bluuebunny/crossref_metadata_2025_split huggingface dataset:
A critical assessment of geological weighing lysimeters: Part 2—Modelling field scale soil moisture storage and hydrological fluxes
Authors: Braaten Morgan , Ireson Andrew , Clark Martyn 
Published: October 2024

AbstractLand surface models (LSMs) are used to simulate the terrestrial component of water, energy, and biogeochemical cycles. These simulations are useful for water resources management, drought and flood prediction, and numerical climate/weather prediction. However, the usefulness of LSMs are dependent by their ability to reproduce states and fluxes realistically. Accurate measurements of water storage are useful to calibrate and validate LSMs outputs. Geological weighing lysimeters (GWLs) are instruments that can provide field‐scale estimates of integrated total water storage within a soil profile. We use field estimates of total water storage and subsurface storage to critically evaluate two different land surface models: the Modélisation Environnementale communautaire—Surface Hydrology (MESH) which uses the Canadian Land Surface Scheme (CLASS), and the Structure for Unifying Multiple Modeling Alternatives: (SUMMA). These models have differences in how the processes and properties of the land surface are represented. We attempted to parameterize each model in an equivalent manner, to minimize model differences. Both models were able to reproduce observations of total water storage and subsurface storage reasonably well. However, there were inconsistencies in the simulated timing of snowmelt; depth of soil freezing; total evapotranspiration; partitioning of evaporation between soil evaporation and evaporation of intercepted water; and soil drainage. No one model emerged as better overall, though each model had specific strengths and weaknesses that we describe. Insights from this study can be used to improve model physics and performance.
Therapy adherence after interdisciplinary tumour board discussion is associated with improved outcome in soft tissue sarcoma: A Charité Comprehensive Cancer Centre analysis
Authors: Strönisch Annika , Rau Daniel , Wittenberg Silvan , Kaul David , Koulaxouzidis Georgios , Öllinger Robert , von Laffert Maximilian , Jarosch Armin , Schäfer Frederik , Keilholz Ulrich , Bullinger Lars , Märdian Sven , Striefler Jana , Flörcken Anne 
Published: October 2024

AbstractCentralising soft tissue sarcoma (STS) treatment in expert centres and implementing comprehensive therapy concepts through interdisciplinary tumour boards (ITB) has led to significant treatment progress. However, our knowledge on the implementation of the ITB recommendations and its impact on patient outcome is limited. In this retrospective analysis, we examined a cohort of 222 adult patients (pts) with primary STS who were presented to the ITB of the Charité Comprehensive Cancer Centre between 2015 and 2020. In localised disease (n = 188), resection was recommended in 71% (n = 134) of pts. The treatment modalities chemotherapy with or without regional deep hyperthermia, and radiotherapy were recommended in 37% (n = 69), 26% (n = 48) and 52% (n = 97), respectively. Complex multidisciplinary concepts were established in 29% (n = 54) including ≥3 treatment modalities. Only partial adherence, either by choice of patient or treating physician, was associated with a higher risk of both progression (HR 4.0 95%‐CI 1.6–9.7 p < .01) and mortality (HR 5.3 95%‐CI 1.7–16.4 p < .01). Pts inable to follow the ITB recommendations due to complications or rapid progression showed a high‐risk profile with increased mortality and progression rates (HR 18.1 95%‐CI 8.5–38.2 p < .001; HR 21.5 95%‐CI 8.5–54.7 p < .001). To our knowledge, this represents the first German Comprehensive Cancer Centre analysis of therapy adherence in STS. It provides further real‐world evidence that full adherence to ITB recommendations and the ability to adhere to them are of prognostic value for patient outcome and underlines the importance of interdisciplinary decision‐making and treatment planning for STS patients.
TP53 mutations and survival in ovarian carcinoma patients receiving first‐line chemotherapy plus bevacizumab: Results of the MITO16A/MaNGO OV‐2 study
Authors: Bignotti Eliana , Simeon Vittorio , Ardighieri Laura , Kuhn Elisabetta , Marchini Sergio , Califano Daniela , Cecere Sabrina Chiara , Bugatti Mattia , Spina Anna , Scognamiglio Giosuè , Paracchini Lara , Russo Daniela , Arenare Laura , Tognon Germana , Lorusso Domenica , Beltrame Luca , D'Incalci Maurizio , Sartori Enrico , De Censi Andrea , Odicino Franco , Perrone Francesco , Chiodini Paolo , Pignata Sandro 
Published: October 2024

AbstractTo date, there are no biomarkers that define a patient subpopulation responsive to bevacizumab (BEV), an effective treatment option for advanced ovarian carcinoma (OC). In the context of the MITO16A/MaNGO OV‐2 trial, a Phase IV study of chemotherapy combined with BEV in first‐line treatment of advanced OC, we evaluated TP53 mutations by next‐generation sequencing and p53 expression by immunohistochemistry (IHC) on 202 and 311 cases, respectively. We further correlated TP53 mutations in terms of type, function, and site, and IHC data with patients' clinicopathological characteristics and survival. TP53 missense mutations of unknown function (named unclassified) represented the majority of variants in our population (44.4%) and were associated with a significantly improved overall survival (OS) both in univariable (hazard ratio [HR] = 0.43, 95% confidence interval [CI] = 0.20–0.92, p = .03) and multivariable analysis (HR = 0.39, 95% CI = 0.18–0.86, p = .02). Concordance between TP53 mutational analysis and IHC was 91%. We observed an HR of 0.70 for OS in patients with p53 IHC overexpression compared to p53 wild‐type, which however did not reach statistical significance (p = .31, 95% CI = 0.36–1.38). Our results indicate that the presence of unclassified TP53 mutations has favorable prognostic significance in patients with OC receiving upfront BEV plus chemotherapy. In particular, unclassified missense TP53 mutations characterize a subpopulation of patients with a significant survival advantage, independently of clinicopathological characteristics. Our findings warrant future investigations to confirm the prognostic impact of TP53 mutations in BEV‐treated OC patients and deserve to be assessed for their potential predictive role in future randomized clinical studies.
Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides
Authors: Fan Shen , Qin Peng , Lu Jie , Wang Shuaitao , Zhang Jie , Wang Yan , Cheng Aifang , Cao Yan , Ding Wei , Zhang Weipeng 
Published: October 2024

AbstractAntimicrobial peptides (AMPs) have become a viable source of novel antibiotics that are effective against human pathogenic bacteria. In this study, we construct a bank of culturable marine biofilm bacteria constituting 713 strains and their nearly complete genomes and predict AMPs using ribosome profiling and deep learning. Compared with previous approaches, ribosome profiling has improved the identification and validation of small open reading frames (sORFs) for AMP prediction. Among the 80,430 expressed sORFs, 341 are identified as candidate AMPs with high probability. Most potential AMPs have less than 40% similarity in their amino acid sequence compared to those listed in public databases. Furthermore, these AMPs are associated with bacterial groups that are not previously known to produce AMPs. Therefore, our deep learning model has acquired characteristics of unfamiliar AMPs. Chemical synthesis of 60 potential AMP sequences yields 54 compounds with antimicrobial activity, including potent inhibitory effects on various drug‐resistant human pathogens. This study extends the range of AMP compounds by investigating marine biofilm microbiomes using a novel approach, accelerating AMP discovery.
Gut microbial 3α‐hydroxysteroid dehydrogenase promotes depression in males via degrading testosterone
Authors: Li Di , Cheng Jingru , Zhang Wei , Cheng Pengfei , He Yuan , Jia Jinghan , Wang Chao , Liu Zhongchun , Sun Zhou , Wang Jinxi 
Published: October 2024

AbstractAbnormal gut microbiota is associated with the occurrence of depression, but the specific pathophysiological role of gut microbiota in the pathogenesis of depression is still unknown. We found that the levels of serum steroid hormone testosterone in male patients with depression were lower than in healthy controls. Using testosterone as the only carbon source, the testosterone‐degrading bacteria Arthrobacter koreensis was isolated from fecal of low testosterone male patients with depression. We found that A. koreensis administration in mice led to reduced serum testosterone levels and depression‐like behaviors, which were improved by antibiotic treatment. Using whole genome sequencing, the gene mediating testosterone degradation in A. koreensis was identified and annotated as 3α‐hydroxysteroid dehydrogenase (3α‐HSD). Escherichia coli heterologously expressing 3α‐HSD obtained the capacity to degrade testosterone, causing depression‐like behaviors after gavage to mice. Testosterone supplementation improves depression‐like behavior in mice induced by gavage of Escherichia coli heterologously expressing 3α‐HSD. Finally, the universality of 3α‐HSD in gut of male patients with depression was higher than that of healthy controls. Overall, our results revealed a new pathway that potentially links testosterone degradation by gut microbes harboring 3α‐HSD enzymes to the pathogenesis of depression. Gut microbial 3α‐HSD can induce depression in mice via testosterone degradation. This means that 3α‐HSD expressed by gut bacteria may be a potential target for depression in men.
Genetic variations in NER pathway gene polymorphisms and Wilms tumor risk: A six‐center case–control study in East China
Authors: Zhan Xueli , Zhou Haixia , Deng Changmi , Hua Rui‐Xi , Pan Lingling , Zhang Shouhua , Lu Hongting , He Shaohua , Wang Yizhen , Ruan Jichen , Zhou Chunlei , He Jing 
Published: October 2024

AbstractThe nucleotide excision repair (NER) system is one of the main ways to protect organisms from DNA damage caused by endogenous and exogenous carcinogens. NER deficiency increases genome mutations, chromosomal aberrations, and cancer viability. However, the genetic association between Wilms tumor and NER pathway gene polymorphisms needs to be further validated. We assessed the associations between 19 NER gene polymorphisms and Wilms tumor susceptibility in 416 cases and 936 controls from East China via the TaqMan method. We found that xeroderma pigmentosum group D (XPD) rs238406 and rs13181 significantly decreased the risk of Wilms tumor [adjusted odds ratio (OR) = 0.59, 95% confidence interval (CI) = 0.46–0.75, p <.0001; adjusted OR = 0.63, 95% CI = 0.44–0.89, p = .009, respectively]. Furthermore, the rs751402 and rs2296147 polymorphisms in the xeroderma pigmentosum group G (XPG) gene were significantly correlated with an increased risk for Wilms tumor (adjusted OR = 1.47, 95% CI = 1.03–2.09, p = .034; adjusted OR = 2.14, 95% CI = 1.29–3.56, p = .003, respectively). Expression quantitative trait loci (eQTL) analysis revealed that these four polymorphisms may affect the expression of genes that are adjacent to XPD and XPG. Our study provides evidence that XPD and XPG gene polymorphisms are associated with Wilms tumor risk. Nonetheless, these findings should be confirmed in a larger sample size.
Coexisting bacterial aminoacyl‐tRNAsynthetase paralogs exhibit distinct phylogenetic backgrounds and functional compatibility withEscherichia coli
Authors: Radecki Alexander A. , Fantasia‐Davis Ariana , Maldonado Juan S. , Mann Joshua W. , Sepulveda‐Camacho Stephanie , Morosky Pearl , Douglas Jordan , Vargas‐Rodriguez Oscar 
Published: October 2024

AbstractAminoacyl‐tRNA synthetases (aaRSs) are universally essential enzymes that synthesize aminoacyl‐tRNA substrates for protein synthesis. Although most organisms require a single aaRS gene for each proteinogenic amino acid to translate their genetic information, numerous species encode multiple gene copies of an aaRS. Growing evidence indicates that organisms acquire extra aaRS genes to sustain or adapt to their unique lifestyle. However, predicting and defining the function of repeated aaRS genes remains challenging due to their potentially unique physiological role in the host organism and the inconsistent annotation of repeated aaRS genes in the literature. Here, we carried out comparative, phylogenetic, and functional studies to determine the activity of coexisting paralogs of tryptophanyl‐, tyrosyl‐, seryl‐, and prolyl‐tRNA synthetases encoded in several human pathogenic bacteria. Our analyses revealed that, with a few exceptions, repeated aaRSs involve paralogous genes with distinct phylogenetic backgrounds. Using a collection ofEscherichia colistrains that enabled the facile characterization of aaRS activity in vivo, we found that, in almost all cases, one aaRS displayed transfer RNA (tRNA) aminoacylation activity, whereas the other was not compatible withE.coli. Together, this work illustrates the challenges of identifying, classifying, and predicting the function of aaRS paralogs and highlights the complexity of aaRS evolution. Moreover, these results provide new insights into the potential role of aaRS paralogs in the biology of several human pathogens and foundational knowledge for the investigation of the physiological role of repeated aaRS paralogs across bacteria.
Role of Ultrasonography in the Evaluation of Peripheral Nerve Pathologies: A Study of 200 Cases
Authors: Kachare Manohar B. , Gamanagatti Shanta A. , Satish Patil , Umesh Joshi 
Published: October 2024

ABSTRACTAimThe aim of this study is to ascertain the role of ultrasonography in appraising the structural intricacies of peripheral nerve pathologies.Objectives(1) To scrutinize the anatomy of both normal and abnormal peripheral nerves. (2) Assess different parameters like continuity of the nerve, echotexture, vascularity, cross‐sectional area, and thickness of the nerve in various pathologies.Methods and MaterialsIn a prospective observational study conducted at the Department of Radio Diagnosis, Tertiary Care Centre, the study design focused on the examination of 200 cases utilizing a high‐resolution 9–14 Mhz and 17 Mhz linear array transducer, integrated into the Aplio 400 Canon Ultrasound System.ResultsAmong the total cases, 62 were identified as traumatic neuropathy cases, 52 as entrapment neuropathy cases, 14 as infective neuropathy cases, 54 as thermal neuropathy cases, 14 as metabolic neuropathy cases, and 4 as nerve‐tumor cases.ConclusionsIn conclusion, this investigation illuminates the dynamic role of ultrasonography as an invaluable diagnostic instrument in appraising peripheral nerve pathologies. The noninvasive attributes, widespread availability, and economic viability of ultrasonography render it a pragmatic choice for clinicians. This inquiry buttresses the escalating significance of ultrasonography within neurology, emphasizing its potential to revolutionize the terrain of peripheral nerve pathology assessment.
The prognostic impact of C‐reactive protein and albumin in patients diagnosed with acute myeloid leukaemia
Authors: Skar Espen Talseth , Wendelbo Øystein , Reikvam Håkon 
Published: October 2024

AbstractBackgroundAcute myeloid leukaemia (AML) is an aggressive and heterogeneous malignant disease. Patient age, comorbidities and disease‐specific genetic abnormalities are recognized as primary determinants of treatment response. Recent years have elucidated the significance of nutritional status and inflammation across various malignancies, including AML, in influencing treatment outcomes.AimsTo assess the prognostic value of the C‐reactive protein‐albumin ratio (CAR) and the Glasgow Prognostic Score (GPS) in predicting overall survival (OS) rates among patients diagnosed with AML.Material and methods189 AML patients receiving standard cytarabine and anthracycline‐based induction treatment were included. Baseline demographic, clinical and laboratory data were collected, and treatment outcomes and survival were registered for all patients.ResultsNo significant association between CAR and prognosis among AML patients was found, even in subgroup analyses. Hypoalbuminemia was an independent predictor of poor survival among all patients (OS 28 vs. 16 months; p < 0.02). Patients with a GPS of 0 or 1 demonstrated superior OS compared to those with a GPS of 2 (median OS 28 vs. 16 months, respectively; p = 0.015). Results remained consistent among patients ≥ 60 years (median OS 15 vs. 6 months; p = 0.020).ConclusionHeightened inflammation and suboptimal nutritional status correlate with unfavourable prognoses in AML patients. Such insights hold the potential for guiding clinical decision‐making, offering easily accessible prognostic information for the induction treatment of eligible AML patients.
Advances in the Synthesis of 3‐Acyl‐2‐Pyridones: Strategies and Methods for Accessing the Versatile Scaffold
Authors: Rani Reena , Devi Sheetu , Yadav Neelam , Sangwan Sarita , Dhanda Vidhi , Kumar Vipan , Chauhan Sonu , Duhan Anil , Kumar Ravi 
Published: October 2024

ABSTRACTThe syntheses and bioevaluation of 3‐acyl‐2‐pyridones have garnered significant interest in recent years as a novel class of compounds with diverse biological activities. The bioactivities cover a wide range of therapeutic areas including antimicrobial, antitumor, anti‐inflammatory, antifungal, antibiotic, neuritogenic, cytotoxic, and antiviral activities. Therefore, 3‐acyl‐2‐pyridone scaffold offers a versatile platform for the development of new molecules with potential applications in medicinal chemistry. The recent exploration on synthesis and bioevaluation of 3‐acyl‐2‐pyridones has yielded promising results, making them attractive targets for further optimization and development of new therapeutic agents. This review summarizes the available information on total synthesis of 3‐acyl‐2‐pyridone containing natural products, and the other synthetic strategies developed for accessing the 3‐acyl pyridones such as multicomponent synthesis, condensation reaction, microwave‐assisted synthesis, catalytic hydrogenation reactions, metalation reaction, Michael addition, and formylation reactions. The presented information may serve as a valuable resource for researchers working in the field of medicinal chemistry and drug discovery, stimulating further exploration and development of this intriguing scaffold.
The Influence of the Isosteric Exchange of Benzene by Thiophene‐Core of Phthalocyanine: The Synthesis, Structure and Opto‐Electronic Behavior of π‐Conjugated Unit Blocks in Materials
Authors: Kendrová Dominika , Gašparová Marcela , Andicsová‐Eckstein Anita , Váry Tomáš , Tokár Kamil , Tokárová Zita 
Published: October 2024

ABSTRACTThe strategy of isosteric replacement of the benzene ring with a thiophene core was applied in the design of phthalocyanine 1 with the aim for reaching an effective organic chromophore as employable content in organic photovoltaic devices. The formation of the desired product was not achieved but the approach created organic small‐molecules 2 and 3. These, representing the reactive intermediates, were converted to novel hemiphthalocyanine 4. Although undesired, all exhibit absorbance in the visible region (λmax ~ 400 nm) and proximity of the HOMO/LUMO band edge (Eg: 2.0–3.5 eV), suggesting that compounds 2–4 behaves as an effective π‐conjugated linkers in donor‐π‐acceptor type dyes for dye sensitized solar cells and related high performing energetic devices.
A Review of Melanoma Subtypes: Genetic and Treatment Considerations
Authors: Druskovich Christina , Kelley Jesse , Aubrey Jason , Palladino Leah , Wright G. Paul 
Published: October 2024

ABSTRACTMelanoma affects over one million people in the United States. This review explores genetic mutations and markers of all seven subtypes. Current treatment options and prognosis of each subtype are also discussed. For lentigo maligna, spitzoid, and nodular subtypes, BRAF was the most common mutation reported. For superficial spreading, TP53 was the most common. Acral lentiginous demonstrated CCDN1 and desmoplastic NF1 most frequently. No mutations have been identified in the nevoid subtype. Nodular melanoma is the deadliest subtype. Evidence suggests that the subtypes differ in regard to genetic markers/mutations, treatment and prognosis. Therefore, subtype should be considered when treating a melanoma patient.
Impact of Adjuvant Interferon Therapy on Survival Outcomes for Cutaneous Melanoma With Parotid Involvement
Authors: Kim Erin , Raven Sarah A. , Lenze Nicholas R. , Farlow Janice L. , McLean Scott A. 
Published: October 2024

ObjectivesTo determine the relative 5‐year overall survival (OS) and 5‐year recurrence‐free survival (RFS) outcomes for adjuvant interferon therapy in the treatment of head and neck cutaneous melanoma (HNCM) with parotid gland involvement.MethodsA retrospective cohort study was conducted at a single tertiary care institution to analyze patients undergoing parotidectomy for cutaneous head and neck melanoma involving the parotid gland from 2000 to 2014. Time‐to‐event analyses were performed using Kaplan–Meier curves with log‐rank p‐values and Cox proportional hazards models.ResultsThe sample consisted of 82 patients who underwent surgical resection of stage III HNCM with parotid involvement. The mean follow‐up was 67.8 months (SD 65) after diagnosis. Twenty‐one patients received adjuvant interferon therapy, 12 patients received adjuvant radiation therapy, and 49 patients received no adjuvant therapy. Crude 5‐year OS rates were 95.0% for interferon therapy, 33.3% for adjuvant RT, and 40.4% for no adjuvant therapy. Crude 5‐year RFS rates were 75.2%, 19.5%, and 40.8% respectively. In the fully adjusted model, adjuvant interferon therapy was associated with improved 5‐year OS compared to adjuvant RT (HR 0.10, 95% CI 0.011–0.837; p = 0.034). There was no significant association between adjuvant interferon therapy and 5‐year RFS in the fully adjusted model.ConclusionAdjuvant interferon therapy for surgically resected stage III cutaneous melanoma with parotid gland involvement may be associated with improved survival outcomes. These findings support the growing evidence for the use of immunotherapy in melanoma, and potentially a unique role for when melanoma involves the lymphatic‐rich parotid gland.Level of Evidence3 Laryngoscope, 135:1098–1104, 2025