bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of enhancing EDM machining performance of INCONEL alloy using composite electrodes
Authors: KT Shabarinathan , K Senthilkumar , N Kathiravan , RM Udhayachandran 
Published: January 2024

Abstract
In this research, an attempt was made to reinforce aluminium with graphite particles and use it as a tool material with the objective of combining the properties of aluminium and graphite. The micrograph confirms that the graphite particles were uniformly distributed over the aluminium matrix, density reduces and thermal conductivity increases with the addition of graphite particles. Material Removal Rate (MRR) peaks at 12 A current before declining due to plasma channel expansion, an optimal Ton of 8 μs ws observed, with 4 μs Toff yielding higher MRR. Copper electrodes excel due to thermal conductivity, while 5% graphite in aluminum boosts MRR to 31.89 mm3 min−1, additional graphite decreases MRR. TWR rises with shorter Toff until 6 μs, then decreases. Gap control impacts TWR, with lower spark gaps causing higher TWR due to intense material removal, and higher gaps leading to increased TWR due to incomplete flushing. Copper electrodes have the lowest TWR due to their high melting temperature. The addition of graphite in aluminum reduces TWR at low currents but is less effective at higher currents. Surface roughness (Ra) decreases with higher current, reaching a minimum of 7.02 μm at 12 A. Optimal Ton is 8 μs (7.56 μm), while shorter Toff at 4 μs and a 3 mm gap yield the best Ra of 7.36 μm with A4 composite tool. Copper electrodes result in higher Ra at higher currents, while graphite in aluminum improves surface quality, especially at 5% content. Arcing, an undesirable electrical discharge phenomenon in EDM, adversely affects machining. Experiments revealed a strong correlation between high duty cycles, duty ratios, and arcing propensity, with composite tools being more susceptible due to their variable conductivity. In contrast, non-composite tools, exemplified by copper, withstand higher duty ratios without arcing.
Problematizing Possible -isms in Adult Second Language Classrooms
Authors: Tadic Nadja 
Published: January 2024

Abstract
While addressing issues of prejudice and exclusion is crucial for helping adult second language (L2) learners acquire and critique socio-interactional norms of their pluralistic communities, there is still a lack of work examining how teachers can problematize prejudiced talk when it arises in the classroom. Within the detail-oriented frameworks of conversation analysis and membership categorization analysis, this study examines teacher practices for problematizing students’ hearably prejudiced, stereotypical, or exclusionary talk—that is, students’ possible -isms. Drawing on data from 55 hours of video-recorded English L2 classes in the United States, I explore three problematizing responses to possible -isms: (i) introducing complexities, (ii) offering counter examples, and (iii) treating -isms as absurd. While introducing complexities neutralizes students’ hearable -isms as somehow inadequate, the latter two practices treat the -isms as entirely inaccurate through illustrated and invited corrections. The analysis reveals these practices to be finely attuned to the institutional goals and features of the adult L2 classroom, allowing teachers to incorporate a critical perspective and delicately problematize possible -isms without threatening solidarity with their diverse adult learners.
A fast machine learning dataloader for epigenetic tracks from BigWig files
Authors: Retel Joren Sebastian , Poehlmann Andreas , Chiou Josh , Steffen Andreas , Clevert Djork-Arné 
Published: January 2024

Abstract

Summary
We created bigwig-loader, a data-loader for epigenetic profiles from BigWig files that decompresses and processes information for multiple intervals from multiple BigWig files in parallel. This is an access pattern needed to create training batches for typical machine learning models on epigenetics data. Using a new codec, the decompression can be done on a graphical processing unit (GPU) making it fast enough to create the training batches during training, mitigating the need for saving preprocessed training examples to disk.

Availability and implementation
The bigwig-loader installation instructions and source code can be accessed at https://github.com/pfizer-opensource/bigwig-loader
ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining
Authors: Beasley Jon-Michael T , Korn Daniel R , Tucker Nyssa N , Alves Erick T M , Muratov Eugene N , Bizon Chris , Tropsha Alexander 
Published: January 2024

Abstract

Summary
Knowledge graphs are being increasingly used in biomedical research to link large amounts of heterogenous data and facilitate reasoning across diverse knowledge sources. Wider adoption and exploration of knowledge graphs in the biomedical research community is limited by requirements to understand the underlying graph structure in terms of entity types and relationships, represented as nodes and edges, respectively, and learn specialized query languages for graph mining and exploration. We have developed a user-friendly interface dubbed ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research) to aid reasoning over biomedical knowledge graphs and assist with data-driven research and hypothesis generation. We explain the key functionalities of ExEmPLAR and demonstrate its use with a case study considering the relationship of Trypanosoma cruzi, the etiological agent of Chagas disease, to frequently associated cardiovascular conditions.

Availability and implementation
ExEmPLAR is freely accessible at https://www.exemplar.mml.unc.edu/. For code and instructions for the using the application, see: https://github.com/beasleyjonm/AOP-COP-Path-Extractor.
Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging
Authors: Cang Hu , Liu Yang , Xing Jianhua 
Published: January 2024

Abstract

Motivation
Ultra-multiplexed fluorescence imaging has revolutionized our understanding of biological systems, enabling the simultaneous visualization and quantification of multiple targets within biological specimens. A recent breakthrough in this field is PICASSO, a mutual-information-based technique capable of demixing up to 15 fluorophores without their spectra, thereby significantly simplifying the application of ultra-multiplexed fluorescence imaging. However, this study has identified a limitation of mutual information (MI)-based techniques. They do not differentiate between spatial colocalization and spectral mixing. Consequently, MI-based demixing may incorrectly interpret spatially co-localized targets as non-colocalized, leading to overcorrection.

Results
We found that selecting regions within a multiplex image with low-spatial similarity for measuring spectroscopic mixing results in more accurate demixing. This method effectively minimizes overcorrections and promises to accelerate the broader adoption of ultra-multiplex imaging.

Availability and implementation
The codes are available at https://github.com/xing-lab-pitt/mosaic-picasso.
Elimination and penetration of amikacin into urine in patients with decreased glomerular filtration rate
Authors: Hartinger Jan Miroslav , Dvořáčková Eliška , Krátký Vojtěch , Hrušková Zdenka , Mysliveček Marek , Bobek Daniel , Benáková Hana , Závora Jan , Kroneislová Gabriela , Halouzková Barbora Agatha , Brejníková Martina , Martínková Vendula , Tesař Vladimír , Slanař Ondřej 
Published: January 2024

ABSTRACT

Background
Amikacin monotherapy is recommended for urinary tract infection (UTI) treatment with multi-resistant pathogens. Even though amikacin efficacy in the treatment of UTIs is dependent on its urinary concentration, there are no robust data proving that sufficiently high urinary concentration is reached in patients with reduced glomerular filtration rate (GFR).

Methods
A prospective study to monitor amikacin penetration into urine of 70 patients [40 males, median (interquartile range) age 70 (65–79) years] with different levels of glomerular filtration decline, including patients treated by dialysis, was conducted. The bactericidal efficacy of amikacin in urine samples has been evaluated.

Results
Patients with estimated GFR (eGFR) &lt;30 mL/min had significantly lower median amikacin urinary concentration than patients with eGFR &gt;30 mL/min (89.75 vs 186.0 mg/L, P &lt; .0001; 200.5 vs 830.0 mg/L, P &lt; .0001; and 126.0 vs 408.0 mg/L, P &lt; .0001 for minimal, maximal and minimal together with maximal concentrations, respectively). The amount of amikacin eliminated in the first 10–13 h after dose administration was dependent on eGFR (r2 = 0.6144, P &lt; .0001). The urinary concentration of amikacin in patients treated by dialysis was indirectly proportional to pH of urine. The plasma concentrations of amikacin did not correlate with urinary levels in patients in either of the GFR categories. Microbiological evaluation showed that the critical urinary concentration for efficacy of amikacin during UTI monotherapy in patients treated by dialysis is 100 mg/L. We found that 4 out of 11 patients treated by dialysis did not reach this level during the treatment.

Conclusion
Systemic administration of amikacin monotherapy in patients treated by dialysis is questionable as the concentrations of amikacin in their urine are often below the threshold of effectivity. Amikacin plasma concentrations are not a major determinant of amikacin concentration in urine, therefore pulse dosing is neither necessary nor safe in patients treated by dialysis, and may cause undesirable toxicity.
Emerging Biomarkers for Monitoring Chimeric Antigen Receptor T-Cell Therapy
Authors: Mamo Theodros , Dreyzin Alexandra , Stroncek David , McKenna David H 
Published: January 2024

Abstract

BACKGROUND
Chimeric antigen receptor (CAR) T-cell therapy has revolutionized treatment of hematologic malignancies and holds promise for solid tumors. While responses to CAR T-cell therapy have surpassed other available options for patients with refractory malignancies, not all patients respond the same way. The reason for this variability is not currently understood. Therefore, there is a strong need to identify characteristics of patients as well as cellular products that lead to an effective response to CAR T-cell therapy.

CONTENT
In this review, we discuss potential biomarkers that may predict clinical outcomes of CAR T-cell therapy. Based on correlative findings from clinical trials of both commercially available and early-phase products, we classify biomarkers into categories of pre- and post-infusion as well as patient and product-related markers. Among the biomarkers that have been explored, measures of disease burden both pre- and post-infusion, as well as CAR T-cell persistence post-infusion, are repeatedly identified as predictors of disease response. Higher proportions of early memory T cells at infusion appear to be favorable, and tracking T-cell subsets throughout treatment will likely be critical.

SUMMARY
There are a growing number of promising biomarkers of CAR T-cell efficacy described in the research setting, however, none of these have been validated for clinical use. Some potentially important predictors of response may be difficult to obtain routinely under the current CAR T-cell therapy workflow. A collaborative approach is needed to select biomarkers that can be validated in large cohorts and incorporated into clinical practice.
Epidemiology of Cancer
Authors: Schwartz Stephen M 
Published: January 2024

Abstract

Background
Cancers are a large and heterogeneous group of malignant tumors that collectively accounted for approximately 600 000 US deaths in 2020; only heart disease claimed more lives. A large amount of knowledge has accumulated regarding the epidemiology of most cancer types, including their causes.

Content
The cancer types most frequently diagnosed among adults in most high-income countries are lung, colorectal, female breast, cutaneous melanoma, and prostate. In general cancer incidence and mortality is very low in children and adolescents, rising exponentially with increasing age during adulthood. There is marked international variation in the incidence of most cancers. The most important causes of cancer are tobacco use (primarily cigarette use), excess alcohol consumption, obesity, lack of physical activity, diets low in fruits and vegetables, infectious agents, and sun exposure. Early detection can reduce the chances that a person will die of cancers of the female breast, uterine cervix, colon and rectum, lung, and prostate.

Summary
Although the most common cancers in the United States continue to have a substantial impact on public health, they are caused in whole or part by factors over which people and governments have control through choices they make. Among these are tobacco and alcohol use, obesity, diets low in fruits and vegetables and lack of physical activity, and sun exposure. Thus, a very large proportion of cancer’s impact could be ameliorated if more people avoided these exposures.
Predictive performance of surgical mortality risk scores in infective endocarditis
Authors: El Hatimi Safwane , Erpelding Marie-Line , Selton-Suty Christine , Botros Jean-Baptiste , Goehringer François , Berthelot Emmanuelle , Elfarra Mazen , Deconinck Laurène , Para Marylou , Provenchere Sophie , Hoen Bruno , Agrinier Nelly , Duval Xavier , Iung Bernard 
Published: January 2024

Abstract

OBJECTIVES
This observational study aimed to evaluate Association pour l’Etude et la Prévention de l’Endocardite Infectieuse (AEPEI) surgery score predictive performance in comparison to general (EuroSCORE I, II) and specific (De Feo, PALSUSE) surgical risk scores for infective endocarditis (IE).

METHODS
The study included patients who underwent surgery for IE during the acute phase at Bichat University Hospital (Paris, France) between 1 January 2006 and 31 December 2016 and at Nancy University Hospital (Nancy, France) between 1 January 2009 and 31 December 2019. Patients with IE complicating percutaneous aortic valve implantations or implantable intra-cardiac devices were excluded. Discrimination and calibration were assessed using receiver operating characteristic curve analysis, calibration curves and the Hosmer–Lemeshow test.

RESULTS
In-hospital mortality rates were 18% at Bichat and 16% at Nancy. Discrimination was high for all risk scores at Bichat (area under the receiver operating characteristic curve = 0.77 for EuroSCORE I, 0.78 for EuroSCORE II, 0.76 for De Feo score, 0.72 for PALSUSE and 0.73 for AEPEI with 95% confidence interval ranging from 0.67 to 0.83), but lower at Nancy (0.56 for EuroSCORE I, 0.65 for EuroSCORE II, 0.63 for De Feo score, 0.67 for PALSUSE and 0.66 for AEPEI score with 95% confidence interval ranging from 0.47 to 0.75). With Brier score, all scores were adequately calibrated in both populations between 0.129 (De Feo) and 0.135 (PALSUSE) for Bichat and between 0.128 (De Feo) and 0.135 (EuroSCORE I) for Nancy. With the Hosmer–Lemeshow test, the AEPEI score exhibited the best calibration (observed/predicted ratio 1.058 in Bichat, 1.087 in Nancy).

CONCLUSIONS
This surgical score external validation in 2 large independent populations demonstrated that the AEPEI surgical score had the best predictive performance compared to other prognosis scores. It could be helpful in clinical practice to assist the endocarditis team in decision-making.
Analysis of factors affecting outcome in acute type A aortic dissection complicated by preoperative cardiopulmonary resuscitation
Authors: Montagner Matteo , Kofler Markus , Pitts Leonard , Gasser Simone , Stastny Lukas , Kurz Stephan D , Grimm Michael , Falk Volkmar , Kempfert Jörg , Dumfarth Julia 
Published: January 2024

AbstractOBJECTIVESCardiopulmonary resuscitation (CPR) aggravates the pre-existing dismal prognosis of patients suffering from acute type A aortic dissection (ATAAD). We aimed to identify factors affecting survival and outcome in ATAAD patients requiring CPR at presentation at 2 European aortic centres.METHODSData on 112 surgical candidates and undergoing preoperative CPR were retrospectively evaluated. Patients were divided into 2 groups according to 30-day mortality. A multivariable model identified predictors for 30-day mortality.RESULTSPreoperative death occurred in 23 patients (20.5%). In the remaining 89 surgical patients (79.5%) circulatory arrest time (41 ± 20 min in 30-day non-survivors vs 30 ± 13 min in 30-day survivor, P = 0.003) as well as cardiopulmonary bypass time (320 ± 132 min in 30-day non-survivors vs 252 ± 140 min in 30-day survivor, P = 0.020) time was significantly longer in patients with worse outcome. Thirty-day mortality of the total cohort was 61.6% (n = 69) with cardiac failure in 48% and aortic rupture or haemorrhagic shock (28%) as predominant reasons of death. Age [odds ratio (OR) 1.04, 95% confidence interval (CI) 1.01–1.09, P = 0.034], preoperative coronary (OR 3.42, 95% CI 1.34–9.26, p = 0.012) and spinal malperfusion (OR 12.49, 95% CI 1.83–225.02, P = 0.028) emerged as independent predictors for 30-day mortality while CPR due to tamponade was associated with improved early survival (OR 0.29, 95% CI 0.091–0.81, P = 0.023).CONCLUSIONSAssessment of underlying cause for CPR is mandatory. Pericardial tamponade, rapidly resolved with pericardial drainage, is a predictor for improved survival, while age and presence of coronary and spinal malperfusion are associated with dismal outcome in this high-risk patient group.
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads
Authors: Hu Jiang , Wang Zhuo , Liang Fan , Liu Shan-Lin , Ye Kai , Wang De-Peng 
Published: January 2024

Abstract
The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here, we describe an upgraded genome polishing tool — NextPolish2, which can fix base errors remaining in those “highly accurate” genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors. We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere (T2T) genomes. NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.
New approach for combined aortic valve and coronary procedures through the left anterior minithoracotomy
Authors: Babliak Oleksandr , Demianenko Volodymyr , Babliak Dmytro , Marchenko Anton , Melnyk Yevhenii , Stohov Oleksii 
Published: January 2024

Abstract

OBJECTIVES
We have developed a novel technique for accessing the aortic valve (AoV) through the left anterior minithoracotomy (LAmT). This approach has been used in patients requiring both AoV surgery and coronary artery bypass grafting (CABG).

METHODS
From April 2023 to July 2023, we performed 6 concomitant AoV procedures and CABG through the LAmT. The mean age was 71.5 [standard deviation (SD): 5.8; 64; 82] years, and the mean left ventricular ejection fraction was 53% (SD: 12.1; 30; 60). Surgical technique includes LAmT in the fourth intercostal space, peripheral cardiopulmonary bypass, aortic cross-clamping using transthoracic clamp, cold blood cardioplegia, conventional oblique aortotomy and special surgical exposure manoeuvres, aimed to position the ascending aorta and AoV close to the surgical incision.

RESULTS
AoV was effectively visualized and the procedure was performed as planned in all 6 patients. No conversion to sternotomy was required. AoV replacement with biological prosthesis was performed in 6 (100%) patients. Conventional surgical instruments were used in all cases. The long-shafted instruments were not required. Knot-pusher was used in 4 (67%)cases. Concomitant complete revascularization was achieved in all cases. The mean number of distal anastomosis was 2.0 (SD: 0.6; 1; 3). Total operation time was 371 (SD: 43; 300; 420) min, cardiopulmonary bypass time was 253 (SD: 36; 193; 284) min and cross-clamp time was - 162 (SD: 29; 128; 214) min. intensive care unit stay was—1.5 (SD: 0.55; 1; 2) days, total hospital stay was—7.3 (SD: 1; 6; 9) days. There were no revisions for bleeding, no strokes or other major complications, and no hospital or 30-days mortality.

CONCLUSIONS
The simultaneous performance of AoV replacement and multivessel CABG through a single left anterior thoracotomy is technically feasible and can be carried out by experienced surgeons. However, a larger number of cases are required to fully comprehend the potential limitations of this procedure.
B-Side Spirituality: An Empathetic Theory of Religion and Ethnographic Data About Spiritual (but Not Religious) Belonging
Authors: Johnston Lucas 
Published: January 2024

AbstractAccording to some cognitive and neuroscientific theories, religion is not an evolved adaptation but rather an artifact, one that may lead to adaptive behaviors. Here I relate (a) an empathetic theory of religion with (b) a functional theory of musicality to clarify religion’s adaptive features. This theory contributes to previous research by explaining the link between spirituality and music and makes the nontrivial prediction that increasing numbers of people who are disaffected by traditional religious institutions will find modes of meaning-making and fellow-feeling in contemporary festival and live music scenes.
A fast and reliable LC–MS-MS method for the quantification of saxitoxin in blood plasma samples
Authors: Odehnalová Klára , Přibilová Petra , Maršálek Blahoslav , Babica Pavel 
Published: January 2024

Abstract
Saxitoxins (STXs) are potent neurotoxins produced by marine dinoflagellates or freshwater cyanobacteria known to cause acute and eventually fatal human intoxications, which are classified as paralytic shellfish poisonings (PSPs). Rapid analysis of STXs in blood plasma can be used for a timely diagnosis and confirmation of PSPs. We developed a fast and simple method of STX extraction based on plasma sample acidification and precipitation by acetonitrile, followed by quantification using liquid chromatography-tandem mass spectrometry (LC–MS-MS). Our approach provides the results ≤30 min, with a limit of detection of 2.8 ng/mL and a lower limit of quantification of 5.0 ng/mL. Within-run and between-run precision experiments showed good reproducibility with ≤15% values. Standard curves for calibration were linear with correlation coefficients ≥0.98 across the assay calibration range (5–200 ng/mL). In an interlaboratory analytical exercise, the method was found to be 100% accurate in determining the presence or absence of STX in human plasma specimens, with recovery values of 86–99%. This simple method for STX determination in animal or human plasma can quickly and reliably diagnose STX exposures and confirm suspected PSP cases to facilitate patient treatment or expedite necessary public health or security actions.