bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternatives assessment: An analysis on progress and future needs for research and practice
Authors: Bechu Aude M. , Roy Monika A. , Jacobs Molly , Tickner Joel A. 
Published: December 2023

Abstract
Alternatives assessment is a science-policy approach to support the informed substitution of chemicals of concern in consumer products and industries, with the intent of avoiding regrettable substitution and facilitating the transition to safer, more sustainable chemicals and products. The field of alternatives assessment has grown steadily in recent decades, particularly after the publication of specific frameworks and the inclusion of substitution and alternatives assessment requirements in a number of policy contexts. Previously, 14 research and practice needs for the field were outlined across five critical areas: comparative hazard assessment, comparative exposure characterization, lifecycle considerations, decision-making and decision analysis, and professional practice. The aim of the current article is twofold: to highlight methodological advances in the growing field of alternatives assessment based on identified research and practice needs and to propose areas for future developments. We assess advances in the field based on the analysis of a broad literature review that captured 154 sources published from 2013 to 2022. The results indicate that research conducted advanced many of the needs identified, but several remain underaddressed. Although the field has clearly grown and taken root over the past decade, there are still research and practice gaps, most notably on the hazard assessment of mixtures or different forms of chemicals, the integration of lifecycle considerations, and the development of practical approaches to address trade-offs in decision-making. We propose modifications to four of the prior research and practice needs in addition to new needs, including the development of standardized hazard assessment approaches for chemical mixtures as well as better integration of equity and/or justice considerations into assessments. Integr Environ Assess Manag 2024;20:1337–1354. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
Key Points
The field of alternatives assessment is a growing science-policy field that has advanced according to five critical areas, most notably in professional practice and comparative hazard assessment. Despite clear advances in certain research and practice needs, methodological gaps remain, most notably on the hazard assessment of mixtures or different forms of chemicals, the consistent use of lifecycle considerations, and methods to approach trade-offs in decision-making. Based on the literature analyzed and activities in aligned fields, we propose six additional research and practice needs to further advance the field, which include the development of best practice guidelines, implementation analysis, and the consideration for equity in alternatives assessment.
Bioinformatics and system biology analysis revealed the crosstalk between COVID‐19 and osteoarthritis
Authors: Lai Bowen , Jiang Heng , Liao Taotao , Gao Yuan , Zhou Xuhui 
Published: December 2023

AbstractBackgroundThe global coronavirus disease 2019 (COVID‐19) outbreak has significantly impacted public health. Moreover, there has been an association between the incidence and severity of osteoarthritis (OA) and the onset of COVID‐19. However, the optimal diagnosis and treatment strategies for patients with both diseases remain uncertain. Bioinformatics is a novel approach that may help find the common pathology between COVID‐19 and OA.MethodsDifferentially expressed genes (DEGs) were screened by R package “limma.” Functional enrichment analyses were performed to find key biological functions. Protein–protein interaction (PPI) network was constructed by STRING database and then Cytoscape was used to select hub genes. External data sets and OA mouse model validated and identified the hub genes in both mRNA and protein levels. Related transcriptional factors (TF) and microRNAs (miRNAs) were predicted with miRTarBase and JASPR database. Candidate drugs were obtained from Drug Signatures database. The immune infiltration levels of COVID‐19 and OA were evaluated by CIBERSORT and scRNA‐seq.ResultsA total of 74 common DEGs were identified between COVID‐19 and OA. Receiver operating characteristic curves validated the effective diagnostic values (area under curve > 0.7) of four hub genes (matrix metalloproteinases 9, ATF3, CCL4, and RELA) in both the training and validation data sets of COVID‐19 and OA. Quantitative polymerase chain reaction and Western Blot showed significantly higher hub gene expression in OA mice than in healthy controls. A total of 84 miRNAs and 28 TFs were identified to regulate the process of hub gene expression. The top 10 potential drugs were screened including “Simvastatin,” “Hydrocortisone,” and “Troglitazone” which have been proven by Food and Drug Administration. Correlated with hub gene expression, Macrophage M0 was highly expressed while Natural killer cells and Mast cells were low in both COVID‐19 and OA.ConclusionFour hub genes, disease‐related miRNAs, TFs, drugs, and immune infiltration help to understand the pathogenesis and perform further studies, providing a potential therapy target for COVID‐19 and OA.
High‐mobility group box 1 emerges as a therapeutic target for asthma
Authors: Yang Qianni , Li Min , Hou Yunjiao , He Huilin , Sun Shibo 
Published: December 2023

AbstractHigh‐mobility group box 1 (HMGB1) is a highly conserved nonhistone nuclear protein found in the calf thymus and participates in a variety of intracellular processes such as DNA transcription, replication and repair. In the cytoplasm, HMGB1 promotes mitochondrial autophagy and is involved in in cellular stress response. Once released into the extracellular, HMGB1 becomes an inflammatory factor that triggers inflammatory responses and a variety of immune responses. In addition, HMGB1 binding with the corresponding receptor can activate the downstream substrate to carry out several biological effects. Meanwhile, HMGB1 is involved in various signaling pathways, such as the HMGB1/RAGE pathway, HMGB1/NF‐κB pathway, and HMGB1/JAK/STAT pathway, which ultimately promote inflammation. Moreover, HMGB1 may be involved in the pathogenesis of asthma by regulating downstream signaling pathways through corresponding receptors and mediates a number of signaling pathways in asthma, such as HMGB1/TLR4/NF‐κB, HMGB1/RAGE, HMGB1/TGF‐β, and so forth. Accordingly, HMGB1 emerges as a therapeutic target for asthma.
Automated preparation of nanoscopic structures: Graph‐based sequence analysis, mismatch detection, and pH‐consistent protonation with uncertainty estimates
Authors: Csizi Katja‐Sophia , Reiher Markus 
Published: December 2023

AbstractStructure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three‐dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time‐consuming and error‐prone process. Here, we present a fast and robust protocol for the automated structure analysis and pH‐consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for p prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system‐focused atomistic modeling described in Brunken and Reiher (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph‐based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human‐machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH‐state through on‐the‐fly system‐focused reparametrization during a molecular simulation at virtually no extra computational cost.
Placenta acrreta spectrum—first trimester, 2D and 3D ultrasound, and magnetic resonance imaging findings
Authors: Araujo Júnior Edward , Caldas João Victor Jacomele , Sun Sue Yasaki , Castro Pedro Teixeira , Passos Jurandir Piassi , Werner Heron 
Published: December 2023

AbstractBackgroundThe term placenta accreta spectrum (PAS) is commonly used to describe abnormal trophoblastic invasion of the myometrium, serosa, or organs adjacent to the uterus. It is of great obstetric importance because of its high morbidity, risk of hemorrhage, admission to the intensive care unit, risk of hysterectomy, and high risk of iatrogenic pelvic lesions and even death. These risks are minimized when prenatal diagnosis is performed. Prenatal diagnosis of PAS is based on imaging findings suggestive of abnormal and pathologically adherent placentation, including placental lacunae (intraplacental sonolucent spaces), disruption of the bladder‐uterine serosa interface, turbulent flow on color Doppler, and bridging vessels.ObjectiveIn this article, we review the major prenatal imaging features of PAS using diagnostic modalities (first trimester, two‐dimensional ultrasound, three‐dimensional ultrasound, and magnetic resonance imaging) for the diagnosis of PAS.
Attitudes of parents of children with ADHD towards genetic testing: Data from a Turkish sample
Authors: Beyazit Utku , Şirin Hande , Uzun Mehmet Erdem , Kuru Alev , Yurdakul Yeşim , Bütün Ayhan Aynur , Yilmaz Serkan 
Published: December 2023

AbstractThis study aimed to examine the opinions of parents with children diagnosed with attention deficit/hyperactivity disorder about genetic tests. A total of 540 parents living in Turkey participated in the study face‐to‐face and online. A questionnaire form prepared by the researchers was used as the data collection instrument. Face‐to‐face data were collected in different institutions in the cities of İzmir, Bursa and Antalya, while online data were collected through Google Forms. The results revealed that parents' views on genetic testing differed according to the sex and age of the child, as well as the parents' level of education and income, and whether the parents had genetic testing during pregnancy (p < 0.05). In the analysis, it was determined that parents' knowledge and awareness levels about genetic tests were generally low, while parents who reported that they would consider having genetic tests had concerns about the storage of their DNA materials, family conflicts that could be caused by genetic tests, and the compatibility of genetic tests with their religious beliefs.
Evaluation of Serum Neurofilament Light Chain and Nerve Ultrasound in Diabetic Neuropathy
Authors: Nasr‐Eldin Yasmin K. , Cartwright Michael S. , Hamed Ahmed , Ali Lamia Hamdy , Abdel‐Nasser Ahmed M. 
Published: December 2023

ObjectiveTo assess the role of serum neurofilament light chain (NfL) levels in individuals with diabetic polyneuropathy (DPN) compared with controls, as well as to highlight the different sonographic changes in DPN and determine if NfL correlates with sonographic, clinical, and functional parameters.MethodsDiabetic individuals with signs or symptoms consistent with peripheral nerve involvement were recruited. They were evaluated by examination, functional neuropathy severity scores, laboratory assessments (including NfL), nerve conduction studies (NCS), and ultrasound. Ultrasound was performed of the bilateral median, ulnar, tibial, fibular, sural, and vagus nerves, and cervical roots 5 and 6. Results were compared with age, sex, and body mass index matched healthy controls.ResultsA total of 320 nerves from 20 patients and 480 nerves from 30 controls were evaluated. NfL was significantly elevated in those with diabetes with a mean and standard deviation of 6.95 ± 2.95 pg/mL in the diabetic group and 2.83 ± 0.77 pg/mL in controls (P < .001). Nerve cross‐sectional area and serum NfL levels correlated significantly with clinical and functional parameters and with each other (P < .05).ConclusionIndividuals with DPN have significantly higher NfL levels than healthy controls, and NfL levels correlate with ultrasonographic parameters. These findings may be useful for the diagnosis, prognosis, and disease monitoring of those with DPN, though further exploration is needed.
A Chinese patient with Rothmund–Thomson syndrome
Authors: Zeng Juan , Li Jiayi , Liu Yuwei , Liang Rui , Wang Lin , Zhou Qing , Sun Jinghua , Liu Zhongzhen , Wang Wen‐Jing , Zhu Sujun 
Published: December 2023

AbstractIntroductionRothmund–Thomson syndrome (RTS) is a rare autosomal recessive disorder that has been reported in all ethnicities, with several identifiable pathogenic variants. There have been reported cases indicating that RTS may lead to low birth weight in fetuses, but specific data on the fetal period are lacking. Genetic testing for RTS II is currently carried out by identifying pathogenic variants in RECQL4.MethodsIn order to determine the cause, we performed whole‐genome sequencing (WGS) analysis on the patient and his parents. Variants detected by WGS were confirmed by Sanger sequencing and examined in family members.ResultsAfter analyzing the WGS data, we found a heterozygous nonsense mutation c.2752G>T (p.Glu918Ter) and a novel frameshift insertion mutation c.1547dupC (p.Leu517AlafsTer23) of RECQL4, which is a known pathogenic/disease‐causing variant of RTS. Further validation indicated these were compound heterozygous mutations from parents.ConclusionOur study expands the mutational spectrum of the RECQL4 gene and enriches the phenotype spectrum of Chinese RTS patients. Our information can assist the patient's parents in making informed decisions regarding their future pregnancies. This case offers a new perspective for clinicians to consider whether to perform prenatal diagnosis.
Standardizing and improving dose predictions for head and neck cancers using complete sets of OAR contours
Authors: Buatti Jacob S. , Kirby Neil , Stathakis Sotirios , Li Ruiqi , Sivabhaskar Sruthi , de Oliveira Michelle , Duke Kristen , Kabat Christopher N. , Papanikolaou Niko , Paragios Nikos 
Published: December 2023

AbstractBackgroundRadiotherapy dose predictions have been trained with data from previously treated patients of similar sites and prescriptions. However, clinical datasets are often inconsistent and do not contain the same number of organ at risk (OAR) structures. The effects of missing contour data in deep learning‐based dose prediction models have not been studied.PurposeThe purpose of this study was to investigate the impacts of incomplete contour sets in the context of deep learning‐based radiotherapy dose prediction models trained with clinical datasets and to introduce a novel data substitution method that utilizes automated contours for undefined structures.MethodsWe trained Standard U‐Nets and Cascade U‐Nets to predict the volumetric dose distributions of patients with head and neck cancers (HNC) using three input variations to evaluate the effects of missing contours, as well as a novel data substitution method. Each architecture was trained with the original contour (OC) inputs, which included missing information, hybrid contour (HC) inputs, where automated OAR contours generated in software were substituted for missing contour data, and automated contour (AC) inputs containing only automated OAR contours. 120 HNC treatments were used for model training, 30 were used for validation and tuning, and 44 were used for evaluation and testing. Model performance and accuracy were evaluated with global whole body dose agreement, PTV coverage accuracy, and OAR dose agreement. The differences in these values between dataset variations were used to determine the effects of missing data and automated contour substitutions.ResultsAutomated contours used as substitutions for missing data were found to improve dose prediction accuracy in the Standard U‐Net and Cascade U‐Net, with a statistically significant difference in some global metrics and/or OAR metrics. For both models, PTV coverage between input variations was unaffected by the substitution technique. Automated contours in HC and AC datasets improved mean dose accuracy for some OAR contours, including the mandible and brainstem, with a greater improvement seen with HC datasets. Global dose metrics, including mean absolute error, mean error, and percent error were different for the Standard U‐Net but not for the Cascade U‐Net.ConclusionAutomated contours used as a substitution for contour data improved prediction accuracy for some but not all dose prediction metrics. Compared to the Standard U‐Net models, the Cascade U‐Net achieved greater precision.
Caffeine and cortical excitability, as measured with paired‐pulse transcranial magnetic stimulation
Authors: Strunge Kristine , Bostock Hugh , Howells James , Cengiz Bülent , Samusyte Gintaute , Koltzenburg Martin , Tankisi Hatice 
Published: December 2023

AbstractIntroduction/AimsThe transcranial magnetic stimulation tests of short‐interval intracortical inhibition (SICI) by both conventional amplitude measurements (A‐SICI) and threshold‐tracking (T‐SICI) are important methods to investigate intracortical inhibitory circuits, and T‐SICI has been proposed to aid the diagnosis of amyotrophic lateral sclerosis. Beverages containing caffeine are widely consumed, and caffeine has been reported to affect cortical excitability. The aim of this study was to determine whether these SICI tests are affected by caffeine.MethodsTwenty‐four healthy subjects (13 females, 11 males, aged from 19 to 31, mean: 26.2 ± 2.4 years) were studied in a single fixed‐dose randomized double‐blind placebo‐controlled cross‐over trial of 200 mg caffeine or placebo ingested as chewing gum. A‐SICI and T‐SICI, using parallel tracking (T‐SICIp), were performed before and after chewing gum.ResultsThere was no significant change in SICI parameters after placebo in A‐SICI (p > .10) or T‐SICIp (p > .30), and no significant effect of caffeine was found on A‐SICI (p > .10) or T‐SICIp (p > .50) for any of the interstimulus intervals.DiscussionThere is no need for caffeine abstention before measurements of SICI by either the T‐SICI or A‐SICI measurements.
Generalizing Horn's conditions for preemptive scheduling on identical parallel machines via network flow techniques
Authors: Shioura Akiyoshi , Strusevich Vitaly A. , Shakhlevich Natalia V. 
Published: December 2023

AbstractWe study the use of flow‐based algorithmic and proof techniques applied to preemptive scheduling of jobs on parallel identical machines. For the classical problem in which the jobs have individual release dates and must be finished by a common deadline, we present and prove unified necessary and sufficient conditions for the existence of a feasible schedule by examining the structure of minimum cuts in a special network. We then study an enhanced model that allows the presence of additional resources, provided that some jobs at any time of their processing require one unit of a particular resource. We extend our argument developed for the classical case to this enhanced model. The generalized necessary and sufficient conditions for the existence of a feasible schedule are presented and proved using the max‐flow/min‐cut reasoning.
Rehabilitation after brain tumor resection: A national study of postacute care service use through insurance claims data
Authors: McLarney Mitra , Fergestrom Nicole , Zheng Jasmine , Pezzin Liliana E. 
Published: December 2023

AbstractObjectiveTo assess postacute rehabilitation service use and length of stay among a national sample of patients with brain tumors after surgery.DesignA retrospective review was conducted of health care claims data of a national sample of patients via The Optum Clinformatics DataMart.Setting and ParticipantsThis study included adult individuals (≥18 years of age) who were diagnosed with a brain tumor between 2015 and 2019 and underwent a craniotomy or craniectomy within 180 days of diagnosis.MethodsDescriptive statistics were used to characterize patients by tumor type. Multivariate models assessed factors associated with discharge setting and length of stay.ResultsOf the 10,275 individuals identified, 69% had malignant tumors. Over two thirds of patients were discharged directly home (with or without home health care) and 9.3% and 9.5% were discharged to acute rehabilitation facilities (inpatient rehabilitation facilities [IRF]) and skilled nursing facilities (SNF/ICF), respectively. About 13.5% were discharged to other settings. The average length of stay during the episode of care was 8.6 (SD = 9.6) days. After adjusting for confounders, individuals with benign brain tumors were more likely to be discharged to either IRF or SNF/ICF than return home after acute care stay, as were those with greater comorbidities, older age, fee‐for‐service and health maintenance organization insurance. Wealthier patients were less likely to be discharged to a SNF/ICF than home, although income was not a factor affecting discharge to an IRF. Patients with benign tumors, the oldest old (80+), those with more comorbidities as well as Black and Hispanic patients had a longer length of stay during the acute hospitalization.ConclusionsIndividuals with brain tumors have deficits amenable to rehabilitation; however, this study finds that service use differs by tumor type and demographic and socioeconomic factors. Further study is needed to identify if there are barriers to access and use of rehabilitation services in this population.