bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social Media and the Unmediated in Early African Americanist Scholarship
Authors: Saillant John 
Published: November 2024

Abstract
The Odyssey of Phillis Wheatley: A Poet’s Journeys through American Slavery and Independence (2023), by David Waldstreicher, analyzes Wheatley in her context in Revolutionary America. Waldstreicher provides reasonable interpretation of her poetry, especially fine for his understanding of her classical allusions. An added bonus is an appendix of anonymous poems that he argues should be attributed to her. His book is guided by a conviction that Wheatley must have been—and must be recognized today as—important. By this, he means influential in her time. His definition of influence seems to draw from early twenty-first-century social media, finding power in touching many people through words and images. Print was, he writes, “the internet of the eighteenth century” (41). Reading Pleasures: Everyday Black Living in Early America (2023), by Tara A. Bynum, expresses a parallel relationship to social media. She discusses #BlackLivesMatter, while her scholarship itself is often discussed in social media. The immediacy and ubiquity of social media in our lives give us a sense of unmediated access to those we encounter in it. In this, Bynum shines on and with the printed page. Her focus is Black pleasure in scenes in which scholars have slighted it—friendship, religion, revolution, even the talking book.
Orchid phylogenetics and evolution: history, current status and prospects
Authors: Freudenstein John V 
Published: November 2024

Abstract

Background
Orchidaceae are one of the two largest families of angiosperms; they exhibit a host of changes – morphological, ecological and molecular – that make them excellent candidates for evolutionary study. Such studies are most effectively performed in a phylogenetic context, which provides direction to character change. Understanding of orchid relationships began in the pre-evolutionary classification systems of the 1800s, which were based solely on morphology, and now is largely based on genomic analysis. The resulting patterns have been used to update family classification and to test many evolutionary hypotheses in the family.

Scope
Recent analyses with dense sampling and large numbers of nuclear loci have yielded well-supported trees that have confirmed many longstanding hypotheses and overturned others. They are being used to understand evolutionary change and diversification in the family. These include dating the origination of the family, analysis of change in ecological habit (from terrestrial to epiphytic and back again in some cases), revealing significant plastid genome change in leafless holomycotrophs, studying biogeographic patterns in various parts of the world, and interpreting patterns of fungal associations with orchids.

Conclusions
Understanding of orchid relationships has progressed significantly in recent decades, especially since DNA sequence data have been available. These data have contributed to an increasingly refined classification of orchids and the pattern has facilitated many studies on character evolution and diversification in the family. Whole-genome studies of the family are just beginning and promise to reveal fine-level details underlying structure and function in these plants, and, when set in a phylogenetic context, provide a much richer understanding of how the family has been so successful in diversification.
Source–sink manipulations through shading, crop load and water deficit affect plant morphogenesis and carbon sink priorities leading to contrasted plant carbon status in grapevine
Authors: Poupard Magali , Gallo Agustina , Boulord Romain , Guillem Pablo , Rolland Gaëlle , Simonneau Thierry , Christophe Angélique , Pallas Benoît 
Published: November 2024

Abstract

Background and Aims
Shading, water deficit and crop load shape plant development in a very plastic way. They directly influence the plant’s carbon supply and demand to and from the different organs via metabolic, hydraulic and hormonal mechanisms. However, how the multiple environmental factors combine through these mechanisms and how they interplay with carbon status, vegetative and reproductive development and carbon assimilation of the plant needs to be investigated in the context of current climatic and technological constraints.

Methods
With this aim, two experiments were conducted on potted grapevines, subjected to ten combinations of treatments. Leaf area growth rates, berry characteristics at harvest (weight, number and total soluble content) and a series of leaf traits (gas exchanges, non-structural carbohydrate contents, water potential and SPAD [Soil–Plant Analysis Development] values) were measured.

Key Results
Grapevine development showed different responses corresponding to different sink priorities: under shade, vegetative development was maintained at the expense of berries, whereas under high crop load and water deficit, berry growth was the priority sink. These responses were accompanied by changes in specific leaf area in agreement with the shade avoidance syndrome. These different strategies affected plant carbon status as estimated through starch content in leaves. Leaf starch content was not affected by shade, while it decreased under water deficit and crop load conditions. Carbon assimilation was decreased under water deficit, low crop load and shading conditions. Hydraulic properties and leaf nitrogen content correlated with this decrease while plant carbon status had a very low impact. Finally, no major interaction between the different types of constraint was observed on both morphological and functional variables.

Conclusions
Depending on the type of abiotic constraints, grapevine exhibits specific morphogenetic responses at plant and leaf levels. The absence of interaction between the different constraints showed that grapevine is able to exhibit independent responses to shade and water deficit. This result is of major importance for the further design of new agricultural systems facing multiple abiotic constraints, such as those in agroforestry and agrivoltaic systems.
Ripples in the Historiography: Harlem Studio Photographer James Van Der Zee and Cecil Beaton’s New York, 1938
Authors: Chesnutt Boone Emilie 
Published: November 2024

Abstract
In 1938, the well-known British photographer Cecil Beaton published his travelogue Cecil Beaton’s New York for American and British audiences. The book was the first to publish and consider works by the African American studio photographer James Van Der Zee. Yet this account of Van Der Zee has been overlooked by scholars and relegated to footnotes, feasibly because of Beaton’s dismissive and tactless consideration of the now highly regarded photographer. With commitments to exploring the overlooked and unexpected moments in Van Der Zee’s historiography, this essay approaches Cecil Beaton’s New York as an opportunity to begin thinking about Van Der Zee in ways that transgress established narratives. It does so by inserting Van Der Zee within an avant-garde circle in which he is rarely considered, and attending to the possibility of an early-twentieth century-critical Black readership of Beaton’s book. With the aim of centring Van Der Zee, this essay demonstrates his relevance to a multitude of interwar contexts animated by the practice of photography. As a result, it becomes conceivable to shift the very terms through which we interpret the early account of Van Der Zee’s work, and the transatlantic contexts that scholars may choose to consider.
Is Vibration Anesthesia Effective and Safe for Pain Reduction in Botulinum Toxin Injection? A Randomized Split-Face Controlled Trial and Cadaver Experiment
Authors: Hua Tianzhen , Li Huan , Liang Chun , Zhang Guangliang , Luo Libo , Jia Haoran , Liu Xin , Chi Yuan , An Yang , Chen Youbai 
Published: November 2024

Abstract

Background
Pain is an important issue in botulinum toxin injection. Vibration anesthesia is a noninvasive method for pain alleviation, but few studies have reported its use during botulinum toxin injection.

Objectives
The aim of this study was to investigate whether vibration anesthesia was effective and safe for pain reduction during botulinum toxin injection for masseter reduction.

Methods
A randomized split-face controlled trial was performed in patients who required masseter reduction. Vibration anesthesia was randomly administered on either side. Study outcomes were pain scores on a visual analog scale, duration of effect, satisfaction, and complications. Intergroup comparison and linear regression analyses were performed.

Results
In a total of 216 patients, the pain score on the vibration side (2.97 ± 1.44) was significantly lower than that on the nonvibration side (4.72 ± 2.13) (P &lt; .0001), with a higher proportion of mild pain. Linear regression showed that a history of injection and more injection points and doses increased the pain, whereas a 2-mL syringe reduced the pain compared to a 1-mL syringe. Side effects were found in 19 patients and 21 sides (7%), but were not associated with vibration. High satisfaction was reported. A cadaver experiment confirmed that vibration did not alter the diffusion radius and depth of injection.

Conclusions
Vibration anesthesia significantly relieved pain during botulinum toxin injection for masseter reduction, and it did not cause adverse effects and or affect duration of effect. Therefore, we recommend vibration anesthesia, a larger syringe size, and fewer injection points to improve patient experience and satisfaction.

Level of Evidence: 3 (Therapeutic)
Optimizing multi-omics data imputation with NMF and GAN synergy
Authors: Ansari Md Istiaq , Ahmed Khandakar Tanvir , Zhang Wei 
Published: November 2024

Abstract

Motivation
Integrating multiple omics datasets can significantly advance our understanding of disease mechanisms, physiology, and treatment responses. However, a major challenge in multi-omics studies is the disparity in sample sizes across different datasets, which can introduce bias and reduce statistical power. To address this issue, we propose a novel framework, OmicsNMF, designed to impute missing omics data and enhance disease phenotype prediction. OmicsNMF integrates Generative Adversarial Networks (GANs) with Non-Negative Matrix Factorization (NMF). NMF is a well-established method for uncovering underlying patterns in omics data, while GANs enhance the imputation process by generating realistic data samples. This synergy aims to more effectively address sample size disparity, thereby improving data integration and prediction accuracy.

Results
For evaluation, we focused on predicting breast cancer subtypes using the imputed data generated by our proposed framework, OmicsNMF. Our results indicate that OmicsNMF consistently outperforms baseline methods. We further assessed the quality of the imputed data through survival analysis, revealing that the imputed omics profiles provide significant prognostic power for both overall survival and disease-free status. Overall, OmicsNMF effectively leverages GANs and NMF to impute missing samples while preserving key biological features. This approach shows potential for advancing precision oncology by improving data integration and analysis.

Availability and implementation
Source code is available at: https://github.com/compbiolabucf/OmicsNMF.
Protein structure alignment by Reseek improves sensitivity to remote homologs
Authors: Edgar Robert C 
Published: November 2024

Abstract

Motivation
Recent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, presenting new opportunities and challenges to bioinformatics.

Results
Reseek is a novel protein structure alignment algorithm based on sequence alignment where each residue in the protein backbone is represented by a letter in a “mega-alphabet” of 85 899 345 920 (∼1011) distinct states. Reseek achieves substantially improved sensitivity to remote homologs compared to state-of-the-art methods including DALI, TMalign, and Foldseek, with comparable speed to Foldseek, the fastest previous method. Scaling to large databases of AI-predicted folds is analyzed. Foldseek E-values are shown to be under-estimated by several orders of magnitude, while Reseek E-values are in good agreement with measured error rates.

Availability and implementation
https://github.com/rcedgar/reseek.
Topical application of the Hedgehog inhibitor patidegib in patients with Gorlin syndrome: a phase II trial
Authors: Lear John T , Harwood Catherine A , Hasan Zeeshaan , Kentley Jonathan , Thomson Jason , Khoo Andre , Alderman Alix , DeSouza Mark , Epstein Ervin H , Kochendoerfer Gerd G , Tang Jean Y 
Published: November 2024

Abstract

Background
Patients with Gorlin (basal cell naevus) syndrome (GS) have numerous phenotypic abnormalities due to overactivity of the hedgehog (HH) signalling pathway, most commonly caused by a heritable mutation in PTCH1, which encodes a major inhibitor of this pathway. Oral HH inhibitors (HHi) can reverse some of the manifestations, most prominent of which is the development of numerous cutaneous basal cell carcinomas (BCCs). In order to improve the benefit–risk ratio, we developed a gel containing a small cyclopamine-derived molecule that can be applied topically in expectation that this mode of delivery can reduce the burden of BCCs without producing the systemic adverse effects that cause patients to stop oral HHi treatment.

Objectives
To determine whether or not patidegib topical gel 2% or 4% can accumulate in high enough concentrations to have local anti-BCC efficacy but not so high that systemic drug levels produce the adverse effects typical of oral HHi treatment.

Methods
We conducted a small randomized double-blinded phase IIA trial at two sites in the UK, to assess the clinical and molecular efficacy and adverse effects of 6 months of twice-daily application of patidegib topical gel to the entire face, as well as to treatment-targeted surgically eligible BCCs at other anatomical sites.

Results
Post hoc analyses suggested that patidegib topical gel reduced the number of new, surgically eligible BCCs and the level of HH signalling, with minimal adverse effects.

Conclusions
Patidegib topical gel warrants further clinical development.
Mapping sentence comprehension and syntactic complexity: evidence from 131 stroke survivors
Authors: Biondo Nicoletta , Ivanova Maria V , Pracar Alexis L , Baldo Juliana , Dronkers Nina F 
Published: November 2024

Abstract
Understanding and interpreting how words are organized in a sentence to convey distinct meanings is a cornerstone of human communication. The neural underpinnings of this ability, known as syntactic comprehension, are far from agreed upon in current neurocognitive models of language comprehension. Traditionally, left frontal regions (e.g. left posterior inferior frontal gyrus) were considered critical, while more recently, left temporal regions (most prominently, left posterior middle temporal gyrus) have been identified as more indispensable to syntactic comprehension. Syntactic processing has been investigated by using different types of non-canonical sentences i.e. those that do not follow prototypical word order and are considered more syntactically complex. However, non-canonical sentences can be complex for different linguistic reasons, and thus, their comprehension might rely on different neural underpinnings. In this cross-sectional study, we explored the neural correlates of syntactic comprehension by investigating the roles of left hemisphere brain regions and white matter pathways in processing sentences with different levels of syntactic complexity. Participants were assessed at a single point in time using structural MRI and behavioural tests. Employing lesion–symptom mapping and indirect structural disconnection mapping in a cohort of 131 left hemisphere stroke survivors, our analysis revealed the following left temporal regions and underlying white matter pathways as crucial for general sentence comprehension: the left mid-posterior superior temporal gyrus, middle temporal gyrus and superior temporal sulcus and the inferior longitudinal fasciculus, the inferior fronto-occipital fasciculus, the middle longitudinal fasciculus, the uncinate fasciculus and the tracts crossing the most posterior part of the corpus callosum. We further found significant involvement of different white matter tracts connecting the left temporal and frontal lobes for different sentence types. Spared connections between the left temporal and frontal regions were critical for the comprehension of non-canonical sentences requiring long-distance retrieval (spared superior longitudinal fasciculus for both subject and object extraction and spared arcuate fasciculus for object extraction) but not for comprehension of non-canonical passive sentences and canonical declarative sentences. Our results challenge traditional language models that emphasize the primary role of the left frontal regions, such as Broca’s area, in basic sentence structure comprehension. Our findings suggest a gradient of syntactic complexity, rather than a clear-cut dichotomy between canonical and non-canonical sentence structures. Our findings contribute to a more nuanced understanding of the neural architecture of language comprehension and highlight potential directions for future research.
Development and Validation of Rapid and Cost-Effective RP-HPLC/UV Method for Determination of Cetirizine/Levocetirizine in Blood Plasma of Smokers and Non Smokers: a Two Cohort Comparative Study
Authors: Khattak Mashal , Iqbal Zafar , Jan Asif , Ali Niaz , Nasir Fazli , Shahbaz Naila 
Published: November 2024

Abstract
In this research study, a simple, rapid, sensitive, and cost-effective Reverse Phase High Performance Liquid Chromatography method was developed and validated for determination of Cetirizine and Levocetirizine in human plasma. The drugs were separated on an ACE Generix100–5 C18 RP (250 × 4.6 mm, 5 μm) column, using Acetonitrile and Distilled water pH 7 (59:41 v/v) as mobile phase with a flow rate of 1.5 mL/min, retention time of 3.39 ± 0.02 min, detection wavelength of 230 nm, and column oven temperature at 26°C. The drug was extracted from human plasma using Methanol, the percent recovery was 97%. The LOD and LOQ for Cetirizine and Levocetirizine were 0.5 ng and 1 ng. The method was linear over the concentration range of 0.5–1000 ng /mL for Cetirizine and Levocetirizine. The method was applied for analysis of drugs in plasma following oral administration of Cetirizine (10 mg) and Levocetirizine (5 mg) in smokers and nonsmokers of Pashtun ethnicity belonging from different districts of Khyber Pakhtunkhwa, Pakistan. The difference between Cetirizine plasma levels in smokers and non-smokers was significant with p -value 0.0279.
Impact of arteriovenous fistula formation on trajectory of kidney function decline: a target trial emulation
Authors: Loureiro Harrison Luis , Fu Edouard L , Thomson Peter C , Traynor Jamie P , Mark Patrick B , Stoumpos Sokratis 
Published: November 2024

ABSTRACT

Background
Prior nonrandomized studies have suggested nephroprotective effects of arteriovenous fistula (AVF) formation, but these are plausibly susceptible to immortal time and selection biases.

Methods
We studied patients attending nephrology clinics in the West of Scotland during 2010–22 with an estimated glomerular filtration rate (eGFR) ≤15 mL/min/1.73 m2 and no prior AVF. Using target trial emulation and a sequential trial design, we simulated a hypothetical trial that would randomize patients to either undergo AVF formation immediately or not to undergo AVF formation. The primary outcome was the difference in eGFR slope for the first 6 months of follow-up, estimated using a mixed-effects model. The secondary outcomes were 5-year absolute risks of dialysis and death, estimated using the Aalen–Johansen and Kaplan–Meier estimators respectively.

Results
A total of 1364 unique patients (mean age 51.1 years, 55.7% male) contributed 3125 person-trials, with 561 in the AVF and 2564 in the no AVF group. Mean eGFR was 12.6 mL/min/1.73 m2 and the median number of eGFR measurements per person-trial was 7 (interquartile range 4–12). Slope of eGFR decline did not differ significantly between the AVF and no AVF groups (between-group difference –0.67 mL/min/1.73 m2/year, 95% CI –1.43, 0.10). The 5-year absolute risk of dialysis was 87% (95% CI 84, 91) in the AVF group and 75% (95% CI 73, 77) in the no AVF group, and the 5-year survival probability was 77% (95% CI 70, 83) in the AVF group and 67% (95% CI 64, 69) in the no AVF group.

Conclusions
In this study of patients with advanced chronic kidney disease, there was no evidence of a nephroprotective effect of AVF formation.
Prospective and External Validation of an Ensemble Learning Approach to Sensitively Detect Intravenous Fluid Contamination in Basic Metabolic Panels
Authors: Spies Nicholas C , Militello Leah , Farnsworth Christopher W , El-Khoury Joe M , Durant Thomas J S , Zaydman Mark A 
Published: November 2024

Abstract

Background
Intravenous (IV) fluid contamination within clinical specimens causes an operational burden on the laboratory when detected, and potential patient harm when undetected. Even mild contamination is often sufficient to meaningfully alter results across multiple analytes. A recently reported unsupervised learning approach was more sensitive than routine workflows, but still lacked sensitivity to mild but significant contamination. Here, we leverage ensemble learning to more sensitively detect contaminated results using an approach which is explainable and generalizable across institutions.

Methods
An ensemble-based machine learning pipeline of general and fluid-specific models was trained on real-world and simulated contamination and internally and externally validated. Benchmarks for performance assessment were derived from in silico simulations, in vitro experiments, and expert review. Fluid-specific regression models estimated contamination severity. SHapley Additive exPlanation (SHAP) values were calculated to explain specimen-level predictions, and algorithmic fairness was evaluated by comparing flag rates across demographic and clinical subgroups.

Results
The sensitivities, specificities, and Matthews correlation coefficients were 0.858, 0.993, and 0.747 for the internal validation set, and 1.00, 0.980, and 0.387 for the external set. SHAP values provided plausible explanations for dextrose- and ketoacidosis-related hyperglycemia. Flag rates from the pipeline were higher than the current workflow, with improved detection of contamination events expected to exceed allowable limits for measurement error and reference change values.

Conclusions
An accurate, generalizable, and explainable ensemble-based machine learning pipeline was developed and validated for sensitively detecting IV fluid contamination. Implementing this pipeline would help identify errors that are poorly detected by current clinical workflows and a previously described unsupervised machine learning-based method.