bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of the Geophysical Strata Rating in Sedimentary Environments
Authors: Medhurst TP 
Published: December 2024

Abstract
The Geophysical Strata Rating (GSR) is an empirical rock mass classification method based on the estimation of clay content, porosity and P-wave velocity from geophysical logs. It was first developed in 2005 for the Australian mining industry and is now routinely used in many operating mines. By allowing a continuous estimate of rock mass quality along the borehole column 3D geotechnical models can be developed for a range of planning and design purposes. The availability of these models provides a means to develop relationships between ground conditions and ground behaviour that can be back analysed and verified. This has allowed several new design methods to be developed to assist in the geotechnical management process such as ground support design, prediction of caving behaviour and stability of shafts. The characterisation models can be used for a range of applications such as porosity/permeability variations within the strata and is particularly useful for delineation of stress related impacts in deep mines. This paper outlines the basic premise of the GSR and provides a few examples of its application.
Rock Mass Classification in the Digital Era: A transformation in Hard Rock Tunnelling
Authors: Klein Lasse , Lehmann Gabriel , Tröndle Johannes , Benedetto Diego di 
Published: December 2024

Abstract
The construction industry has witnessed a transformative shift with the advent of digitalization, and tunnelling especially in hard rock is no exception. This study delves into the profound influence of digitalization on rock mass assessment methods employed in tunnelling endeavours. Conventional rock mass classification systems, such as the widely embraced RMR (Rock Mass Rating) and Q-system, have traditionally played a pivotal role in evaluating geological conditions and providing guidance for engineering decisions in hard rock tunnelling projects. While these systems are invaluable for project selection and execution, it is noteworthy that they may not always offer a comprehensive representation, and their applicability can be limited, especially in smaller-diameter tunnelling projects, as evidenced by experience from numerous past projects. The development in the field of machine intelligence and the connectivity of IT systems has increased significantly. The introduction of BIM and numerous independent platforms for construction companies, the processes of all project participants are becoming increasingly digitalized, with professional data management now an essential component of successful process management. Modern OT and IT interfaces make it possible to combine different data sources and to display and analyse them in data management tools. A comparison between geotechnical data and operational parameters can provide important conclusions for the further course of the project. In increasingly complex contract situations, the comparison between expected and encountered geology, in combination with real-time machine data, can be a crucial element between for all involved construction project shareholders.
Stope Dimension Analysis Based on Geomechanical Properties Using Brute Force Algorithm
Authors: Army Mohammad , Karian Tri 
Published: December 2024

Abstract
Mining operations play a crucial role in meeting global resource demands, emphasizing the importance of determining optimal stope dimensions for safe and efficient ore extraction. However, the complexity arising from multiple geomechanical factors affecting stope stability poses challenges in identifying ideal dimensions. Traditionally, engineers use an iterative process for stability analysis, but its limited scope and time-consuming nature call for more efficient algorithms. This research proposes a series of algorithms based on the brute force method using Potvin’s empirical stability criterion. The algorithm efficiently generates and evaluates stope dimension scenarios, enabling comprehensive stability analysis. Testing on case studies demonstrates its remarkable speed and effectiveness, making it a valuable tool for mine planning and optimization.
The impact of underground support and mine opening profiles on the economics of underground mining projects
Authors: Putra Danu , Karian Tri , Sulistianto Budi , Husain Taherdito Ali 
Published: December 2024

Abstract
Underground mines, particularly in the cut and fill method, require careful consideration of stope or slice dimensions and support. Determining the appropriate and efficient dimensions and mine support is crucial to ensuring mine safety. An increase in stope size affects the amount and quality of mine support needed, thus increasing the overall mining cost, which can impact the feasibility of the project. On the other hand, it can lower overall mining costs, as the amount of extracted ore increases. Optimization by implementing mining scenarios is performed to assess the impact of support costs on the economy of a mining block. This study attempts to examine the feasibility of three mining scenarios with various excavation profiles. Excavation profiles of stope cut and fill with variations of 2 mW x 2.5 mH, 3 mW x 3 mH, and 5 mW x 5 mH, further referred to as scenarios 1, 2, and 3, respectively, are established as the base scenarios for optimization. The mine support requirements were determined based on the material load per square meter of tunnel progress and the available mine support specifications. Based on the types of supported requirements in the model, the analysis groups the required support into two categories: one for scenarios 1 and 2, and another for scenario 3. The categorization was made because the possibility of using one set of mine supports for the whole scenario wasn’t possible. Scenario 3 necessitates stronger and more robust mine support, including the requirement for 18 pcs/m of dome plate type 47 (un-galvanized) and split set type 47 (un-galvanized), respectively, as well as 2 pcs of H-beam per meter of other primary support. The calculation of mine support costs was then performed and combined with other mining cost components to form the required cost parameter in the optimization process. The optimum stope shape for each scenario is then created through the optimization process using a widely known stope optimization module, Stope Shape Optimization (SSO), that is available in the Micromine educational package. The stope optimization results show the stope layout in the zone with high grade, where the total estimated reserves for each scenario are 20,482 metric tons, 30,057 metric tons, and 43,508 metric tons, with an average gold grade of 2.74 g/t, 2.73 g/t, and 2.71 g/t, respectively. Economic value calculations have also been performed on the amount of mined reserves in the optimization process, with the highest mining cost shown in scenario 1 at $1.40 million, resulting in a mining cost per ton of 59.93 $/ton. The highest revenue is obtained in scenario 3 with an economic value of $112.58 million, which is consistent with the profit of $109.17 million, indicating that scenario 3 is economically feasible.
Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae)
Authors: He Guan-Hao , Meng Ying , Zhang Meng-Hua , Wang Da , Meng Ran , Zhang Lei , Chu Zhao-Fu , Wen Jun , Nie Ze-Long 
Published: December 2024

Abstract

Background and Aims
Nekemias is a small genus of the grape family, with nine species discontinuously distributed in temperate to subtropical zones of the Northern Hemisphere but mostly in East Asia. Previous phylogenetic studies on Nekemias have mainly been based on a few chloroplast markers, and the phylogenetic framework and systematic relationships are still highly contested.

Methods
We carried out a systematic framework reconstruction of Nekemias and intra-generic reticulate evolutionary analyses based on extensive single-copy nuclear and chloroplast genomic data obtained by the Hyb-Seq approach, combining genome skimming and target enrichment.

Key Results
Both nuclear and chloroplast genomic data strongly support the monophyly of Nekemias with its division into two major lineages from East Asia and North America, respectively. There are strong and extensive topological conflicts among nuclear gene trees and between nuclear and chloroplast topologies within the genus, especially within the East Asian clade.

Conclusions
Rapid radiation through predominant incomplete lineage sorting (ILS) throughout the evolutionary history of the East Asian taxa is supported to explain the relatively high species diversity of Nekemias in East Asia. This study highlights the important role of short periods of rapid evolutionary radiations accompanied by ILS as a mechanism for the complex and fast species diversifications in the grape family as well as potentially in many other plant lineages in East Asia and beyond.
Semi-parametric local variable selection under misspecification
Authors: Rossell D , Seong A K , Saez I , Guindani M 
Published: December 2024

Abstract
Local variable selection aims to test for the effect of covariates on an outcome within specific regions. We outline a challenge that arises in the presence of nonlinear effects and model misspecification. Specifically, for common semiparametric methods even slight model misspecification can result in a high false positive rate, in a manner that is highly sensitive to the chosen basis functions. We propose a methodology based on orthogonal cut splines that avoids false positive inflation for any choice of knots, and achieves consistent local variable selection. Our approach offers simplicity, handles both continuous and categorical covariates, and provides theory for high-dimensional covariates and model misspecification. We discuss settings with either independent or dependent data. Our proposal allows including adjustment covariates that do not undergo selection, enhancing the model’s flexibility. Our examples describe salary gaps associated with various discrimination factors at different ages, and the effects of covariates on functional data measuring brain activation at different times.
Assessing the effectiveness of acoustic signals in mark-recapture studies to estimate dolphins’ population size
Authors: Papale Elena , Ceraulo Maria , Gregorietti Martina , De Vita Clarissa , Buscaino Giuseppa 
Published: December 2024

Abstract
Accurate estimations of animal population size are pivotal for implementing management strategies properly. Recapture technique based on sounds as a specimen identification mark has barely been used for marine mammals. However, inferring abundance estimates from acoustic methods could enhance the accuracy and precision of population size assessments. Here, we tested the possibility of using signature whistles as individual marks for estimating the size of common bottlenose dolphin (Tursiops truncatus) populations. Data were continuously collected for 326 days in 2015–2016, by using a fixed acoustic device located in the Sicily Strait (Italy). The SIGID method was applied to identify Signature Whistles Types (SWTs) over 7,000 h of recordings. Eighty SWTs were detected as long as their stereotyped fundamental frequency contours were repeated in bouts of at least 6 renditions. The mean SWTs monthly recording rate resulted in 0.19 (Standard deviation = 0.16), with 20 SWTs recorded over 5 or more different encounters (until a maximum of 30 encounters). The Jolly–Seber model (with POPAN formulation) was run in Mark software to estimate the population size. The estimated population size resulted in 171 bottlenose dolphins (95% confidence interval = 137–215). Even if the detection and identification of signature whistles required crucial precautions, and animals could be detected differently from visual techniques, the population size estimate obtained was comparable with previous results based on physical marks data. These outcomes demonstrated that signature whistles can be considered a strongly effective tool for integrating traditional mark-recapture techniques with finely estimated dolphins’ population abundances.
Loving Life? Loving Science? Quality of Life Perceptions Predict Public Attitudes Toward Science
Authors: Fuglsang Simon 
Published: December 2024

Abstract
This study explores a previously unstudied avenue of understanding public attitudes toward science, suggesting that perceived quality of life predicts science attitudes. This relationship is investigated in two cross-national surveys, the Special Eurobarometer 516 and the World Values Survey round 7. As a theoretical basis for the relationship, three mechanisms are proposed; that people employ quality of life perceptions as an evaluative tool for gauging the success of science, affective spillover between individual concerns and science attitudes, and expected exclusion from science based on life circumstance. Across measures of quality of life perceptions, and across the clear majority of countries investigated, higher quality of life perceptions are positively related to promise of science (societal impact), but not to reservations about science (moral and social consequences).
Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer
Authors: Junca Howard , Steube Arndt , Mrowietz Simon , Stallhofer Johannes , Vital Marius , dos Anjos Borges Luiz Gustavo , Pieper Dietmar H , Stallmach Andreas 
Published: December 2024

Abstract
Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population
Authors: Takano Sotaro , Umetani Miki , Nakaoka Hidenori , Miyazaki Ryo 
Published: December 2024

Abstract
Most of the microbes in nature infrequently receive nutrients and are thus in slow- or non-growing states. How quickly they can resume their growth upon an influx of new resources is crucial to occupy environmental niches. Isogenic microbial populations are known to harbor only a fraction of cells with rapid growth resumption, yet little is known about the physiological characteristics of those cells and their emergence in the population. Here, we tracked growth of individual Escherichia coli cells in populations under fluctuating nutrient conditions. We found that shifting from high- to low-nutrient conditions caused stalling of cell growth with few cells continuing to divide extremely slowly, a process which was dependent on lipid turnover. Resuming high-nutrient inflow after low-nutrient conditions resulted in cells resuming growth and division, but with different lag times and leading to varying progeny. The history of cell growth during low-nutrient but not high-nutrient conditions was determinant for resumption of growth, which cellular genealogy analysis suggested to originate from inherited physiological differences. Our results demonstrate that cellular growth dynamics become diverse by nutrient limitations, under which a fraction of cells experienced a particular growth history can reproduce progeny with new resources in the future.
Descriptive epidemiology demonstrating the All of Us database as a versatile resource for the rare and undiagnosed disease community
Authors: Magee Drenen J , Kicker Sierra , Thomas Aeisha 
Published: December 2024

Abstract

Objective
We aim to demonstrate the versatility of the All of Us database as an important source of rare and undiagnosed disease (RUD) data, because of its large size and range of data types.

Materials and Methods
We searched the public data browser, electronic health record (EHR), and several surveys to investigate the prevalence, mental health, healthcare access, and other data of select RUDs.

Results
Several RUDs have participants in All of Us [eg, 75 of 100 rare infectious diseases (RIDs)]. We generated health-related data for undiagnosed, sickle cell disease (SCD), cystic fibrosis (CF), and infectious (2 diseases) and chronic (4 diseases) disease pools.

Conclusion
Our results highlight the potential value of All of Us with both data breadth and depth to help identify possible solutions for shared and disease-specific biomedical and other problems such as healthcare access, thus enhancing diagnosis, treatment, prevention, and support for the RUD community.
When Did Growth Begin? New Estimates of Productivity Growth in England from 1250 to 1870
Authors: Bouscasse Paul , Nakamura Emi , Steinsson Jón 
Published: December 2024

Abstract
We estimate productivity growth in England from 1250 to 1870. Real wages over this period were heavily influenced by plague-induced swings in the population. Our estimates account for these Malthusian dynamics. We find that productivity growth was zero before 1600. Productivity growth began in 1600—almost a century before the Glorious Revolution. Thus, the onset of productivity growth preceded the bourgeois institutional reforms of seventeenth-century England. We estimate productivity growth of 2% per decade between 1600 and 1800, increasing to 5% per decade between 1810 and 1860. Much of the increase in output growth during the Industrial Revolution is explained by structural change—the falling importance of land in production—rather than faster productivity growth. Stagnant real wages in the eighteenth and early nineteenth centuries—Engels’ Pause—is explained by rapid population growth putting downward pressure on real wages. Yet feedback from population growth to real wages is sufficiently weak to permit sustained deviations from the “iron law of wages” prior to the Industrial Revolution.
Diagnosis and Management of Neuropathic Breast Pain
Authors: Bejar-Chapa Maria , Caragher Seamus P. , Gfrerer Lisa , Valerio Ian L. , Colwell Amy S. , Winograd Jonathan M. 
Published: December 2024

Summary:
Chronic postoperative pain after breast surgery is a significant concern, with studies indicating varying rates depending on the type of surgical procedure. The risk of developing neuropathic pain is notably increased with axillary lymph node dissection due to potential nerve injuries. Additionally, the method of breast reconstruction may influence postsurgical pain rates, with conflicting findings on the impact of reconstruction type. Recent advancements in techniques such as targeted muscle reinnervation, among others, show promise in addressing postoperative pain in these patients. As the prevalence of these procedures rises, future research is likely to focus on assessing and managing pain in this patient population. The development of patient-reported outcome measures specific to breast surgery pain can aid in clinical assessment and treatment planning. This review emphasizes the importance of gaining a deeper understanding of risk factors, nerve anatomy, and treatment options to enhance outcomes and quality of life for individuals undergoing breast surgery.
Retinal Imaging Analysis Performed By ChatGPT-4o And Gemini Advanced: The Turning Point Of The Revolution?
Authors: Carlà Matteo Mario , Crincoli Emanuele , Rizzo Stanislao 
Published: December 2024

Purpose:
To assess the diagnostic capabilities of the most recent chatbots releases, GPT-4o and Gemini Advanced, facing different retinal diseases.

Methods:
Exploratory analysis on 50 cases with different surgical (n=27) and medical (n=23) retinal pathologies, whose optical coherence tomography/angiography (OCT/OCTA) scans were dragged into ChatGPT and Gemini’s interfaces. Then, we asked “Please describe this image” and classified the diagnosis as: 1) Correct; 2) Partially correct; 3) Wrong; 4) Unable to assess exam type and 5) Diagnosis not given.

Results:
ChatGPT indicated the correct diagnosis in 31/50 cases (62%), significantly higher than Gemini Advanced 16/50 cases (p=0.0048). In 24% of cases, Gemini Advanced was not able to produce any answer, stating “That’s not something I’m able to do yet”. For both, primary misdiagnosis was macular edema, given erroneously in 16% and 14% of cases, respectively. ChatGPT-4o showed higher rates of correct diagnoses either in surgical (52% vs 30%) and medical retina (78% vs 43%). Notably, when presented without the corresponding structural image, in any case Gemini was able to recognize OCTA scans, confusing images for artworks.

Conclusion:
ChatGPT-4o outperformed Gemini Advanced in terms of diagnostic accuracy facing OCT/OCTA images, even if the range of diagnoses is still limited.
Clinical and Radiologic Predictors of Response to Teprotumumab: A 3D Volumetric Analysis of 35 Patients
Authors: Ugradar Shoaib , Parunakian Emanuil , Zimmerman Erin , Malkhasyan Emil , Raika Pershanjit , Douglas Raymond N. , Kossler Andrea L. , Douglas Raymond S. 
Published: December 2024

Purpose:
Teprotumumab, a novel human monoclonal antibody, has been shown to reverse the clinical manifestations of thyroid eye disease. Previous reports have suggested that it demonstrates disease-modifying properties through the reduction of orbital fat and muscle volumes. This study aims to analyze orbital volumetric change following treatment and to identify clinical and radiological predictors of response.

Methods:
This was a prospective longitudinal study with 35 consecutive patients who had available pre- and posttreatment orbital imaging. Three-dimensional volumetric calculations of orbital fat, extraocular muscles, and proptosis were measured using previously validated image processing software. This information was used with demographic data to create a multivariate regression model to review which baseline clinical or radiological factors were predictors of proptosis response.

Results:
In the study orbit, 20 patients (57%) had a proptosis reduction of ≥2 mm. In the fellow orbit, 18 patients (51%) had a proptosis reduction of ≥2 mm. Regression modeling revealed that baseline proptosis and baseline muscle volumes were significant predictors of proptosis response (p < 0.01 and p < 0.05, respectively). Further, changes in muscle volume and fat volume were significantly associated with proptosis response (r = 0.5, p < 0.001 and r = 0.3, p = 0.012, respectively).

Conclusion:
Teprotumumab significantly reduces orbital fat and muscle volumes. This is manifested by a significant reduction in proptosis. Baseline proptosis and muscle volumes are significant predictors of proptosis response.