bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and temporal characterization of a recurrent scalloped hammerhead shark Sphyrna lewini aggregation using drones
Authors: López N A , McAuley R B , van Elden S , Meeuwig J J 
Published: October 2023

Abstract
Scalloped hammerhead sharks Sphyrna lewini are threatened throughout their distribution. The species forms aggregations, which can potentially increase its vulnerability to human impacts. Identification and characterization of aggregation sites are essential to inform management and conservation. We used drones to characterize the spatial and temporal distribution of a recently documented scalloped hammerhead aggregation within the Shoalwater Islands Marine Park, in southwest Western Australia. A total of 267 drone transects were conducted across the Austral summers of 2019–2020 and 2020–2021. The presence or absence of the sharks was examined in relation to fine scale patterns in habitat type, environmental conditions, and the occurrence of human activities. Scalloped hammerhead sharks had a small spatial and temporal distribution within the study area. Their presence in the study area was higher on days associated with higher lunar illumination phases, which could indicate that the aggregation site is potentially acting as a refuge for resting and/or predatory avoidance. The extent to which human interactions affect scalloped hammerhead sharks at the aggregation site remains unclear and raises questions about the adequacy of management measures at Shoalwater Islands Marine Park. Recommendations are proposed to limit potential impacts, such as establishing spatiotemporal fishing restrictions and regulating public interactions.
Early aortic valve neocuspidization failure due to xenograft leaflet tear in a young adult
Authors: Lee Kwok Fai Lucius , Mak Ka Lun Tony , Chen Qiang , Yam Nicholson 
Published: October 2023

Abstract
Aortic valve neocuspidization, initially described by Ozaki and colleagues, has become an increasingly popular treatment approach for aortic valve disease in both adult and paediatric populations. We report a case of an 18-year-old man with severe aortic regurgitation who underwent the Ozaki procedure using photo-oxidized bovine pericardium. Around 5 weeks after the surgery, he developed early symptomatic valve failure due to multiple leaflet tears requiring urgent reoperation.
Optimization of the EUCAST reference broth microdilution method for echinocandin susceptibility testing of Aspergillus fumigatus
Authors: Siopi Maria , Georgiou Panagiota-Christina , Pournaras Spyros , Meletiadis Joseph 
Published: October 2023

Abstract

Background
Because of the high inoculum (105 cfu/mL) used in the EUCAST susceptibility testing of Aspergillus spp., determination of the minimal effective concentration (MEC) of echinocandins is challenging as the morphological differences are subtle.

Methods
The MECs of 10 WT and 4 non-WT Aspergillus fumigatus isolates were determined with the EUCAST E.Def 9.4. Plates were inoculated with increasing inocula (102–105 cfu/mL) and after 24 and 48 h of incubation, MECs were determined macroscopically (magnifying mirror) and microscopically (inverted microscope) by two observers, spectrophotometrically (OD at 405 nm) and colorimetrically (absorbance at 450/630 nm after 2 h incubation with 400 mg/L XTT/6.25 μM menadione). The interobserver (between observers)/intermethod (compared with the microscopic method) essential agreement (EA, ±1 2-fold dilution) and categorical agreement (CA) were determined for each inoculum.

Results
Echinocandin-induced microscopic hyphal alterations or macroscopic changes in turbidity were subtle with a 105 cfu/mL inoculum compared with the lower inocula of 103 and 102 cfu/mL, where more distinct changes in turbidity and formation of characteristic rosettes were obvious at the MEC after 48 h. A 105 cfu/mL inoculum resulted in wider MEC distributions (3–6 dilutions) and lower interobserver EA (69%), macroscopic–microscopic EA (26%) and CA (71%) compared with a 103 cfu/mL inoculum (2–3 dilutions, 100%, 100% and 100%, respectively). Spectrophotometric readings using a 103 cfu/mL inoculum showed good EA (57–93%) and excellent CA (86%–100%), while the XTT assay demonstrated excellent EA (93%) and CA (100%).

Conclusions
A 48 h incubation using a 103 cfu/mL inoculum improved echinocandin MEC determination for A. fumigatus with the EUCAST method, while the colorimetric assay could allow automation.
Chromogenic and Clot-Based Bivalirudin Assays for Monitoring Anticoagulation
Authors: Raghavendran Prashant , Tillman Benjamin F , Wheeler Allison P , Gailani David 
Published: October 2023

Abstract

Background
Direct thrombin inhibitors (DTIs) are usually monitored with the activated partial thromboplastin time (aPTT) or activated clotting time (ACT). Both are complex assays with multiple enzymatic steps, and performance may be influenced by physiologic and pathologic factors unrelated to the DTI. Simpler systems, such as clot-based dilute thrombin time (dTT) and chromogenic anti-factor IIa assays, have been developed for monitoring DTIs, but there is limited data on their performance in clinical settings.

Methods
Medical records of patients who received bivalirudin between March 2020 and April 2022 at a single institution were reviewed for demographic data and adverse outcomes. Plasma samples drawn for aPTT testing were analyzed with chromogenic anti-IIa and dTT bivalirudin assays. Results were compared to bivalirudin dosing.

Results
Results of aPTT assays from 32 patients were compared with the chromogenic (n = 136) and dTT (n = 120) bivalirudin assays. Correlations between the aPTT and the chromogenic and dTT assays were poor (Spearman coefficients 0.55 and 0.62, respectively). There was a stronger correlation when results of the chromogenic and dTT assays were compared to each other (Spearman coefficient 0.92). When assay results were compared to bivalirudin dose, there were stronger correlations with the chromogenic and dTT assays than with the aPTT (Spearman coefficients 0.51, 0.63 and 0.22, respectively).

Conclusions
There was considerable variation between results of specific bivalirudin assays and the aPTT. While bivalirudin assay results correlated better with administered drug dose, suggesting improving reliability, more studies are needed to determine if there is correlation between testing and clinical outcomes.
Effects of ensiling sugarcane tops with bacteria-enzyme inoculants on growth performance, nutrient digestibility, and the associated rumen microbiome in beef cattle
Authors: Tang Qingfeng , He Renchun , Huang Feng , Liang Qimei , Zhou Zhiyang , Zhou Junhua , Wang Qizhi , Zou Caixia , Gu Qichao 
Published: October 2023

Abstract
Major challenges when ensiling sugarcane tops include fermentation that results in high quantities of alcohol and decrease in nutrient digestibility due to the accumulation of fiber components. Increased efforts to apply bacteria-enzyme inoculants in silage have the potential to improve nutrient digestibility. This study aimed to evaluate the effects of ensiling sugarcane tops with bacteria-enzyme inoculants or mixed bacterial inoculants on growth performance, nutrient digestibility, and rumen microbiome in beef cattle. Chopped sugarcane tops were ensiled in plastic bags for 60 d after application of 1) no inoculant (control check, CK); 2) bacteria-enzyme inoculants containing Pediococcus acidilactici, Saccharomyces cerevisiae, cellulase, and xylanase (T1, viable colony-forming units of each bacterial strain ≥108 CFU/g; enzyme activity of each enzyme ≥200 U/g); or 3) mixed bacterial inoculants containing Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae (T2, viable colony-forming units of each bacterial strain ≥107 CFU/g). Silages were fed to eighteen Holstein bull calves (n = 6/treatment) weighing 163.83 ± 7.13 kg to determine intake in a 49-d experimental period. The results showed that beef cattle-fed T1 silage or T2 silage had a significantly higher (P &lt; 0.05) average daily gain than those fed CK silage, but the difference in dry matter intake was not significant (P &gt; 0.05). The apparent digestibility of crude protein (CP) and acid detergent fiber (ADF) were higher (P &lt; 0.05) for beef cattle-fed T1 silage or T2 silage than for those fed CK silage. The rumen bacterial community of beef cattle-fed T1 silage or T2 silage had a tendency to increase (P &gt; 0.05) abundance of Firmicutes and Rikenellaceae_RC9_gut_group than those fed CK silage. Rumen fungal communities of beef cattle-fed T1 or T2 silage had a tendency to increase (P &gt; 0.05) abundance of Mortierellomycota and of Mortierella than those fed CK silage. Spearman’s rank correlation coefficient showed that the apparent digestibility of ADF for beef cattle was positively correlated with unclassified_p_Ascomycota of the fungal genera (P &lt; 0.05). Neocalimastigomycota of the fungal phyla was strongly positively correlated with the apparent digestibility of neutral detergent fiber (NDF) (P &lt; 0.05). Ruminococcus was positively correlated with the apparent digestibility of CP (P &lt; 0.05). It was concluded that both T1 and T2 improved the growth performance of beef cattle by improving the ruminal apparent digestibility of CP and ADF, and had no significant impact on major rumen microbial communities in beef cattle.
The SH3 binding site in front of the WH1 domain contributes to the membrane binding of the BAR domain protein endophilin A2
Authors: Sim Pei Fang , Chek Min Fey , Nguyen Nhung Thi Hong , Nishimura Tamako , Inaba Takehiko , Hakoshima Toshio , Suetsugu Shiro 
Published: October 2023

Abstract
The Bin–Amphiphysin–Rvs (BAR) domain of endophilin binds to the cell membrane and shapes it into a tubular shape for endocytosis. Endophilin has a Src-homology 3 (SH3) domain at their C-terminal. The SH3 domain interacts with the proline-rich motif (PRM) that is found in proteins such as neural Wiskott–Aldrich syndrome protein (N-WASP). Here, we re-examined the binding sites of the SH3 domain of endophilin in N-WASP by machine learning-based prediction and identified the previously unrecognized binding site. In addition to the well-recognized PRM at the central proline-rich region, we found a PRM in front of the N-terminal WASP homology 1 (WH1) domain of N-WASP (NtPRM) as a binding site of the endophilin SH3 domain. Furthermore, the diameter of the membrane tubules in the presence of NtPRM mutant was narrower and wider than that in the presence of N-WASP and in its absence, respectively. Importantly, the NtPRM of N-WASP was involved in the membrane localization of endophilin A2 in cells. Therefore, the NtPRM contributes to the binding of endophilin to N-WASP in membrane remodeling.
The impact of client-overlap hiring on PSF client embeddedness
Authors: Kim Yeongsu Anthony , Skaggs Bruce C 
Published: October 2023

Abstract
Professional service firms (PSFs) are commonly perceived to attain success through the acquisition of new clients. However, these firms are not solely reliant on this strategy as PSFs may also achieve competitive advantage by improving their relationships with existing clients. Despite the significance of these established client relationships, limited information exists regarding how PSFs can effectively enhance and utilize them. This study examines how a PSF’s client-related knowledge can be obtained and developed through its hiring practices in order to strengthen relationships with existing clients. Results reveal that when hiring from other PSFs who share similar clients (i.e., client-overlapping PSFs), that this has a positive impact on the firm’s overall relationships with its clients, with the effect being impacted by the firm’s level of practice overlap with the new hires and the degree of co-mobility of the hires.
SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding
Authors: Yang Zhiquan , Luo Chengfang , Pei Xinxin , Wang Shengbo , Huang Yiming , Li Jiawei , Liu Baohui , Kong Fanjiang , Yang Qing-Yong , Fang Chao 
Published: October 2023

Abstract
Advanced multi-omics technologies offer much information that can uncover the regulatory mechanisms from genotype to phenotype. In soybean, numerous multi-omics databases have been published. Although they cover multiple omics, there are still limitations when it comes to the types and scales of omics datasets and analysis methods utilized. This study aims to address these limitations by collecting and integrating a comprehensive set of multi-omics datasets. This includes 38 genomes, transcriptomes from 435 tissue samples, 125 phenotypes from 6686 accessions, epigenome data involving histone modification, transcription factor binding, chromosomal accessibility and chromosomal interaction, as well as genetic variation data from 24 501 soybean accessions. Then, common analysis pipelines and statistical methods were applied to mine information from these multi-omics datasets, resulting in the successful establishment of a user-friendly multi-omics database called SoyMD (https://yanglab.hzau.edu.cn/SoyMD/#/). SoyMD provides researchers with efficient query options and analysis tools, allowing them to swiftly access relevant omics information and conduct comprehensive multi-omics data analyses. Another notable feature of SoyMD is its capability to facilitate the analysis of candidate genes, as demonstrated in the case study on seed oil content. This highlights the immense potential of SoyMD in soybean genetic breeding and functional genomics research.
Yeast ribosome biogenesis factors Puf6 and Nog2 and ribosomal proteins uL2 and eL43 act in concert to facilitate the release of nascent large ribosomal subunits from the nucleolus
Authors: LaPeruta Amber J , Hedayati Stefanie , Micic Jelena , Fitzgerald Fiona , Kim David , Oualline Grace , Woolford John L 
Published: October 2023

Abstract
Large ribosomal subunit precursors (pre-LSUs) are primarily synthesized in the nucleolus. At an undetermined step in their assembly, they are released into the nucleoplasm. Structural models of yeast pre-LSUs at various stages of assembly have been collected using cryo-EM. However, which cryo-EM model is closest to the final nucleolar intermediate of the LSU has yet to be determined. To elucidate the mechanisms of the release of pre-LSUs from the nucleolus, we assayed effects of depleting or knocking out two yeast ribosome biogenesis factors (RiBi factors), Puf6 and Nog2, and two ribosomal proteins, uL2 and eL43. These proteins function during or stabilize onto pre-LSUs between the late nucleolar stages to early nucleoplasmic stages of ribosome biogenesis. By characterizing the phenotype of these four mutants, we determined that a particle that is intermediate between the cryo-EM model State NE1 and State NE2 likely represents the final nucleolar assembly intermediate of the LSU. We conclude that the release of the RiBi factors Nip7, Nop2 and Spb1 and the subsequent stabilization of rRNA domains IV and V may be key triggers for the release of pre-LSUs from the nucleolus.
SORC: an integrated spatial omics resource in cancer
Authors: Zhou Weiwei , Su Minghai , Jiang Tiantongfei , Yang Qingyi , Sun Qisen , Xu Kang , Shi Jingyi , Yang Changbo , Ding Na , Li Yongsheng , Xu Juan 
Published: October 2023

Abstract
The interactions between tumor cells and the microenvironment play pivotal roles in the initiation, progression and metastasis of cancer. The advent of spatial transcriptomics data offers an opportunity to unravel the intricate dynamics of cellular states and cell–cell interactions in cancer. Herein, we have developed an integrated spatial omics resource in cancer (SORC, http://bio-bigdata.hrbmu.edu.cn/SORC), which interactively visualizes and analyzes the spatial transcriptomics data in cancer. We manually curated currently available spatial transcriptomics datasets for 17 types of cancer, comprising 722 899 spots across 269 slices. Furthermore, we matched reference single-cell RNA sequencing data in the majority of spatial transcriptomics datasets, involving 334 379 cells and 46 distinct cell types. SORC offers five major analytical modules that address the primary requirements of spatial transcriptomics analysis, including slice annotation, identification of spatially variable genes, co-occurrence of immune cells and tumor cells, functional analysis and cell–cell communications. All these spatial transcriptomics data and in-depth analyses have been integrated into easy-to-browse and explore pages, visualized through intuitive tables and various image formats. In summary, SORC serves as a valuable resource for providing an unprecedented spatially resolved cellular map of cancer and identifying specific genes and functional pathways to enhance our understanding of the tumor microenvironment.
Physician, patient, and caregiver support for a formal certification in pediatric neuro-oncology: A survey-based report from the SNO pediatrics working group
Authors: Lindsay Holly B , Cheng Sylvia , Fisher Paul Graham , Peters Katherine B , Walsh Kyle M , Ashley David M , Huang Annie 
Published: October 2023

Abstract

Background
Although CNS tumors are the most common pediatric cancer in the United States, most physicians caring for these patients are not formally certified in the subspecialty. To determine support for developing a formal certification process in pediatric neuro-oncology, the Society for Neuro-Oncology’s Pediatrics Special Interest Track Training and Credentialing working group performed a cross-sectional survey-based study of physicians and patients/caregivers of children with a CNS tumor history.

Methods
Surveys were built in Survey Monkey and were available for 3 months. The physician survey had 34 questions and was open to doctors currently caring for pediatric neuro-oncology patients. The patient/caregiver survey had 13 questions. Both surveys were completed anonymously.

Results
The physician survey was completed by 193 participants, the majority of whom self-identified as oncologists. Only 5.6% of survey participants had ever been board-certified in neuro-oncology; the majority of participating physicians were either unaware that this certification existed or thought they were not eligible due to training in pediatrics rather than neurology or internal medicine. Almost half of the self-identified pediatric neuro-oncologists had not completed any specific clinical neuro-oncology training. Over 75% of physicians were supportive of the implementation of a formal certification process in pediatric neuro-oncology. A total of 30 participants completed the patient/caregiver survey. Although the majority of survey participants were highly satisfied with their oncologist, 70% would have been more comfortable if their oncologist had been specifically certified in pediatric neuro-oncology.

Conclusions
There is support from physicians, patients, and caregivers to establish a formal certification process in pediatric neuro-oncology.
Spectral analysis of the Galactic supernova remnant Kesteven 69 with Suzaku
Authors: Yamauchi Shigeo , Pannuti Thomas G 
Published: October 2023

Abstract
The results of a Suzaku observation of the supernova remnant (SNR) Kesteven 69 = G21.8−0.6 are presented. To estimate the sky background precisely, we conducted a simultaneous fit of the source region spectrum with the background region spectrum and found that the SNR spectrum is well represented by a two-component ionizing plasma model composed of a low-temperature plasma at kTe = 0.80 ± 0.11 keV and a high-temperature plasma at kTe = 1.5 ± 0.4 keV. The existence of a low-ionized Fe K line at 6.49 ± 0.07 keV was confirmed. The center energy of the line is consistent with those of type Ia SNRs.
Platelet rich plasma could replace tranexemic acid in total knee replacement? A comparative study between their postoperative- bleeding hemostatic effects
Authors: Fahmy Mahmoud , Yasin Ebeed 
Published: October 2023

Background:
The aim of the study is to detect whether platelet rich plasma (PRP) is equal to tranexemic acid (TXA) in reducing blood loss and transfusion rates following total knee arthroplasty (TKA), and compare clinical outcomes, complications, and cost effectiveness between the two groups. This is one of the first randomized, controlled trials that compare both materials in elective knee arthroplasty.

Methods:
120 patients were randomized. Postoperative blood loss was determined and compared by measuring the total drainage suction together with the hemoglobin level and blood transfusion rate. Thromboembolic complications and knee society score were recorded.

Results:
The mean total drain output was 469 mL in the TXA group compared with 698 mL in the PRP group, with statistical significance. There were significant differences in reduction of hemoglobin level (TXA: 1.21 vs. PRP: 2.08). The rate of deep vein thrombosis (DVT) in patients given TXA was higher than those given PRP, however, there were no significant differences. No transfusions were required in either group, and no significant differences were found in the length of hospital stay, pain assessment and knee society score.

Conclusions:
Though the blood loss was significantly bigger in the custom-made PRP group, no transfusions were required. Meanwhile, the rate of DVT in the PRP group tends to be lower than those in TXA group. We concluded that PRP was not superior to TXA in reducing perioperative blood loss, however further large-scale randomized trials are crucial to confirm these results to be added to the calling literature.
Surveillance With Serial Imaging and CA 19-9 Tumor Marker Testing After Resection of Pancreatic Cancer
Authors: Nong Minerva Z. , Dove Devanshi , Fischer Dawn A. , Hourdequin Kathryn C. , Ripple Gregory H. , Amin Manik A. , McGrath Elizabeth B. , Zaki Bassem I. , Smith Kerrington D. , Brooks Gabriel A. 
Published: October 2023

Objectives:
Most patients receiving curative-intent surgery for pancreatic cancer will experience cancer recurrence. However, evidence that postoperative surveillance testing improves survival or quality of life is lacking. We evaluated the use and characteristics of surveillance with serial imaging and CA 19-9 tumor marker testing at an NCI-designated comprehensive cancer center.

Methods:
We conducted a retrospective cohort study of patients who entered surveillance after curative-intent resection of pancreatic adenocarcinoma. We abstracted information from the electronic medical record about oncology office visits, surveillance testing (cross-sectional imaging and CA 19-9 tumor marker testing), and pancreatic cancer recurrence, with follow-up through 2 years after pancreatectomy. We conducted analyses to describe the use of surveillance testing and to characterize the sensitivity and specificity of CA 19-9 tumor marker testing for the identification of cancer recurrence.

Results:
We identified 90 patients entering surveillance after pancreatectomy. CA 19-9 was the most frequently used surveillance test, followed by CT imaging. Forty-seven patients (52.2%) experienced recurrence within two years of pancreatectomy. Recurrence risk was 58.8% versus 31.8% in patients with elevated versus normal CA 19-9 at diagnosis (P=0.03). Elevated CA 19-9 at any point during surveillance was significantly associated with 2-year recurrence risk (P<0.001). Elevated CA 19-9 had a sensitivity of 83% (95% CI 0.72–0.95) and specificity of 87% (0.76–0.98) for identification of recurrence within 2 years of pancreatectomy.

Conclusions:
CA 19-9 demonstrates clinical validity for identifying recurrence of pancreatic cancer during surveillance. Surveillance approaches with reduced reliance on imaging should be prospectively evaluated.