bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decomposing dependency analysis: revisiting the relation between annotation scheme and structure-based textual measures
Authors: Yih Tsy , Liu Haitao 
Published: January 2025

Abstract
Standardized quantitative measurement of texts lies at the heart of digital approaches to humanities. Structure-based textual measures are known to be influenced by the choice of syntactic annotation schemes. Building on previous research, the present article further explores the relation between annotation schemes and the index of mean dependency distance (MDD) by comparing the treebanks of seventeen languages, respectively, within a tree representation (basic universal dependencies, BUD) and within a graphic representation (enhanced universal dependencies, EUD). Following the idea of decomposing annotation schemes into the combinations of analyses of specific constructions (coordinate structures, control constructions, and relative clauses), we design algorithms to identify them in the CoNLL-U format treebanks and explore their influences. It is found that the overall MDD of the EUD representation is statistically higher than that of BUD at corpus level, primarily affected by the coordinate structure due to its high frequency. At sentence level, all three constructions might contribute to either increased or decreased MDD, with stochastically intervening words and word order being two important determinants of the values of the measure. Finally, we propose and argue for the view that MDDs calculated under different annotation schemes should be regarded as different textual measures in nature. In sum, the present study provides another case study to deepen our understanding of the nature of syntactic annotation schemes and its relation with textual indices, which paves the way for standard measurement of texts in future humanities research.
Identifying Concepts to Establish Problematic Medications in Active Duty Servicemembers (ProMADS)
Authors: Costantino Ryan C , Brandt Nicole J , Perfetto Eleanor M , Hull Jessica R , Daniel Mullins C 
Published: January 2025

ABSTRACT

Introduction
The military’s approach to medication use often evolves in response to operational issues that have the potential to impact the medical readiness and combat effectiveness of active duty service members (ADSMs). Historically, medications have been considered problematic because they serve as surrogate markers for deployment limiting health conditions or due to factors that make sustainment challenging in military/austere environments. This study aims to identify key concepts that capture the aspects of a medication that make it problematic in ADSMs. The goal of this effort would be to inform a future policy and establish criteria for Problematic Medications in Active Duty Servicemembers (ProMADS) to enhance the readiness and deployability of ADSMs.

Materials and Methods
Concepts of ProMADS were elicited from 8 key informants (KIs). Key informants included care providers and care recipients from the Army, Navy, Air Force, and Defense Health Agency. Semi-structured interviews were conducted, and a phenomenological approach was used to summarize KI perspectives, and thematic analysis identified core elements and sub-elements.

Results
Five core elements were identified: (1) Adverse cognitive or behavioral effects, (2) sustainment issues, (3) controlled substance compliance and risk mitigation, (4) medication-related hemostasis interference, and (5) combat-readiness inhibitors. Key sub-concepts were related to whether a medication might impact cognition, cause sedation, have complex monitoring requirements (e.g., laboratory, adverse drug reactions, etc.), is temperature sensitive, or impacts the functioning of the immune system.

Conclusion
This study generated core medication-related concepts and sub-concepts that KIs believe make a medication innately problematic among ADSMs. These findings can guide consensus-driven efforts to identify ProMADS which would enable Military Departments and Combat Support Agencies to create programs that improve lethality, warfighting, and readiness by optimizing medication use.
Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability
Authors: McQuail Josh , Krepl Miroslav , Katsuya-Gaviria Kai , Tabib-Salazar Aline , Burchell Lynn , Bischler Thorsten , Gräfenhan Tom , Brear Paul , Šponer Jiří , Luisi Ben F , Wigneshweraraj Sivaramesh 
Published: January 2025

Abstract
The RNA chaperone Hfq plays crucial roles in bacterial gene expression and is a major facilitator of small regulatory RNA (sRNA) action. The toroidal architecture of the Hfq hexamer presents three well-characterized surfaces that allow it to bind sRNAs to stabilize them and engage target transcripts. Hfq-interacting sRNAs are categorized into two classes based on the surfaces they use to bind Hfq. By characterizing a systematic alanine mutant library of Hfq to identify amino acid residues that impact survival of Escherichia coli experiencing nitrogen (N) starvation, we corroborated the important role of the three RNA-binding surfaces for Hfq function. We uncovered two, previously uncharacterized, conserved residues, V22 and G34, in the hydrophobic core of Hfq, to have a profound impact on Hfq’s RNA-binding activity in vivo. Transcriptome-scale analysis revealed that V22A and G34A Hfq mutants cause widespread destabilization of both sRNA classes, to the same extent as seen in bacteria devoid of Hfq. However, the alanine substitutions at these residues resulted in only modest alteration in stability and structure of Hfq. We propose that V22 and G34 have impact on Hfq function, especially critical under cellular conditions when there is an increased demand for Hfq, such as N starvation.
Chemical and Isotopic Exchanges in Serpentinites during Hydration and Dehydration Events in the Erro-Tobbio Massif (Italy): from Ocean to Subduction
Authors: Vesin Coralie , Ulrich Michelle , Rubatto Daniela , Hermann Joerg , Scambelluri Marco 
Published: January 2025

Abstract
Subducted serpentinites are important for recycling water and fluid mobile elements into the deep Earth. Here we present a texturally controlled in situ oxygen and boron isotope and trace element study of the Erro-Tobbio ultramafic rocks (Western Alps, Italy) that have experienced exhumation to the seafloor, hydration and subsequent dehydration upon subduction. High variability in δ18O from +0.2‰ to +12.5‰ in the low-temperature serpentine polymorph lizardite coupled to strong enrichment in fluid mobile elements are associated to variable serpentinisation conditions at the ocean floor during the opening of the Piemonte-Liguria Ocean. Incipient oceanic serpentinisation, i.e. mesh formation after mantle olivine, occurred at approximately 160–325°C ± 20–60°C. Subsequently, mantle pyroxene was transformed into serpentine bastite with decreasing temperatures down to 75°C to 100°C. The transition metals V, Sc, Co, Zn and Mn, and the Ni/Cr in lizardite are indicative of precursor olivine or orthopyroxene. Remarkably, some lizardite in partially serpentinised and undeformed mantle peridotites remained metastable during subsequent subduction. During early subduction, with increasing temperature, the serpentine polymorph antigorite replaced lizardite in highly serpentinised ultramafic rocks. Antigorite shows a narrower δ18O range from +5.3‰ to +7.5‰, indicating isotopic homogenisation at the regional scale. A redistribution of the transition metals is observed at the sample scale, and the fluid mobile elements B, Cl and Li are partly lost. The isotopic homogenisation and the element redistribution are likely the results of (i) sample internal equilibration during antigorite crystallisation and (ii) mobility of serpentinite-derived fluids during the lizardite-to-antigorite transition. During the peak subduction stage at 1.8 to 2.5 GPa and 550°C to 650°C, metamorphic olivine with δ18O of ~+4‰ to +5‰ is formed from the dehydration of brucite + antigorite. This olivine is enriched in fluid mobile elements such as Li and B compared to primitive mantle and is in oxygen isotopic equilibrium with the co-existing antigorite. Based on this equilibrium and the coupled trace element systematics, there is no evidence of large influxes of external slab fluids from other lithologies. Recrystallised mantle olivine has lower B and Li contents compared to metamorphic olivine formed during brucite dehydration, and has similar δ18O values, XMg and Ni/Mn as mantle olivine, and is not in isotopic equilibrium with the antigorite. Such metamorphic olivine produced by recrystallisation, as well as the metastable lizardite during subduction, cannot be used as indicators of fluid production from serpentine dehydration.
“Me Llamo Luchadora Social”: Trans Latina Immigrants as Nepantleras Generating Change in the Southern United States
Authors: Alvarez-Hernandez Luis Roberto , Maria Bermúdez J 
Published: January 2025

Abstract
Many trans Latina immigrants have utilized their individual and collective strengths to resist oppression and generate change in their communities; however, their efforts remain largely invisible to those outside of their communities. The current study aimed to explore the meaning trans Latinas make of their experiences as agents of change in the southern United States. Informed by Chicana feminisms, authors used interpretive phenomenology to explore the testimonios of six trans Latina immigrants living in Georgia, Louisiana, North Carolina, and Texas. Three themes were constructed: (1) the burden of discrimination, violence, and unmet needs; (2) luchadoras being and doing social change; and (3) finding strength in caring for each other. Anzaldúa’s nepantlera concept informed how authors situated findings as acts of resistance to societal violence, discrimination, and struggles at the micro, mezzo, and macro levels. The participants’ sense of agency was a response to the complexity of their identities within hostile contexts, and their resilience and resistance hinged upon building caring communities and becoming luchadoras sociales to affect empowerment and change. The authors offer suggestions for guiding social work researchers, practitioners, and educators to engage in strengths-based approaches to advocate for the human rights, needs, and strengths of trans Latina immigrants and their communities.
Metabolomic and proteomic changes in leaves of rubber seedlings infected by Phytophthora palmivora
Authors: Kruaweangmol Pongsakorn , Ekchaweng Kitiya , Morakul Sumallika , Phaonakrop Narumon , Roytrakul Sittiruk , Tunsagool Paiboon 
Published: January 2025

Abstract
Phytophthora palmivora, an oomycete pathogen, induces leaf fall disease in rubber trees (Hevea brasiliensis), causing significant economic losses. Effective disease management requires an understanding metabolic dynamics during infection. This study employed untargeted metabolomic and proteomic analyses to investigate the response of rubber seedling leaves to P. palmivora infection. Metabolomic profiling revealed 1702 and 979 metabolite peaks in positive and negative ionization modes, respectively, with 212 metabolites identified after duplicate removal. Principal component analysis demonstrated distinct metabolic profiles between infected and non-infected leaves. Volcano plots indicated significant changes in 90 metabolites (P &lt; 0.05, fold-change ≥ 2), with 20 showing increased levels and 70 showing decreased levels in infected leaves. Pathway analysis highlighted nine metabolic pathways, with alanine, aspartate, and glutamate metabolism being the most impacted. Proteomic analysis identified 391 proteins, with 283 in infected leaves and 253 in control leaves. Among these, 145 were common to both conditions, suggesting their roles in maintaining homeostasis and responding to stress. Unique proteins in infected leaves were linked to oxidative phosphorylation, ATP synthesis and metabolic adjustments, reflecting the increased energy demands. Control samples showed proteins related to growth and photosynthesis. Integrating metabolomic and proteomic data revealed significant alterations in energy metabolism pathways in response to infection. These findings enhance our understanding of rubber seedlings’ defense strategies against P. palmivora, with implications for improving plant resistance and disease management strategies.
New approaches in childhood IgE-mediated food allergy treatment
Authors: Gurel Deniz Ilgun , Anagnostou Aikaterini , Fiocchi Alessandro , Sharon Chinthrajah , Sahiner Umit , Sindher Sayantani , Arasi Stefania 
Published: January 2025

Purpose of review
This review aims to provide an overview of the current and future treatment options for children with food allergies (FAs), highlighting the latest research findings and the potential impact of these new approaches on improving patients’ and caregivers’ quality of life.

Recent findings
In the last decade, many promising approaches have emerged as an alternative to the standard avoidance of the culprit food with the risk of severe accidental reactions. Desensitization through oral immunotherapy has been introduced in clinical settings as a therapeutic approach, and more recently also omalizumab. In addition, alternative routes of administration for immunotherapy, other biologics, small molecules, probiotics or prebiotics, microbiota transplantation therapy, IGNX001, and PVX108 are being investigated.

Summary
The portfolio of available treatment options for food allergies is increasing but several relevant unmet needs remain. This review aims to provide a brief overview of the existing and future treatment options for IgE-mediated food allergies.
Occupational allergy and climate change
Authors: Raulf Monika , Annesi-Maesano Isabella 
Published: January 2025

Purpose of review
Climate change influences working conditions in various ways, affecting employee health and safety across different sectors. Climatic factors like rising temperatures, increased UV radiation, and more frequent extreme weather events pose risks to in both indoor and outdoor workers. Allergic diseases of the respiratory tract and the skin may emerge due to climate change. This review summarizes current aspects of both direct and indirect consequences of climate change and associated exposures in diverse work environments, focusing on occupational allergies.

Recent findings
Outdoor workers, in particular, are increasing susceptible to ubiquitous pollen allergens. Additionally, they may experience climate-related increases in allergens typically associated with specific workplaces, such as Cryptostroma corticale. Changes in production processes, along with altered workplaces exposures, can lead to new sensitizations and trigger allergies, representing indirect consequences of climate change. Furthermore, lifestyle changes aimed to promoting climate protection and sustainability (e.g. the introduction of insects as a protein source or using enzymes), may also contribute to the emergence of new allergens.

Summary
The emergence of new occupational sensitization sources from novel or modified allergen exposures must be addressed within the framework of workplace safety and health, necessitating proactive measures to safeguard workers and mitigate risks.
Adipose-derived Stem Cells and Wound Healing Are Progressively Impaired Long-term After Radiotherapy in Mice
Authors: Yoshizumi Kayo , Saito Natsumi , Wu Yunyan , Shirado Takako , Asahi Rintaro , Mori Masanori , Yamamoto Yoshihiro , Sowa Yoshihiro , Yoshimura Kotaro 
Published: January 2025

Background:
The pathogenesis of deterministic radiation damage is not clearly understood, but it has been reported that fibroinflammatory pathways are up-regulated. We hypothesized that the number of adipose-derived stem/stromal cells (ASCs) decline after radiotherapies, preventing normalization of fibrosis and angiogenesis, resulting in chronic radiation damages that progress over time.

Methods:
Dorsal skin of 8-week-old male BALB/cfC3H mice was irradiated with 10 Gy weekly for 4 weeks. At 1, 3, 6, 9, and 12 months after radiotherapy (n = 5, 5, 5, 5, and 4), tissue hemoglobin oxygen saturation, and time until epithelialization were evaluated. Skin biopsies were measured for thickness and CD34+/isolectin− stem/stromal cell count. Nonirradiated (NRT) controls were evaluated at each time point as well (n = 5 each).

Results:
Compared with NRT controls, time until epithelialization was significantly longer at 1 month (28 ± 3, P < 0.01); not statistically different at 3 months (16 ± 2, P = 0.32); and lengthened over time at 6 months (20 ± 2, P = 0.21), 9 months (28 ± 2, P < 0.01), and 12 months (26 ± 3, P < 0.01), as did tissue oxygen saturation. The number of CD34+/isolectin– ASCs decreased over time, at 1 month (5.3 ± 1.3, P = 0.01), 3 months (6.0 ± 1.4, P = 0.03), 6 months (4.0 ± 0.8, P < 0.01), 9 months (1.7 ± 0.5, P < 0.01), and 12 months (0.3 ± 0.5, P < 0.01). The subcutaneous fatty layer was significantly thinner at 3 months (116 ± 33, P < 0.01), 6 months (147 ± 22, P = 0.02), 9 months (52 ± 12, P = 0.04), and 12 months (89 ± 19, P = 0.04), but not at 1 month (141 ± 18, P = 0.43).

Conclusions:
After 6 months postirradiation, the number of ASCs continued to decline over time, accompanied by irreversible progression of fibrosis, atrophy, and ischemia, which resulted in impaired wound healing.
Secondary Healing Over NovoSorb BTM in the Management of Complex Nasal Defects
Authors: McMahon Mary Ellen , Browne Robert , Ibrahim Safwat 
Published: January 2025

Background:
The use of PolyNovo NovoSorb biodegradable temporizing matrix (BTM) has become popular for the management of complex wounds, often with the subsequent application of a split-thickness skin graft. To date, there are no published case series describing healing via secondary intention over BTM in the management of small, complex nasal wounds following excision of skin malignancy in the elective setting.

Methods:
This study consisted of a single-center, consecutive case series. Inclusion criteria consisted of defects with exposed cartilage or bone in wounds located on the nasal dorsum or nasal sidewall resulting from the elective excision of nasal skin malignancies. BTM without skin grafting was used as a single-stage reconstruction in all patients following oncological clearance. After delamination, the wound was left to heal by secondary intention. The Patient and Observer Scar Assessment Scale was used to measure the aesthetic outcome.

Results:
All 32 cases exhibited 100% integration of BTM and successful wound closure. Two cases required further excision following review of the final histology. The median (SD) overall Patient and Observer Scar Assessment Scale score was 2.7 (±0.81), and the median overall observer score was 3.2 (±0.73).

Conclusions:
When planning nasal reconstruction following oncological resection, one should consider the patient’s comorbidities; their ability to tolerate the anesthetic, surgery, donor skin deficit, and risks; and the technical ability of the operating surgeon. We suggest that the use of BTM without harvesting a skin graft represents a simple, low-risk option for reconstruction of nasal defects that produces acceptable functional and aesthetic outcomes.
Characterization changes and research waste in randomized controlled trials of global gastroesophageal reflux disease and hiatus hernia over the past 20 years
Authors: Lin Bin , Guo Xiao-Jing , Jiang Yi-Ming , Shang-Guan Zhi-Xin , Zhong Qing , Chen Qi-Yue , Xie Jian-Wei , Li Ping , Zheng Chao-Hui , Huang Chang-Ming , Lin Jian-Xian 
Published: January 2025

Background:
The results of many large randomized clinical trials (RCTs) have transformed clinical practice in gastroesophageal reflux disease (GERD) and esophageal hiatal hernia (HH). However, research waste (i.e., unpublished data, inadequate reporting, or avoidable design limitations) remains a major challenge to evidence-based medicine. To explore the characteristics of GERD and HH RCTs over the past 20 years and whether there is research waste, and to explore potential targets for improvement.

Method:
A cross-sectional analysis was conducted to comprehensively review and evaluate RCTs related to GERD and esophageal HH, registered in the ClinicalTrials.gov database between 2003 and 2023. A sample of eligible RCTs was identified by excluding early-stage trials, pediatric studies, and duplicate studies. Publication status was tracked using PubMed and Scopus databases, reporting adequacy was assessed according to the CONSORT guidelines, and design flaws were checked with the help of Cochrane tools. Shortcomings of RCT studies in different regions and intervention types were identified by quantifying RCT conduct, recruitment, reporting adequacy, risk of bias, and guideline citations.

Results:
From 2003 to 2023, a total of 182 RCTs were included in the analysis, of which 69.8% (127 trials) were drug-related, and 71.4% of the principal investigators were located in North America and Asia (65 trials [35.7%] in both). Among them, the country with the most RCTs is the United States. RCTs in Asia were under-conducted in “procedure” and “other” types and fewer RCTs were conducted in Europe in “drug” type. RCTs in Oceania and South America were relatively under-conducted in the device and “other.” The study revealed that more than 86.7% of RCTs were characterized by at least one type of research waste. Research waste was associated with the size of the RCT, blinded design, and regional healthcare access and quality index.

Conclusions:
This study describes for the first time the characteristics of RCTs for GERD and esophageal HH over the past 20 years and the conduct of various types of RCTs at the continental level. It identifies the burden of research waste and shortcomings in the conduct of RCT programs on each continent, which may provide evidence for the development of rational RCTs and the reduction of waste in the future.
Dense stroma activates the TGF-β1/FBW7 axis to induce metabolic subtype switching in pancreatic cancer
Authors: Rong Zeyin , Yang Jianhui , Liu Jiang , Meng Qingcai , Hua Jie , Tan Zhen , Zhang Bo , Liu Yuan , Du Qiong , Wang Wei , Yu Xianjun , Xu Jin , Liang Chen 
Published: January 2025

Background:
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal diseases. Although several chemotherapy regimens have been developed over the past decades, few targeted therapies have shown a significant improvement in overall survival, partly due to the identification of PDAC as a single disease.

Methods:
Combining metabolomic analysis and immunohistochemistry staining with Oil Red O staining, analysis for the oxygen consumption rate and extracellular acidification rate, we stratified pancreatic cancer cells into two subtypes. The impact of transforming growth factor β (TGF-β)-1/F-box and WD repeat domain-containing 7 (FBW7) on the switch of the metabolic subtype was further validated in vitro and in vivo. Finally, cell growth was performed to identify the TGF-β1/FBW7 ratio as a molecular marker for gemcitabine resistance.

Results:
PDAC was stratified into the glycolytic subtype and lipogenic subtype. Furthermore, pancreatic cancer-associated fibroblasts-derived TGF-β1 and tumor cell-derived FBW7 were demonstrated to co-determine the metabolic phenotypes in PDAC. A high TGF-β1/FBW7 ratio always represented the glycolytic PDAC with dense stroma. This subtype of PDAC exhibited mesenchymal features and was predictive of unfavorable prognoses, despite being more sensitive than the lipogenic subtype to combination treatment with gemcitabine and an inhibitor of TGF-β receptor I (TGF-βR1).

Conclusions:
The TGF-β1/FBW7 ratio could be regarded as a molecular marker of metabolic phenotypes in PDAC and may contribute to the development of effective therapeutic strategies to improve the survival of PDAC patients.