bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intelligent ontology alignment to improve semantic data integration across research domains in biomedicine
Authors: Malik Muhammad Shoaib , Inau Esther Thea 
Published: August 2023

Abstract
Ontology alignment is a key component of semantic web interoperability, with a long history of applications in traditional data integration tasks that address the problem of semantic heterogeneity. Ontology alignment tools take two ontologiesas input and determine alignments as output i.e. a set of correspondences between semantically related units of these ontologies. These correspondences can then be used to merge ontologies, link data across knowledge domains, answer semantic queries, navigate through knowledge graphs, and many more. The process of determining alignments, called matching, therefore is a basic requirement for linking knowledge across scientific domains covered by one or more ontologies. A matching exists if entities from different ontologies are semantically equivalent. The goal of this study is to find all semantically equivalent entity pairs given a source ontology Os and a target ontology Ot, each consisting of a set of entities. We propose to use Inverse Document Frequency (IDF) and Jaccard distance to find candidate entities with high precision and less computational effort. Our goal to cross-link different research fields in the biomedical and clinical domains.
Construction of a predictive model for osteoporosis risk in men: using the IOF one-minute Osteoporosis Test
Authors: Zhang Kun , Wang Min , Yi Weihong , Yang Dazhi 
Published: August 2023

Abstract
Objective To construct a clinical prediction nomogram model using the one-minute IOF osteoporosis risk test as an evaluation tool for male osteoporosis.
Methods The one-minute test results and the incidence of osteoporosis were collected from 354 patients in the osteoporotic clinic of our hospital. LASSO regression model and multi-factor Logtisic regression were used to analyze the risk factors of osteoporosis in patients, and the risk prediction model of osteoporosis was established. Verify with an additional 140 objects.
Results We used logtisic regression to construct a nomogram model. According to the model, the AUC value of the training set was 0.760 (0.704-0.817). The validation set has an AUC value of 0.806 (0.733-0.879). The test set AUC value is 0.714 (0.609-0.818). The calibration curve shows that its advantage is that the deviation correction curve of the nomogram model can maintain a good consistency with the ideal curve. In terms of clinical applicability, compared with the "total intervention" and "no intervention" schemes, the clinical net return rate of the nomogram model showed certain advantages.
Conclusion Using the one-minute osteoporosis risk test provided by IOF, we built a male osteoporosis risk prediction model with good prediction effect, which can provide greater reference and help for clinicians.
Ultra-high µC* beyond 10 000 F cm-1 V-1 s-1 in organic electrochemical transistors
Authors: Bardagot Olivier , Durand Pablo , Guchait Shubhradip , Rebetez Gonzague , Cavassin Priscila , Réhault Julien , Brinkmann Martin , Leclerc Nicolas , Banerji Natalie 
Published: August 2023

Abstract

Organic electrochemical transistors (OECTs) are the heart of promising high-sensitivity biosensors, electrophysiological monitors, and neuromorphic devices. In a context of growing interest for such strategic electronics, we investigate a novel PBTTT polymer bearing single ether side chains (PBTTT-8O) in OECTs. Pristine, non-aligned, devices match state-of-the-art transconductance, confirming the value of single ethers for designing next-generation organic mixed ionic-electronic conductors (OMIECs). Moreover, a ten-fold enhancement of 𝜇C*, reaching 12 000 F cm-1 V-1 s-1, is achieved by unidirectional alignment of PBTTT-8O, opening doors to unprecedented device sensitivity. Such improvement is mainly attributed to enhanced hopping along ordered polymer chains, resulting in ultra high mobility over 25 cm2 V-1 s-1. Interestingly, aligned channels dope twice and dedope fifteen times faster than pristine ones, offering a path to achieve rapid ON/OFF device switching. This study reports an easily transferable solution to concomitantly boost the signal amplification and switching speed of bioelectronic devices.
Climate and humans interact to shape the fire regime of a chir pine forest in eastern Bhutan
Authors: Tenzin Karma , Nitschke Craig R , Allen Kathryn J , Krusic Paul J , Cook Edward R , Nguyen Thiet V , Baker Patrick J 
Published: August 2023

Abstract

Background: Chir pine (pinus roxburghii Sarg.) forests are distributed in the dry valleys of Bhutan Himalaya. These forests are heavily influenced by biotic activities such as grazing, resin tapping and NWFP (non-wood forests produce) collection. Understanding the relationship between past and present climate and the frequency and severity of forest fires is important for assessing the relative importance of potential drivers on fire occurrence and extent. This study aimed to reconstruct the fire history of a forested landscape dominated by chir pine in eastern Bhutan using crossdated fire scars disc samples.
Results: The chir pine fire chronology extended to the early 1900s. Between 1900 and ~1970 fires were typically small and limited to a small number of sites within the larger study area. After 1970 a distinct shift in fire activity occurred with fires in 1985, 1989, 1996, 2000, and 2013 burning >90% of sample plots. Fire activity was positively associated with La Niña conditions (wetter, cooler) in the preceding year, which likely contributed to a greater accumulation of fuels on the forest floor.
Conclusions: Historical reconstruction of fire activity from a site in eastern Bhutan highlights the interaction between human activity and climatic conditions. Prior to 1970 fire activity was dominated by patchy, low-intensity fires. After 1970 fires became larger and more damaging. This shift is associated with the enactment of the Bhutan Forest Act in 1969, which regulated grazing and implemented a policy of strict fire exclusion in government-reserved forests. This led to large build-ups of fuels, particularly after La Niña years. The ubiquity of ignition sources and strong rainfall seasonality ensured that fire could occur in most years. However, the change in forest policy and local community activities in the forests altered the amount and connectivity of fuels within the landscape, reshaping the fire regime in the chir pine forests of eastern Bhutan.
The Association Between CYP7B1 and Diabetes in Prostate Cancer patients (DIAMOND study)
Authors: Russo Giorgio Ivan , Durukan Emil , Broggi Giuseppe , Asmundo Maria Giovanna , Giudice Arturo Lo , Salzano Serena , Cimino Sebastiano , Morgia Giuseppe , Fode Mikkel , Caltabiano Rosario 
Published: August 2023

Abstract

Background: Prostate cancer (PCa) is the second most frequently diagnosed cancer in men, and the extent of CYP7B1's involvement in androgen metabolism and its impact on the progression of PCa is still uncertain. The aim of this study is to investigate the role of the CYP7B1 enzyme in prostate cancer aggressiveness.
Methods: A retrospective analysis was performed on 390 patients with prostate cancer (PCa) or benign prostatic hyperplasia (BPH) at the Department of Urology, University of Catania, where we examined CYP7B1 protein expression through immunohistochemical analysis in malignant and benign prostatic tissue. We investigated the interactions between CYP7B1 expression and proteins associated with PCa and metabolic processes, followed by an analysis of the risk of biochemical recurrence based on CYP7B1 expression.
Results: Among 286 patients with PCa and 104 patients with BPH, CYP7B1 expression was higher in malignant tissue. Of the 139 patients with elevated CYP7B1 expression, 92.8% had prostate cancer. Logistic regression revealed significantly higher positive scores for IR-α (OR 5.73, CI: 2.77-11.84, p < 0.01), IR-β (OR 6.61, CI: 2.19-19.96, p < 0.01), SRSF-1 (OR 2.04, CI: 1.27-3.29, p < 0.01), FAS (OR 2.15, CI: 1.28-3.62, p < 0.01), PSMA (OR 1.66, CI: 1.04-2.66, p = 0.03), and ACC-1 (OR 1.83, CI: 1.14-2.93, p = 0.01). Overall, no increased risk of biochemical recurrence was associated with CYP7B1 expression. However, in a non-diabetic subgroup analysis, higher CYP7B1 expression indicated a higher risk of biochemical recurrence with HR of 1.78 (CI: 1.0-3.2, p = 0.05).
Conclusion: PCa is associated with elevated CYP7B1 expression. In a subgroup of non-diabetic patients, elevated CYP7B1 expression was associated with increased risk of biochemical recurrence, suggesting increased cancer aggressiveness.
Convolutional neural networks from the perspective of the problems of multivalued logic
Authors: Vitulyova Yelizaveta S , Matrassulova Dinara , SULEIMENOV IBRAGIM , Bakirov Akhat 
Published: August 2023

Abstract
It is shown that it is possible to reduce the operations performed by convolutional neural networks to algebraic, and then to operations of multivalued logic. The tool for this is signal models, which are functions that take values in Galois fields and algebraic rings. This approach, among other things, allows us to switch to the use of partial convolutions, which significantly simplify the analysis of digital signals and images. Such convolutions are performed directly in terms of Galois fields, which makes it possible to use a digital analogue of the classical convolution theorem. The advantage in this regard is the possibility of using a digital analogue of transfer functions, because in terms of Fourier-Galois spectra, the convolution operation is reduced to the multiplication operation by the transfer function. This, in turn, allows us to exhaustively describe a convolutional neural network through a set of transfer functions that take values in Galois fields. The close connection between Galois fields and multivalued logics makes it possible to describe the functioning of convolutional neural networks using variables of multivalued logic.
The real-world outcomes of multiple myeloma treated with elotuzumab, pomalidomide, and dexamethasone
Authors: Nakayama Hitomi , Aisa Yoshinobu , Ito Chisako , Sakurai Aki , Kurosawa Shuhei , Nakazato Tomonori 
Published: August 2023

Abstract
Background
We present the outcome of relapsed/refractory multiple myeloma (RRMM) patients heavily pre-treated who received a combination of elotuzumab, pomalidomide, and dexamethasone (EPd) outside of clinical trials to evaluate the safety and efficacy of this combination in a real-world setting.
Patients and Methods
The medical records of 22 patients who received EPd for RRMM at our institution between January 2020 and July 2021 were reviewed.
Results
The median age was 73.5 years. The overall response rate was 55%. With a median follow-up of 20.2 months, the median progression-free survival (PFS) was 9.1 months (95% confidence interval [CI], 2.5–23.0 months). The median PFS was shorter in patients with a poor performance status (PS) than in those with favorable PS (2.5 vs. 10.8 months; P<0.01). Patients with prior daratumumab had significantly shorter PFS than those without prior daratumumab (2.1 vs. 23.0 months; P<0.01). In the multivariate analysis, poor PS (hazard ratio [HR]=4.1, 95% CI: 1.1–15.6; P=0.04) and prior exposure to daratumumab (HR=3.8, 95% CI: 1.1–13.8; P=0.04) remained significantly associated with shorter PFS.
Conclusions
Our results suggest that EPd is an active and well-tolerated regimen in RRMM, even in real-world patients. Furthermore, EPd may be useful, especially in daratumumab-naïve patients.
Porphyry Copper Prospectivity using Machine Learning Methods: A Case Study of the Shahr-e-Babak Prospecting Area, South Eastern Iran
Authors: Jahantigh Moslem , Ramazi Hamidreza 
Published: August 2023

Abstract
Mineral prospectivity modelling (MPM) is an essential step in reducing cost and time at the reconnaissance stage of mineral exploration. In this paper, the MPM was conducted in the Shahr-e-Babak study area for porphyry copper prospectivity. For achieving this goal, the evidential layers, including geology, remote sensing, airborne geophysics, geochemistry, and elevation model, were used as the input of training models. Four machine learning methods, consisting of multilayer perceptron (MLP), Adaptive neuro fuzzy inference system (ANFIS), random forest (RF), and generalized regression neural network (GRNN), were used to generate the models. Then, the fractal method and the prediction area plot were applied to evaluate the models. The models were divided into low potential, moderate potential, and high potential zones. The effective weight of evidential layers was extracted using the P-A plot method. The weight of Cu anomalies, phyllic, argillic and iron oxide alterations, elevation data, PC1 geochemical anomalies, magnetic anomalies, and subvolcanic bodies were 0.71, 0.62, 0.49, 0.4, 0.32, 0.25, 0.25 and -0.49, respectively. In the next step, the weights were extracted for MLP, ANFIS, RF, and GRNN as 0.85, 0.78, 1.26, and 0.76, respectively. The statistical correlation coefficients between argillic, phyllic, and iron oxide alterations were calculated. In the final step, an integrated model was generated using machine learning methods. Then, the integrated model was divided into low, moderate, and high potential zones based on the fractal method. Favorable areas are located in the western and eastern parts of the study area based on the integrated model.
A conserved signaling axis integrates conflicting environmental drought and heat signals to control stomatal aperture in plants
Authors: De Smet Ive , Xu Xiangyu , Praat Myrthe , Pizzio Gaston , Jiang Zhang , Driever Steven , Wang Ren , de Cotte Brigitte van , Villers Selwyn , Gevaert Kris , LEONHARDT Nathalie , Nelissen Hilde , Kinoshita Toshinori , Vanneste Steffen , Rodriguez Pedro , Zanten Martijn van , Vu Lam 
Published: August 2023

Abstract
Plants continuously respond to changing environmental conditions to prevent damage and maintain optimal performance. To regulate gas exchange with the environment and to control abiotic stress relief, plants have pores in their leaf epidermis, called stomata 1. Multiple environmental signals affect the opening and closing of these stomata 2. Heat promotes stomatal opening (to cool down) and drought induces stomatal closing (to prevent water loss). Coinciding stress conditions, however, may evoke conflicting stomatal responses, but the cellular mechanisms to resolve these conflicts are unknown. Here, we demonstrate that the high temperature-associated kinase TARGET OF TEMPERATURE 3 (TOT3) directly controls the activity of plasma membrane H+-ATPases to induce stomatal opening. This TOT3 activity is directly antagonized by OPEN STOMATA 1 (OST1), to prevent water loss during drought stress. This signaling axis harmonizes conflicting heat and drought signals to regulate stomatal aperture. In the context of global climate change, understanding how conflicting stress signals converge on stomatal regulation allows the development of climate change-ready crops.
Association of gut microbiota with dyslipidemia and chronic coronary syndrome patients undergoing coronary angiography
Authors: Luangphiphat Wongsakorn , Prombutara Pinidphon , Muangsillapasart Viroj , Sukitpunyaroj Damrong , Eeckhout Eric , Taweechotipatr Malai 
Published: August 2023

Abstract
Chronic coronary syndrome (CCS) has a high mortality rate, and dyslipidemia is a major risk factor. Atherosclerosis, a cause of CCS, is influenced by gut microbiota dysbiosis and its metabolites. We aimed to study the diversity and composition of gut microbiota and related clinical parameters among CCS patients undergoing coronary angiography and dyslipidemia patients in comparison to healthy volunteers in Thailand. We reported that CCS patients had more risk factors and higher inflammatory marker, high-sensitivity C-reactive protein (hs-CRP) than others. We showed that the alpha diversity was lower in dyslipidemia and CCS patients than in the healthy group. A significant difference in the composition of gut microbiota was observed among the three groups. The relative abundance of Proteobacteria, Fusobacteria, Enterobacteriaceae, Prevotella and Streptococcus were significantly increased while Roseburia, Ruminococcus and Faecalibacterium were lower in CCS patients. In CCS patients, Lachnospiraceae, Peptostreptococcaceae and Pediococcus were positively correlated with hs-CRP. In dyslipidemia patients, Megasphaera was strongly positively correlated with triglyceride (TG) level and negatively correlated with high-density lipoprotein cholesterol (HDL-C). The modification of gut microbiota was associated with changes in clinical parameters involved in the development of coronary artery disease (CAD) in CCS patients.
Exclusive Radio±chemoTherapy versus upfront Surgery in the treatment of HPV-related localized or locally ADvanced Oropharyngeal squamous cell Carcinoma (RT-SHADOC): a tricentric study of efficacy, tolerance and quality of life
Authors: Baude Jérémy , Guigou Caroline , Thibouw David , Vulquin Noémie , Folia Mireille , Constantin Guillaume , Boustani Jihane , Duvillard Christian , Ladoire Sylvain , Truc Gilles , Bertaut Aurélie , Chevalier Cédric 
Published: August 2023

Abstract
Background The treatment of stage I-III HPV + oropharyngeal squamous cell carcinoma (HPV-OPSCC) is based on either surgery ± adjuvant therapy or exclusive radio ± chemotherapy. We sought to compare these two therapeutic strategies in terms of efficacy, tolerance and quality of life (QoL).Methods Patients treated for stage I-III HPV-OPSCC from 2010 to 2021in 3 academic centers were included and sorted according to the treatment strategy: surgery or exclusive radio ± chemotherapy. Efficacy and tolerance were retrospectively assessed, and QoL was prospectively evaluated using QoL assessment instruments.Results Eighty-three patients were included, 21 underwent surgery and 62 definitive radio-±chemotherapy. 2-year progression-free survival (PFS) and overall survival (OS) were respectively 80% and 86% in the surgical group and 92% and 95% in the non-surgical group, with no significant difference. At the end of treatment, 64.5% of patients presented a grade III symptom, without significant difference between the two groups. No patient had late grade III toxicity at 24 months. Forty-five patients (11 in the surgical group, 34 in the nonsurgical group) participated in the prospective quality-of-life analysis. Patients reported significantly more fatigue and loss of appetite after surgery, whereas patients in the radio ± chemotherapy group described significantly more salivary and oral problems and difficulty swallowing. The global quality of life score tended to be better in the radio ± chemotherapy group (EORTC QLQ-C30 77.6 vs 65.2, p = 0.07).Conclusion No significant difference in terms of efficacy, physician-reported toxicity and patient-reported quality of life was found between surgery and radio ± chemotherapy in the treatment of stage I-III HPV-OPSCC.
Integrating Behavioral Health Services into Primary Care Clinics within a Large Public Healthcare System: Provider Satisfaction and Patient Outcomes
Authors: Miller Emily K. , O’Donnell Kari , Fiegl Jordan , Berko Eric , Leon Janeen , Kaelber David C. , Luca Susan 
Published: August 2023

Abstract

Background: Behavioral health integration within primary care has demonstrated improved access to mental health services, patient outcomes, and satisfaction with care. This pre-post, mixed-methods quality improvement study examined factors of healthcare provider satisfaction in 10 integrated behavioral health (IBH) clinics in a Midwestern public healthcare system. This study also examined implementation indicators, including referral rates, scheduling time from referral to initial behavioral health encounter, and emergency department (ED) utilization to better understand patient experiences and outcomes.
Methods: Providers were asked to complete online pre- and post-surveys (n = 110 patients, n = 115 patients, respectively) related to provider satisfaction with IBH services between October 2021 and April 2022. All other analyses were completed using electronic health record (EHR) patient data corresponding to IBH implementation across the 10 sites (pre-integration n = 42,397 patients, post-integration n = 37,129 patients).
Results: Increases in organizational and relational scores were associated with significant improvements in provider satisfaction scores. Additionally, the results showed a significant increase in referrals to behavioral health in the post-integration period and a significant reduction in days to a behavior health appointment in the post-integration timeframe. Finally, ED utilization dropped from pre- to post-integration, but this was not statistically significant. Analysis of opened-ended questions revealed two main themes: positive regard for the value of IBH and structural and organizational barriers to IBH.
Conclusions: Findings suggest that IBH implementation resulted in improvements in some areas of patient care and coordination and, importantly, points to areas where even more improvement is needed. This study highlights the value of collaboration among different providers toward creating a more supportive primary care environment for the patient.
Daily streamflow of Argentinian rivers analysis using information theory quantifiers.
Authors: Suriano Micaela , Caram Leonidas Facundo , Rosso Osvaldo Anibal 
Published: August 2023

AbstractThis paper analyzes the temporal evolution of the streamflow for different rivers in Argentina, based on information quantifiers such as statistical complexity and permutation entropy. The main objective is to identify essential details of the dynamics of the processes to differentiate the degrees of randomness and chaos. The permutation entropy is used with the probability distribution of Ordinal Patterns and the Jensen-Shannon divergence to calculate the disequilibrium and then the statistical complexity. Daily streamflow series at different river stations were analyzed to classify the different hydrological systems. The Complexity Entropy Causality Plane (CEPC) and the representation of the Shannon Entropy and Fisher Information Measure (FIM) show that the daily discharge series could be represented approximately with Gaussian noise, but the variances highlight the difficulty of modeling a series of natural phenomena. An analysis of stations downstream from the Yacyretá dam shows that the operation affects the randomness of the daily discharge series in hydrometric stations near the dam, but when the station is further downstream this effect is attenuated. The size of the basin plays a relevant role in modulating the process, large catchments have smaller values for entropy and the signal is less noisy due to integration over larger time scales. The small and mountain basins present a rapid response that influences the behavior of daily discharge while presenting a higher entropy and lower complexity. The results obtained characterize the behavior of the daily discharge series in Argentinian rivers and provide key information for hydrological modeling.