bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach
Authors: Filip Ewa , Strzała Tomasz , Stępień Edyta , Cembrowska-Lech Danuta 
Published: June 2023

AbstractThe aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene forCapreolus capreolus,Dama dama, andCervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminatingCervidaespecies, with BLOG and WEKAs SMO classifier performing the best.
Association between marital status and all-cause mortality of patients with metastatic breast cancer: a population-based study
Authors: Zhu Shouqiang , Lei Chong 
Published: June 2023

AbstractThis study aimed to investigate the association between marital status and the prognosis of patients with metastatic breast cancer (MBC). Data of patients with MBC were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Patients were classified into married and unmarried groups. Kaplan–Meier analysis with the log-rank test was conducted to compare breast cancer-specific survival (BCSS) and overall survival (OS) between the groups. Univariable and multivariable Cox proportional models were used to determine whether marital status was independently associated with OS, and the Fine–Gray subdistribution hazard method was performed to determine whether marital status was independently associated with BCSS. In total, 16,513 patients with MBC were identified, including 8949 married (54.19%) and 7564 unmarried (45.81%) patients. The married patients were significantly younger [median age (interquartile range), 59.0 (50.0–68.0) vs. 63.0 (53.0–75.0); p < 0.001] and received more aggressive treatments, such as chemotherapy (p < 0.001) and surgery (p < 0.001), than the unmarried patients. Moreover, married patients had higher 5-year BCSS (42.64% vs. 33.17%, p < 0.0001) and OS (32.22% vs. 21.44%, p < 0.0001) rates. Multivariable analysis revealed that marital status was an independent prognostic factor, and married status was associated with a significant reduction in the risk of breast cancer-specific (sub-hazard ratio, 0.845; 95% confidence interval, 0.804–0.888; p < 0.001) and all-cause (hazard ratio, 0.810; 95% confidence interval, 0.777–0.844; p < 0.001) mortality. Unmarried patients had a 15.5% increased risk of breast cancer-specific mortality and a 19.0% increased risk of overall mortality compared with married patients with MBC. BCSS and OS were superior in married populations compared with unmarried populations in most subgroups. Marital status was an independent prognostic indicator for survival in patients with MBC and was associated with significant survival benefits.
Validation of self-report of uterine fibroid diagnosis using a transvaginal ultrasound scan
Authors: Adebamowo Clement A. , Morhason-Bello Imran O. ,   The ACCME Research Group as part of the H3Africa Consortium, Famooto Ayotunde O. , Offiong Richard , Olaniyan Olayinka , Obende Kayode , Adebayo Amos , Ologun Sanni , Alabi Bunmi , Achara Peter , Adebamowo Sally N. 
Published: June 2023

AbstractSelf-report of uterine fibroids (UF) has been used for epidemiologic research in different environments. Given the dearth of studies on the epidemiology of UF in Sub-Saharan Africa (SSA), it is valuable to evaluate its performance as a potential tool for much needed research on this common neoplasm in SSA women. We conducted a cross-sectional study of self-report of UF compared with transvaginal ultrasound diagnosis (TVUS) among 486 women who are members of the African Collaborative Center for Microbiome and Genomics Research (ACCME) Study Cohort in central Nigeria. We used log-binomial regression models to compute the classification, sensitivity, specificity, and predictive values of self-report compared to TVUS, adjusted for significant covariates. The prevalence of UF on TVUS was 45.1% (219/486) compared to 5.4% (26/486) based on self-report of abdominal ultrasound scan and 7.2% (35/486) based on report of healthcare practitioner’s diagnosis. Self-report correctly classified 39.5% of the women compared to TVUS in multivariable adjusted models. The multivariable adjusted sensitivity of self-report of healthcare worker diagnosis was 38.8%, specificity was 74.5%, positive predictive value (PPV) was 55.6%, and negative predictive value (NPV) was 59.8%. For self-reported abdominal ultrasound diagnosis, the multivariable adjusted sensitivity was 40.6%, specificity was 75.3%, PPV was 57.4%, and NPV was 60.6%. Self-report significantly underestimates the prevalence of UF and is not accurate enough for epidemiological research on UF. Future studies of UF should use population-based designs and more accurate diagnostic tools such as TVUS.
Association between changes in serum alkaline phosphatase levels and radiographic progression in ankylosing spondylitis
Authors: Kim Tae-Hwan , Park Seo Young , Shin Ji Hui , Lee Seunghun , Joo Kyung Bin , Koo Bon San 
Published: June 2023

AbstractThis retrospective study evaluated the electronic medical records of patients with ankylosing spondylitis (AS) (January 2001–December 2018) to determine the relationship between serum alkaline phosphatase (ALP) levels and radiographic changes over time. Longitudinal data, including serum ALP levels, were imputed by linear interpolation at 3-month intervals. Among the serum ALP levels calculated for 8 years prior to modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS) measurement, those having the highest beta coefficient with the mSASSS were selected in the correlation between ALP and longitudinal mSASSS. Linear mixed models with the selected serum ALP levels, mSASSS, and clinical variables were investigated. We included 1122 patients (mean follow-up, 8.20 [standard deviation: 2.85] years). The serum ALP level from 5 years and 3 months prior showed the highest beta coefficient with the mSASSS. In the linear mixed model, the serum ALP level at 5 years and 3 months before radiographic changes was significantly associated with the mSASSS (β = 0.021, 95% confidence interval: 0.017–0.025,p < 0.001). Serum ALP levels measured approximately 5 years before may be a surrogate marker for predicting spinal radiographic changes. Long-term prospective clinical and experimental studies of > 5 years are required for biomarker discovery or therapeutic research on AS radiographic progression.
Characteristic of phosphorus rich compounds in the incinerated sewage sludge ashes: a case for sustainable waste management
Authors: Kasina Monika , Jarosz Kinga , Stolarczyk Mateusz , Göttlicher Jörg , Steininger Ralph , Michalik Marek 
Published: June 2023

AbstractGrowing concern over mineral resources supply forces us to search for alternative sources of Phosphorus. The possibility to recover phosphorus from incinerated sewage sludge ashes appears to be an important aspect in anthropogenic phosphorus cycle and sustainable economy. To make phosphorus recovery efficient it is important to learn the chemical and mineral composition of ash and phosphorus speciation. The phosphorus content in the ash was over 7%, what corresponds to medium rich phosphorus ores. The main phosphorus rich mineral phases were phosphate minerals. The most widespread was tri-calcium phosphate Whitlockite with various Fe, Mg and Ca proportions. In minority Fe–PO4 and Mg–PO4 were detected. Whitlockite commonly overgrown with hematite, influences negatively mineral solubility and thus recovery potential and indicates low bioavailability of phosphorus. Considerable amount of phosphorus was found in the low crystalline matrix where phosphorus content was around 10 wt% however low crystallinity and dispersed phosphorus also does not strengthen the potential to recover this element.
Inherent seizure susceptibility in patients with antihistamine-induced acute symptomatic seizure: a resting-state EEG analysis
Authors: Kim Hayom , Wang In-Nea , Park Jun-Su , Kim Keun-Tae , Kong Jooheon , Kim Jung Bin , Kim Dong-Joo 
Published: June 2023

AbstractWe compared neural activities and network properties between the antihistamine-induced seizures (AIS) and seizure-free groups, with the hypothesis that patients with AIS might have inherently increased neural activities and network properties that are easily synchronized. Resting-state electroencephalography (EEG) data were collected from 27 AIS patients and 30 healthy adults who had never had a seizure. Power spectral density analysis was used to compare neural activities in each localized region. Functional connectivity (FC) was measured using coherence, and graph theoretical analyses were performed to compare network properties between the groups. Machine learning algorithms were applied using measurements found to be different between the groups in the EEG analyses as input features. Compared with the seizure-free group, the AIS group showed a higher spectral power in the entire regions of the delta, theta, and beta bands, as well as in the frontal areas of the alpha band. The AIS group had a higher overall FC strength, as well as a shorter characteristic path length in the theta band and higher global efficiency, local efficiency, and clustering coefficient in the beta band than the seizure-free group. The Support Vector Machine, k-Nearest Neighbor, and Random Forest models distinguished the AIS group from the seizure-free group with a high accuracy of more than 99%. The AIS group had seizure susceptibility considering both regional neural activities and functional network properties. Our findings provide insights into the underlying pathophysiological mechanisms of AIS and may be useful for the differential diagnosis of new-onset seizures in the clinical setting.
A global analysis of violence against women defenders in environmental conflicts
Authors: Tran Dalena , Hanaček Ksenija 
Published: June 2023

AbstractWomen environmental defenders face retaliation for mobilizing against extractive and polluting projects, which perpetrate violence against Indigenous, minority, poor and rural communities. The issue matters because it highlights the gendered nature of extractive violence and the urgent need to address the systemic patterns of violence that affect women defenders, who are often overlooked and underreported. Here we analyse violence against women defenders in environmental conflicts around the world. We use data from the Environmental Justice Atlas and employ log-linear and binomial regressions to find statistically significant patterns in displacement, repression, criminalization, violent targeting and assassinations committed against women defenders in extractive conflicts. Statistical results indicate that violence against women defenders is concentrated among mining, agribusiness and industrial conflicts in the geographical South. Repression, criminalization and violent targeting are closely linked, while displacement and assassination appear as extreme outcomes when conflict violence worsens. Women defenders experience high rates of violence regardless of countries’ governance accountability and gender equality. This work contributes to the broader sustainability agenda by highlighting the need to address the impacts of extractive activities on women.
Compensation for atmospheric appropriation
Authors: Fanning Andrew L. , Hickel Jason 
Published: June 2023

AbstractResearch on carbon inequalities shows that some countries are overshooting their fair share of the remaining carbon budget and hold disproportionate responsibility for climate breakdown. Scholars argue that overshooting countries owe compensation or reparations to undershooting countries for atmospheric appropriation and climate-related damages. Here we develop a procedure to quantify the level of compensation owed in a ‘net zero’ scenario where all countries decarbonize by 2050, using carbon prices from IPCC scenarios that limit global warming to 1.5 °C and tracking cumulative emissions from 1960 across 168 countries. We find that even in this ambitious scenario, the global North would overshoot its collective equality-based share of the 1.5 °C carbon budget by a factor of three, appropriating half of the global South’s share in the process. We calculate that compensation of US$192 trillion would be owed to the undershooting countries of the global South for the appropriation of their atmospheric fair shares by 2050, with an average disbursement to those countries of US$940 per capita per year. We also examine countries’ overshoot of equality-based shares of 350 ppm and 2 °C carbon budgets and quantify the level of compensation owed using earlier and later starting years (1850 and 1992) for comparison.
C11orf54 promotes DNA repair via blocking CMA-mediated degradation of HIF1A
Authors: Tan Junyang , Wang Wenjun , Liu Xinjie , Xu Jinhong , Che Yaping , Liu Yanyan , Hu Jiaqiao , Hu Liubing , Li Jianshuang , Zhou Qinghua 
Published: June 2023

AbstractC11orf54 is an ester hydrolase highly conserved across different species. C11orf54 has been identified as a biomarker protein of renal cancers, but its exact function remains poorly understood. Here we demonstrate that C11orf54 knockdown decreases cell proliferation and enhances cisplatin-induced DNA damage and apoptosis. On the one hand, loss of C11orf54 reduces Rad51 expression and nuclear accumulation, which results in suppression of homologous recombination repair. On the other hand, C11orf54 and HIF1A competitively interact with HSC70, knockdown of C11orf54 promotes HSC70 binding to HIF1A to target it for degradation via chaperone-mediated autophagy (CMA). C11orf54 knockdown-mediated HIF1A degradation reduces the transcription of ribonucleotide reductase regulatory subunit M2 (RRM2), which is a rate-limiting RNR enzyme for DNA synthesis and DNA repair by producing dNTPs. Supplement of dNTPs can partially rescue C11orf54 knockdown-mediated DNA damage and cell death. Furthermore, we find that Bafilomycin A1, an inhibitor of both macroautophagy and chaperone-mediated autophagy, shows similar rescue effects as dNTP treatment. In summary, we uncover a role of C11orf54 in regulating DNA damage and repair through CMA-mediated decreasing of HIF1A/RRM2 axis.
Insight into the formation of bismuth-tungsten carbonyl clusters
Authors: Beuthert Katrin , Peerless Benjamin , Dehnen Stefanie 
Published: June 2023

AbstractMultimetallic clusters play a key role as models to doped metals, as candidates to new types of superatomic catalysts and as precursors to new multimetallic solids. Understanding formation pathways is an essential and necessary step forward in the development of cluster synthesis and research, yet remains considerably lacking owing to difficulty in identification of intermediates and the ill-defined nature of common starting materials. Here we show progress in this regard by investigating the reactivity of an intermetallic solid of nominal composition ‘K5Ga2Bi4’ with [W(cod)(CO)4] upon extraction with ethane-1,2-diamine (en) and 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane (crypt-222). Several polybismuthide intermediates and by-products were identified along the reaction pathway, ultimately forming the new polybismuthide salt [K(crypt-222)]3[µ:η3-Bi3{W(CO)3}2]∙en∙tol. DFT calculations revealed plausible reaction schemes for the transformations taking place in the reaction mixture providing insight into the complex reactivity of ‘K5Ga2Bi4’ on the basis of in situ generation of Bi22−.
Multi pathways temporal distance unravels the hidden geometry of network-driven processes
Authors: Bontorin Sebastiano , De Domenico Manlio 
Published: June 2023

AbstractNetwork-based interactions allow one to model many technological and natural systems, where understanding information flow between nodes is important to predict their functioning. The complex interplay between network connectivity and dynamics can be captured by scaling laws overcoming the paradigm of information spread being solely dependent on network structure. Here, we capitalize on this paradigm to identify the relevant paths for perturbation propagation. We introduce a multi-pathways temporal distance between nodes that overcomes the limitation of focussing only on the shortest path. This metric predicts the latent geometry induced by the dynamics in which the signal propagation resembles the traveling wave solution of reaction-diffusion systems. We validate the framework on a set of synthetic dynamical models, showing that it outperforms existing approaches in predicting arrival times. On a set of empirical contact-based social systems, we show that it can be reliably used also for models of infectious diseases spread - such as the Susceptible-Infected-Susceptible - with remarkable accuracy in predicting the observed timing of infections. Our framework naturally encodes the concerted behavior of the ensemble of paths connecting two nodes in conveying perturbations, with applications ranging from regulatory dynamics within cells to epidemic spreading in social networks.
Flux-flow instability across Berezinskii Kosterlitz Thouless phase transition in KTaO3 (111) based superconductor
Authors: Kumar Ojha Shashank , Mandal Prithwijit , Kumar Siddharth , Maity Jyotirmay , Middey Srimanta 
Published: June 2023

AbstractThe nature of energy dissipation in 2D superconductors under perpendicular magnetic field at small current excitations has been extensively studied over the past two decades. However, dissipation mechanisms at high current drives remain largely unexplored. Here we report on the distinct behavior of energy dissipation in the AlOx/KTaO3 (111) system hosting 2D superconductivity in the intermediate disorder regime. The results show that below the Berezinskii Kosterlitz Thouless (BKT) phase transition temperature (TBKT), hot-spots and Larkin Ovchinnikov type flux-flow instability (FFI) are the major channels of dissipation, leading to pronounced voltage instability at large currents. Furthermore, such FFI leads to a rare observation of clockwise hysteresis in current-voltage characteristics within the temperature range TBKT < T < TC (TC is superconducting transition temperature). These findings deepen our understanding of how a BKT system ultimately transforms to a normal state under increasing current.
The incretin co-agonist tirzepatide requires GIPR for hormone secretion from human islets
Authors: El Kimberley , Douros Jonathan D. , Willard Francis S. , Novikoff Aaron , Sargsyan Ashot , Perez-Tilve Diego , Wainscott David B. , Yang Bin , Chen Alex , Wothe Donald , Coupland Callum , Tschöp Mattias H. , Finan Brian , D’Alessio David A. , Sloop Kyle W. , Müller Timo D. , Campbell Jonathan E. 
Published: June 2023

AbstractThe incretins glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide 1 (GLP-1) mediate insulin responses that are proportionate to nutrient intake to facilitate glucose tolerance1. The GLP-1 receptor (GLP-1R) is an established drug target for the treatment of diabetes and obesity2, whereas the therapeutic potential of the GIP receptor (GIPR) is a subject of debate. Tirzepatide is an agonist at both the GIPR and GLP-1R and is a highly effective treatment for type 2 diabetes and obesity3,4. However, although tirzepatide activates GIPR in cell lines and mouse models, it is not clear whether or how dual agonism contributes to its therapeutic benefit. Islet beta cells express both the GLP-1R and the GIPR, and insulin secretion is an established mechanism by which incretin agonists improve glycemic control5. Here, we show that in mouse islets, tirzepatide stimulates insulin secretion predominantly through the GLP-1R, owing to reduced potency at the mouse GIPR. However, in human islets, antagonizing GIPR activity consistently decreases the insulin response to tirzepatide. Moreover, tirzepatide enhances glucagon secretion and somatostatin secretion in human islets. These data demonstrate that tirzepatide stimulates islet hormone secretion from human islets through both incretin receptors.
Assessing social contracts for urban adaptation through social listening on Twitter
Authors: Doshi Deepal , Garschagen Matthias 
Published: June 2023

AbstractAdapting to climate change impacts requires a coherent social contract in which different actors agree on a clear distribution of roles and responsibilities. An urgent requirement is to understand the imagined social contracts on expected roles and responsibilities, which is particularly relevant in cities where very diverse social groups come together. However, there is limited empirical evidence on these expectations as they are often tacit and hard to capture across large populations and heterogeneous groups. Here we assess the social contract on flood risk management in Mumbai, using the concept of social listening in combination with Twitter data. We find wide gaps between and within imagined social contracts. Sentiments such as frustration and apathy expressed in tweets explain these gaps and highlight the need to build trust for achieving accepted and effective social contracts for adaptation. Theoretical, empirical, and methodological lessons can be transferred to other cities and beyond.
Rethinking Literacy Intervention: Addressing a Practice Gap With Best Practices From Multisensory Structured Language Approaches
Authors: Bowers Lisa M. , Ramsdell Heather L. 
Published: June 2023

Purpose:
Dyslexia is increasingly being defined, assessed, diagnosed, and treated in the educational system. The purpose of this clinical focus article is to elucidate ways in which speech-language pathologists (SLPs) can rethink how to implement literacy interventions to incorporate best practices from multisensory structured language (MSL) approaches and how they can be influential participants in the conversations of how to define and implement services for students who have written language disorders, including dyslexia, in the school setting.

Method:
This clinical focus article provides an operational definition of dyslexia, discusses the various roles and responsibilities of SLPs with respect to dyslexia, and describes the well-established evidence-based practices of MSL approaches as a means of rethinking literacy intervention.

Results:
Using a case study scenario based on an individual diagnosed with dyslexia, this clinical focus article presents similarities and differences between traditional speech-language pathology intervention approaches and MSL approaches to literacy intervention.

Conclusions:
MSL strategies may be considered in literacy intervention as a means to optimize the academic gains of children with dyslexia in a school setting. Furthermore, SLPs should be considered integral participants in discussions of policies and practices related to the diagnosis and treatment of literacy disorders, including dyslexia.

Supplemental Material:

https://doi.org/10.23641/asha.23228483