bluuebunny/crossref_metadata_2025_split huggingface dataset:
Envisioning a sustainable agricultural water future across spatial scales
Authors: Troy Tara J , Bowling Laura C , Jame Sadia A , Lee Charlotte I , Liu Jing , Perry Chris , Richter Brian 
Published: June 2023

Abstract
Sustainable agricultural water systems are critical to ensure prosperous agricultural production, secure water resources, and support healthy ecosystems that sustain livelihoods and well-being. Many growing regions are using water unsustainably, leading to groundwater and streamflow depletion and polluted water bodies. Often, this is driven by global consumer demands, with environmental and social impacts occurring in regions far from where the crop is ultimately consumed. This letter defines sustainable agricultural water limits, both for quantity and quality, tying them to the impacts of agricultural water use, such as impacts on ecosystems, economies, human health, and other farmers. Imposing these limits will have a range of both positive and negative impacts on agricultural production, food prices, ecosystems, and health. Pathways forward exist and are proposed based on existing studies, showing the gains that can be made from the farm to global scale to ensure sustainable water systems while sustaining agricultural production.
Plasma synthesis of various polymorphs of tungsten trioxide nanoparticles using gliding electric discharge in humid air: characterization and photocatalytic properties
Authors: SEUTCHA Romaric L , KAMGANG-YOUBI Georges , ACAYANKA Elie , VERMILE Valeria , DEVRED François , GAIGNEAUX Eric M , LAMINSI Samuel 
Published: June 2023

Abstract
A gliding electric arc (glidarc) discharge generates a low-temperature plasma at atmospheric pressure. When the discharge occurs in humid air as the feed gas, the chemistry of a glidarc plasma consists of in situ formation of HO° and NO° as the primary chemical species. Tungsten trioxide (WO3) nanoparticles were successfully prepared by exposure of a liquid precursor to glidarc plasma. The WO3 samples were calcined at three different temperatures (300 °C, 500 °C and 800 °C), resulting in different pure polymorphs: γ-WO3 (at 300 °C), β-WO3 (at 500 °C) and α-WO3 (at 800 °C) according to x-ray diffraction analysis. The identification of WO3 compounds was also confirmed by attenuated total reflection Fourier transform infrared spectroscopy analysis. Increase in the calcination temperature of WO3 induced a decrease in its specific surface area according to Brunauer–Emmett–Teller nitrogen physisorption analysis. The UV-visible results showed that the absorption bands of plasma-WO3 samples were more intense than those of WO3 samples obtained by a precipitation route, a classical method used for comparison. Consequently, this parameter can improve the photocatalytic properties of WO3 under visible light. The photodegradation (in sunlight conditions) of gentian violet, chosen as a model pollutant, confirmed the photocatalytic properties of plasma-WO3 samples. This novel synthesis method has great potential to improve the efficiency of advanced tungsten trioxide-based functional material preparation, as well as in pollution-reducing and energy-saving tungsten extractive metallurgy.
Evaluation of a pharmacist-provider collaborative clinic for treatment of iron deficiency in patients with heart failure
Authors: Kido Kazuhiko , Fang Wei , Broscious Rachael , Colvin Bailey M , Kamal Khalid M , Bianco Christopher , Caccamo Marco , Felpel Kevin , Sokos George 
Published: June 2023

Abstract

Purpose
Intravenous iron therapy is recommended to improve symptoms and exercise tolerance in patients with heart failure (HF) with ­reduced ejection fraction and iron deficiency (ID), but there are limited published data on the implementation of intravenous iron therapy in practice. A pharmacist-provider collaborative ID treatment clinic was established within an advanced HF and pulmonary hypertension service to optimize IV iron therapy. The objective was to evaluate the clinical impacts of the pharmacist-provider collaborative ID treatment clinic.

Methods
A retrospective cohort study was performed to compare clinical outcomes among patients of the collaborative ID treatment clinic (the postimplementation group) and a cohort of patients who received usual care (the preimplementation group). The study included patients 18 years of age or older with diagnosed HF or pulmonary hypertension who met prespecified criteria for ID. The primary outcome was adherence to institutional intravenous iron therapy guidance. A key secondary outcome was ID treatment goal achievement.

Results
A total of 42 patients in the preimplementation group and 81 in the postimplementation group were included in the study. The rate of adherence to the institutional guidance was significantly improved in the postimplementation group (93%) compared to the preimplementation group (40%). There was no significant difference in the ID therapeutic target achievement rate between the pre- and postimplementation groups (38% vs 48%).

Conclusion
Implementing a pharmacist-provider collaborative ID treatment clinic significantly increased the number of patients who adhered to intravenous iron therapy guidance compared to usual care.
CroMaSt: a workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment
Authors: Dhondge Hrishikesh , Chauvot de Beauchêne Isaure , Devignes Marie-Dominique 
Published: June 2023

Abstract

Motivation
Protein domains can be viewed as building blocks, essential for understanding structure–function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, domain models and boundaries differ from one domain database to the other, raising the question of domain definition and enumeration of true domain instances.

Results
We propose an automated iterative workflow to assess protein domain classification by cross-mapping domain structural instances between domain databases and by evaluating structural alignments. CroMaSt (for Cross-Mapper of domain Structural instances) will classify all experimental structural instances of a given domain type into four different categories (‘Core’, ‘True’, ‘Domain-like’ and ‘Failed’). CroMast is developed in Common Workflow Language and takes advantage of two well-known domain databases with wide coverage: Pfam and CATH. It uses the Kpax structural alignment tool with expert-adjusted parameters. CroMaSt was tested with the RNA Recognition Motif domain type and identifies 962 ‘True’ and 541 ‘Domain-like’ structural instances for this domain type. This method solves a crucial issue in domain-centric research and can generate essential information that could be used for synthetic biology and machine-learning approaches of protein domain engineering.

Availability and implementation
The workflow and the Results archive for the CroMaSt runs presented in this article are available from WorkflowHub (doi: 10.48546/workflowhub.workflow.390.2).

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
A cross-validation-based statistical theory for point processes
Authors: Cronie Ottmar , Moradi Mehdi , Biscio Christophe A N 
Published: June 2023

Abstract
Motivated by the general ability of cross-validation to reduce overfitting and mean square error, we develop a cross-validation-based statistical theory for general point processes. It is based on the combination of two novel concepts for general point processes: cross-validation and prediction errors. Our cross-validation approach uses thinning to split a point process/pattern into pairs of training and validation sets, while our prediction errors measure discrepancy between two point processes. The new statistical approach, which may be used to model different distributional characteristics, exploits the prediction errors to measure how well a given model predicts validation sets using associated training sets. Having indicated that our new framework generalizes many existing statistical approaches, we then establish different theoretical properties for it, including large sample properties. We further recognize that nonparametric intensity estimation is an instance of Papangelou conditional intensity estimation, which we exploit to apply our new statistical theory to kernel intensity estimation. Using independent thinning-based cross-validation, we numerically show that the new approach substantially outperforms the state-of-the-art in bandwidth selection. Finally, we carry out intensity estimation for a dataset in forestry and a dataset in neurology.
Under pressure—mechanisms and risk factors for orthodontically induced inflammatory root resorption: a systematic review
Authors: Dawood Hassan M , Kroeger Annika , Chavda Vinay , Chapple Iain L C , Kebschull Moritz 
Published: June 2023

Summary

Background
The application of orthodontic forces causes root resorption of variable severity with potentially severe clinical ramifications.

Objective
To systematically review reports on the pathophysiological mechanisms of orthodontically induced inflammatory root resorption (OIIRR) and the associated risk factors based on in vitro, experimental, and in vivo studies.

Search methods
We undertook an electronic search of four databases and a separate hand-search.

Selection criteria
Studies reporting on the effect of orthodontic forces with/without the addition of potential risk factors on OIIRR, including (1) gene expression in in-vitro studies, the incidence root resorption in (2) animal studies, and (3) human studies.

Data collection and analysis
Potential hits underwent a two-step selection, data extraction, quality assessment, and systematic appraisal performed by duplicate examiners.

Results
One hundred and eighteen articles met the eligibility criteria. Studies varied considerably in methodology, reporting of results, and variable risk of bias judgements.
In summary, the variable evidence identified supports the notion that the application of orthodontic forces leads to (1) characteristic alterations of molecular expression profiles in vitro, (2) an increased rate of OIIRR in animal models, as well as (3) in human studies. Importantly, the additional presence of risk factors such as malocclusion, previous trauma, and medications like corticosteroids increased the severity of OIIRR, whilst other factors decreased its severity, including oral contraceptives, baicalin, and high caffeine.

Conclusions
Based on the systematically reviewed evidence, OIIRR seems to be an inevitable consequence of the application of orthodontic forces—with different risk factors modifying its severity. Our review has identified several molecular mechanisms that can help explain this link between orthodontic forces and OIIRR. Nevertheless, it must be noted that the available eligible literature was in part significantly confounded by bias and was characterized by substantial methodological heterogeneity, suggesting that the results of this systematic review should be interpreted with caution.

Registration
PROSPERO (CRD42021243431).
From necessity to opportunity: lessons for integrating phone and in-person data collection
Authors: Zezza Alberto , McGee Kevin , Wollburg Philip , Assefa Thomas , Gourlay Sydney 
Published: June 2023

Abstract
The Coronavirus disease pandemic has disrupted survey systems globally and especially in low- and middle-income countries. Phone surveys started being implemented at a national scale in many places that previously had limited experience with them. As in-person data collection resumes, the experience gained provides the grounds to reflect on how phone surveys may be incorporated into survey and data systems in low- and middle-income countries. Reviewing evidence and experiences from before and during the pandemic, the paper provides guidance on the scope of and considerations for using phone surveys for agricultural data collection and the integration of phone interviews with in-person data.
Communication via Biotremors in the Veiled Chameleon (Chamaeleo calyptratus): Part I- Biotremor Production and Response to Substrate-Borne Vibrations
Authors: Denny Kathryn L , Huskey Steve , Anderson Christopher V , Smith Michael E 
Published: June 2023

Synopsis
Biotremors are vibrations, usually surface waves along the boundary of a medium, produced by an organism. While substrate-borne vibrations are utilized by different reptile species, true conspecific communication via biotremors has not yet been demonstrated in lizards. Recent research revealed that the veiled chameleon (Chamaeleo calyptratus) produces biotremors. The prerequisites for any communication system are the ability of an organism to produce and detect a signal. We tested C. calyptratus behavioral responses to vibrations by placing them on a dowel attached to a shaker, emitting vibrations of 25, 50, 150, 300, and 600 Hz and compared their locomotory velocity before and after the stimulus. Adult chameleons exhibited a freeze response to 50 and 150 Hz, while juveniles exhibited a similar response to frequencies between 50 and 300 Hz. In a second experiment, chameleons were induced to produce biotremors via experimenter contact. These biotremors ranged in mean fundamental frequency from 106.4 to 170.3 Hz and in duration from 0.06 to 0.29 s. Overall, two classes of biotremors were identified, “hoots” and “mini-hoots,” which differed significantly in mean relative signal intensity (−7.5 and −32.5 dB, respectively). Juvenile chameleons 2 months of age were able to produce biotremors, suggesting this behavior may serve a wide range of ecological functions throughout ontogeny. Overall, the data demonstrate that C. calyptratus can both produce and detect biotremors that could be used for intraspecific communication.
Influence of shark tourism on the activity and physiological condition of a non-focal pelagic fish
Authors: Clarke Thomas M , Whitmarsh Sasha K , Champion Curtis , Pederson Hugh , Meyer Lauren , Dennis Joshua D , Dwyer Ross G , Huveneers Charlie 
Published: June 2023

Abstract
Wildlife tourism can have adverse effects on the behaviours and movements of animals, with implications for the health and fitness of individuals and populations. We used acoustic-tracking to show that food-based attractants used in shark-tourism increases activity (15%) and burst behaviours (60%) in yellowtail kingfish (Seriola lalandi, n = 18). Increased activity was restricted to periods when kingfish were on the same side of the island group as berleying tourism vessels, but decreased after operators left the site. Despite the raised activity and frequency of burst swimming events, the physiological condition of kingfish (n = 39, 6 tagged, and 33 untagged) measured using bioelectrical impedance analysis remained consistent with kingfish from control sites not exposed to tourism. This suggests that kingfish were able to compensate raised energy expenditure by feeding on bait and berley used by operators or through natural foraging. We highlight that the effects of provisioning from wildlife tourism can extend beyond changes in behaviours and movements and can additionally influence the energetic condition of non-focal animals through increased activity. However, supplemental food-sources provided through wildlife tourism may be sufficient to compensate for the increased energy expenditure and lessen the effects of tourism on individual fitness and health.
Adversarial ink: componentwise backward error attacks on deep learning
Authors: Beerens Lucas , Higham Desmond J 
Published: June 2023

Abstract
Deep neural networks are capable of state-of-the-art performance in many classification tasks. However, they are known to be vulnerable to adversarial attacks—small perturbations to the input that lead to a change in classification. We address this issue from the perspective of backward error and condition number, concepts that have proved useful in numerical analysis. To do this, we build on the work of Beuzeville, T., Boudier, P., Buttari, A., Gratton, S., Mary, T. and Pralet S. (2021) Adversarial attacks via backward error analysis. hal-03296180, version 3. In particular, we develop a new class of attack algorithms that use componentwise relative perturbations. Such attacks are highly relevant in the case of handwritten documents or printed texts where, for example, the classification of signatures, postcodes, dates or numerical quantities may be altered by changing only the ink consistency and not the background. This makes the perturbed images look natural to the naked eye. Such ‘adversarial ink’ attacks therefore reveal a weakness that can have a serious impact on safety and security. We illustrate the new attacks on real data and contrast them with existing algorithms. We also study the use of a componentwise condition number to quantify vulnerability.
Strategic Ontologies: Narrative and Meso-Level Theorizing in International Politics
Authors: Lerner Adam B , O'Loughlin Ben 
Published: June 2023

Abstract
This paper offers a theory of incremental theoretical evolution connecting the practice of international politics with disciplinary IR. It theorizes how international political actors engaged in strategic local decision-making exert productive power over dominant scientific ontologies of the international system. We refer to the narratives emerging from these processes as strategic ontologies, defined as gradual reformulations of the subjects, objects, and relational logics of the international system according to positionally determined priorities. As strategic ontologies gain acceptance, their innovations endure beyond the context of their utterance, leading to meso-level theoretical evolution. We substantiate this account with comparative case studies of contested strategic ontologies that have yet to become dominant in either the international arena or IR theory. Without strategic ontology as an analytical lens, scholarship might miss embryonic theoretical innovations in the process of gaining traction. First, we examine how Israel and West Germany engaged in strategic ontological contestation when negotiating a reparations agreement following the Holocaust. Second, we analyze how states have used vulnerability in climate negotiations in 2020–2021 to recast global policy priorities. Recognition of strategic ontologies across contexts illuminates theoretical innovations in real-time and opens a path for dynamic new bridges between the academy and policymaking.
DEPLOYR: a technical framework for deploying custom real-time machine learning models into the electronic medical record
Authors: Corbin Conor K , Maclay Rob , Acharya Aakash , Mony Sreedevi , Punnathanam Soumya , Thapa Rahul , Kotecha Nikesh , Shah Nigam H , Chen Jonathan H 
Published: June 2023

Abstract

Objective
Heatlhcare institutions are establishing frameworks to govern and promote the implementation of accurate, actionable, and reliable machine learning models that integrate with clinical workflow. Such governance frameworks require an accompanying technical framework to deploy models in a resource efficient, safe and high-quality manner. Here we present DEPLOYR, a technical framework for enabling real-time deployment and monitoring of researcher-created models into a widely used electronic medical record system.

Materials and Methods
We discuss core functionality and design decisions, including mechanisms to trigger inference based on actions within electronic medical record software, modules that collect real-time data to make inferences, mechanisms that close-the-loop by displaying inferences back to end-users within their workflow, monitoring modules that track performance of deployed models over time, silent deployment capabilities, and mechanisms to prospectively evaluate a deployed model’s impact.

Results
We demonstrate the use of DEPLOYR by silently deploying and prospectively evaluating 12 machine learning models trained using electronic medical record data that predict laboratory diagnostic results, triggered by clinician button-clicks in Stanford Health Care’s electronic medical record.

Discussion
Our study highlights the need and feasibility for such silent deployment, because prospectively measured performance varies from retrospective estimates. When possible, we recommend using prospectively estimated performance measures during silent trials to make final go decisions for model deployment.

Conclusion
Machine learning applications in healthcare are extensively researched, but successful translations to the bedside are rare. By describing DEPLOYR, we aim to inform machine learning deployment best practices and help bridge the model implementation gap.
Integrating sperm cell transcriptome and seminal plasma metabolome to analyze the molecular regulatory mechanism of sperm motility in Holstein stud bulls
Authors: Li Wenlong , Mi Siyuan , Zhang Jinning , Liu Xueqin , Chen Siqian , Liu Shuli , Feng Xia , Tang Yongjie , Li Yanhua , Liu Lin , Fang Lingzhao , Zhang Shengli , Yu Ying 
Published: June 2023

Abstract
Considering that artificial insemination is the most widely used assisted reproductive technique in the dairy industry, the semen quality of bulls is very important for selecting excellent stud bulls. Sperm motility is one of the important traits of semen quality, and related genes may be regulated by environmental factors. Seminal plasma can affect sperm cell transcriptome and further affect sperm motility through exosome or other processes. However, the molecular regulation mechanism of bull sperm motility has not been studied by combining the sperm cell transcriptome with seminal plasma metabolome. The number of motile sperm per ejaculate (NMSPE) is an integrated indicator for assessing sperm motility in stud bulls. In the present study, we selected 7 bulls with higher NMSPE (5,698.55 million +/− 945.40 million) as group H and 7 bulls with lower NMSPE (2,279.76 million +/− 1,305.69 million) as group L from 53 Holstein stud bulls. The differentially expressed genes (DEGs) in sperm cells were evaluated between the two groups (H vs. L). We conducted gene co-expression network analysis (WGCNA) on H and L groups of bulls, as well as two monozygotic twin Holstein bulls with different NMSPE values, to screen candidate genes for NMSPE. The regulatory effect of seminal plasma metabolome on the candidate genes of NMSPE was also investigated. A total of 1,099 DEGs were identified in the sperm cells of H and L groups. These DEGs were primarily concentrated in energy metabolism and sperm cell transcription. The significantly enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways of the 57 differential metabolites were the aminoacyl–tRNA biosynthesis pathway and vitamin B6 metabolism pathway. Our study discovered 14 genes as the potential candidate markers for sperm motility, including FBXO39. We observed a broad correlation between transcriptome of sperm cells and seminal plasma metabolome, such as three metabolites, namely, mesaconic acid, 2-coumaric acid, and 4-formylaminoantipyrine, might regulate FBXO39 expression through potential pathways. The genes related to seminal plasma metabolites expressed in sperm cells are not only located near the quantitative trait loci of reproductive traits, but also enriched in the genome-wide association study signal of sire conception rate. Collectively, this study was the first to investigate the interplays among transcriptome of sperm cells and seminal plasma metabolome from Holstein stud bulls with different sperm motility.