community composition estimation, including diversity, ordination, and differential abundance analysis. Our tool aids in the standardization of computational workflows, thus supporting reproducibility of scientific sequencing studies. It is adaptable to small- and large-scale experimental designs and offers a user-friendly interface, thus making it an invaluable tool for both clinical and research-oriented metagenomic studies. Mibianto is freely available without the need for a login at: https://www.ccb.uni-saarland.de/mibianto.
Anthropogenic warming is a key climate indicator of rising urban fire activity in China
Authors: Yao Qichao , Jiang Dabang , Zheng Ben , Wang Xiaochun , Zhu Xiaolin , Fang Keyan , Shi Lamei , Wang Zhou , Wang Yongli , Zhong Linhao , Pei Yanyan , Hudson Amy , Xu Shuai , Bai Maowei , Huang Xinyan , Trouet Valerie 
Published: May 2024

ABSTRACT
China, one of the most populous countries in the world, has suffered the highest number of natural disaster-related deaths from fire. On local scales, the main causes of urban fires are anthropogenic in nature. Yet, on regional to national scales, little is known about the indicators of large-scale co-varying urban fire activity in China. Here, we present the China Fire History Atlas (CFHA), which is based on 19 947 documentary records and represents fires in urban areas of China over the twentieth century (1901–1994). We found that temperature variability is a key indicator of urban fire activity in China, with warmer temperatures being correlated with more urban fires, and that this fire–temperature relationship is seasonally and regionally explicit. In the early twentieth century, however, the fire–temperature relationship was overruled by war-related fires in large urban areas. We further used the fire–temperature relationship and multiple emissions scenarios to project fire activity across China into the twenty-first century. Our projections show a distinct increase in future urban fire activity and fire-related economic loss. Our findings provide insights into fire–climate relationships in China for densely-populated areas and on policy-relevant time scales and they contribute spatial coverage to efforts to improve global fire models.
PSEUDO-RESPONSE REGULATOR 3b and transcription factor ABF3 modulate abscisic acid-dependent drought stress response in soybean
Authors: Li Cong , Chen Yanhang , Hu Qing , Yang Xiaolan , Zhao Yunfeng , Lin Yan , Yuan Jianbo , Gu Jinbao , Li Yang , He Jin , Wang Dong , Liu Bin , Wang Zhen-Yu 
Published: May 2024

Abstract
The circadian system plays a pivotal role in facilitating the ability of crop plants to respond and adapt to fluctuations in their immediate environment effectively. Despite the increasing comprehension of PSEUDO-RESPONSE REGULATORs and their involvement in the regulation of diverse biological processes, including circadian rhythms, photoperiodic control of flowering, and responses to abiotic stress, the transcriptional networks associated with these factors in soybean (Glycine max (L.) Merr.) remain incompletely characterized. In this study, we provide empirical evidence highlighting the significance of GmPRR3b as a crucial mediator in regulating the circadian clock, drought stress response, and abscisic acid (ABA) signaling pathway in soybeans. A comprehensive analysis of DNA affinity purification sequencing and transcriptome data identified 795 putative target genes directly regulated by GmPRR3b. Among them, a total of 570 exhibited a significant correlation with the response to drought, and eight genes were involved in both the biosynthesis and signaling pathways of ABA. Notably, GmPRR3b played a pivotal role in the negative regulation of the drought response in soybeans by suppressing the expression of abscisic acid-responsive element-binding factor 3 (GmABF3). Additionally, the overexpression of GmABF3 exhibited an increased ability to tolerate drought conditions, and it also restored the hypersensitive phenotype of the GmPRR3b overexpressor. Consistently, studies on the manipulation of GmPRR3b gene expression and genome editing in plants revealed contrasting reactions to drought stress. The findings of our study collectively provide compelling evidence that emphasizes the significant contribution of the GmPRR3b-GmABF3 module in enhancing drought tolerance in soybean plants. Moreover, the transcriptional network of GmPRR3b provides valuable insights into the intricate interactions between this gene and the fundamental biological processes associated with plant adaptation to diverse environmental conditions.
Weak-formulated physics-informed modeling and optimization for heterogeneous digital materials
Authors: Zhang Zhizhou , Lee Jeong-Ho , Sun Lingfeng , Gu Grace X 
Published: May 2024

Abstract
Numerical solutions to partial differential equations (PDEs) are instrumental for material structural design where extensive data screening is needed. However, traditional numerical methods demand significant computational resources, highlighting the need for innovative optimization algorithms to streamline design exploration. Direct gradient-based optimization algorithms, while effective, rely on design initialization and require complex, problem-specific sensitivity derivations. The advent of machine learning offers a promising alternative to handling large parameter spaces. To further mitigate data dependency, researchers have developed physics-informed neural networks (PINNs) to learn directly from PDEs. However, the intrinsic continuity requirement of PINNs restricts their application in structural mechanics problems, especially for composite materials. Our work addresses this discontinuity issue by substituting the PDE residual with a weak formulation in the physics-informed training process. The proposed approach is exemplified in modeling digital materials, which are mathematical representations of complex composites that possess extreme structural discontinuity. This article also introduces an interactive process that integrates physics-informed loss with design objectives, eliminating the need for pretrained surrogate models or analytical sensitivity derivations. The results demonstrate that our approach can preserve the physical accuracy in data-free material surrogate modeling but also accelerates the direct optimization process without model pretraining.
Nano-ZnO-modified hydroxyapatite whiskers with enhanced osteoinductivity for bone defect repair
Authors: Wei Penggong , Wang Ning , Zhang Qiyue , Wang Wanfeng , Sun Hui , Liu Zengqian , Yan Tingting , Wang Qiang , Qiu Lihong 
Published: May 2024

Abstract
Hydroxyapatite (HA) whisker (HAw) represents a distinct form of HA characterized by its high aspect ratio, offering significant potential for enhancing the mechanical properties of bone tissue engineering scaffolds. However, the limited osteoinductivity of HAw hampers its widespread application. In this investigation, we observed HAw-punctured osteoblast membranes and infiltrated the cell body, resulting in mechanical damage to cells that adversely impacted osteoblast proliferation and differentiation. To address this challenge, we developed nano-zinc oxide particle-modified HAw (nano-ZnO/HAw). Acting as a reinforcing and toughening agent, nano-ZnO/HAw augmented the compressive strength and ductility of the matrix materials. At the same time, the surface modification with nano-ZnO particles improved osteoblast differentiation by reducing the mechanical damage from HAw to cells and releasing zinc ion, the two aspects collectively promoted the osteoinductivity of HAw. Encouragingly, the osteoinductive potential of 5% nano-ZnO/HAw and 10% nano-ZnO/HAw was validated in relevant rat models, demonstrating the efficacy of this approach in promoting new bone formation in vivo. Our findings underscore the role of nano-ZnO particle surface modification in enhancing the osteoinductivity of HAw from a physical standpoint, offering valuable insights into the development of bone substitutes with favorable osteoinductive properties while simultaneously bolstering matrix material strength and toughness.
EMA-Positive Superficial ALK–Rearranged Myxoid Spindle Cell Neoplasm Masquerading as Perineurioma/Hybrid Nerve Sheath Tumor
Authors: Hegazy Shaymaa , Naous Rana 
Published: May 2024

Abstract:
Superficial anaplastic lymphoma kinase (ALK)–rearranged myxoid spindle cell neoplasm (SAMS) is a recently described entity which coexpresses ALK, CD34, and commonly S100. These neoplasms are characterized morphologically by concentric spindle cell whorls and cords and are commonly set in an abundant myxoid to myxocollagenous stroma, thus mimicking perineurioma or hybrid nerve sheath tumor. EMA immunostain has been reported to be negative in SAMS which helps in excluding the latter entities. Herein, we report the first EMA-positive SAMS of the right leg in a 37-year-old female patient masquerading as perineurioma/hybrid nerve sheath tumor. The tumor morphologically was comprised of spindle cells arranged in loose whorls and short fascicles set in myxoid to collagenous stroma and coexpressed CD34 and EMA, reminiscent of perineurioma. S100 showed focal staining. ALK immunostain was subsequently performed and was positive. ALK gene rearrangement was identified by fluorescence in situ hybridization break-apart assay and was further confirmed by next-generation sequencing–based RNA sequencing demonstrating FLNA::ALK fusion, thus supporting the diagnosis of SAMS. In conclusion, EMA can be expressed in SAMS, thus posing as a diagnostic pitfall. ALK immunostain and molecular studies are essential for confirming the diagnosis of SAMS and excluding potential mimickers, particularly perineurioma or hybrid nerve sheath tumor.