bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of pulmonary rehabilitation duration on exercise capacity and health‐related quality of life in people with chronic obstructive pulmonary disease (PuRe Duration Trial): A randomized controlled equivalence trial
Authors: Bishop Joshua A. , Spencer Lissa M. , Dwyer Tiffany J. , McKeough Zoe J. , McAnulty Amanda , Leung Regina , Alison Jennifer A. 
Published: September 2024

AbstractBackground and ObjectiveThere is no strong evidence on the optimal duration of pulmonary rehabilitation (PR) programmes. The aim of the study was to determine whether an 8‐week PR programme was equivalent to a 12‐week PR programme in improving endurance exercise capacity in people with chronic obstructive pulmonary disease (COPD).MethodsParticipants with COPD were randomized to either an 8‐week (8‐wk Group) or 12‐week (12‐wk Group), twice weekly, supervised PR programme consisting of endurance and strength training and individualized self‐management education. Between group comparisons were made at completion of each programme (i.e., week 8 or week 12), for both programmes at week 12, and at 6–12‐month follow‐up. The primary outcome was endurance exercise capacity measured by the endurance shuttle walk test (ESWT) with the minimally important difference of 186 s set as the equivalence limit.ResultsSixty‐six participants [mean (SD); age 69 (7) years, FEV1 48 (17) %predicted] were randomized (33 per group). Between‐group comparisons demonstrated that the ESWT time was equivalent for the 12‐wk Group compared to the 8‐wk Group at programme completion [mean (95% CI)] [71 s (−61 to 203)], week 12 [70 s (−68 to 208)], and 6–12‐month follow‐up [93 s (−52 to 239)], though superiority of the 12‐wk Group could not be ruled out at each time point.ConclusionEquivalence was shown between 8‐and 12‐week PR programmes for endurance exercise capacity, but superiority could not be ruled out for the 12‐wk Group. Decisions about programme duration may depend on local waitlist times, healthcare budgets and patient preference.
Parametric Modeling Method for 3D Symbols of Fault Structures
Authors: Li An‐Bo , Chen Hao , Xie Xian‐Li , Lü Guo‐Nian , Fox Matthew 
Published: September 2024

ABSTRACTAs the research and application of three‐dimensional (3D) Geographic Information Science (GIS) continue to advance, the abstract representation and symbolic modeling of geological entities in three dimensions have become one of the research focuses in the current GIS field. To address the need for the symbolic representation of complex and diverse fault structures, this paper proposes a parametric modeling method for 3D fault symbols. This method includes (1) constructing a 3D stratum model and a fault plane model based on stratum and fault plane parameters, (2) performing a 3D cutting operation based on the fault plane model to generate the fault block model, and (3) translating the strata in two faultblocks according to the parameters of fault motion to generate a fault symbol model. The experimental results show that the proposed method requires only a small number of parameters to efficiently and intuitively construct diverse 3D fault symbol models. This method breaks through the excessive dependence on geological survey data in the process of 3D geological modeling. It is suitable for 3D geological symbol modeling of folds, joints, intrusions, and other geological structures, as well as 3D modeling of typical geological structures with relatively simple spatial morphology. This paper's parametric modeling method has essential research significance and application value in various applications such as digital earth, digital city, and virtual geoscience exploration.
Machine learning analysis of contrast-enhanced ultrasound (CEUS) for the diagnosis of acute graft dysfunction in kidney transplant recipients
Authors: Moisoiu Tudor , Elec Alina Daciana , Muntean Adriana Milena , Badea Alexandru Florin , Budusan Anca , Stancu Bogdan , Iacob Gheorghiță , Oana Antal , Andries Alexandra , Zaro Razvan , Socaciu Mihai A. , Badea Radu Ion , Oniscu Gabriel C. , Elec Florin Ioan 
Published: September 2024

Aim: The aim of the study was to develop machine learning algorithms (MLA) for diagnosing acute graft dysfunction (AGD) in kidney transplant recipients based on contrast-enhanced ultrasound (CEUS) analysis of the graft.Materials and methods: This prospective study involved 71 patients with kidney transplant undergoing CEUS during follow-up. AGD wasdefined as an increase in serum creatinine levels of at least 25% compared to the baseline of the last three months. The control group consisted of patients with stable kidney graft function (SGF). The top five CEUS parameters that achieved the best discrimination between the AGD and SGF groups were selected based on ANOVA testing and then employed as input for training MLA (naïve Bayes (NB), k-nearest neighbors (k-NN), and logistic regression (LR)). The models were validated by leave-one-out cross-validation.Results: Among the 111 CEUS analyses, 21 corresponded to the AGD group and 90 to the SGF group. CEUS analyses yielded 44 parameters, from which five were selected: the wash out rate in segmental arteries,time to peak in segmental arteries, medullary mean transit time, renal mean transit time, and medullary time to fall. These five parameters were employed as input for MLA, yielding an AUROC of 0.68 for NB and k-NN and 0.72 for LR. The inclusion of graft survival in the MLA significantly improved discrimination accuracy, yielding an AUROC of 0.79 for NB, 0.76 for k-NN,and 0.81 for LR.Conclusions: The use of MLA represents a promising strategy for analyzing CEUS-derived parameters in the setting AGD.
Discovery of new acetamide derivatives of 5-indole-1,3,4-oxadiazol-2-thiol as inhibitors of HIV-1 Tat-mediated viral transcription
Authors: Shin YoungHyun , Park Chul Min , Kim Dong-Eun , Kim Sungmin , Lee Sang-Yeop , Lee Jun Young , Jeon Won-Hui , Kim Hong Gi , Bae Songmee , Yoon Cheol-Hee 
Published: September 2024

ABSTRACT

Human immunodeficiency virus-1 (HIV-1) encodes a transcriptional factor called Tat, which is critical for viral transcription. Tat-mediated transcription is highly ordered apart from the cellular manner; therefore, it is considered a target for developing anti-HIV-1 drugs. However, drugs targeting Tat-mediated viral transcription are not yet available. Our high-throughput screen of a compound library employing a dual-reporter assay identified a 1,3,4-oxadiazole scaffold against Tat and HIV-1 infection. Furthermore, a serial structure–activity relation (SAR) study performed with biological assays found 1,3,4-oxadiazole derivatives (
9
and
13
) containing indole and acetamide that exhibited potent inhibitory effects on HIV-1 infectivity, with half-maximal effective concentrations (EC
50
) of 0.17 (
9
) and 0.24 µM (
13
), respectively. The prominent derivatives specifically interfered with the viral transcriptional step without targeting other infection step(s) and efficiently inhibited the HIV-1 replication cycle in the T cell lines and peripheral blood mononuclear cells infected with HIV-1. Additionally, compared to the wild type, the compounds exhibited similar potency against anti-retroviral drug-resistant HIV-1 strains. In a series of mode-of-action studies, the compounds inhibited the ejection of histone H3 for facilitating viral transcription on the long-terminal repeat (LTR) promoter. Furthermore, SAHA (a histone deacetylase inhibitor) treatment abolished the compound potency, revealing that the compounds can possibly target Tat-regulated epigenetic modulation of LTR to inhibit viral transcription. Overall, our screening identified novel 1,3,4-oxadiazole compounds that inhibited HIV-1 Tat, and subsequent SAR-based optimization led to the derivatives
9
and
13
development that could be a promising scaffold for developing a new class of therapeutic agents for HIV-1 infection.
Non-invasive multimodal CT deep learning biomarker to predict pathological complete response of non-small cell lung cancer following neoadjuvant immunochemotherapy: a multicenter study
Authors: Ye Guanchao , Wu Guangyao , Qi Yu , Li Kuo , Wang Mingliang , Zhang Chunyang , Li Feng , Wee Leonard , Dekker Andre , Han Chu , Liu Zaiyi , Liao Yongde , Shi Zhenwei 
Published: September 2024

ObjectivesAlthough neoadjuvant immunochemotherapy has been widely applied in non-small cell lung cancer (NSCLC), predicting treatment response remains a challenge. We used pretreatment multimodal CT to explore deep learning-based immunochemotherapy response image biomarkers.MethodsThis study retrospectively obtained non-contrast enhanced and contrast enhancedbubu CT scans of patients with NSCLC who underwent surgery after receiving neoadjuvant immunochemotherapy at multiple centers between August 2019 and February 2023. Deep learning features were extracted from both non-contrast enhanced and contrast enhanced CT scans to construct the predictive models (LUNAI-uCT model and LUNAI-eCT model), respectively. After the feature fusion of these two types of features, a fused model (LUNAI-fCT model) was constructed. The performance of the model was evaluated using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, positive predictive value, and negative predictive value. SHapley Additive exPlanations analysis was used to quantify the impact of CT imaging features on model prediction. To gain insights into how our model makes predictions, we employed Gradient-weighted Class Activation Mapping to generate saliency heatmaps.ResultsThe training and validation datasets included 113 patients from Center A at the 8:2 ratio, and the test dataset included 112 patients (Center B n=73, Center C n=20, Center D n=19). In the test dataset, the LUNAI-uCT, LUNAI-eCT, and LUNAI-fCT models achieved AUCs of 0.762 (95% CI 0.654 to 0.791), 0.797 (95% CI 0.724 to 0.844), and 0.866 (95% CI 0.821 to 0.883), respectively.ConclusionsBy extracting deep learning features from contrast enhanced and non-contrast enhanced CT, we constructed the LUNAI-fCT model as an imaging biomarker, which can non-invasively predict pathological complete response in neoadjuvant immunochemotherapy for NSCLC.
Duodenal–Jejunal Bypass Restores Sweet Taste Receptor‐Mediated Glucose Sensing and Absorption in Diabetic Rats
Authors: Sun Sipeng , Wang Anping , Kou Rongguan , Xue Hantao , Zhao Xiangyu , Yang Ben , Shi Mengqi , Wang Yubing , Yan Qingtao , Qu Meihua , Wang Yi , Gao Zhiqin 
Published: September 2024

Aim: The aim of the study is to identify the regulatory role of intestinal sweet taste receptors (STRs) and glucose transporters (SGLT1, GLUT2) and gut peptide secretion in duodenal–jejunal bypass (DJB)–ameliorated glycemic control in Type 2 diabetes.Materials and Methods: DJB and sham surgeries were performed in streptozotocin‐induced diabetic male rats. The blood GLP‐1 and GLP‐2 levels were evaluated under feeding and fasting conditions. The expression of STRs (T1R2, T1R3), sweet taste signaling effector (Gα‐gustducin), SGLT1, and GLUT2 was detected in the intestinal alimentary limb (A limb), biliopancreatic limb (BP limb), and common limb (C limb). The effects of STR inhibition on glucose control were measured with lactisole.Results: Glucose tolerance was improved in DJB‐operated rats compared with the sham group, similar to that of normal control rats, without significant differences in food intake and body weight. The plasma GLP‐1 levels of DJB rats were increased under diet‐fed condition, and GLP‐2 levels were increased after fasting. The villus height and crypt depth were significantly increased in the A limb of DJB‐operated rats. In addition, GLP‐1 expression was restored in enterocytes. The expression of T1R2, Gα‐gustducin, and SGLT1 was elevated in the A limb after DJB, while GLUT2 was downregulated in the A, BP, and C limbs. The localization of GLUT2 was normalized in the three intestinal limbs after DJB. However, the beneficial effects of DJB on glucose control were abolished in the presence of lactisole in vivo.Conclusion: DJB ameliorates glycemic control probably by restoring STR‐mediated glucose sensing and absorption with the responses of GLP‐1 and GLP‐2 to carbohydrate.
ARID1A-Deficient Tumors Acquire Immunogenic Neoantigens during the Development of Resistance to Targeted Therapy
Authors: Okada Masahiro , Yamasaki Satoru , Nakazato Hiroshi , Hirahara Yuhya , Ishibashi Takuya , Kawamura Masami , Shimizu Kanako , Fujii Shin-ichiro 
Published: September 2024

Abstract
Neoantigen-based immunotherapy is an attractive potential treatment for previously intractable tumors. To effectively broaden the application of this approach, stringent biomarkers are crucial to identify responsive patients. ARID1A, a frequently mutated subunit of SWI/SNF chromatin remodeling complex, has been reported to determine tumor immunogenicity in some cohorts; however, mutations and deletions of ARID1A are not always linked to clinical responses to immunotherapy. In this study, we investigated immunotherapeutic responses based on ARID1A status in targeted therapy-resistant cancers. Mouse and human BRAFV600E melanomas with or without ARID1A expression were transformed into resistant to vemurafenib, an FDA-approved specific BRAFV600E inhibitor. Anti-PD-1 antibody treatment enhanced antitumor immune responses in vemurafenib-resistant ARID1A-deficient tumors but not in ARID1A-intact tumors or vemurafenib-sensitive ARID1A-deficient tumors. Neoantigens derived from accumulated somatic mutations during vemurafenib resistance were highly expressed in ARID1A-deficient tumors and promoted tumor immunogenicity. Furthermore, the newly generated neoantigens could be utilized as immunotherapeutic targets by vaccines. Finally, targeted therapy resistance–specific neoantigen in experimental human melanoma cells lacking ARID1A were validated to elicit T-cell receptor responses. Collectively, the classification of ARID1A-mutated tumors based on vemurafenib resistance as an additional indicator of immunotherapy response will enable a more accurate prediction to guide cancer treatment. Furthermore, the neoantigens that emerge with therapy resistance can be promising therapeutic targets for refractory tumors.
Significance: Chemotherapy resistance promotes the acquisition of immunogenic neoantigens in ARID1A-deficient tumors that confer sensitivity to immune checkpoint blockade and can be utilized for developing antitumor vaccines, providing strategies to improve immunotherapy efficacy.
Dimensions: Calculating disruption indices at scale
Authors: Sixt Joerg , Pasin Michele 
Published: September 2024

Abstract
Assessing the disruptive nature of a line of research is a new area of academic evaluation that moves beyond standard citation-based metrics by taking into account the broader citation context of publications or patents. The “CD index” and a number of related indicators have been proposed in order to characterize the disruptiveness of scientific publications or patents. This research area has generated a lot of attention in recent years, yet there is no general consensus on the significance and reliability of disruption indices. More experimentation and evaluation would be desirable, but it is hampered by the fact that the calculation of these indicators is time-consuming, especially if done at scale on large citation networks. We present a novel SQL-based method to calculate disruption indices for the Dimensions publications data on Google BigQuery. This reduces the computational time taken to produce such indices by an order of magnitude, as well as making available such functionalities within an online environment that requires no setup efforts. We explain the novel algorithm and describe how its results align with preexisting implementations of disruption indicators. This method will enable researchers to develop, validate, and improve disruption models more quickly and with more precision.
2. De Morgan and Logic
Authors: Heinemann Anna-Sophie 
Published: September 2024

From 1847 onwards, Augustus De Morgan propounded an extension of classical syllogistic logic by the introduction of ‘contraries’. These are negative terms in the sense that, for example, x means non-x within a given ‘universe’. In this chapter, we will focus on De Morgan’s early research on logic between 1847 and 1850, and address De Morgan’s revisions of traditional syllogistic logic in his ‘system of contraries’ and his ‘numerically definite system’. We will discuss his approach to determining portions of ‘universes’, which is based on determining extensions by numbers of instances of terms. The main point will be that De Morgan conceived of logical quantities as scopes and of conjunctive or disjunctive enumeration as quantifications over given domains—which is one of the systematic reasons behind his being involved in a long-lasting debate over the ‘quantification of the predicate’. It will be argued that, despite its relative lack of influence on later developments, De Morgan’s work still represented a notable departure from traditional syllogistic methods and anticipated the modern understanding of quantification in logic.
3. Augustus De Morgan, Astronomy and Almanacs
Authors: Belteki Daniel 
Published: September 2024

Augustus De Morgan never identified himself as an astronomer, and blindness in one eye rendered him unable to make reliable observations with astronomical instruments. Yet he participated actively in the British astronomical community during the mid-nineteenth century, becoming involved as Secretary of the Royal Astronomical Society in major events and controversies that shaped both British and international astronomical practice during the 1840s, and making himself through his writings an authoritative ‘expounder and historian’ of astronomy and its instruments.
This chapter revisits De Morgan’s interest in astronomy and his close relationships with leading astronomers of the nineteenth century. It discusses his activities as a writer, arguing that while he raised awareness of history’s forgotten and overlooked astronomers, his publications also reaffirmed the contemporary and historical boundaries of the astronomical community. Finally, it examines De Morgan’s writings about calendrical reforms and an apparent paradox regarding the determination of the date of Easter, to demonstrate how he combined his interests in antiquarianism, ecclesiastical and legal history with his knowledge of mathematics and astronomy to participate in a debate of interest to the wider public.
4. De Morgan, Periodicals and Encyclopaedias
Authors: Bruneau Olivier 
Published: September 2024

Through his many books and publications in various periodicals, Augustus De Morgan was a disseminator of mathematics, particularly to the general public. An active member of the Society for the Diffusion of Useful Knowledge, founded by the same people who established University College London, De Morgan was also a great promoter of mathematics via its publications. The most striking example is his significant involvement as a contributor to the Penny Cyclopaedia (27 vols., 1833-1843), for which he authored more than 700 articles on mathematics and astronomy, some of which are very long.
In this chapter we propose to contextualise these articles by comparing them with the mathematical production in other encyclopedic works of the time, such as the well-known Encyclopaedia Brittanica (with its several editions), Rees’ Encyclopaedia (1802-1820), the Edinburgh Encyclopaedia (1808-1830) and the Encyclopedia Metropolitana (1845). Through this comparative study, we will give an overview of De Morgan’s scholarly and journalistic output, showing the extent of his writings for a general audience, and revealing him to have been one of early Victorian Britain’s most prolific and gifted mathematical expositors.
Irrigation Effects on Regional Circulation and Climate in the U.S. Great Plains: A Case Study
Authors: Hu Qi , Achugbu Ifeanyi Chukwudi , Chen Liang 
Published: September 2024

Abstract
Observations have indicated that compared to the six decades before 1960, the frequency of dry summers in the U.S. Great Plains was lowered by 20% in the six decades after 1960. In the meantime, there was a sharp increase in the recent six decades in both the rate and coverage of groundwater irrigation in the region repeated every summer for agricultural production. The potential effect of irrigation on the changes of growing season precipitation in the Great Plains is examined in this study using models from the perspective of regional circulation and climate, broadened from prior studies of irrigation effects focused on changes of specific weather elements. As the first step, the dry year of 2012 is used in this case study to minimize wet circulation impacts and also the possibility for the irrigation effect being skewed by decadal variations/trends in climate itself. It is found that massive irrigation in the Great Plains does not alter the frequency and duration of individual precipitation events. Irrigation does, however, modify the regional thermodynamic properties of the atmosphere enough to amplify the precipitation rate and amount in most weather events. In addition to these direct effects, irrigation further influences large-scale circulations, especially the Great Plains low-level jet (GPLLJ) and, through them, indirectly affects the growing season climate in the irrigated region. Analysis of physical processes explains the weakening of the GPLLJ and reduction of its northward moisture flux by irrigation. Budget analysis shows that this negative indirect effect of irrigation on moisture and precipitation is surpassed by the direct effect in the irrigated region, resulting in a net increased precipitation rate for individual rainfall events.
Plasmin generation analysis in patients with bleeding disorder of unknown cause
Authors: Mehic Dino , Reitsma Stéphanie E. , de Moreuil Claire , Haslacher Helmuth , Koeller Maximilian C. , de Laat Bas , Ay Cihan , Pabinger Ingrid , Wolberg Alisa S. , Gebhart Johanna 
Published: September 2024

Abstract
Bleeding disorder of unknown cause (BDUC) is a diagnosis of exclusion after evaluation of plasma coagulation and platelet function. Patients with BDUC (n = 375) recorded in the Vienna Bleeding Biobank were analyzed in comparison with healthy controls (HCs; n = 100) in this case-control study. Plasmin generation (PG) parameters were analyzed using calibrated fluorescence detection in citrated plasma. Turbidimetric plasma clot formation/lysis of 293 (78%) patients with BDUC and confocal microscopy of clots from representative patients with BDUC (n = 6) and HCs (n = 9) were assessed. In the PG analysis, patients with BDUC exhibited lower velocity and peak plasmin levels but a higher endogenous plasmin potential than HCs. Peak plasmin levels correlated with maximum clot absorbance but not with clot lysis time. Clot absorbance is an indicator of clot fiber density. Confocal microscopy analysis revealed a tendency towards thicker fibers in clots of patients with BDUC, which negatively correlated with peak plasmin (r = −0.561; P = .030). Peak plasmin correlated weakly with factor XIII, but not with other fibrinolytic factors (alpha2-antiplasmin, thrombin activatable fibrinolysis inhibitor, or plasminogen activator inhibitor 1) or bleeding severity. A model comprising fibrinogen and parameters of PG yielded high predictive power in discriminating between patients with BDUC and HCs across a fivefold stratified cross validation (80% of data; mean area under the curve [AUC], 0.847). The model generalized well to unseen data (20% of data; AUC, 0.856). Overall, patients with BDUC counterintuitively exhibited reduced peak plasmin levels, potentially related to altered clot structure.