bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying homologous recombination deficiency in breast cancer: genomic instability score distributions differ among breast cancer subtypes
Authors: Lenz Lauren , Neff Chris , Solimeno Cara , Cogan Elizabeth S. , Abramson Vandana G. , Boughey Judy C. , Falkson Carla , Goetz Matthew P. , Ford James M. , Gradishar William J. , Jankowitz Rachel C. , Kaklamani Virginia G. , Marcom P. Kelly , Richardson Andrea L. , Storniolo Anna Maria , Tung Nadine M. , Vinayak Shaveta , Hodgson Darren R. , Lai Zhongwu , Dearden Simon , Hennessy Bryan T. , Mayer Erica L. , Mills Gordon B. , Slavin Thomas P. , Gutin Alexander , Connolly Roisin M. , Telli Melinda L. , Stearns Vered , Lanchbury Jerry S. , Timms Kirsten M. 
Published: August 2023

Abstract
Purpose
A 3-biomarker homologous recombination deficiency (HRD) score is a key component of a currently FDA-approved companion diagnostic assay to identify HRD in patients with ovarian cancer using a threshold score of ≥ 42, though recent studies have explored the utility of a lower threshold (GIS ≥ 33). The present study evaluated whether the ovarian cancer thresholds may also be appropriate for major breast cancer subtypes by comparing the genomic instability score (GIS) distributions of BRCA1/2-deficient estrogen receptor–positive breast cancer (ER + BC) and triple-negative breast cancer (TNBC) to the GIS distribution of BRCA1/2-deficient ovarian cancer.

Methods
Ovarian cancer and breast cancer (ER + BC and TNBC) tumors from ten study cohorts were sequenced to identify pathogenic BRCA1/2 mutations, and GIS was calculated using a previously described algorithm. Pathologic complete response (pCR) to platinum therapy was evaluated in a subset of TNBC samples. For TNBC, a threshold was set and threshold validity was assessed relative to clinical outcomes.

Results
A total of 560 ovarian cancer, 805 ER + BC, and 443 TNBC tumors were included. Compared to ovarian cancer, the GIS distribution of BRCA1/2-deficient samples was shifted lower for ER + BC (p = 0.015), but not TNBC (p = 0.35). In the subset of TNBC samples, univariable logistic regression models revealed that GIS status using thresholds of ≥ 42 and ≥ 33 were significant predictors of response to platinum therapy.

Conclusions
This study demonstrated that the GIS thresholds used for ovarian cancer may also be appropriate for TNBC, but not ER + BC. GIS thresholds in TNBC were validated using clinical response data to platinum therapy.
Computational thinking and repetition patterns in early childhood education: Longitudinal analysis of representation and justification
Authors: Acosta Yeni , Alsina Ángel , Pincheira Nataly 
Published: August 2023

AbstractThis paper provides a longitudinal analysis of the understanding of repetition patterns by 24 Spanish children ages 3, 4 and 5, through representation and the type of justification. A mixed quantitative and qualitative study is conducted to establish bridges between algebraic thinking and computational thinking by teaching repetition patterns in technological contexts. The data are obtained using: a) participant observations; b) audio-visual and photographic records; and c) written representations, in drawing format, from the students. The analysis involves, on the one hand, a statistical analysis of the representations of patterns, and on the other, an interpretive analysis to describe the type of justification that children use in technological contexts: “elaboration”, “validation”, “inference” and “prediction or decision-making”. The results show that: a) with respect to the representation of patterns, errors decreased by 27.3% in 3-to-5-year-olds, with understanding and correct representation of repetition patterns gaining prominence in more than 50% of the sample from the age of 4; b) on the type of justification used, it is evident that in 3-and-4-year-olds, “elaboration” predominates, and at 5, progress is made towards “validation”. We conclude that it is necessary to design learning sequences connected with theory and upheld through practice, and that foster the active role of the teacher as a promoter of teaching situations that help spur the beginning of computational and algebraic thinking.
Inequitable Gains and Losses from Conservation in a Global Biodiversity Hotspot
Authors: Platts Philip J. , Schaafsma Marije , Turner R. Kerry , Burgess Neil D. , Fisher Brendan , Mbilinyi Boniface P. , Munishi Pantaleo K. T. , Ricketts Taylor H. , Swetnam Ruth D. , Ahrends Antje , Ashagre Biniam B. , Bayliss Julian , Gereau Roy E. , Green Jonathan M. H. , Green Rhys E. , Jeha Lena , Lewis Simon L. , Marchant Rob , Marshall Andrew R. , Morse-Jones Sian , Mwakalila Shadrack , Njana Marco A. , Shirima Deo D. , Willcock Simon , Balmford Andrew 
Published: August 2023

AbstractA billion rural people live near tropical forests. Urban populations need them for water, energy and timber. Global society benefits from climate regulation and knowledge embodied in tropical biodiversity. Ecosystem service valuations can incentivise conservation, but determining costs and benefits across multiple stakeholders and interacting services is complex and rarely attempted. We report on a 10-year study, unprecedented in detail and scope, to determine the monetary value implications of conserving forests and woodlands in Tanzania’s Eastern Arc Mountains. Across plausible ranges of carbon price, agricultural yield and discount rate, conservation delivers net global benefits (+US$8.2B present value, 20-year central estimate). Crucially, however, net outcomes diverge widely across stakeholder groups. International stakeholders gain most from conservation (+US$10.1B), while local-rural communities bear substantial net costs (-US$1.9B), with greater inequities for more biologically important forests. Other Tanzanian stakeholders experience conflicting incentives: tourism, drinking water and climate regulation encourage conservation (+US$72M); logging, fuelwood and management costs encourage depletion (-US$148M). Substantial global investment in disaggregating and mitigating local costs (e.g., through boosting smallholder yields) is essential to equitably balance conservation and development objectives.
Monitoring of cyanobacterial breakthrough and accumulation by in situ phycocyanin probe system within full-scale treatment plants
Authors: Ma Liya , Maldonado Juan Francisco Guerra , Zamyadi Arash , Dorner Sarah , Prévost Michèle 
Published: August 2023

AbstractWorldwide, there has been an increase in the presence of potentially toxic cyanobacterial blooms in drinking water sources and within drinking water treatment plants (DWTPs). The objective of this study is to validate the use of in situ probes for the detection and management of cyanobacterial breakthrough in high and low-risk DWTPs. In situ phycocyanin YSI EXO2 probes were devised for remote control and data logging to monitor the cyanobacteria in raw, clarified, filtered, and treated water in three full-scale DWTPs. An additional probe was installed inside the sludge holding tank to measure the water quality of the surface of the sludge storage tank in a high-risk DWTP. Simultaneous grab samplings were carried out for taxonomic cell counts and toxin analysis. A total of 23, 9, and 4 field visits were conducted at the three DWTPs. Phycocyanin readings showed a 93-fold fluctuation within 24 h in the raw water of the high cyanobacterial risk plant, with higher phycocyanin levels during the afternoon period. These data provide new information on the limitations of weekly or daily grab sampling. Also, different moving averages for the phycocyanin probe readings can be used to improve the interpretation of phycocyanin signal trends. The in situ probe successfully detected high cyanobacterial biovolumes entering the clarification process in the high-risk plant. Grab sampling results revealed high cyanobacterial biovolumes in the sludge for both high and low-risk plants.
Influence of Particle Size on the Flammability and Explosibility of Biomass Dusts: Is a New Approach Needed?
Authors: Castells Blanca , Tascón Alberto , Amez Isabel , Fernandez-Anez Nieves 
Published: August 2023

AbstractThe influence of particle size on the flammability and explosion severity has been widely demonstrated for coals along the years: the thinner the particle size, the more flammable is the dust and more severe are the explosions. Later, the increase on the use of biomass led to using the same resources and techniques for both groups of materials, considering them similar enough. However, there are basic differences between biomass and coal dust particles that leads to different behaviours when focusing on industrial fire safety. This difference is the starting point of this review, where a study on the existing knowledge in relation to the size and shape of biomass dust is presented. The methodologies and parameters used to determine particle size are described and discussed, showing the inconvenience of using only one parameter (d50) to describe dust, as well as the need of a standardized methodology to homogenise the results. The biomass data gathered from scientific literature and the following analysis carried out has also highlighted the importance of identifying samples in an accurate way and the strong necessity of further research on these materials and on the interdependence between particle size and the experimental procedures for flammability and explosibility properties.
On the affective threshold of power and privilege
Authors: Rattray Julie 
Published: August 2023

AbstractHigher education is facing increasing calls to engage in a process of intellectual decolonisation. This process necessitates that we take time to consider both the content of our curriculum and the pedagogic practices used to facilitate its understanding. Drawing on discussions of both intellectual decolonisation and its underpinning principles of epistemic justice, I consider the implications of these ideas for the threshold concept framework. These implications are likely to relate to both the identification of potential future threshold concepts and the experience of engaging with them. As threshold scholars, we may need to reconsider our ideas about who the experts are within a discipline or practice in our efforts to identify candidate threshold concepts and consider alternative sources of evidence in support of this. In addition, we need to reflect on how the learning experiences that arise as a result of encounters with thresholds that have emerged as a result of the privileging of knowledge and ways of knowing from the ‘global north’ might serve as a source of epistemic trouble to learners from the ‘global south’. Such learning experiences are likely to be highly emotive and represent a significant source of troublesome learning.
Habitat quality, not patch isolation, drives distribution and abundance of two light-demanding butterflies in fragmented coppice landscapes
Authors: Graser Anne , Kelling Marit , Pabst Rebecca , Schulz Meike , Hölzel Norbert , Kamp Johannes 
Published: August 2023

AbstractCoppice forests are socio-ecological systems especially rich in biodiversity. They have been transformed into high forest and abandoned across large areas of Europe over the past 200 years. Coppice loss is likely an important driver of insect declines. It is currently unclear whether habitat quality or decreasing connectivity of the remaining fragments is more important for the survival of insect populations. We related the abundance of two coppice-associated butterflies of conservation concern, Satyrium ilicis and Melitaea athalia, to indicators of habitat quality and habitat connectivity. We estimated butterfly densities using Distance Sampling along a successional gradient (time since last cut: 1–9 years; N = 130 plots) across one of the largest remaining simple oak-birch coppice landscapes in Central Europe. Both species reached abundance peaks within four to six years after the last cut, declining rapidly in abundance with subsequent succession. We found no evidence that coupe size, coppice availability and patch (= coupe) connectivity were related to the density of the species. Besides stand age, the cover of larval foodplants explained predicted butterfly densities well. Only Satyrium ilicis benefitted from high Red Deer densities.Implications for insect conservation: Our results suggest that habitat quality and sufficient availability of coppice of suitable age matters more than coupe size and fragmentation within a traditional managed coppice landscape. Coppice restoration aiming at the study species should ensure a shifting mosaic of successional habitat to provide a large availability of resprouting oak stools and bilberry vegetation that holds dense Melampyrum pratense stands.
Convexity and Monotonicity in Language Coordination: Simulating the Emergence of Semantic Universals in Populations of Cognitive Agents
Authors: Gierasimczuk Nina , Kalociński Dariusz , Rakowski Franciszek , Uszyński Jakub 
Published: August 2023

AbstractNatural languages vary in their quantity expressions, but the variation seems to be constrained by general properties, so-calleduniversals. Their explanations have been sought among constraints of human cognition, communication, complexity, and pragmatics. In this article, we apply a state-of-the-art language coordination model to the semantic domain of quantities to examine whether two quantity universals—monotonicity and convexity—arise as a result of coordination. Assuming precise number perception by the agents, we evolve communicatively usable quantity terminologies in two separate conditions: a numeric-based condition in which agents communicate about a number of objects and a quotient-based condition in which agents communicate about the proportions. We find out that both universals take off in all conditions but only convexity almost entirely dominates the emergent languages. Additionally, we examine whether the perceptual constraints of the agents can contribute to the further development of universals. We compare the degrees of convexity and monotonicity of languages evolving in populations of agents with precise and approximate number sense. The results suggest that approximate number sense significantly reinforces monotonicity and leads to further enhancement of convexity. Last but not least, we show that the properties of the evolved quantifiers match certain invariance properties from generalized quantifier theory.
Terrestrial versus aquatic source identification of sedimentary n-alkane and sugar biomarkers: a case study from the Bale Mountains, Ethiopia
Authors: Mekonnen Betelhem , Bittner Lucas , Bromm Tobias , Lemma Bruk , Glaser Bruno , Zech Wolfgang , Nemomissa Sileshi , Bekele Tamrat , Zech Michael 
Published: August 2023

AbstractOrganic matter in sedimentary archives is abundantly used to reconstruct paleoenvironmental and climate histories. Thereby, distinguishing between the terrestrial and aquatic origin of sedimentary organic matter is often a prerequisite for robust interpretations. In this case study, we use published data for modern plants and topsoils to identify the terrestrial versus aquatic source of n-alkane and sugar biomarkers in two afro-alpine sediment archives (Lake Garba Guracha and Depression B4) in the Bale Mountains, Ethiopia. The results of our comparative approach show that the long-chain n-alkanes C29, C31, and C33 in the sedimentary archives yielded patterns similar to those typical for the potential terrestrial input. By contrast, the relative abundances of the sedimentary mid-chain n-alkanes C23 and C25, and at least partly C27, are significantly increased compared to the plants and topsoils. This suggests that they are primarily produced by aquatic macrophytes and micro-organisms. The Paq ratio (C23 + C25)/(C23 + C25 + C29 + C31) is validated as a suitable source identification proxy in our study area. The sugar biomarkers xylose (xyl) and arabinose (ara) are abundant in the plant and topsoil samples. By comparison, high relative abundances of fucose (fuc) and rhamnose (rham) are generally only observed in sediments. This indicates that these sugar biomarkers are primarily produced by aquatic macrophytes or micro-organisms. Therefore, the ratio (fuc + rham)/(ara + xyl) is a suitable sugar biomarker proxy for organic matter source identification. The relative abundances of galactose and mannose are systematically decreasing and increasing, respectively, from leaves over O-layers to Ah-horizons. Furthermore, they are not significantly different from the abundances found in the sediments. This hinders terrestrial versus aquatic source identification using galactose and mannose.
The Effect of Relative Pubertal Maturation and Perceived Popularity on Symptoms of Depression and Social Anxiety in Adolescent Boys and Girls
Authors: van Rijn Rebecca , Lee Nikki C. , Hollarek Miriam , Sijtsma Hester , Walsh Reubs J. , van Buuren Mariët , Braams Barbara R. , Krabbendam Lydia 
Published: August 2023

AbstractResearch has shown that adolescents – particularly girls – who mature relatively early often experience more internalizing problems. This effect is thought to be partially driven by psychosocial mechanisms, but previous research based relative pubertal maturation on complete samples or population standards, instead of considering the adolescents’ direct peer environment. In the current study the level of adolescents’ pubertal development was assessed relative to their classmates in order to examine relative pubertal maturation. The effects of adolescents’ relative pubertal status, and their perceived popularity, on symptoms of social anxiety and depression in adolescents were studied. All analyses were also performed for absolute pubertal maturation. Participants were 397 young adolescents (Mage = 13.06, SD = 0.36, 49.9% girls) at timepoint 1, and 307 (Mage = 14.08, SD = 0.36, 50.5% girls) at timepoint 2. A significant positive relationship was found between relative pubertal timing and symptoms of depression for girls but not boys. Social anxiety symptoms were not significantly related to relative pubertal timing in either sex. Relative pubertal maturation had no effect on change in or persistence of depressive and social anxiety symptoms one year later. The effects of the comparison with the immediate peer environment, did not seem to explain more variance in internalizing symptoms than the effects of early maturation.
Open areas associated with traditional agriculture promote functional connectivity among amphibian demes in Mediterranean agrosystems
Authors: Albero Luis , Martínez-Solano Íñigo , Hermida Miguel , Vera Manuel , Tarroso Pedro , Bécares Eloy 
Published: August 2023

Abstract
Context
Functional connectivity across fragmented habitat patches is essential for the conservation of animal populations in humanized landscapes. Given their low dispersal capacity, amphibians in the Mediterranean region are threatened by habitat fragmentation and loss due to changes in land use, including agricultural intensification.

Objectives
We assessed patterns of functional connectivity of a Near Threatened Mediterranean amphibian, the sharp ribbed newt (Pleurodeles waltl), in an agricultural landscape matrix in NW Spain subject to different intensification regimes.

Methods
We sampled newts in 17 ponds embedded in a terrestrial habitat matrix dominated by agricultural land uses. Genome-wide molecular markers (1390 SNPs) were used to assess patterns of genetic diversity and gene flow among ponds. We tested the role of landscape features on functional connectivity using isolation by resistance models incorporating information on Normalized Difference Vegetation Index (NDVI) data.

Results
We found low levels of genetic diversity in all sampled populations. Global FST estimates and cluster analyses revealed shallow but significant genetic structure in the study area, with NDVI-based resistance models showing that open areas (rainfed crops and grasslands) offer lower resistance to gene flow and thus promote functional connectivity among demes.

Conclusions
Our study highlights the important role of landscape features, such as open areas resulting from traditional rainfed agriculture, in promoting functional connectivity between amphibian populations in Mediterranean agrosystems. Conservation policies must adopt a functional network strategy and protect groups of inter-connected temporary ponds across the traditional agricultural matrix to efficiently preserve their associated biotic communities.
Racial/Ethnic Disparities Impact the Real-World Effectiveness of a Multicomponent Maternal Smoking Cessation Program: Findings from the CTTP Cohort
Authors: Wiles Stacey D. , Lee Jerry W. , Nelson Anna , Petersen Anne Berit , Singh Pramil N. 
Published: August 2023

Abstract
Introduction
Smoking during pregnancy adversely affects perinatal outcomes for both women and infants. We conducted a retrospective cohort study of the state-funded Comprehensive Tobacco Treatment Program (CTTP) – the largest maternal tobacco cessation program in San Bernardino County, California – to determine the real-world program effectiveness and to identify variables that can potentially improve effectiveness.

Methods
During 2012–2019, women who smoked during pregnancy were enrolled in CTTP’s multicomponent behavioral smoking cessation program that implemented components of known efficacy (i.e., incentives, biomarker testing, feedback, and motivational interviewing).

Results
We found that 40.1% achieved prolonged abstinence by achieving weekly, cotinine-verified, 7-day abstinence during 6 to 8 weeks of enrollment. Using intention-to-treat analyses, we computed that the self-reported point prevalence abstinence rate (PPA) at the six-month telephone follow-up was 36.7%. Cohort members achieving prolonged abstinence during the CTTP were five times more likely to achieve PPA six months after CTTP. Several non-Hispanic ethnicities (Black, Native American, White, or More than one ethnicity) in the cohort were two-fold less likely (relative to Hispanics) to achieve prolonged abstinence during CTTP or PPA at six months after CTTP. This disparity was further investigated in mediation analysis. Variables such as quitting during the first trimester and smoking fewer cigarettes at enrollment were also associated with achieving PPA at six months.

Discussion
Racial/ethnic health disparities that have long been linked to a higher rate of maternal smoking persist even when the pregnant smoker enrolls in a smoking cessation program.
An optimized enhanced-multi learner approach towards speaker identification based on single-sound segments
Authors: Shahamiri Seyed Reza 
Published: August 2023

AbstractSpeaker Identification (SI) is the task of identifying an unknown speaker of an utterance by comparing the voice biometrics of the unknown speaker with previously stored and known speaker models. Although deep learning algorithms have been successful in different speech and speaker recognition systems, they are computationally expensive and require considerable run-time resources. This paper approaches this issue by proposing an optimized text-independent SI system based on convolutional neural networks (CNNs) that not only delivers accuracies on par with state-of-the-art benchmarks but also demands significantly fewer trainable parameters. The proposed system integrates an Enhanced Multi-Active Learner framework, which distributes the complexity of the learning task among an array of learners, with a novel SI approach in which speakers are identified based on a single sound segment of voice biometrics. Here, experiments were conducted with all 1881 VoxCeleb 1 and TIMIT speakers, and results were compared with the SI systems reported in the literature that were assessed on the same speakers’ data. Results indicate that first, the proposed system outperformed the benchmark systems’ performances by delivering up to 2.43% better top-1 accuracy, and second, it reduced the number of deep learning trainable parameters by up to 95%. The proposed SI could bring offline, large-scale speaker identification to low-end computing machines without specific deep learning hardware and make the technology more affordable.