bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolving perspectives in Hymenoptera systematics: Bridging fossils and genomes across time
Authors: Zhang Y. Miles , Bossert Silas , Spasojevic Tamara 
Published: July 2024

AbstractThe recent advances in sequencing technologies, phylogenomics and divergence dating methods call for an integrative review of the current state of Hymenoptera systematics. We here explore the impact of these latest developments on the Hymenoptera phylogeny and our understanding of the timing of Hymenoptera evolution, while identifying the current methodological constraints and persistent knowledge gaps that warrant further investigation. Our review highlights the lack of consensus among the backbone phylogeny of Hymenoptera between key phylogenomic studies, as the higher level phylogeny remains unresolved in key nodes such as the relationships among Eusymphyta, the relationships within the Infraorder Proctotrupomorpha and the placements of the superfamilies Ichneumonoidea, Ceraphronoidea and Vespoidea. Furthermore, we underline the huge variation in divergence age estimates for Hymenoptera and detect several major gaps and/or disagreements between the fossil record and available age estimates, either due to the poorly studied fossil record or problematic age estimates, or both. To better understand the timing of Hymenoptera evolution and the role of key diversification factors, we will need continuous efforts to (i) reconcile conflicts among morphological and molecular phylogenies, by improving taxon sampling of underrepresented lineages, applying novel techniques to study morphology, making use of genome‐scale data and critically assessing incongruences in genetic markers; (ii) improve the Hymenoptera fossil record, by exercising integrative taxonomy and bringing together paleontologists and neontologists; and (iii) reconcile age estimates, by relying on tip dating approaches to bridge fossils, morphology and genomes across time.
Characterizing collaborative mapping projects. A methodological framework for analyzing volunteered geographic information and spatial data infrastructure convergence
Authors: Pedregal Belén , Orozco Gabriel , Osorio Joaquin , Díaz‐Cuevas Pilar 
Published: July 2024

AbstractIn this article, we compile and characterize a total of 43 collaborative web map projects by a set of parameters that enable the understanding and comparability of current and future projects. We then develop a comprehensive methodological framework to explore volunteered geographic information (VGI) and spatial data infrastructure (SDI) convergence based on this review. The main results show the dominance of citizen science projects, followed by initiatives promoting sustainability values, local development, and governance. Although values remain low, the potential to achieve convergence in VGI–SDI features is very high in citizen science projects, where the presence of experts and the funding of these projects by governments and decision‐making entities enable quality standards in the collection and distribution of the contributed information. The work concludes by addressing two major challenges facing current VGI projects: firstly, accessing affordable technological solutions that allow the creation of collaborative web maps with SDI‐like functions. Secondly, guaranteeing the project's sustainability and the preservation of the information gathered.
Complete genome sequence of
Arcanobacterium wilhelmae
strain DSM 102162 isolated from the genital tract of a
Rhinoceros unicornis
Authors: Borowiaka Maria , Kreitlow Antonia , Malorny Burkhard , Lämmler Christoph , Rau Jörg , Plötz Madeleine , Abdulmawjood Amir 
Published: July 2024

ABSTRACT

Previous case reports indicate
Arcanobacterium
’s opportunistic pathogenic potential. However, the true diversity of the genus remains understudied. Here, we present the complete genome of
Arcanobacterium wilhelmae
isolated from a diseased rhinoceros, suspected to play a role in its condition. These genomic data may enable future advancements in understanding
Arcanobacterium
pathogenicity.
Passages
Authors: Groce Alex 
Published: July 2024

Richard W. Hamming's The Art of Doing Science and Engineering: Learning to Learn is one of the true essentials, a book to be read by every scientist or engineer (and certainly software engineer) interested in the big picture; it may be safely skipped by those who aim only at a life and career where one has "merely survived and amused" oneself, as Hamming himself puts it in his final, summative, chapter.
The essence of this book is a combination of anecdote and aphorism drawn from a mature, active mind, reflecting on a great career spent at great places (Los Alamos, and then Bell Labs in its heyday, to be precise). There is also a great deal of mathematics, but the aphorism, backed by well-chosen anecdote(s), is fundamental; you do not need to know or care much about differential equations (and there are many here) to benefit from this book. It is hard to convey the value of the anecdotes, in a short review. The aphorisms, however, can be more than mentioned; what follows is, in reverse order, the entire set of Hamming's bolded, inset, aphorisms, by chapter (combining multiple chapters on the same topic, e.g., simulation). I have truncated one long item, which offers up a description of pure mathematics; you will have to read the book to get that one. The focus on aphorism is appropriate; I think Hamming himself would have agreed that this entire wonderful book is a kind of elaboration and proof of Pasteur's "Luck favors the prepared mind", which Hamming quotes not once, not twice, but seven times.
Cryoablation Does Not Significantly Contribute to Systemic Effector Immune Responses in a Poorly Immunogenic B16F10 Melanoma Model
Authors: Yakkala Chakradhar , Corria-Osorio Jesus , Kandalaft Lana , Denys Alban , Koppolu Bhanu , Duran Rafael 
Published: July 2024

Abstract

Purpose:
Cryoablation is a minimally invasive procedure implemented to destroy solid tumors. It also results in the release of tumor antigens into the systemic circulation. Preclinical studies using immunogenic tumor models have shown that cryoablation evokes antitumor immune responses. The mechanisms by which cryoablation impacts immune responses in poorly immunogenic tumors have not been sufficiently explored.

Experimental Design:
We used a bilateral B16F10 melanoma model devoid of strong immunogenic antigens. Cryoablation-induced effector immune responses were investigated, also in combination with a peritumoral STING agonist and systemic anti–PD-1. Selective immune cell depletion, T-cell migration arrest, in vivo T-cell transplantation, and cryoablation versus surgical removal techniques were used to determine the contribution of cryoablation and immunotherapies to systemic antitumor effector immune responses.

Results:
Treatment of a tumor with cryoablation + STING agonist + anti–PD-1 resulted in the rejection of unablated, contralateral tumors. Depletion studies demonstrated that tumor rejection is essentially dependent on CD8+ T cells. T-cell arrest in the lymph nodes had no effect on the rejection process. Splenic CD8+ T cells isolated from cryoablation-treated mice with B16F10 melanoma, upon transplantation into melanoma-bearing recipients, did not impact the recipient’s tumor growth. Finally, comparison of cryoablation + STING agonist + anti–PD-1 versus surgery + STING agonist + anti–PD-1 in the bilateral tumor model showed no difference in the rejection of contralateral tumors.

Conclusions:
Cryoablation does not significantly contribute to systemic antitumor effector immune responses in a B16F10 melanoma model. Cryoablation primarily performs tumor debulking, and immunotherapy functions independently of cryoablation in eliciting antitumor effector immune responses.
Engineered CAR-NK Cells with Tolerance to H2O2 and Hypoxia Can Suppress Postoperative Relapse of Triple-Negative Breast Cancers
Authors: Liu Yan , Chen Jiahui , Tian Jia , Hao Yu , Ma Xinxing , Zhou Yehui , Feng Liangzhu 
Published: July 2024

Abstract
Surgical resection is a primary treatment option for patients with triple-negative breast cancer (TNBC), but it is associated with a high rate of postoperative local and metastatic relapse. Although chimeric antigen receptor–engineered NK (CAR-NK) cell therapy can specifically recognize and eradicate tumor cells, its therapeutic potency toward TNBCs is markedly suppressed by the hostile tumor microenvironment, which restricts the infiltration, survival, and effector functions of CAR-NK cells inside tumor masses. In this study, HER1-overexpressing TNBC-targeted CAR-NK (HER1-CAR-NK) cells were genetically engineered with catalase to endow them with tolerance toward the high levels of oxidative stress and hypoxia inside TNBC tumors through the catalytic decomposition of hydrogen peroxide, which is a principle reactive oxygen species inside tumors, into O2. We refer to these cells as HER1-CAR-CAT-NK cells. Upon intratumoral fixation with an injectable alginate hydrogel, HER1-CAR-CAT-NK cells enabled sustained tumor hypoxia attenuation and exhibited markedly enhanced persistence and effector functions inside TNBC tumors. As a result, locoregional HER1-CAR-CAT-NK cell therapy not only inhibited the growth of local primary residual tumors but also elicited systemic antitumor activity to suppress the growth of distant tumors. This study highlights that genetic engineering of HER1-CAR-NK cells with catalase is a promising strategy to suppress the postoperative local and distant relapse of TNBC tumors.
Children's Memory for Events: The Challenge of Free Recall
Authors: Benear Susan L. , Onwukanjo Obinnaya J. , Olson Ingrid R. , Newcombe Nora S. 
Published: July 2024

Abstract
Early childhood is a critical period for episodic memory development, with sharp behavioral improvements between ages 4 to 7 years. Prior work has demonstrated this extensively with prompted memory tasks, but we explored performance on unprompted, free recall of a naturalistic experience in children, and how their performance relates to other cognitive measures. We asked children and adults to view a television episode, a naturalistic task for which there exists a ground truth, and assessed their free recall memory for the episode. Children's free recall performance improved dramatically with age, with many young children producing no verbal free recall whatsoever, although prompted recognition memory measures showed retention of material. However, the detail in free recall was related to both recognition and temporal order forced-choice memory performance in our full sample, showing agreement among memory measures. Free recall was strongly predicted by verbal skills, suggesting that children's sparse recall reflects verbal skill development rather than a pure mnemonic deficit. We propose that free recall has a more protracted developmental trajectory because it requires more substantial verbal skills as well as metacognitive skills that direct memory search, as compared with forced-choice memory tasks.
Neutrophil extracellular traps are associated with airways inflammation and increased severity of lung disease in cystic fibrosis
Authors: Law Sheonagh M. , Hardisty Gareth , Gillan Jonathan L. , Robinson Nicola J. , Davidson Donald J. , Whyte Moira K.B. , Dransfield Ian , Gray Robert D. 
Published: July 2024

BackgroundCystic fibrosis (CF) is characterised by inflammatory lung disease and large numbers of airways neutrophils. In health, neutrophils undergo apoptosis and removal from the airway. Since CF neutrophils are known to engage in apoptosis less efficiently, we wanted to assess whether alternative forms of neutrophil clearance such as NETosis were prominent in the CF airway.MethodsSputum and blood were collected from 45 CF and 15 healthy control (HC) participants. Neutrophil morphology and biochemical properties were assessed in CF and HC sputum. Neutrophil extracellular traps (NETs) were measured by a novel histone-calprotectin ELISA. NET levels were compared with established measurements of airway inflammation. CF participants were followed up for 1 year and the number of exacerbations recorded. Neutrophil and macrophage co-culture experiments were undertaken with cells from CF and HC.ResultsNeutrophil numbers were significantly higher in CF and associated with abnormal morphology. Several inflammatory mediators were elevated in CF sputum, as was cell-free DNA. This was highly correlated with sputum calprotectin, a known NET-associated protein. Using a histone-calprotectin NET ELISA, we demonstrated higher levels of NETs in the CF airway. CF participants treated with DNase had fewer sputum NETs, and in neutrophil/macrophage co-culture experiments, DNase effectively attenuated the pro-inflammatory potential of NETs, suggesting a previously unrecognised anti-inflammatory role for this treatment.ConclusionsNETs in the CF airway are associated with increased levels of inflammatory mediators and more severe lung disease. NET effects on macrophages can be blocked by DNase, suggesting an anti-inflammatory role for this treatment in CF.
FnR: R package for computing inbreeding and numerator relationship coefficients
Authors: Nilforooshan Mohammad Ali 
Published: July 2024

Abstract
Background
Inbreeding and relationship coefficients are essential for conservation and breeding programs. Whether dealing with a small conserved population or a large commercial population, monitoring the inbreeding rate and designing mating plans that minimize the inbreeding rate and maximize the effective population size is important. Free, open-source, and efficient software may greatly contribute to conservation and breeding programs and help students and researchers. Efficient methods exist for calculating inbreeding coefficients. Therefore, an efficient way of calculating the numerator relationship coefficients is via the inbreeding coefficients. i.e., the relationship coefficient between parents is twice the inbreeding coefficient of their progeny. A dummy progeny is introduced where no progeny exists for a pair of individuals. Calculating inbreeding coefficients is very fast, and finding whether a pair of individuals has a progeny and picking one from multiple progenies is computationally more demanding. Therefore, the R package introduces a dummy progeny for any pair of individuals whose relationship coefficient is of interest, whether they have a progeny or not.

Results
Runtime and peak memory usage were benchmarked for calculating relationship coefficients between two sets of 250 and 800 animals (200,000 dummy progenies) from a pedigree of 2,721,252 animals. The program performed efficiently (200,000 relationship coefficients, which involved calculating 2,721,252 + 200,000 inbreeding coefficients) within 3:45 (mm:ss). Providing the inbreeding coefficients (for real animals), the runtime was reduced to 1:08. Furthermore, providing the diagonal elements of D in $$\textbf{A} = \textbf{TDT}^{\prime }$$

A
=

TDT
′

(d), the runtime was reduced to 54s. All the analyses were performed on a machine with a total memory size of 1 GB.

Conclusions
The R package FnR is free and open-source software with implications in conservation and breeding programs. It proved to be time and memory efficient for large populations and many dummy progenies. Calculation of inbreeding coefficients can be resumed for new animals in the pedigree. Thus, saving the latest inbreeding coefficient estimates is recommended. Calculation of d coefficients (from scratch) was very fast, and there was limited value in storing those for future use.
Sorbate metal complexes as newer antibacterial, antibiofilm, and anticancer compounds
Authors: Abousaty Amira I. , Reda Fifi M. , Hassanin Wessam A. , Felifel Walaa M. , El-Shwiniy Walaa H. , Selim Heba M. R. M. , Bendary Mahmoud M. 
Published: July 2024

Abstract
Background
The ineffectiveness of treatments for infections caused by biofilm-producing pathogens and human carcinoma presents considerable challenges for global public health organizations. To tackle this issue, our study focused on exploring the potential of synthesizing new complexes of Co(II), Cu(II), Ni(II), and Zn(II) with sorbic acid to enhance its antibacterial, antibiofilm, and anticancer properties.

Methods
Four novel complexes were synthesized as solid phases by reacting sorbic acid with Co(II), Cu(II), Ni(II), and Zn(II). These complexes were characterized by various technique, including infrared spectra, UV–Visible spectroscopy, proton nuclear magnetic resonance (1H NMR), and thermal analysis techniques, including thermogravimetry (TG).

Results
The data acquired from all investigated chemical characterization methods confirmed the chemical structure of the sorbate metal complexes. These complexes exhibited antibacterial and antibiofilm properties against both Gram-positive and Gram-negative bacteria. Furthermore, these complexes enhanced the antibacterial effects of commonly used antibiotics, such as gentamicin and imipenem, with fractional inhibitory concentration (FIC) indices ≤ 0.5. Notably, the Cu(II) complex displayed the most potent antibacterial and antibiofilm activities, with minimum inhibitory concentration (MIC) values of 312.5 µg/mL and 625.0 µg/mL for Bacillus cereus and Escherichia coli, respectively. Additionally, in vitro assays using the methyl thiazolyl tetrazolium (MTT) method showed inhibitory effects on the growth of the human colon carcinoma cell line (HCT-116 cells) following treatment with the investigated metal complexes. The IC50 values for Co(II), Cu(II), Zn(II), and Ni(II) were 3230 µg/mL, 2110 µg/mL, 3730 µg/mL, and 2240 µg/mL, respectively.

Conclusion
Our findings offer potential for pharmaceutical companies to explore the development of novel combinations involving traditional antibiotics or anticancer drugs with sorbate copper complex.
Comparison of anesthesia methods for intra-arterial therapy of patients with acute ischemic stroke: an updated meta-analysis and systematic review
Authors: Chen Huijun , Xing Yang , Lang Zekun , Zhang Lei , Liao Mao , He Ximin 
Published: July 2024

Abstract
Objectives
Currently, there remains debate regarding the optimal anesthesia approach for patients undergoing intra-arterial therapy for acute ischemic stroke. Therefore, we conducted a comparative analysis to assess the effects of general anesthesia versus non general anesthesia on patient outcomes.

Methods
The research methodology entailed comprehensive searches of prominent databases such as the Cochrane Library, PubMed, Scopus, and Web of Science, covering the period from January 1, 2010, to March 1, 2024. Data synthesis employed techniques like risk ratio or standardized mean difference, along with 95% confidence intervals. The study protocol was prospectively registered with PROSPERO (CRD42024523079).

Results
A total of 27 trials and 12,875 patients were included in this study. The findings indicated that opting for non-general anesthesia significantly decreased the risk of in-hospital mortality (RR, 1.98; 95% CI: 1.50 to 2.61; p<0.00001; I2 = 20%), as well as mortality within three months post-procedure (RR, 1.24; 95% CI: 1.15 to 1.34; p<0.00001; I2 = 26%), while also leading to a shorter hospitalization duration (SMD, 0.24; 95% CI: 0.15 to 0.33; p<0.00001; I2 = 44%).

Conclusion
Ischemic stroke patients who undergo intra-arterial treatment without general anesthesia have a lower risk of postoperative adverse events and less short-term neurological damage. In routine and non-emergency situations, non-general anesthetic options may be more suitable for intra-arterial treatment, offering greater benefits to patients. In addition to this, the neuroprotective effects of anesthetic drugs should be considered more preoperatively and postoperatively.
Identifying the obstacles facing emergency nurses regarding treating CTAS1 and CTAS2 in Saudi Arabia
Authors: AlZahrani Rawan , Al Thobaity Abdulellah , Saleh Manal Saleh Moustafa 
Published: July 2024

Abstract
Background
Emergency nurses play a pivotal role in delivering efficient emergency healthcare, yet they often encounter numerous challenges, especially while managing life-threatening cases, impacting both their well-being and patient satisfaction. This study seeks to identify the prevalent challenges faced by these nurses in Saudi hospitals when handling Canadian Triage and Acuity Scale (CTAS1 and CTAS2) cases, with the aim of mitigating or managing these issues in the future.

Methods
This study incorporated a mixed-method approach to identify obstacles in Emergency Department (ED) nursing treatment of CTAS1 and CTAS2 cases in two major Saudi Arabian hospitals. The research began with qualitative focus group interviews with expert ED nurses, followed by a quantitative survey to measure and explore relationships among the qualitative findings. Data analysis leveraged qualitative thematic analysis and principal component analysis, ensuring rigorous examination and validation of data to drive meaningful conclusions.

Findings
From expert interviews, key challenges for emergency nurses were identified, including resource management, communication, training compliance, and psychological factors. A survey of 172 nurses further distilled these into five major issues: patient care management, handling critical cases, administration support, patient care delay, and stress from patients’ families.

Conclusion
Through a mixed-method approach, this study pinpoints five pivotal challenges confronting emergency nurses in Saudi hospitals. These encompass difficulties in patient care management, the psychological toll of handling critical cases, inadequate administrative support, delays due to extended patient stays, and the stress induced by the presence of patients’ families, all of which significantly impede emergency department efficiency and compromise nurse well-being.
Accuracy, thoroughness, and quality of outpatient primary care documentation in the U.S. Department of Veterans Affairs
Authors: Weiner Michael , Flanagan Mindy E. , Ernst Katie , Cottingham Ann H. , Rattray Nicholas A. , Franks Zamal , Savoy April W. , Lee Joy L. , Frankel Richard M. 
Published: July 2024

Abstract
Background
Electronic health records (EHRs) can accelerate documentation and may enhance details of notes, or complicate documentation and introduce errors. Comprehensive assessment of documentation quality requires comparing documentation to what transpires during the clinical encounter itself. We assessed outpatient primary care notes and corresponding recorded encounters to determine accuracy, thoroughness, and several additional key measures of documentation quality.

Methods
Patients and primary care clinicians across five midwestern primary care clinics of the US Department of Veterans Affairs were recruited into a prospective observational study. Clinical encounters were video-recorded and transcribed verbatim. Using the Physician Documentation Quality Instrument (PDQI-9) added to other measures, reviewers scored quality of the documentation by comparing transcripts to corresponding encounter notes. PDQI-9 items were scored from 1 to 5, with higher scores indicating higher quality.

Results
Encounters (N = 49) among 11 clinicians were analyzed. Most issues that patients initiated in discussion were omitted from notes, and nearly half of notes referred to information or observations that could not be verified. Four notes lacked concluding assessments and plans; nine lacked information about when patients should return. Except for thoroughness, PDQI-9 items that were assessed achieved quality scores exceeding 4 of 5 points.

Conclusions
Among outpatient primary care electronic records examined, most issues that patients initiated in discussion were absent from notes, and nearly half of notes referred to information or observations absent from transcripts. EHRs may contribute to certain kinds of errors. Approaches to improving documentation should consider the roles of the EHR, patient, and clinician together.