bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
Authors: Zuffa Simone , Schmid Robin , Bauermeister Anelize , Gomes Paulo Wender P. , Caraballo-Rodriguez Andres M. , Abiead Yasin El , Aron Allegra T. , Gentry Emily C. , Zemlin Jasmine , Meehan Michael J. , Avalon Nicole E. , Cichewicz Robert H. , Buzun Ekaterina , Terrazas Marvic Carrillo , Hsu Chia-Yun , Oles Renee , Ayala Adriana Vasquez , Zhao Jiaqi , Chu Hiutung , Kuijpers Mirte C. M. , Jackrel Sara L. , Tugizimana Fidele , Nephali Lerato Pertunia , Dubery Ian A. , Madala Ntakadzeni Edwin , Moreira Eduarda Antunes , Costa-Lotufo Leticia Veras , Lopes Norberto Peporine , Rezende-Teixeira Paula , Jimenez Paula C. , Rimal Bipin , Patterson Andrew D. , Traxler Matthew F. , de Cassia Pessotti Rita , Alvarado-Villalobos Daniel , Tamayo-Castillo Giselle , Chaverri Priscila , Escudero-Leyva Efrain , Quiros-Guerrero Luis-Manuel , Bory Alexandre Jean , Joubert Juliette , Rutz Adriano , Wolfender Jean-Luc , Allard Pierre-Marie , Sichert Andreas , Pontrelli Sammy , Pullman Benjamin S , Bandeira Nuno , Gerwick William H. , Gindro Katia , Massana-Codina Josep , Wagner Berenike C. , Forchhammer Karl , Petras Daniel , Aiosa Nicole , Garg Neha , Liebeke Manuel , Bourceau Patric , Kang Kyo Bin , Gadhavi Henna , de Carvalho Luiz Pedro Sorio , dos Santos Mariana Silva , Pérez-Lorente Alicia Isabel , Molina-Santiago Carlos , Romero Diego , Franke Raimo , Brönstrup Mark , de León Arturo Vera Ponce , Pope Phillip Byron , La Rosa Sabina Leanti , Barbera Giorgia La , Roager Henrik M. , Laursen Martin Frederik , Hammerle Fabian , Siewert Bianka , Peintner Ursula , Licona-Cassani Cuauhtemoc , Rodriguez-Orduña Lorena , Rampler Evelyn , Hildebrand Felina , Koellensperger Gunda , Schoeny Harald , Hohenwallner Katharina , Panzenboeck Lisa , Gregor Rachel , O’Neill Ellis Charles , Roxborough Eve Tallulah , Odoi Jane , Bale Nicole J. , Ding Su , Sinninghe Damsté Jaap S. , Guan Xueli Li , Cui Jerry J. , Ju Kou-San , Silva Denise Brentan , Ribeiro Silva Fernanda Motta , da Silva Gilvan Ferreira , Koolen Hector H. F. , Grundmann Carlismari , Clement Jason A. , Mohimani Hosein , Broders Kirk , McPhail Kerry L. , Ober-Singleton Sidnee E. , Rath Christopher M. , McDonald Daniel , Knight Rob , Wang Mingxun , Dorrestein Pieter C. 
Published: July 2023

AbstractMicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, withouta prioriknowledge, will vastly enhance the understanding of microorganisms’ role in ecology and human health.
Seafloor Incubation Experiments at Deep-Sea Hydrothermal Vents Reveal Distinct Biogeographic Signatures of Autotrophic Communities
Authors: Fullerton Heather , Smith Lindsey , Enriquez Alejandra , Butterfield David , Wheat C. Geoffrey , Moyer Craig L. 
Published: July 2023

AbstractThe discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon dioxide and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama’ehuakanaloa Seamount (Hawai’i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama’ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. These results provide insights to nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
A positive association between gut microbiota diversity and vertebrate host performance in a field experiment
Authors: Härer Andreas , Thompson Ken A. , Schluter Dolph , Rennison Diana J. 
Published: July 2023

AbstractThe vertebrate gut microbiota is a critical determinant of organismal function, yet it remains unclear if and how gut microbial communities affect host fitness under natural conditions. Here, we investigate associations between growth rate (a fitness proxy) and gut microbiota diversity and composition in a field experiment with threespine stickleback fish (Gasterosteus aculeatus). We detected on average 63% more bacterial taxa in the guts of high-fitness fish compared to low-fitness fish (i.e., higher α-diversity), suggesting that higher diversity promotes host growth. The microbial communities of high-fitness fish had higher similarity (i.e., lower β-diversity) than low-fitness fish, supporting the Anna Karenina principle— that there are fewer ways to have a functional microbiota than a dysfunctional microbiota. Our findings provide a basis for functional tests of the fitness consequences of host-microbiota interactions.Significance statementThe vertebrate gut microbiota is important for many aspects of their hosts’ biology—such as nutrient metabolism and defense against pathogens—that could ultimately affect host fitness. However, studies investigating the effects of gut microbiota composition on vertebrate host fitness under natural conditions remain exceedingly rare. We tested for associations between gut microbiota diversity and growth rate (a fitness proxy) in threespine stickleback fish reared in large outdoor ponds. We found evidence that a more diverse gut microbiota was predictive of higher growth rate and therefore increased host fitness. Notably, high-fitness fish had higher gut microbiota similarity to one another than did low-fitness fish, providing experimental evidence for the Anna Karenina principle—that there are fewer ways to have a functional microbiota than a dysfunctional microbiota—as it relates to host fitness.
Carbon dioxide emissions and the economic growth: competitiveness and economic development view
Authors: Hamdan Allam 
Published: July 2023

Purpose
This study aims to shed light on the experience of the United Arab Emirates (UAE) in balancing three main pillars: the environmental criteria, the reduction of CO2 emissions and the economic growth. Based on the environmental Kuznets curve (EKC) framework, it will assess the causal relationship between economic indicators such as gross domestic product (GDP) per capita, trade openness and energy use and environmental indicators such as CO2 emissions.

Design/methodology/approach
The analysis relies on a period of 40 years (1981–2020) where data is extracted from the World Bank database. This study uses the unit root test for time series stationarity, the optimal lag length test, the “Johansen” test for co-integration and the vector error correction model.

Findings
The paper concludes to two major findings. On a short-term basis, CO2 emissions and economic indicators are negatively correlated, whereas on a long-term basis, there is no association between CO2 emissions and economic indicators in the UAE.

Research limitations/implications
The research ends with important recommendations. It illustrates the importance of rationalizing the use of primary resources and the necessity to embrace successful and efficient policies in the energy production.

Practical implications
More specifically, UAE is urged to address the problem of CO2 emissions in the electricity sector and increase awareness of the use of environmentally friendly processes in the transport and industrial sectors. While setting their economic agendas, UAE are encouraged to meet environmental criteria and invest in renewable energy projects such as “Shams 1”, the largest solar power plant outside of Spain and the USA.

Originality/value
The current study is significant in its research on the environmental impact of economic development, trade openness and energy use policies in the UAE. It uses CO2 emissions as an environmental proxy and evaluates the environmental policies adopted in the UAE to reduce its impact.
The effects of national and international tourism on income inequality: evidence from Asia-Pacific economies
Authors: Paramati Sudharshan Reddy , Nguyen Thanh Pham Thien 
Published: July 2023

PurposeThis paper explores the effect of tourism (national and international) indicators on income inequality in a sample of 21 Asia Pacific economies.Design/methodology/approachThis study uses panel data set from 1995 to 2020 and employs panel autoregressive distributed lag (ARDL) method for the empirical investigation.FindingsThe empirical findings from the panel ARDL models suggest that all of the considered tourism indicators have significant negative impacts on income inequalities. The results remain consistent with alternative indicators and methods.Social implicationsThe findings of this study will be critical for the policymakers to take effective measures to reduce the income inequality. Such measures could include promoting tourism in general, focusing on attracting international tourists or domestic tourists, and putting more weight on developing leisure or business tourism, which will boost the overall economic performance and alleviates inequalities in the society.Originality/valueThis is the first study to consider various forms of tourism indicators to see their impact on income inequality in the Asia–Pacific region, and offers important implications for the policy actions.
Automation of tree‐ring detection and measurements using deep learning
Authors: Poláček Miroslav , Arizpe Alexis , Hüther Patrick , Weidlich Lisa , Steindl Sonja , Swarts Kelly 
Published: July 2023

Abstract

Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour‐intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network‐based implementation that automates detection and measurement of tree‐ring boundaries from coniferous species.

We trained our Mask R‐CNN extensively on over 8000 manually annotated ring boundaries from microscope‐imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post‐processing on real‐world data generated from our core processing pipeline.

The CNN after post‐processing performed well, with recognition of over 98% of ring boundaries (recall) with a precision in detection of 96% when tested on real‐world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure.

We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN‐based system provides high predictive performance in terms of both tree‐ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re‐training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring‐width measurements in a commonly used .pos format, facilitating the efficient generation of large ring‐width measurement datasets from increment core samples, an important source of environmental data.
Low‐molecular‐weight heparin in thrombophilic women receiving in vitro fertilization/intracytoplasmic sperm injection: A meta‐analysis
Authors: Chen Jingsi , Bie Jia , Jiang Fangjie , Wu Yanzhi , Pan Zhengmei , Meng Yushi , Song Jiamei , Liu Yang 
Published: July 2023

AbstractIntroductionThis meta‐analysis aimed to evaluate the efficacy and safety of low‐molecular‐weight heparin (LMWH) on pregnancy outcomes in thrombophilic women receiving in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI).Material and methodsA systematic literature search of PubMed, EMBASE, the Cochrane Library, and China National Knowledge Infrastructure was performed to identify randomized controlled trials (RCTs) comparing LMWH with no treatment or placebo published from database inception until February 19, 2023. Primary outcomes were the clinical pregnancy rate and implantation rate, and secondary outcomes were the live birth rate, miscarriage rate, and the risk of bleeding events. The certainty of the evidence was rated using the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) system. Meta‐analysis was conducted using STATA 14.0.ResultsFive RCTs involving 1094 thrombophilic women receiving IVF/ICSI were finally included. Administration of LMWH was associated with statistically higher clinical pregnancy rate (4 RCTs, risk ratio [RR] 1.50, 95% confidence interval [CI] 1.23–1.82, p < 0.001, low certainty evidence), implantation rate (5 RCTs, RR 1.49, 95% CI 1.25–1.78, p < 0.001, very low certainty evidence), and live birth rate (2 RCTs, RR 2.15, 95% CI 1.60–2.89, p < 0.001, very low certainty evidence), but with statistically lower miscarriage rate (2 RCTs, RR 0.36, 95% CI 0.15–0.86, p = 0.021, very low certainty evidence). However, using LMWH was linked to a higher risk of bleeding events (2 RCTs, RR 2.36, 95% CI 1.49–3.74, p < 0.001, very low certainty evidence).ConclusionsVery low certainty evidence suggests that administration of LMWH may benefit pregnancy outcomes in thrombophilic women receiving IVF/ICSI treatment, although it may also increase the risk of bleeding events. However, before putting our findings into practice, healthcare professionals should conduct an in‐depth evaluation of the available evidence and specific patient situations. Furthermore, due to the low methodological quality of the included studies, more high‐quality studies are needed to validate our findings in the future.
Sexual health in diabetes care is a ‘hot topic’–A qualitative study with Diabetes Specialist Nurses
Authors: Yin Janina , Rämgård Margaret , Wangel Anne‐Marie 
Published: July 2023

AbstractAimThe aim of this study is to illuminate Diabetes Specialist Nurses' experiences of having a conversation about sexual health with adults with diabetes.BackgroundIt is well known that diabetes mellitus may affect a person's sexual function. Interview studies with men and women living with diabetes show that conversations about sexual health are important. However, research on Diabetes Specialist Nurses' experiences of having such conversations is limited.DesignA qualitative approach, with individual interviews, was used.MethodPurposive sampling was used to recruit 12 informants from adult diabetes care, within primary health care and within hospital settings in southern Sweden, between September and November 2021. A qualitative latent content analysis was used for data analysis. The COREQ guidelines were followed to ensure rigour for this study.ResultsOne theme, ‘Sexual health is a hot topic’, could be understood in light of three categories: ‘Obstructive factors that complicate the conversation’, ‘Promoting factors that facilitate the conversation’ and ‘Improvements that may facilitate the conversation’. The findings embrace the Diabetes Specialist Nurses' experiences of having a conversation about sexual health with persons with diabetes.ConclusionsDiabetes Specialist Nurses often experience difficulty having a conversation about sexual health with their patients. The findings provide a deeper understanding of their experiences of obstructive as well as promoting factors related to conversations about what is considered a ‘hot topic’.Relevance to Clinical PracticeTo increase knowledge on how to have a conversation about sexual health within diabetes care, support is needed from the organisation; the organisation could, for instance, support the diabetes care staff in gaining education and training regarding sexual health.Patient or Public ContributionNot applicable due to the current method.
Histone deacetylase MdHDA6 is an antagonist in regulation of transcription factor MdTCP15 to promote cold tolerance in apple
Authors: Guo Meimiao , Wang Shicong , Liu Han , Yao Senyang , Yan Jinjiao , Wang Caixia , Miao Bingjie , Guo Junxing , Ma Fengwang , Guan Qingmei , Xu Jidi 
Published: July 2023

SummaryUnderstanding the molecular regulation of plant cold response is the basis for cold resistance germplasm improvement. Here, we revealed that the apple histone deacetylase MdHDA6 can perform histone deacetylation on cold‐negative regulator genes and repress their expression, leading to the positive regulation of cold tolerance in apples. Moreover, MdHDA6 directly interacts with the transcription factor MdTCP15. Phenotypic analysis of MdTCP15 transgenic apple lines and wild types reveals that MdTCP15 negatively regulates cold tolerance in apples. Furthermore, we found that MdHDA6 can facilitate histone deacetylation of MdTCP15 and repress the expression of MdTCP15, which positively contributes to cold tolerance in apples. Additionally, the transcription factor MdTCP15 can directly bind to the promoter of the cold‐negative regulator gene MdABI1 and activate its expression, and it can also directly bind to the promoter of the cold‐positive regulator gene MdCOR47 and repress its expression. However, the co‐expression of MdHDA6 and MdTCP15 can inhibit MdTCP15‐induced activation of MdABI1 and repression of MdCOR47, suggesting that MdHDA6 suppresses the transcriptional regulation of MdTCP15 on its downstream genes. Our results demonstrate that histone deacetylase MdHDA6 plays an antagonistic role in the regulation of MdTCP15‐induced transcriptional activation or repression to positively regulate cold tolerance in apples, revealing a new regulatory mechanism of plant cold response.
Rose bengal–encapsulated chitosan nanoparticles for the photodynamic treatment of Trichophyton species
Authors: Bekmukhametova Alina , Antony Anu , Halliday Catriona , Chen Sharon , Ho Chun‐Hoong , Uddin Mir Muhammad Nasir , Longo Leonardo , Pedrinazzi Christian , George Laurel , Wuhrer Richard , Myers Simon , Mawad Damia , Houang Jessica , Lauto Antonio 
Published: July 2023

AbstractRose bengal (RB) solutions coupled with a green laser have proven to be efficient in clearing resilient nail infections caused by Trichophyton rubrum in a human pilot study and in extensive in vitro experiments. Nonetheless, the RB solution can become diluted or dispersed over the tissue and prevented from penetrating the nail plate to reach the subungual area where fungal infection proliferates. Nanoparticles carrying RB can mitigate the problem of dilution and are reported to effectively penetrate through the nail. For this reason, we have synthesized RB‐encapsulated chitosan nanoparticles with a peak distribution size of ~200 nm and high reactive oxygen species (ROS) production. The RB‐encapsulated chitosan nanoparticles aPDT were shown to kill more than 99% of T. rubrum, T. mentagrophytes, and T. interdigitale spores, which are the common clinically relevant pathogens in onychomycosis. These nanoparticles are not cytotoxic against human fibroblasts, which promotes their safe application in clinical translation.
Mismatch between syntax and prosody and complex sentence structure in Hittite
Authors: Sideltsev Andrei V. 
Published: July 2023

Abstract
Hittite attests a set of complex sentences in which (mostly) relative clauses (other subordinate clauses are also attested) appear in linear syntax to be within another subordinate (usually conditional, rarely temporal) clause or main clause. The relative clause can be preceded by a very limited array of constituents from the matrix clause, e.g., mān ‘if’ or the quotative particle ⸗wa(r). There are also examples which attest the conditional subordinator and the irrealis particle in two positions simultaneously, at the left edge of the whole sentence and in the conditional clause (= main clause for the relative clause). I provide a fine-grained descriptive and structural analysis of the structure and show that the type cannot be explained as bare indefinites, embedded relative clauses or parenthetic clauses. It is shown that, structurally, the sentences containing subordinate (mostly relative) clauses within other clauses are heterogenous and of three types. The difference lies in the elements that precede the relative clause and in the structure of the sentences, whereby a standard Hittite relative clause adjoins at different heights. All three types display the same mismatch between prosodic domains and syntax/semantics—the constituent that is part of the main clause from the semantic and syntactic perspective is prosodically part of the relative clause. Since there is a clause boundary delimiting the end of the subordinate clause within the main clause, it makes sense to treat the surface structure as a distinct taxonomic unit, which is correspondingly labelled a mismatch sentence. The new evidence allows us to obtain a fuller understanding of the Hittite left periphery than was previously possible. It thus offers an important window into hitherto unrecognized aspects of the underlying structure of the complex sentence in Hittite.