bluuebunny/crossref_metadata_2025_split huggingface dataset:
hydrographr: An R package for scalable hydrographic data processing
Authors: Schürz Marlene , Grigoropoulou Afroditi , García Márquez Jaime , Torres‐Cambas Yusdiel , Tomiczek Thomas , Floury Mathieu , Bremerich Vanessa , Schürz Christoph , Amatulli Giuseppe , Grossart Hans‐Peter , Domisch Sami 
Published: October 2023

Abstract

Freshwater ecosystems are considered biodiversity hotspots, but assessing the spatial distribution of species remains challenging. One major obstacle lies in the complex geospatial processing of large amounts of data, such as stream network, sub‐catchment and basin data, that are necessary for addressing the longitudinal connectivity among water bodies. Workflows thus need to be scalable, especially when working across large spatial extents and at high spatial resolution. This in turn requires advanced command‐line GIS skills and programming language integration, which often poses a challenge for freshwater researchers.

To address this challenge, we developed the package hydrographr that provides scalable hydrographic data processing in R. The package contains functions for downloading data of the high‐resolution Hydrography90m dataset, processing, reading and extracting information, as well as assessing network distances and connectivity. While the functions are, by default, tailored toward the Hydrography90m data, they can also be generalised toward other data and purposes, such as efficient cropping and merging of raster and vector data, point‐raster extraction, raster reclassification and data aggregation. The package depends on the open‐source software GDAL/OGR, GRASS‐GIS and the AWK programming language in the Linux environment, allowing a seamless language integration. Since the data is processed outside R, hydrographr allows creating scalable geo‐processing workflows.

We illustrate the hydrographr functions using two workflows that focus on (i) a freshwater species distribution modelling approach, and (ii) assessing stream connectivity given the fragmentation by dams. We also provide a detailed guide for the initial installation of the required software. Windows users need to first enable the Windows Subsystem for Linux (WSL) feature, and can then follow the same software installation as Linux users. hydrographr is maintained on GitHub at https://github.com/glowabio/hydrographr.

hydrographr provides a set of key functions for processing freshwater geospatial data. We expect that the package will support the freshwater‐related research communities given the easy‐to‐use wrapper functions that allow capitalizing on powerful open‐source command‐line software, which may otherwise require a steep learning curve. Users can thus perform large‐scale freshwater‐specific longitudinal connectivity and network analyses across large geographic extents while staying within the R environment.
Exploring congruent diversification histories with flexibility and parsimony
Authors: Andréoletti Jérémy , Morlon Hélène 
Published: October 2023

Abstract

Using phylogenies of present‐day species to estimate diversification rate trajectories—speciation and extinction rates over time—is a challenging task due to non‐identifiability issues. Given a phylogeny, there exists an infinite set of trajectories that result in the same likelihood; this set has been coined a congruence class. Previous work has developed approaches for sampling trajectories within a given congruence class, with the aim to assess the extent to which congruent scenarios can vary from one another. Based on this sampling approach, it has been suggested that rapid changes in speciation or extinction rates are conserved across the class. Reaching such conclusions requires to sample the broadest possible set of distinct trajectories.

We introduce a new method for exploring congruence classes that we implement in the R package CRABS. Whereas existing methods constrain either the speciation rate or the extinction rate trajectory, ours provides more flexibility by sampling congruent speciation and extinction rate trajectories simultaneously. This allows covering a more representative set of distinct diversification rate trajectories. We also implement a filtering step that allows selecting the most parsimonious trajectories within a class.

We demonstrate the utility of our new sampling strategy using a simulated scenario. Next, we apply our approach to the study of mammalian diversification history. We show that rapid changes in speciation and extinction rates need not be conserved across a congruence class, but that selecting the most parsimonious trajectories shrinks the class to concordant scenarios.

Our approach opens new avenues both to truly explore the myriad of potential diversification histories consistent with a given phylogeny, embracing the uncertainty inherent to phylogenetic diversification models, and to select among these different histories. This should help refining our inference of diversification trajectories from extant data.
Clozapine augmentation with long‐acting antipsychotic injections: A case series and systematic review
Authors: Oloyede Ebenezer , Dima Aikaterini , Taylor David , Cheung Henry , Dzahini Olubanke , Shergill Sukhi , Whiskey Eromona 
Published: October 2023

AbstractBackgroundUp to 30% of patients with a diagnosis of treatment‐resistant psychosis remain symptomatic despite an optimal trial with the gold standard treatment, clozapine. Emerging evidence suggests the clinical utility of long‐acting injections (LAI) in such clinical scenarios. In this study, we aimed to describe clozapine augmentation with LAIs in an inner London hospital and explore the literature on the clinical effectiveness of this treatment modality.MethodsPatients prescribed clozapine, who were commenced on a LAI between 2007 and 2023 by the United Kingdom's largest mental health trust, were identified from electronic patient records. First, routine clinical data were used to describe the use, effectiveness, and safety of this augmentation strategy. Second, we conducted a literature search up to 1st June 2023 to identify published studies describing clinical outcomes after clozapine augmentation with a LAI. Clinical outcomes were collated and presented in a table, including hospitalisation rates and quantitative clinical assessments using validated scales.ResultsOf the 1248 patients prescribed clozapine in SLaM, three patients (0.2%) received augmentation with the following LAIs: olanzapine embonate, paliperidone palmitate and pipotiazine palmitate. This treatment strategy was clinically effective and generally well tolerated in all three cases. Twelve published studies between 2010 and 2022 were included in the review. Eight distinct LAIs were reported (4 first and 4 second generation antipsychotics), with risperidone and paliperidone most widely studied. All the identified studies were observational including mirror‐image studies, case series and case reports. Duration of follow up varied from 3 months to 3 years. There was evidence that the use of LAIs with clozapine can significantly reduce clinical symptoms, hospitalisation rates and bed days. No serious adverse effects were reported.ConclusionThis preliminary evidence suggests clinical utility of LAIs in alleviating residual symptoms and subsequently reducing hospitalisation rates in patients optimised on clozapine treatment. The current study warrants further investigations including a randomised controlled study to establish the clinical efficacy, tolerability, and place in therapy of this treatment modality.
Talking to and around children: Socializing learners, participants, and speakers in an urban Zapotec community
Authors: Toledo Bustamante Nadxieli 
Published: October 2023

AbstractThis article examines caregivers' everyday language choices and interactions with children in an urban Zapotec community in Mexico, where Diidxazá is being displaced by Spanish in everyday use. It argues that caregivers' language choices and interactions get entangled in complex ways with the socio‐cultural organization of everyday life and with local pedagogies and understandings of children's development, which, in turn, shape children's participation roles and long‐term developmental trajectories as learners and speakers.
Is increased subjective thirst associated with greater interdialytic weight gains, extracellular fluid and dietary sodium intake?
Authors: Chhabra Roohi , Davenport Andrew 
Published: October 2023

AbstractBackgroundSome previous studies have reported an effect of increasing subjective thirst and interdialytic weight gains (IDWG), and that this may be influenced by nonadherence to dietary sodium restrictions, whereas others reported no such association. As such we wished to review the effect of self‐reported thirst on IDWGs and dietary sodium intake.MethodsDialysis patients were asked to complete visual analogues thirst, distress thermometer (DT) scores and complete a sodium food frequency questionnaire (SFFQ). IDWG and pre and post dialysis volumes were measured with multifrequency bioelectrical impedance.ResultsOne hundred and eleven patients completed the questionnaires and had bioimpedance measurements: 63% male, mean age 63.8 ± 16.1 years, 33% diabetic with a median thirst score 3 (0–5) and SFFQ 52.0 ± 18, and IDWG 2.1 ± 1.3%. Thirst was associated with DT (r = 0.28, p = 0.004) and negatively with age (r = −0.31, p < 0.001), but not SFFQ, IDWG, extracellular water, or dialysate sodium, or dialysate to plasma gradient. Patients with higher thirst scores were younger (58.0 ± 15.2 vs. 69.4 ± 15.0 years, p < 0.001) with higher DT scores (5 [2–7] vs. 2 [0–5], p < 0.001). On multivariate logistic analysis, only age was associated with self‐reported thirst (odds ratio 0.95, 95% confidence limits 0.92–0.98, p < 0.001).ConclusionWe found that subjective thirst was greater for younger patients and those who reported higher levels of distress, but no association with IDWGs, dietary sodium intake, or dialysate sodium. However, most of our patients followed the dietary advice, as evidenced by the low SFFQ scores and % IDWGs. Whether thirst increases distress or distress increases subjective thirst remains to be determined.
The power of ethical words
Authors: Alda Mercedes , Muñoz Fernando , Vargas María 
Published: October 2023

AbstractIn this research, we analyse the impact of the inclusion of ethical expressions in the prospectuses of socially responsible (SR) mutual funds on money flows. We contribute to the existing literature by proposing a text‐based measure that integrates three attributes that are relevant to whether clients are attracted: exclusiveness, intensity and lexical diversity. We analyse a sample formed of 266 SR US equity mutual funds in the period 1999–2019. Our findings show that both the proposed indicator and other alternative partial proxies based on textual data have a positive impact on the money flows of the SR funds. This effect is more relevant in the case of SR mutual funds belonging to smaller families. Besides, persistence in money flows is more intense for SR mutual funds that are more attractive because of their ethical expressions. Another finding shows that return‐chaser behaviour occurs among all SR investors, independently of the level of text attractiveness of the mutual funds in which they invest, revealing that they take into account both financial and non‐financial outcomes. Our results indicate that policymakers should control fund prospectus information, given its importance for investors' decisions. In addition, managers should be especially cautious with the information provided in prospectuses because of its impact on investor decisions.
Factors associated with respectful maternity care and influence of HIV status among women giving birth in Kilimanjaro, Tanzania
Authors: Barabara Mariam L. , Cohen Susanna R. , Masenga Gileard , Minja Linda M. , Mlay Pendo S. , Stephens Maya J. , Olomi Gaudensia A. , Mlay Janeth , Marchand Virginie , Weglarz Anya , Hanson Olivia , Mmbaga Blandina T. , Watt Melissa H. 
Published: October 2023

AbstractBackgroundRespectful maternity care (RMC) is a rights‐based approach to childbirth that centers the dignity, autonomy, and well‐being of birthing women. This study aimed to examine factors associated with RMC among women giving birth in Tanzania and to examine whether HIV status was associated with self‐reported RMC.MethodsWe enrolled 229 postpartum women in six clinics in the Kilimanjaro Region; of them, 103 were living with HIV. Participants completed a survey within 48 h after birth before being discharged. RMC was measured using a 30‐item scale with three subscales (dignity and respect; supportive care; communication and autonomy), each standardized from 0 to 100. Univariable and multivariable regression models examined factors associated with RMC.ResultsThe median score of the full RMC score was 74, differing slightly by subscale: 83 for dignity and respect, 76 for supportive care, and 67 for communication and autonomy. RMC did not differ by HIV status (median 67.0 vs. 67.0, p = 0.89). In multivariable linear regression, women who would not recommend the birth facility to their friends and who did not receive breastfeeding education had significantly lower RMC scores on the full RMC scale. In the dignity and respect subscale, variables associated with significantly lower RMC scores were not being able to read and write, delivering in a public facility, and delivering vaginally.ConclusionsAlthough self‐reported RMC was generally high, we identified areas for improvement. Practitioners need ongoing training on RMC principles and the delivery of equitable care.
Mentalistic and normative frameworks in children's explanations of others' behaviors
Authors: Brandone Amanda C. , Stout Wyntre 
Published: October 2023

AbstractAs they learn to navigate the social world, children construct frameworks to interpret others' behavior. The present studies examined two such frameworks: a mentalistic framework, which construes behavior as driven by internal mental states; and a normative framework, which presumes people act in accordance with social norms. Participants included 101 children (ages 4, 7, and 10; 81% White; 41% female) and 35 adults (66% female) tested in the northeastern United States from 2019 to 2021. Children and adults utilized both mentalistic and normative frameworks to explain others' behaviors. Framework use depended on features of the behavior being explained. Minimal developmental differences were observed. The relative independence and the utility of the mentalistic and normative frameworks for naïve reasoning about behavior are considered.
Antecedents to and outcomes associated with teacher–child relationship perceptions in early childhood: Further evidence for child‐driven effects
Authors: Dede Yildirim Elif , Frosch Cynthia A. , Santos António J. , Veríssimo Manuela , Bub Kristen , Vaughn Brian E. 
Published: October 2023

AbstractPreschool teachers' perceptions about relationships with students (teacher–child relationships [TCRs]) predict children's subsequent social competence (SC) and academic progress. Why this is so remains unclear. Do TCRs shape children's development, or do child attributes influence both TCRs and subsequent development? Relations between TCRs and other measures were examined for 185 preschoolers (107 girls, 89 longitudinal, and ~75% European American). Teachers rated TCRs and child social/affective behaviors. Teacher–child interactions (TCIs) and children's affect expressiveness were observed. Child SC and receptive vocabulary were assessed. TCRs were significantly correlated with each type of outcome. TCIs, SC, expressed affect, and teacher‐rated behaviors also predicted TCRs longitudinally. Results suggest that TCR ratings predict subsequent adaptation because they summarize children's behavioral profiles rather than on TCR quality per se.
Is residential care a risk factor for teenage pregnancy? A study on the experiences of young women's discharge and transition from residential care in Trinidad and Tobago
Authors: Roberts Petra 
Published: October 2023

AbstractSome English‐speaking Caribbean nations continue to maintain large residential homes for children and youth who need out‐of‐home care. My doctoral study with alumni from a number of these homes reported that their overall experiences were positive. However, transition and discharge were less favourable, with women suffering more hardships than men. These hardships included homelessness, which often led to sexual exploitation for women. A number of young women became pregnant within a year of discharge from the home (which normally happened at the age of 16 or 18). An unplanned pregnancy can have immediate and lasting consequences for a young woman's health, education, and income‐earning potential. It often alters the course of her entire life. This study provides information from a sample of 15 young adult women in Trinidad and Tobago on the risk factor of living in a residential care facility and unplanned teenage pregnancy. Recommendations are proposed to better prepare young women who grew up in residential care.
De novo enhancer deletion of LMX1B produces a mild nail‐patella clinical phenotype
Authors: Francis David , Lall Paula , Ayres Samantha , Van Bergen Nicole J. , Christodoulou John , Brown Natasha J. , Kalitsis Paul 
Published: October 2023

AbstractCritical genes involved in embryonic development are often transcription factors, regulating many downstream genes. LMX1B is a homeobox gene that is involved in formation of the limbs, eyes and kidneys, heterozygous loss‐of‐function sequence variants and deletions cause Nail‐Patella syndrome. Most of the reported variants are localised within the gene's coding sequence, however, approximately 5%–10% of affected individuals do not have a pathogenic variant identified within this region. In this study, we present a family with four affected individuals across two generations with a deletion spanning a conserved upstream LMX1B‐binding sequence. This deletion is de novo in the mother of three affected children. Furthermore, in this family, the manifestations appear limited to the nails and limbs, and therefore may reflect an attenuated phenotype of the classic Nail‐Patella phenotype that includes ophthalmological and renal manifestations.
Carbon offsets and agriculture: Options, obstacles, and opinions
Authors: van Kooten G. Cornelis , Zanello Rebecca 
Published: October 2023

AbstractWhile carbon offsets in agriculture can play a role in addressing climate change, they are not a perfect substitute for direct emission reductions. As shown in this paper through various arguments and case studies, climate policies in Canada have avoided the use of offsets to be sold in carbon markets, preferring instead to incentivize adoption of best management practices (BMPs) that provide environmental benefits along with climate mitigation benefits. We argue that this is a preferred policy option due to the perils and pitfalls inherent in the measurement and monitoring required to identify offset credits. While an appropriate approach might be to penalize Canadian farmers for any emissions their activities cause, this may do more harm than good. Canadian agricultural production is highly efficient and technologically advanced; therefore, reductions in Canada's contribution to the global food supply will result in less‐efficient production occurring elsewhere (i.e., leakage) that increases global greenhouse gas emissions.
Naturalization of introduced plants is driven by life‐form‐dependent cultivation biases
Authors: Dong Bi‐Cheng , Yang Qiang , Kinlock Nicole L. , Pouteau Robin , Pyšek Petr , Weigelt Patrick , Yu Fei‐Hai , van Kleunen Mark 
Published: October 2023

AbstractAimsMost naturalized plants are escapees from cultivation. Inventories of cultivated introduced species thus offer unique, still underutilized, opportunities to assess naturalization drivers of introduced plants. We used a comprehensive inventory of 13,718 introduced species cultivated in China's botanical gardens to test which species characteristics distinguish the 739 species that have naturalized.LocationsChina.MethodsWe used generalized linear models to test whether the naturalization of cultivated introduced plants in China is associated with functional traits, propagule pressure, environmental niche and introduction history. To test direct and indirect effects of those variables and their relative importance in driving naturalization, we used structural equation models.ResultsWe showed that species were more likely to naturalize when they originate from the Americas, are more widely cultivated, and have a longer residence time. Moreover, species were more likely to naturalize if they have a good environmental match, are short‐lived herbs, are predominantly propagated from seeds, and, in the case of herbs, are relatively tall compared to other herbs. Part of the latter effects are mediated by how these variables relate to propagule pressure proxies, and this varies among short‐lived herbs, long‐lived herbs and woody plants.Main ConclusionsNaturalization is partly driven by life‐form‐dependent cultivation biases.
Utilization and outcome disparities in allogeneic hematopoietic stem cell transplant in the United States
Authors: Ashok Kumar Prashanth , Ghimire Krishna , Haroun Elio , Kassab Joseph , Saba Ludovic , Gentile Teresa , Dutta Dibyendu , Lim Seah H. 
Published: October 2023

AbstractAllogeneic hematopoietic stem cell transplant (allo‐HSCT) is increasingly being used in the United States (US) and across the world as a curative therapeutic option for patients with certain high‐risk hematologic malignancies and non‐malignant diseases. However, racial and ethnic disparities in utilization of the procedure and in outcome following transplant remain major problems. Racial and ethnic minority patients are consistently under‐represented in the proportion of patients who undergo allo‐HSCT in the US. The transplant outcomes in these patients are also inferior. The interrelated driving forces responsible for the differences in the utilization and transplant outcome of the medical intervention are socioeconomic status, complexity of the procedure, geographical barriers, and the results of differences in the genetics and comorbidities across different races. Bridging the disparity gaps is important not only to provide equity and inclusion in the utilization of this potentially life‐saving procedure but also in ensuring that minority groups are well represented for research studies about allo‐HSCT. This is required to determine interventions that may be more efficacious in particular racial and ethnic groups. Various strategies at the Federal, State, and Program levels have been designed to bridge the disparity gaps with varying successes. In this review paper, we will examine the disparities and discuss the strategies currently available to address the utilization and outcome gaps between patients of different races in the US.