bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying gastric cancer by optical coherence tomography based on an optimized depth-resolved attenuation estimation
Authors: Zhao Chao , Shu Yukang , Cui Lin , He Xiang , Mao Weizheng , Shi Xiaofeng , Zhao Hang , Ma Jun 
Published: June 2024

Abstract
Optical coherence tomography (OCT) is a reliable technique for cancer detection, with the potential to improve accuracy in identifying cancerous tissue through effective use of OCT image data. We proposed an optimized depth resolution estimation based optical attenuation coefficient (OAC) mapping method to reduce the error effect caused by discretization without considering whether the light is completely attenuated or not. The attenuation coefficient maps of gastric tissue were reconstructed using this method. Features were extracted from these maps using gray-level co-occurrence matrix and gray histogram, and a support vector machine was employed as a classifier for identifying gastric cancer tissues. The recognition accuracy achieved was 98.60%, which was higher than the 94.30% accuracy in the control group without OACs. This approach enhances the utilization of OCT image information and improves its practical application ability by increasing the recognition accuracy.
Effect of tin doping and tin-bromine co-doping on electronic and optical properties of BiOCl crystal: density functional theory
Authors: Wakjira Tadesse Lemma , Tadele Kumneger , Gemta Abebe Belay , Kassahun Gashaw Beyene 
Published: June 2024

Abstract
Bismuth oxychloride (BiOCl) is a layered compound known for its exceptional physical, chemical, and optical characteristics, along with notable photocatalytic performance under visible light irradiation. This investigation employed density functional theory (DFT) to analyze the electronic band structure, projected density of states (PDOS), joint density of states (JDOS), and dielectric functions of both pristine BiOCl and various doped crystalline structures utilizing a projected augmented wave basis set. The crystallographic symmetry of doped and co-doped configurations exhibited congruency with the pristine crystals. Electronic band structures were evaluated for pristine, doped, and co-doped crystalline forms. In the case of the co-doped SnxBi1−xOBrxCl1−x crystal (x = 0.0625, 0.125, and 0.25), energy band gaps of 1.40 eV, 1.42 eV, and 1.5 eV were determined, respectively, signifying a reduction in the energy band gap compared to the single doped and undoped BiOCl crystal. Analysis of the PDOS revealed that the valence band (VB) of the SnxBi1−xOBrxCl1−x crystal was characterized by Cl (p), Br (p), O (p), and Sn (s, p) states, while the conduction band (CB) primarily consisted of Bi (p) states. JDOS calculations indicated a shift in peak energy towards lower values, indicating that dopants promoted electron transitions from Cl, Sn, O, and Br p states to the Bi p state. Moreover, investigation of the dielectric function for both pure and doped BiOCl demonstrated that tin-bromine co-doping induced modifications in the static dielectric constant and dielectric permittivity of the unmodified BiOCl crystal. Ultimately, the incorporation of tin and bromine through co-doping exerted a substantial influence on the electronic and optical properties of the doped crystalline materials. Based on our computational assessments, the SnxBi1−xOBrxCl1−x configuration with x = 0.25 showcased superior visible light absorption efficiency compared to other doped variations and pristine BiOCl.
Amphistomy: stomata patterning inferred from 13C content and leaf-side-specific deposition of epicuticular wax
Authors: Askanbayeva Balzhan , Janová Jitka , Kubásek Jiří , Zeisler-Diehl Viktoria V , Schreiber Lukas , Muir Christopher D , Šantrůček Jiří 
Published: June 2024

Abstract

Background and Aims
The benefits and costs of amphistomy (AS) vs. hypostomy (HS) are not fully understood. Here, we quantify benefits of access of CO2 through stomata on the upper (adaxial) leaf surface, using 13C abundance in the adaxial and abaxial epicuticular wax. Additionally, a relationship between the distribution of stomata and epicuticular wax on the opposite leaf sides is studied.

Methods
We suggest that the 13C content of long-chain aliphatic compounds of cuticular wax records the leaf internal CO2 concentration in chloroplasts adjacent to the adaxial and abaxial epidermes. This unique property stems from: (1) wax synthesis being located exclusively in epidermal cells; and (2) ongoing wax renewal over the whole leaf lifespan. Compound-specific and bulk wax 13C abundance (δ) was related to amphistomy level (ASL; as a fraction of adaxial in all stomata) of four AS and five HS species grown under various levels of irradiance. The isotopic polarity of epicuticular wax, i.e. the difference in abaxial and adaxial δ (δab − δad), was used to calculate the leaf dorsiventral CO2 gradient. Leaf-side-specific epicuticular wax deposition (amphiwaxy level) was estimated and related to ASL.

Key Results
In HS species, the CO2 concentration in the adaxial epidermis was lower than in the abaxial one, independently of light conditions. In AS leaves grown in high-light and low-light conditions, the isotopic polarity and CO2 gradient varied in parallel with ASL. The AS leaves grown in high-light conditions increased ASL compared with low light, and δab − δad approached near-zero values. Changes in ASL occurred concomitantly with changes in amphiwaxy level.

Conclusions
Leaf wax isotopic polarity is a newly identified leaf trait, distinguishing between hypo- and amphistomatous species and indicating that increased ASL in sun-exposed AS leaves reduces the CO2 gradient across the leaf mesophyll. Stomata and epicuticular wax deposition follow similar leaf-side patterning.
Temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal communities with ontogenetic and phenological development in Prasophyllum (Orchidaceae)
Authors: Freestone Marc , Reiter Noushka , Swarts Nigel D , Linde Celeste C 
Published: June 2024

Abstract

Background and Aims
Plant–fungus symbioses may experience temporal turnover during the ontogenetic or phenological development of the host, which can influence the ecological requirements of the host plant. In this study, we investigate temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal (OMF) communities in Prasophyllum (Orchidaceae), asking whether OMF communities are subject to temporal change attributable to orchid phenology or ontogeny.

Methods
Roots of adult Prasophyllum frenchii, Prasophyllum lindleyanum and Prasophyllum sp. aff. validum from Australia were sampled between autumn and spring. Seed was sown in situ as ‘baits’ to explore the mycorrhizal associations of germinating protocorms, which were compared with OMF in roots of co-occurring adult plants. Culture-dependent and -independent sequencing methods were used to amplify the internal transcribed spacer and mitochondrial large subunit loci, with sequences assigned to operational taxonomic units (OTUs) in phylogenetic analyses. Germination trials were used to determine whether fungal OTUs were mycorrhizal.

Key Results
A persistent core of OMF was associated with Prasophyllum, with Ceratobasidiaceae OMF dominant in all three species. Phenological turnover occurred in P. lindleyanum and P. sp. aff. validum, but not in P. frenchii, which displayed specificity to a single OTU. Ontogenetic turnover occurred in all species. However, phenological and ontogenetic turnover was typically driven by the presence or absence of infrequently detected OTUs in populations that otherwise displayed specificity to one or two dominant OTUs. Ex situ germination trials showed that 13 of 14 tested OTUs supported seed germination in their host orchid, including eight OTUs that were not found in protocorms in situ.

Conclusions
An understanding of OMF turnover can have practical importance for the conservation of threatened orchids and their mycorrhizal partners. However, frameworks for classifying OMF turnover should focus on OTUs important to the life cycle of the host plant, which we suggest are likely to be those that are frequently detected or functionally significant.
Themis: advancing precision oncology through comprehensive molecular subtyping and optimization
Authors: Xi Yue , Zheng Kun , Deng Fulan , Liu Yujun , Sun Hourong , Zheng Yingxia , Tong Henry H Y , Ji Yuan , Zhang Yingchun , Chen Wantao , Zhang Yiming , Zou Xin , Hao Jie 
Published: June 2024

Abstract
Recent advances in tumor molecular subtyping have revolutionized precision oncology, offering novel avenues for patient-specific treatment strategies. However, a comprehensive and independent comparison of these subtyping methodologies remains unexplored. This study introduces ‘Themis’ (Tumor HEterogeneity analysis on Molecular subtypIng System), an evaluation platform that encapsulates a few representative tumor molecular subtyping methods, including Stemness, Anoikis, Metabolism, and pathway-based classifications, utilizing 38 test datasets curated from The Cancer Genome Atlas (TCGA) and significant studies. Our self-designed quantitative analysis uncovers the relative strengths, limitations, and applicability of each method in different clinical contexts. Crucially, Themis serves as a vital tool in identifying the most appropriate subtyping methods for specific clinical scenarios. It also guides fine-tuning existing subtyping methods to achieve more accurate phenotype-associated results. To demonstrate the practical utility, we apply Themis to a breast cancer dataset, showcasing its efficacy in selecting the most suitable subtyping methods for personalized medicine in various clinical scenarios. This study bridges a crucial gap in cancer research and lays a foundation for future advancements in individualized cancer therapy and patient management.
PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity
Authors: Nam Hwanhee , Lee Esder , Yang Hichang , Lee Kyeyoon , Kwak Taeho , Kim Dain , Kim Hyemin , Yang Mihwa , Yang Younjoo , Son Seungwan , Nam Young-Hyean , Minn Il 
Published: June 2024

Abstract
Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.
Strategies for overcoming tumour resistance to immunotherapy: harnessing the power of radiation therapy
Authors: Passelli Katiuska , Repáraz David , Kinj Remy , Herrera Fernanda G 
Published: June 2024

Abstract
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment; yet their efficacy remains variable across patients. This review delves into the intricate interplay of tumour characteristics contributing to resistance against ICI therapy and suggests that combining with radiotherapy holds promise. Radiation, known for its ability to trigger immunogenic cell death and foster an in situ vaccination effect, may counteract these resistance mechanisms, enhancing ICI response and patient outcomes. However, particularly when delivered at high-dose, it may trigger immunosuppressive mechanism and consequent side-effects. Notably, low-dose radiotherapy (LDRT), with its capacity for tumour reprogramming and reduced side effects, offers the potential for widespread application. Preclinical and clinical studies have shown encouraging results in this regard.
Can we screen opportunistically for low bone mineral density using CT scans of the shoulder and artificial intelligence?
Authors: Sebro Ronnie , De la Garza-Ramos Cynthia 
Published: June 2024

Abstract

Objective
To evaluate whether the CT attenuation of bones seen on shoulder CT scans could be used to predict low bone mineral density (BMD) (osteopenia/osteoporosis), and to compare the performance of two machine learning models to predict low BMD.

Methods
In this study, we evaluated 194 patients aged 50 years or greater (69.2 ± 9.1 years; 170 females) who underwent unenhanced shoulder CT scans and dual-energy X-ray absorptiometry within 1 year of each other between January 1, 2010, and December 31, 2021. The CT attenuation of the humerus, glenoid, coracoid, acromion, clavicle, first, second, and third ribs was obtained using 3D-Slicer. Support vector machines (SVMs) and k-nearest neighbours (kNN) were used to predict low BMD. DeLong test was used to compare the areas under the curve (AUCs).

Results
A CT attenuation of 195.4 Hounsfield Units of the clavicle had a sensitivity of 0.577, specificity of 0.781, and AUC of 0.701 to predict low BMD. In the test dataset, the SVM had sensitivity of 0.686, specificity of 1.00, and AUC of 0.857, while the kNN model had sensitivity of 0.966, specificity of 0.200, and AUC of 0.583. The SVM was superior to the CT attenuation of the clavicle (P = .003) but not better than the kNN model (P = .098).

Conclusion
The CT attenuation of the clavicle was best for predicting low BMD; however, a multivariable SVM was superior for predicting low BMD.

Advances in knowledge
SVM utilizing the CT attenuations at many sites was best for predicting low BMD.
National myeloma patient survey shows continuing inappropriate imaging and geographical inequalities
Authors: Quinn Sandra C M , Goh Vicky , Westerland Olwen A , Pratt Guy 
Published: June 2024

Abstract

Objective
To evaluate the provision of imaging at diagnosis of myeloma from the service user perspective with a specific focus on how the experiences of patients align with the National Institute for Health and Care Excellence (NICE) guidelines (NG35, 2016) on first-line imaging practice for myeloma in the United Kingdom.

Methods
A national survey was performed to evaluate access to imaging from the patient’s perspective. Patients with myeloma who received their diagnosis between 2017 and March 2022 were invited to participate. Data were collected using an online survey from 895 patients and carers between 4 and 14 March 2022.

Results
Most patients had more than one imaging test. First-line MRI was used in 69.2% of respondents. First-line skeletal survey (SS, whole body X-rays) remained common (48.7% of respondents). 18F-fluorodexyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) was used least often (23.1% of respondents). SS was used more often in East England (57.9%) and Scotland (61.2%) than in South East England (36.3%).

Conclusions
Despite NICE recommendations, first-line MRI was not used in a third of patients surveyed, with geographical variation in imaging practice. Patients are still undergoing multiple imaging tests at diagnosis. Healthcare professionals should continue to emphasize the superiority of MRI compared to SS to drive for improvements in care.

Advances in knowledge
Current recommendations on first-line imaging for myeloma are not provided consistently across the United Kingdom. There is a need to drive change and support healthcare professionals to deliver guidance-based recommendations to improve experience and outcomes for patients.
Retrospective study of germline variants in patients with hereditary melanoma study criteria in a real clinical practice setting
Authors: Villa-Gonzalez Jose Maria , Carrera Revilla Sergio , Lombardero Gutiérrez Lara , Gardeazabal García Jesús 
Published: June 2024

Abstract

Background
Five to twelve per cent of melanoma cases show aggregation of melanomas or other related tumours within the same family or individual. Genes such as CDKN2A or BAP1, among others, have been associated with this condition.

Objectives
To describe the epidemiology and clinical characteristics of patients in whom a germline genetic study was performed due to suspected hereditary melanoma.

Methods
This was a retrospective descriptive study that included patients from Cruces University Hospital who underwent a germline genetic analysis for hereditary melanoma from 2016 to 2023, having met any of the following criteria: (i) presence of two or more melanomas in the same individual; (ii) a melanoma and a pancreatic cancer in the same individual; (iii) presence of a melanoma in an individual and one or more first- or second-degree relatives with melanoma or pancreatic cancer; (iv) first- or second-degree relative of an individual with a known deleterious variant in genes associated with melanoma predisposition; or (v) incidental discovery of deleterious variants in genes associated with predisposition to melanoma, within hereditary cancer panels carried out for reasons other than melanoma.

Results
In total, 59 families were included, comprising 69 patients (64% women). Among these, 8% of families (13% of patients) presented pathogenic/likely pathogenic (P/LP) variants: 6% of families (6% of patients), excluding criteria (iv) and (v), showed P/LP variants in CDKN2A, and 2% of families (1% of patients) presented P/LP variants in BAP1, BRCA2 and TERF2IP.

Conclusions
The frequencies of P/LP variants in CDKN2A are similar to those previously described. This study could contribute to the knowledge of the characteristics of patients who meet genetic study criteria for hereditary melanoma in a setting of real-world clinical practice.
Sex differences in aberrant functional connectivity of three core networks and subcortical networks in medication-free adolescent-onset major depressive disorder
Authors: Yang Chunyu , Zhou Zilin , Bao Weijie , Zhong Ruihan , Tang Mengyue , Wang Yidan , Gao Yingxue , Hu Xinyue , Zhang Lianqing , Qiu Lihua , Kuang Weihong , Huang Xiaoqi , Gong Qiyong 
Published: June 2024

Abstract
Major depressive disorder demonstrated sex differences in prevalence and symptoms, which were more pronounced during adolescence. Yet, research on sex-specific brain network characteristics in adolescent-onset major depressive disorder remains limited. This study investigated sex-specific and nonspecific alterations in resting-state functional connectivity of three core networks (frontoparietal network, salience network, and default mode network) and subcortical networks in adolescent-onset major depressive disorder, using seed-based resting-state functional connectivity in 50 medication-free patients with adolescent-onset major depressive disorder and 56 healthy controls. Irrespective of sex, compared with healthy controls, adolescent-onset major depressive disorder patients showed hypoconnectivity between bilateral hippocampus and right superior temporal gyrus (default mode network). More importantly, we further found that females with adolescent-onset major depressive disorder exhibited hypoconnectivity within the default mode network (medial prefrontal cortex), and between the subcortical regions (i.e. amygdala, striatum, and thalamus) with the default mode network (angular gyrus and posterior cingulate cortex) and the frontoparietal network (dorsal prefrontal cortex), while the opposite patterns of resting-state functional connectivity alterations were observed in males with adolescent-onset major depressive disorder, relative to their sex-matched healthy controls. Moreover, several sex-specific resting-state functional connectivity changes were correlated with age of onset, sleep disturbance, and anxiety in adolescent-onset major depressive disorder with different sex. These findings suggested that these sex-specific resting-state functional connectivity alterations may reflect the differences in brain development or processes related to early illness onset, underscoring the necessity for sex-tailored diagnostic and therapeutic approaches in adolescent-onset major depressive disorder.
Safety and Effectiveness of 3 Novel All-Oral Shortened Regimens for Rifampicin- or Multidrug-Resistant Tuberculosis in Kazakhstan
Authors: Rashitov Makhmujan , Franke Molly F , Trevisi Letizia , Bekbolatova Gulzhanat , Shalimova Julia , Eshmetov Gafurzhan , Bektasov Sagit , LaHood Allison , Arlyapova Nataliya , Osso Elna , Yedilbayev Askar , Korotych Oleksandr , Ciobanu Anisoara , Skrahina Alena , Mitnick Carole D , Seung Kwonjune J , Algozhin Yerkebulan , Rich Michael L 
Published: June 2024

Abstract

Background
In 2019, the World Health Organization called for operational research on all-oral shortened regimens for multidrug- and rifampicin-resistant tuberculosis (MDR/RR-TB). We report safety and effectiveness of three 9-month all-oral regimens containing bedaquiline (Bdq), linezolid (Lzd), and levofloxacin (Lfx) and reinforced with cycloserine (Cs) and clofazimine (Cfz), delamanid (Dlm) and pyrazinamide (Z), or Dlm and Cfz.

Methods
We conducted a prospective cohort study of patients initiating treatment for pulmonary MDR/RR-TB under operational research conditions at public health facilities in Kazakhstan. Participants were screened monthly for adverse events. Participants with baseline resistance were excluded from the study and treated with a longer regimen. We analyzed clinically relevant adverse events of special interest in all participants and sputum culture conversion and end-of-treatment outcomes among individuals who were not excluded.

Results
Of 510 participants, 41% were women, the median age was 37 years (25th–75th percentile: 28–49), 18% had a body mass index &lt;18.5 kg/m2, and 51% had cavitary disease. A total of 399 (78%) initiated Bdq-Lzd-Lfx-Cs-Cfz, 83 (16%) started Bdq-Lzd-Lfx-Dlm-Z, and 28 (5%) initiated Bdq-Lzd-Lfx-Dlm-Cfz. Fifty-eight individuals (11%) were excluded from the study, most commonly due to identification of baseline drug resistance (n = 52; 90%). Among the remaining 452 participants, treatment success frequencies were 92% (95% CI: 89–95%), 89% (95% CI: 80–94%), and 100% (95% CI: 86–100%) for regimens with Cs/Cfz, Dlm/Z, and Dlm/Cfz, respectively. Clinically relevant adverse events of special interest were uncommon.

Conclusions
All regimens demonstrated excellent safety and effectiveness, expanding the potential treatment options for patients, providers, and programs.