bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Running Velocity and Hypoxic Exposure on Vastus Lateralis Muscle Oxygenation
Authors: Yeap Ming Wei , Loh Tze Chien , Chong Mee Chee , Yeo Wee Kian , Girard Olivier , Tee Chris Chow Li 
Published: September 2024

Purpose: We investigated the effects of manipulating running velocity and hypoxic exposure on vastus lateralis muscle oxygenation levels during treadmill running. Methods: Eleven trained male distance runners performed 7 randomized runs at different velocities (8, 10, 12, 14, 16, 18, and 20 km·h−1), each lasting 45 seconds on an instrumented treadmill in normoxia (fraction of inspired oxygen [FiO2] = 20.9%), moderate hypoxia (FiO2 = 16.1%), high hypoxia (FiO2 = 14.1%), and severe hypoxia (FiO2 = 13.0%). Continuous assessment of Tissue Saturation Index (TSI) in the vastus lateralis muscle was conducted using near-infrared spectroscopy. Subsequently, changes in TSI (ΔTSI) data over the final 20 seconds of each run were compared between velocities and conditions. Results: There was a significant velocity × condition interaction for ΔTSI% (P < .001, ), with a smaller ΔTSI% decline in normoxia compared with high hypoxia and severe hypoxia at 8 km·h−1 (g = 1.30 and 1.91, respectively), 10 km·h−1 (g = 0.75 and 1.43, respectively), and 12 km·h−1 (g = 1.47 and 1.95, respectively) (pooled values for all conditions: P < .037). The ΔTSI% decline increased with each subsequent velocity increment from 8 km·h−1 (−9.2% [3.7%]) to 20 km·h−1 (−22.5% [4.1%]) irrespective of hypoxia severity (pooled values for all conditions: P < .048). Conclusions: Running at slower velocities in conjunction with high and severe hypoxia reduces vastus lateralis muscle oxygenation levels. Muscle ΔTSI% proves to be a sensitive indicator, underscoring the potential use of near-infrared spectroscopy as a reference index of internal load during treadmill runs.
Breadth and polyfunctionality of T cell responses to human cytomegalovirus in men who have sex with men: relationship with HIV infection and frailty
Authors: Zhang Weiying , Nilles Tricia L. , Bream Jay H. , Li Huifen , Malash Eslam , Langan Susan , Leng Sean X. , Margolick Joseph B. 
Published: September 2024

ABSTRACT

Cytomegalovirus (CMV)-seropositive adults have large T cell responses to a wide range of CMV proteins; these responses have been associated with chronic inflammation and frailty in people with or without HIV infection. We analyzed the relationships between chronic HIV infection, frailty, and the breadth and polyfunctionality of CD4 and CD8 T cell responses to CMV. Peripheral blood mononuclear cells from 42 men (20 without HIV and 22 with virologically suppressed HIV) in the Multicenter AIDS Cohort Study (MACS) were stimulated with peptide pools spanning 19 CMV open reading frames (ORFs). As measured by flow cytometry and intracellular cytokine staining for IFN-γ, TNF-α, and IL-2, CD8 T cells from men with HIV responded to significantly more CMV ORFs than those from men without HIV. This was primarily due to a broader response to ORFs that are expressed during the late phase of CMV replication. The number of ORFs to which a participant’s T cells responded was positively correlated with the sum of all that individual’s T cell responses; these correlations were weaker in men with than without HIV. Polyfunctional CMV-specific CD4 responses (production of more than one cytokine) were significantly lower in men with than without HIV. Frailty status did not substantially affect the breadth or magnitude of the CMV-specific T cell responses. These results suggest that immune control of CMV infection is affected more by chronic HIV infection than by frailty. The differences between men with and without HIV were similar to those reported between young and older adults without HIV.

IMPORTANCE
T cell responses to chronic cytomegalovirus (CMV) infection have significant biological and clinical implications in HIV infection and aging. Here, we systematically analyzed the breadth, magnitude, and polyfunctionality of T cell responses to multiple CMV antigens in men with and without HIV in the Multicenter AIDS Cohort Study (MACS), a longstanding study of the natural and treated history of HIV-1 infection in men who have sex with men. We found that the breadth and polyfunctionality of T cell responses to CMV were different between men with chronic, treated HIV and those without HIV. The reason for these differences is unknown, but these findings suggest that people with treated HIV may have more frequent CMV reactivation than people without HIV. Differences between people with and without HIV also resembled differences reported between young and older adults without HIV, supporting a role for the immune responses to CMV in the aging process.
Annotation-free prediction of microbial dioxygen utilization
Authors: Flamholz Avi I. , Goldford Joshua E. , Richter Philippa A. , Larsson Elin M. , Jinich Adrian , Fischer Woodward W. , Newman Dianne K. 
Published: September 2024

ABSTRACT

Aerobes require dioxygen (O
2
) to grow; anaerobes do not. However, nearly all microbes—aerobes, anaerobes, and facultative organisms alike—express enzymes whose substrates include O
2
, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O
2
utilization has wide-ranging effects on microbes: aerobes typically have larger genomes encoding distinctive O
2
-utilizing enzymes, for example. These effects permit high-quality prediction of O
2
utilization from annotated genome sequences, with several models displaying ≈80% accuracy on a ternary classification task for which blind guessing is only 33% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genomic sequence content—e.g., triplets of amino acids—perform as well as intensive annotation-based classifiers, enabling rapid processing of genomes. We further show that amino acid trimers are useful because they encode information about protein composition and phylogeny. To showcase the utility of rapid prediction, we estimated the prevalence of aerobes and anaerobes in diverse natural environments cataloged in the Earth Microbiome Project. Focusing on a well-studied O
2
gradient in the Black Sea, we found quantitative correspondence between local chemistry (O
2
:sulfide concentration ratio) and the composition of microbial communities. We, therefore, suggest that statistical methods like ours might be used to estimate, or “sense,” pivotal features of the chemical environment using DNA sequencing data.

IMPORTANCE

We now have access to sequence data from a wide variety of natural environments. These data document a bewildering diversity of microbes, many known only from their genomes. Physiology—an organism’s capacity to engage metabolically with its environment—may provide a more useful lens than taxonomy for understanding microbial communities. As an example of this broader principle, we developed algorithms that accurately predict microbial dioxygen utilization directly from genome sequences without annotating genes, e.g., by considering only the amino acids in protein sequences. Annotation-free algorithms enable rapid characterization of natural samples, highlighting quantitative correspondence between sequences and local O
2
levels in a data set from the Black Sea. This example suggests that DNA sequencing might be repurposed as a multi-pronged chemical sensor, estimating concentrations of O
2
and other key facets of complex natural settings.
Research priorities for progressive pulmonary fibrosis in the UK
Authors: Fabbri Laura , Russell Anne-Marie , Chaudhuri Nazia , Adams Wendy , Cowan Katherine , Conway John , Dickinson Wendy , Gibbons Michael , Hart Simon , Jones Steve , Lynch-Wilson Jenny , McMillan Tom , Milward Steve , Ward Maureen , Wright Louise Elisabeth , Jenkins Gisli 
Published: September 2024

IntroductionHealth research bodies recommend patient involvement and engagement in research and healthcare planning, although their implementation is not yet widespread. This deficiency extends to progressive pulmonary fibrosis (PPF), where crucial aspects remain unknown, including causal mechanisms, curative treatments and optimal symptom management. This study addresses these gaps by seeking stakeholders’ perspectives to guide research and treatment directions.MethodA priority-setting partnership was established to explore stakeholders’ priorities in the diagnosis, treatment, management and care of PPF, including idiopathic pulmonary fibrosis which is the archetypal PPF. Stakeholders included people living with PPF, their carers, relatives and healthcare professionals involved in their management.ResultsThrough an online open-ended survey, 2542 responses were collected from 638 stakeholders. Thematic analysis identified 48 specific research questions, which were then cross-referenced with academic literature to pinpoint research gaps. Following the evidence check, 44 unanswered questions were shortlisted by 834 stakeholders in a second online survey. Ultimately, a top 10 priority list was established through consensus.The prioritised research questions include (1) improved diagnosis accuracy and timing, (2) development of new treatments, (3) enhanced accuracy in primary care, (4) optimal timing for drug and non-drug interventions, (5) effective cough treatment, (6) early intervention for PPF, (7) improved survival rates, (8) symptom reduction, (9) impact of interventions on life expectancy and (10) new treatments with reduced side effects.ConclusionStakeholders’ priorities can be summarised into five areas: early diagnosis, drug and non-drug treatments, survival and symptom management. Ideally, these topics should guide funding bodies and health policies.
Comparison of established and preliminarily proposed ASAS MRI working group cut-offs for inflammatory MRI lesions in the sacroiliac joints in radiographic and non-radiographic axial spondyloarthritis
Authors: Baraliakos Xenofon , Machado Pedro M , Bauer Lars , Hoepken Bengt , Kim Mindy , Kumke Thomas , Tham Rachel , Rudwaleit Martin 
Published: September 2024

BackgroundA consensus definition for active sacroiliitis by MRI, mentioned in the Assessment of SpondyloArthritis International Society (ASAS) classification criteria for axial spondyloarthritis (axSpA), was published in 2009 and included a qualitative and quantitative MRI cut-off component. In 2021, updates to the quantitative component were preliminarily proposed. This post hoc analysis of part A of the phase 3 open-label C-OPTIMISE study (NCT02505542) explores the differences by applying the 2009 and preliminary 2021 inflammatory cut-offs on clinical outcomes of axSpA patients treated with certolizumab pegol.MethodsBaseline MRI scans were used to classify 657 patients as MRI+ or MRI– according to the quantitative components of the 2009 and preliminary 2021 MRI cut-offs for inflammatory lesions. Clinical outcomes, including ASAS ≥40% improvement (ASAS40), Ankylosing Spondylitis Disease Activity Score and Bath Ankylosing Spondylitis Disease Activity Index, were reported to week 48.ResultsAcross all analysed outcomes, 2009 MRI+ and preliminary 2021 MRI+ subgroups showed similar results. Notably, clinical outcomes for the discordant group (2009 MRI+but preliminary 2021 MRI– group; 53/657 [8.1%]) were close to those seen in MRI– patients according to either 2009 or preliminary 2021 inflammatory cut-offs, and notably different from the totality of MRI+ subgroups.ConclusionThis analysis suggests that the preliminary 2021 cut-offs for MRI inflammatory lesions may slightly increase the specificity of the quantitative part of the 2009 MRI inflammatory lesion definition. The effects of the updated MRI cut-offs need to be assessed on the basis of efficacy outcomes and with the inclusion of aspects of structural changes.Trial registration numberNCT02505542.
Association of Snoring and Daytime Sleepiness With Subsequent Incident Hypertension: A Population-Based Cohort Study
Authors: Balagny Pauline , Vidal-Petiot Emmanuelle , Kab Sofiane , Frija Justine , Steg Philippe Gabriel , Goldberg Marcel , Zins Marie , d’Ortho Marie-Pia , Wiernik Emmanuel 
Published: September 2024

BACKGROUND:
There is a strong association between obstructive sleep apnea and hypertension, but the effects of obstructive sleep apnea symptoms on the risk of incident hypertension are not well documented. The aim of this prospective study was to examine whether snoring and sleepiness are associated with incident hypertension.

METHODS:
Data from the French population-based CONSTANCES cohort were analyzed. Normotensive participants, aged 18 to 69 years, were included between 2012 and 2016 and screened for snoring, morning fatigue, and daytime sleepiness in 2017 using items of the Berlin Questionnaire. We used Cox models, adjusted for multiple potential confounders, including body mass index, baseline blood pressure, sleep duration, and depressive symptoms, to compute hazards ratios of incidentally treated hypertension.

RESULTS:

Among 34 727 subjects, the prevalence of self-reported habitual snoring, morning fatigue, and excessive daytime sleepiness (≥3× a week for each) was 23.6%, 16.6%, and 19.1%, respectively. During a median follow-up of 3.1 years (interquartile range, 3.0–3.5), the incidence of treated hypertension was 3.8%. The risk of de novo treated hypertension was higher in participants who reported habitual snoring (adjusted hazard ratio, 1.17 [95% CI, 1.03–1.32]) and excessive daytime sleepiness (adjusted hazard ratio, 1.42 [95% CI, 1.24–1.62]), and increased with the weekly frequency of symptoms, with a dose-dependent relationship (
P
trend
≤0.02 for all symptoms).

CONCLUSIONS:
Self-reported snoring and excessive daytime sleepiness are associated with an increased risk of developing hypertension. Identification of snoring and daytime sleepiness may be a useful public health screening tool in primary care for hypertension prevention.
Investigating the Neural Basis of the Loud-first Principle of the Iambic–Trochaic Law
Authors: Llanos Fernando , Stump Teagan , Crowhurst Megan 
Published: September 2024

Abstract
The perception of rhythmic patterns is crucial for the recognition of words in spoken languages, yet it remains unclear how these patterns are represented in the brain. Here, we tested the hypothesis that rhythmic patterns are encoded by neural activity phase-locked to the temporal modulation of these patterns in the speech signal. To test this hypothesis, we analyzed EEGs evoked with long sequences of alternating syllables acoustically manipulated to be perceived as a series of different rhythmic groupings in English. We found that the magnitude of the EEG at the syllable and grouping rates of each sequence was significantly higher than the noise baseline, indicating that the neural parsing of syllables and rhythmic groupings operates at different timescales. Distributional differences between the scalp topographies associated with each timescale suggests a further mechanistic dissociation between the neural segmentation of syllables and groupings. In addition, we observed that the neural tracking of louder syllables, which in trochaic languages like English are associated with the beginning of rhythmic groupings, was more robust than the neural tracking of softer syllables. The results of further bootstrapping and brain–behavior analyses indicate that the perception of rhythmic patterns is modulated by the magnitude of grouping alternations in the neural signal. These findings suggest that the temporal coding of rhythmic patterns in stress-based languages like English is supported by temporal regularities that are linguistically relevant in the speech signal.
Do Multi-Document Summarization Models Synthesize?
Authors: DeYoung Jay , Martinez Stephanie C. , Marshall Iain J. , Wallace Byron C. 
Published: September 2024

Abstract
Multi-document summarization entails producing concise synopses of collections of inputs. For some applications, the synopsis should accurately synthesize inputs with respect to a key aspect, e.g., a synopsis of film reviews written about a particular movie should reflect the average critic consensus. As a more consequential example, narrative summaries that accompany biomedical systematic reviews of clinical trial results should accurately summarize the potentially conflicting results from individual trials. In this paper we ask: To what extent do modern multi-document summarization models implicitly perform this sort of synthesis? We run experiments over opinion and evidence synthesis datasets using a suite of summarization models, from fine-tuned transformers to GPT-4. We find that existing models partially perform synthesis, but imperfectly: Even the best performing models are over-sensitive to changes in input ordering and under-sensitive to changes in input compositions (e.g., ratio of positive to negative reviews). We propose a simple, general, effective method for improving model synthesis capabilities by generating an explicitly diverse set of candidate outputs, and then selecting from these the string best aligned with the expected aggregate measure for the inputs, or abstaining when the model produces no good candidate.
11. Recovery and Return
Authors: Fisher Barbara 
Published: September 2024

In 1924, when Trix was fifty-six years old, she was recalled from exile. Jack, sixty-six years old and in declining health, allowed Trix back into the Fleming home in Edinburgh. She was at first treated as if she were incompetent, but she eventually demonstrated that she was not only capable and coherent, but charming and witty. She nursed but also teased and subtly tortured Jack through his final years of ill health. She mourned the death of her brother in 1936 and the loss of her husband in 1942. With Rudyard’s death, Trix became a valued resource for Kipling biographers. When Jack died, she was liberated from the unsatisfying roles of companion and nursemaid. Having outlived her brother and husband, she created her final extravagant persona—playful, garrulous, and eccentric old lady. Trix died on October 25th 1948 at the age of 80.
Trix characterized much of her life as a waste, but it was not entirely so. Her contributions to the Psychic Research Society were important to their work, her editorial and critical support for her friend, Maud Diver was crucial to the composition of her many popular novels, and her early collaboration and life-long encouragement to her brother provided him with sustenance throughout his illustrious career. Her brilliant talk embellished by quotations and ornamented with wit and devilish humor was well remembered by the many who called her “Aunt Trix” and the many others fortunate enough to have shared her company.
But her life was a waste of a brilliant literary gift. Trix had talent, originality, perhaps even genius, but these alone were not enough to secure success. Without the inner resources of self-love, confidence, and persistence she could not persevere through the distractions, frustrations, and vexations of a literary career. She was able to tend to her talent when it burst forth precociously, almost spontaneously, in youth. But as an adult, lacking in internal strength, she needed external support to nurture her gift, and that she did not have. On the contrary, she had to contend with societal disapproval, parental pressure, and spousal incomprehension. She was no match for this much opposition, and her art, blossoming early, withered before it reached full flower.
1. De Morgan and Mathematics
Authors: Rice Adrian 
Published: September 2024

If Augustus De Morgan is remembered at all today, it is primarily for the pair of algebraic laws that bear his name, for he proved no major theorem, made no notable mathematical discoveries, and published no magnum opus. Indeed, it is hard to identify much in today’s mathematics for which he was responsible. Yet he was described by contemporaries as ‘one of the most eminent mathematicians and logicians of his time’ and ‘one of the profoundest and subtlest thinkers of the nineteenth century’. And his mathematical publications spanned a far greater array of subjects than his current limited fame would suggest, including algebra, logic, probability, actuarial mathematics, differential equations, mathematical education, and the history of mathematics—some of which will be discussed in more detail in subsequent chapters.
In this chapter, we explore the range of De Morgan’s activities as a mathematician, including his mathematical research, his philosophy of the subject, and his work as the first professor of mathematics at University College London. In doing so, we aim to answer two questions: why was De Morgan’s mathematical reputation so high in the nineteenth century? And why, in comparison, is he so little-known today?
10. Augustus De Morgan’s Library Revisited
Authors: Attar Karen 
Published: September 2024

Even during his lifetime Augustus De Morgan was well known for his library of nearly 4,000 titles on mathematics and its history published between 1474 and 1870, in which landmarks of mathematical and astronomical literature jostled with multiple editions of popular textbooks and obscure rare works. This library was coveted after his death and continued in the twentieth century to be praised in superlative terms, for example as ‘one of the finest accumulations of books on the history of mathematics in the country’ (1996). It is particularly remarkable because, according to studies of book-collecting, mathematics was not a major collecting area.
Yet De Morgan was neither the first, nor the sole, mathematical collector. His library is known largely because it was one of few mathematical libraries amassed by Victorians to remain intact after the owner’s death, when it was acquired by the University of London. Because De Morgan’s library has not yet been studied within the context of contemporary collecting, this chapter looks at the mathematical libraries, intact and dispersed, of De Morgan and some of his contemporaries to contextualise and reassess his library in comparison to other Victorian mathematical collections. We also discuss how the library fared after De Morgan’s death and why it continues to stand out.