bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenomic Prediction Can Be Improved by Optimization of NIRS Preprocessing
Authors: Braun Vincent , Zhu Xintian , Meyenberg Carina , Hahn Volker , Maurer Hans Peter , Würschum Tobias , Thorwarth Patrick 
Published: February 2025

ABSTRACTIn recent years, phenomic prediction has emerged as a new method in plant breeding that has been shown to have great potential. However, there are still many open questions regarding its practical application. For example, in the field of spectroscopy, it is standard practice to optimize the preprocessing of spectra, which so far has only been done to a limited extent for phenomic prediction. In this study, we therefore used three different data sets of soybean, triticale and maize to identify the best combinations of Savitzky–Golay filter parameters for preprocessing near‐infrared spectra for phenomic prediction. We tested 677 combinations of polynomial order, derivative and window size and evaluated them with Monte Carlo cross‐validation. Our results showed that the predictive ability can be improved with the right settings. However, there was no global optimum that gave the best results for all data sets. Even for different traits within the same data set, different combinations of parameters were necessary to achieve the highest predictive ability. Nevertheless, we show that some combinations generally result in a very low predictive ability and should not be used for preprocessing. In addition, we used the normalized discounted cumulative gain to assess whether preprocessing affected the ranking of individuals, which revealed no major changes in the top 1%, 10% or 20% of predicted individuals. Taken together, our results show the potential of preprocessing near‐infrared spectroscopy data to improve the phenomic predictive ability, but there appears to be no global optimum of parameter settings across data sets and traits.
Unexpected Palatal Lesion: Pistachio Shell Mimicking a Palatal Tumor
Authors: Dikmen Adile , Akdeniz Hande 
Published: February 2025

ABSTRACTA 17‐month‐old child presented with a suspected nodule on the hard palate, initially diagnosed as a possible teratoma or adenoma. MRI showed a mucosal mass limited to the submucosa, leading to an excisional biopsy under general anesthesia. The lesion was ultimately identified as a pistachio shell, emphasizing the challenge of diagnosing foreign bodies in atypical locations. This case highlights the need for vigilance among clinicians in identifying uncommon presentations of foreign body ingestion.
An adversarial risk analysis framework for software release decision support
Authors: Soyer Refik , Ruggeri Fabrizio , Insua David Rios , Pierce Cason , Guevara Cesar 
Published: February 2025

AbstractRecent artificial intelligence (AI) risk management frameworks and regulations place stringent quality constraints on AI systems to be deployed in an increasingly competitive environment. Thus, from a software engineering point of view, a major issue is deciding when to release an AI system to the market. This problem is complex due to, among other features, the uncertainty surrounding the AI system's reliability and safety as reflected through its faults, the various cost items involved, and the presence of competitors. A novel general adversarial risk analysis framework with multiple agents of two types (producers and buyers) is proposed to support an AI system developer in deciding when to release a product. The implementation of the proposed framework is illustrated with an example and extensions to cases with multiple producers and multiple buyers are discussed.
Benefits Conditionality in the United Kingdom: Is It Common, and Is It Perceived to Be Reasonable?
Authors: Geiger Ben Baumberg , Scullion Lisa , Edmiston Daniel , de Vries Robert , Summers Kate , Ingold Jo , Young David 
Published: February 2025

ABSTRACTProgramme‐level data suggest that increasing numbers of claimants are subject to work‐related behavioural requirements in countries like the United Kingdom. Likewise, academic qualitative research has suggested that conditionality is pervasive within the benefits system, and is often felt to be unreasonable. However, there is little quantitative evidence on the extent or experience of conditionality from claimants' perspectives. We fill this gap by drawing on a purpose‐collected survey of UK benefit claimants (n = 3801). We find that the stated application of conditionality was evident for a surprisingly small proportion of survey participants—even lower than programme‐level data suggest. Unreasonable conditionality was perceived by many of those subject to conditionality, but not a majority, with, for example, 26.2% believing that work coaches do not fully take health/care‐related barriers into account. Yet, alongside this, a substantial minority of claimants not currently subject to conditionality (22.4%) report that conditionality has negatively affected their mental health. We argue that reconciling this complex set of evidence requires a more nuanced understanding of conditionality, which is sensitive to methodological assumptions, the role of time and implementation and the need to go beyond explicit requirements to consider implicit forms of conditionality. In conclusion, we recommend a deeper mixed‐methods agenda for conditionality research.
The cis‐prenyltransferase protein family in Taraxacum koksaghyz
Authors: Müller Boje , Niephaus Eva , Eisenreich Wolfgang , Bröker Jan Niklas , Twyman Richard M. , Prüfer Dirk , Schulze Gronover Christian 
Published: February 2025

SUMMARYThe cis‐prenyltransferase (cisPT) enzyme family is involved in diverse biological processes that require the synthesis of linear isoprenoid compounds. Taraxacum koksaghyz is a rubber‐producing species and potential crop that has eight cisPT homologs (TkCPT1–8) but their distribution and functions are unclear. We compared the structural organization and sequence homology of the proteins, and defined two groups: TkCPT and TkCPT‐like (TkCPTL) proteins that form heteromeric cisPT enzymes (TkCPT1–4), and TkCPT proteins that function as homomeric cisPTs (TkCPT5–8). We found that TkCPT1 and TkCPT2 are predominantly expressed in latex whereas TkCPT3 and TkCPT6‐8 are predominantly expressed in leaves. TkCPT4 was constitutively expressed in all T. koksaghyz tissues and TkCPT5 mRNA was detected in flowers. The TkCPT1–4 subunits localized to the endoplasmic reticulum whereas TkCPT5–7 were located in chloroplasts. TkCPT1‐4 interacted with TkCPTL1‐2, forming heteromeric complexes that complemented yeast lacking cisPT. Homomeric TkCPT6 could also complement yeast lacking cisPT but we observed no cisPT activity for TkCPT5, TkCPT7, or TkCPT8 in yeast functional complementation assays. TkCPT1/TkCPTL1 and TkCPT2/TkCPTL1 expressed in yeast produced extra‐long‐chain polyisoprenes, whereas TkCPT3/TkCPTL1 and TkCPT4/TkCPTL1 produced long‐chain dolichols and polyisoprenes, TkCPT5 and TkCPT6 produced medium‐chain polyisoprenes, and TkCPT7 and TkCPT8 catalyzed the formation of nerol. The complexity of cisPT proteins in T. koksaghyz suggests that they synthesize different metabolites in a tissue‐specific manner, and thus play distinct roles in isoprenoid metabolism. This is the first comprehensive analysis of the localization, interactions, and products of the entire T. koksaghyz cisPT family in vivo, also revealing a novel pentaprenol found specifically in flowers.
Accuracy and safety of two landmark‐guided techniques for arthrocentesis and intra‐articular injection of the shoulder in dogs
Authors: McClean Brónach , P. McNally Turlough , Pozzi Antonio , Evans Richard , C. Cuddy Laura 
Published: February 2025

AbstractObjectiveTo determine the accuracy and safety of two landmark‐guided techniques for shoulder arthrocentesis and injection.Study designEx vivo prospective study.AnimalsA total of 36 paired canine cadaver forelimbs.MethodsAn electronic survey was used to assess the prevalence of injection technique amongst surgeons in clinical practice. Thoracic limbs were randomized to technique for shoulder arthrocentesis and injection (subacromial [SA], n = 18, or supratubercular [ST], n = 18). Repositions, attempts, and the acquisition of synovial fluid was recorded. After the needle was placed, contrast was injected into the joint to determine accuracy of position. The radiographic presence of intra‐articular contrast was judged as an accurate injection. Shoulders were disarticulated and India ink assay performed to assess for iatrogenic articular cartilage injury (IACI).ResultsBoth SA and ST techniques were not accurate. Completely accurate injection was identified in 50% SA and 44% ST (p = .80). IACI was identified in 50% SA versus 11% ST (p = .027). There were no significant differences in repositions, attempts, presence of synovial fluid (p = .5, p = .6, p = .7).ConclusionLandmark‐guided shoulder injections performed via SA and ST approaches in cadaveric dog shoulders are overall inaccurate. If performing landmark‐guided shoulder injection, ST technique carries a lower risk of IACI than SA in cadaveric shoulders.Clinical significanceLandmark‐guided shoulder injections are inaccurate in dogs and may result in treatment failure. A ST approach may be considered preferable due to the lower risk of cartilage damage. Future studies should assess ultrasound‐guided techniques to improve accuracy and safety.
High-Speed Visualization and Characterization of Bubbles in a Bubble Absorber with Swirl-Induced Flow of Refrigerant
Authors: Sanikommu Narasimha Reddy , Mani Dr. A. , Tiwari Shaligram 
Published: February 2025

Abstract
The present study experimentally investigates the hydrodynamic characteristics of air bubbles within a glass bubble absorber. A swirl generator designed based on the cavity profile introduces swirl motion to the air entering the water column, and high-speed visualization techniques are employed to analyze the resulting bubble behavior. The optimal swirl generator geometry is determined by performing numerical simulations. The present study considers still, co-current and counter current water flow conditions relative to the airflow. Experiments are also conducted to explore the impact of air and water flow rates on bubble characteristics, such as departure diameter, departure time, rise velocity, etc. Visualization studies revealed that the bubble formation phenomenon can be categorized into three different stages: initiation, growth, and detachment. It is observed that the direction of water flow has a significant effect on bubble characteristics. Based on the experimental data, empirical correlations for non-dimensional departure bubble diameter have been proposed, which can help estimate the primitive bubble size in a bubble absorber.
Transition Wave Interference in Multistable Mechanical Metamaterials
Authors: Bonthron Michael , Tubaldi Eleonora 
Published: February 2025

Abstract
Mechanical metamaterials with multiple stable configurations offer a promising avenue for the design and development of adaptable materials with unprecedented levels of control over physical properties. Specifically, arrays of bistable beam elements represent a unique metamaterial platform with tunable transition waves offering means of passive control, sensing, and memory effects of environmental conditions. Although previous studies have mainly investigated transition waves triggered by a static input in nonlinear metamaterials, the dynamic properties of these structures and the interference of colliding waves are still unknown. Here, we investigate the dynamic properties of arrays of bistable beam elements which are important keys in the further development of applications of these metastructures. We determine the critical force and the optimal location to apply a force to trigger a transition wave and characterize the natural frequencies of the metamaterial. Moreover, we study the interference between two transition waves simultaneously actuated at both ends of the one-dimensional multistable array. Our new insights on the nonlinear dynamic responses of multistable metamaterials pave the way for the ability to design and program adaptable structures with enhanced energy absorption, vibration isolation, and wave steering capabilities.
Embedded Fused Filament Fabrication of Thermoplastics for Biomedical Applications
Authors: Mitchell Kellen , Shackleford Aidan , Bandala Erick , Zhang Chen , Chai Guangrui , Jin Yifei 
Published: February 2025

Abstract
Utilizing material extrusion three-dimensional printing methods, particularly fused filament fabrication (FFF), allows for the creation of complex architectures. Nevertheless, FFF-fabricated structures often suffer from inadequate mechanical properties and elevated surface roughness. In this study, we developed an embedded FFF (e-FFF) approach to produce thermoplastic products with enhanced mechanical characteristics and improved surface quality. This approach was achieved through the development of a thermostable yield-stress fluid made from fumed silica particles and sunflower oil. By tuning the rheological properties of the support bath, thermoplastic filaments were effectively supported in a molten state throughout printing. Biocompatible and biodegradable polycaprolactone (PCL) was selected as the exemplary thermoplastic polymer in this work. Filaments, single-layer sheets, and tensile test samples were printed to fine-tune the printing parameters, assess surface morphology, and certify the mechanical properties of structures printed by e-FFF. To demonstrate the potential biomedical applications of the approach, an orbital implant model was designed using numerical simulation to evaluate mechanical integrity. Then, the orbital implant was printed and measured to confirm the effectiveness of the proposed e-FFF approach. Lastly, cells were successfully incubated on the PCL implant, which was affixed to a mock orbital fracture to confirm that patient-specific orbital implants could be fabricated.
Presenting Hackathon Data for Design Research: A Transcript Dataset
Authors: Flus Meagan , Litster Gregory , Olechowski Alison 
Published: February 2025

Abstract
Hackathons are intensive design experiences during which teams identify a problem and rapidly develop prototypes of solutions. These events offer a promising venue for studying collaborative design: they are naturalistic, short-term, and contained, which mitigate many of the drawbacks of traditional investigations in design research. The objective of this technical brief is to present and describe a transcript dataset of conversations collected from a hackathon team. The dataset includes a transcript of the verbal communication between a four-person hackathon team in the first 2 hours and 9 minutes of their collaboration. This portion of the design process, totalling 908 segments of speech, details the team's problem exploration, brainstorming, idea selection, and premature team dissolution. This brief outlines the advantages of having rich transcript data freely available, with a specific focus on new research directions and impact. We demonstrate the potential for this dataset in an example analysis of premature team dissolution, using inductive coding to explore goal misalignment as a possible explanation. We aim for this brief to encourage the use of this data for future investigations of design, teamwork, and hackathon phenomena, as well as act as an exemplar for future publications of open-access datasets.
Xpert MTB/RIF Ultra-resistant and MTBDR
plus-
susceptible rifampicin results in people with tuberculosis: utility of FluoroType MTBDR and deep sequencing
Authors: Ghebrekristos Yonas , Ahmed Aysha , Beylis Natalie , Singh Sarishna , Opperman Christoffel , Naufal Fahd , Folkerts Megan , Engelthaler David , Auma Erick , Venter Rouxjeane , Booley Ghowa , Metcalfe John , Warren Robin , Theron Grant 
Published: February 2025

ABSTRACT

Xpert MTB/RIF Ultra (Ultra)-detected rifampicin-resistant tuberculosis (TB) is often programmatically confirmed using MTBDR
plus
. There are limited data on discordant results, including when re-tested using newer methods, like FluoroType MTBDR (FT-MTBDR) and targeted deep sequencing. MTBDR
plus
rifampicin-susceptible isolates from people with Ultra rifampicin-resistant sputum were identified from a South African programmatic laboratory. FT-MTBDR and single molecule-overlapping reads (SMOR;
rpoB
,
inhA
,
katG
) on isolate DNA were done (SMOR was used as a reference standard). Between 1 April 2021 and 30 September 2022, 8% (109/1347) of Ultra rifampicin-resistant specimens were MTBDR
plus
-susceptible. Of 89% (97/109) isolates with a sequenceable
rpoB
, SMOR resolved most in favor of Ultra (79% [77/97]). Sputum with lower mycobacterial load was associated with Ultra false-positive resistance (46% [11/24] of “very low” Ultra had false resistance vs 12% [9/73;
P
= 0.0004] of ≥“low”), as were Ultra heteroresistance calls (all wild-type probes, ≥1 mutant probe) (62% [23/37 vs 25% 15/60] for Ultra without heteroresistance calls;
P
= 0.0003). Of the 91% (88/97) of isolates successfully tested by FT-MTBDR, 55% (48/88) were FT-MTBDR rifampicin-resistant and 45% (40/88) susceptible, translating to 69% (47/68) sensitivity and 95% (19/20) specificity. In the 91% (99/109) of isolates with
inhA
and
katG
sequenced, 62% (61/99) were SMOR isoniazid-susceptible. When Ultra and MTBDR
plus
rifampicin results are discordant, Ultra is more likely to be correct, and FT-MTBDR agrees more with Ultra than MTBDR
plus
; however, lower load and the Ultra heteroresistance probe pattern were risk factors for Ultra false rifampicin-resistant results. Most people with Ultra–MTBDR
plus
discordant resistance results were isoniazid-susceptible. These data have implications for drug-resistant TB diagnosis.
Evaluation of two gradient diffusion tests to determine susceptibility to aztreonam and ceftazidime–avibactam in combination
Authors: Khan Ayesha , Manuel Carmila , Maynard Richard , Humphries Romney M. 
Published: February 2025

ABSTRACT

The combination of aztreonam and ceftazidime–avibactam (ATM–CZA) is a last resort regimen against recalcitrant infections caused by metallo-β-lactamase (MBL)-producing organisms. Susceptibility testing is warranted due to emerging resistance to the combination, but there are no widely implemented methods for use in clinical laboratories. Here, we used a cohort of 100 Enterobacterales
, Pseudomonas aeruginosa
, and
Stenotrophomonas maltophilia
strains, including 68 MBL producers, to evaluate the performance of two ETEST strip-based synergy testing methods: the side-by-side (SS) method with an ATM ETEST placed next to a CZA ETEST (10 mm apart) and the strip cross (SX) method with a CZA ETEST placed perpendicularly on top of the ATM ETEST (at the 8 µg/mL mark). By reference broth microdilution (BMD), 89.1% (41/46) of the Enterobacterales, 15% (3/20) of the
P. aeruginosa
, and 97.1% (33/34) of the
S. maltophilia
isolates tested susceptible to the ATM–CZA combination. The SS method yielded 72% categorical agreement with BMD and 28 major errors (ME, 36.4%). Initial testing with the SX method yielded three ME , of which one was resolved upon repeat testing, yielding a final categorical agreement of 98% with BMD with two ME (2.6%). The SX method also yielded 100% reproducibility across three brands of Mueller Hinton agar (BD, Hardy, Remel). Our study demonstrates that the SX method is accurate, precise, and feasible for clinical laboratories to perform ATM–CZA susceptibility testing to guide use of the combination for treatment of multidrug-resistant gram-negative pathogens.
Enhancing
Acanthamoeba
diagnostics: rapid detection of viable
Acanthamoeba
trophozoites and cysts using viability PCR assay
Authors: Veugen J. M. J. , Savelkoul P. H. M. , Nuijts R. M. M. A. , Dickman M. M. , Wolffs P. F. G. 
Published: February 2025

ABSTRACT

Acanthamoeba
keratitis (AK) is a sight-threatening corneal infection that is challenging to diagnose and treat due to the resistance of
Acanthamoeba
to standard antimicrobial agents. Current detection methods have limitations. This study aimed to develop and validate a sensitive viability PCR (v-PCR) assay using a photoreactive dye to distinguish viable from non-viable
Acanthamoeba
for rapid identification of viable
Acanthamoeba
trophozoites and cysts. Propidium monoazide (PMAxx) was used as a photoreactive dye. Mixtures containing decreasing percentages of viable
Acanthamoeba
, including reference strains
Acanthamoeba polyphaga
trophozoites and cysts,
Acanthamoeba castellanii
trophozoites, and
Acanthamoeba castellanii
trophozoites from a clinical sample, were prepared. Disinfectant efficacy against
Acanthamoeba
was also assessed. Samples were divided into PMAxx-treated and non-PMAxx-treated parts, and v-PCR assay was applied to both. The difference in viable
Acanthamoeba
was determined by subtracting the cycle threshold (Ct) value of the PMAxx-treated sample from the non-PMAxx-treated sample. Mixtures with decreasing concentrations of viable
Acanthamoeba
trophozoites and cysts showed increasingly lower delta Ct values as the percentage of viable
Acanthamoeba
decreased, as expected. This relationship was observed across all tested samples. Menicon Progent effectively eliminated
A. polyphaga
trophozoites and cysts, while propamidine, chlorhexidine, or their combination resulted in approximately 2-log reductions in
A. polyphaga
trophozoites and cysts. In the current study, a rapid v-PCR assay was developed that can distinguish between viable and non-viable
Acanthamoeba
, for both trophozoites and cysts, across multiple species. The presence of viable
Acanthamoeba
, as determined by v-PCR, allows monitoring of treatment response and efficacy in AK.

IMPORTANCE

The development of a sensitive viability PCR (v-PCR) assay using propidium monoazide (PMAxx) as a photoreactive dye marks a significant advancement in the diagnosis and treatment of
Acanthamoeba
keratitis (AK), a severe corneal infection notorious for its resistance to conventional antimicrobials. This innovative assay offers a rapid and accurate method to distinguish viable from non-viable
Acanthamoeba
trophozoites and cysts, addressing a critical need in the field. By effectively distinguishing between viable and non-viable
Acanthamoeba
, this test enables monitoring of treatment response and efficacy, essential for guiding clinical interventions in AK cases. The successful validation of this v-PCR assay across various
Acanthamoeba
species and its ability to assess disinfectant efficacy further underline its potential as a valuable tool for improving diagnostic precision and therapeutic outcomes in the treatment of AK.
Supplemental Material: Insights into Cordilleran collisional processes: Early shared history of the Eocene Siletzia and Yakutat terranes as a ridge-centered oceanic plateau
Authors: Donaghy Erin E. , al. et 
Published: February 2025

<p>Sedimentologic characterization of sedimentary units discussed in manuscript text, detailed U-Pb zircon geochronology methods, and raw data. </p>