bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome and phosphoproteome signatures of recurrence for HPV+ head and neck squamous cell carcinoma
Authors: Kaneko Tomonori , Zeng Peter Y. F. , Liu Xuguang , Abdo Rober , Barrett John W. , Zhang Qi , Nichols Anthony C. , Li Shawn Shun-Cheng 
Published: July 2022

Abstract
Background
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and the human papillomavirus (HPV+)-driven subtype is the fastest rising cancer in North America. Although most cases of HPV+ HNSCC respond favorably to the treatment via surgery followed by radiochemotherapy, up to 20% recur with a poor prognosis. The molecular and cellular mechanisms of recurrence are not fully understood.

Methods
To gain insights into the mechanisms of recurrence and to inform patient stratification and personalized treatment, we compared the proteome and phosphoproteome of recurrent and non-recurrent tumors by quantitative mass spectrometry.

Results
We observe significant differences between the recurrent and non-recurrent tumors in cellular composition, function, and signaling. The recurrent tumors are characterized by a pro-fibrotic and immunosuppressive tumor microenvironment (TME) featuring markedly more abundant cancer-associated fibroblasts, extracellular matrix (ECM), neutrophils, and suppressive myeloid cells. Defective T cell function and increased epithelial-mesenchymal transition potential are also associated with recurrence. These cellular changes in the TME are accompanied by reprogramming of the kinome and the signaling networks that regulate the ECM, cytoskeletal reorganization, cell adhesion, neutrophil function, and coagulation.

Conclusions
In addition to providing systems-level insights into the molecular basis of recurrence, our work identifies numerous mechanism-based, candidate biomarkers and therapeutic targets that may aid future endeavors to develop prognostic biomarkers and precision-targeted treatment for recurrent HPV+ HNSCC.
Automatic detection of long-duration transients in Fermi-GBM data
Authors: Kunzweiler F. , Biltzinger B. , Greiner J. , Burgess J. M. 
Published: July 2022

Context. In the era of time-domain, multi-messenger astronomy, the detection of transient events on the high-energy electromagnetic sky has become more important than ever. Previous attempts to systematically search for onboard, untriggered events in the data of Fermi-GBM have been limited to short-duration signals with variability time scales smaller than ≈1 min. This is due to the dominance of background variations on longer timescales.
Aims. In this study, we aim to achieve a detection of slowly rising or long-duration transient events with high sensitivity and a full coverage of the GBM spectrum.
Methods. We made use of our earlier developed physical background model, which allows us to effectively decouple the signal from long-duration transient sources from the complex varying background seen with the Fermi-GBM instrument. We implemented a novel trigger algorithm to detect signals in the variations of the time series that is composed of simultaneous measures in the light curves of the different Fermi-GBM detectors in different energy bands. To allow for a continuous search in the data stream of the satellite, the new detection algorithm was embedded in a fully automatic data analysis pipeline. After the detection of a new transient source, we also performed a joint fit for spectrum and location using the BALROG algorithm.
Results. The results from extensive simulations demonstrate that the developed trigger algorithm is sensitive down to sub-Crab intensities (depending on the search timescale) and has a near-optimal detection performance. During a two month test run on real Fermi-GBM data, the pipeline detected more than 300 untriggered transient signals. We verified, for one of these transient detections, that it originated from a known astrophysical source, namely, the Vela X-1 pulsar, showing pulsed emission for more than seven hours. More generally, this method enables a systematic search for weak or long-duration transients.
The ornithophily of Impatiens sakeriana does not guarantee a preference by sunbirds
Authors: Mundi Onella , Awa Ii Taku , Chmel Kryštof , Ewome Francis Luma , Uceda-Gómez Guillermo , Janečková Petra , Janeček Štěpán 
Published: July 2022

Abstract
In recent decades, the tight mutual specialization between nectarivorous birds and ornithophilous plants has been questioned, and instead, high degrees of generalization and interaction asymmetry have been highlighted. Here, we studied interactions among two sunbirds and four plant species in two Mount Cameroon forests, with two plant species from each forest. First, we investigated whether sunbirds differ in frequencies of visitation to target plant species in natural conditions. Second, using a cage experiment, we investigated whether sunbirds prefer various plant species, plants with which they are more familiar and that occur in the habitat where they were caught and/or the only studied ornithophilous plant, Impatiens sakeriana. In natural conditions, the short-billed sunbird, Cinnyris reichenowi, fed more on flowers with shorter tubes than the long-billed sunbird, Cyanomitra oritis. Likewise, sunbirds differed in their experimental preferences. Local plants were generally preferred. This was most obvious in the case of I. sakeriana, which was often visited by both sunbirds, but only in the habitat where it grows naturally. This study supports the importance of associative learning. Together with other studies, we suggest that the signalling traits of flowers with bird pollination syndromes evolved to filter out other visitors rather than to attract bird pollinators.
Glocal intimacies: theorizing mobile media and intimate relationships
Authors: Cabañes Jason Vincent A , Uy-Tioco Cecilia S 
Published: July 2022

AbstractThis article develops the concept of “glocal intimacies,” capturing the role of mobile media in how people enact and reconfigure their increasingly global experiences of social relationships. It establishes the two foundational assumptions of this concept: the interplay of local and global cultures and the transformative role of mobile media. It then identifies the three key dimensions that characterize glocal intimacies: digital access, contextual localities, and sociotechnical dynamics. To provide empirical flesh to how these dimensions intersect, it comparatively discusses two ethnographic projects on privileged Filipinos and their mediated familial and romantic relationships.
Stool Interleukin-1β Differentiates Clostridioides difficile Infection (CDI) From Asymptomatic Carriage and Non-CDI Diarrhea
Authors: Villafuerte Gálvez Javier A , Pollock Nira R , Alonso Carolyn D , Chen Xinhua , Xu Hua , Wang Lamei , White Nicole , Banz Alice , Miller Mark , Daugherty Kaitlyn , Gonzalez-Luna Anne J , Barrett Caitlin , Sprague Rebecca , Garey Kevin W , Kelly Ciaran P 
Published: July 2022

Abstract

Background
Despite advances in the understanding and diagnosis of Clostridioides difficile infection (CDI), clinical distinction within the colonization–infection continuum remains an unmet need.

Methods
By measuring stool cytokines and antitoxin antibodies in well-characterized cohorts of CDI (diarrhea, nucleic acid amplification test [NAAT] positive), non-CDI diarrhea (NCD; diarrhea, NAAT negative), asymptomatic carriers (ASC; no diarrhea, NAAT positive) and hospital controls (CON; no diarrhea, NAAT negative), we aim to discover novel biological markers to distinguish between these cohorts. We also explore the relationship of these stool cytokines and antitoxin antibody with stool toxin concentrations and disease severity.

Results
Stool interleukin (IL) 1β, stool immunoglobulin A (IgA), and immunoglobulin G (IgG) anti–toxin A had higher (P &lt; .0001) concentrations in CDI (n = 120) vs ASC (n = 43), whereas toxins A, B, and fecal calprotectin did not. Areas under the receiver operating characteristic curve (ROC-AUCs) for IL-1β, IgA, and IgG anti–toxin A were 0.88, 0.83, and 0.83, respectively. A multipredictor model including IL-1β and IgA anti–toxin A achieved an ROC-AUC of 0.93. Stool IL-1β concentrations were higher in CDI compared to NCD (n = 75) (P &lt; .0001) and NCD + ASC+ CON (CON, n = 75) (P &lt; .0001), with ROC-AUCs of 0.83 and 0.86, respectively. Stool IL-1β had positive correlations with toxins A (ρA = +0.55) and B (ρB = +0.49) in CDI (P &lt; .0001) but not in ASC (P &gt; .05).

Conclusions
Stool concentrations of the inflammasome pathway, proinflammatory cytokine IL-1β, can accurately differentiate CDI from asymptomatic carriage and NCD, making it a promising biomarker for CDI diagnosis. Significant positive correlations exist between stool toxins and stool IL-1β in CDI but not in asymptomatic carriers.
A Targeted Liquid Chromatography–Tandem Mass Spectrometry Method for Simultaneous Quantification of Peptides from the Carboxyl-terminal Region of Type III Procollagen, Biomarkers of Collagen Turnover
Authors: Huynh Huu Hien , Forrest Katrina , Becker Jessica O , Emrick Michelle A , Miller Geoffrey D , Moncrieffe Danielle , Cowan David A , Thomas Andreas , Thevis Mario , MacCoss Michael J , Hoffstrom Ben , Byers Peter H , Eichner Daniel , Hoofnagle Andrew N 
Published: July 2022

Abstract

Background
The development of analytical approaches to help reduce the risk of growth hormone (GH) doping is important to fair competition and the health of athletes. However, the reliable detection of GH use remains challenging. The identification of novel biomarkers of GH administration could lead to a better understanding of the physiological response to GH, more sensitive detection of the illicit use of GH in sport, and better management of patients treated for GH disorders.

Methods
We developed a targeted liquid chromatography–tandem mass spectrometry method to simultaneously quantify the carboxyl-terminal propeptide of type III procollagen (P-III-CP) and type III collagen degradation products in human serum. Following proteolysis, we instituted a simple acid precipitation step to reduce digested sample complexity before peptide immunoenrichment, which improved the recovery of one target peptide from serum. We evaluated the concentration of each biomarker at different age ranges and after GH administration in healthy participants.

Results
The assay was linear over an estimated concentration range of 0.3 to1.0 nM and 0.1 to 0.4 nM for each surrogate peptide of P-III-CP and collagen fragments, respectively. Intra-day and inter-day coefficients of variation were ≤15%. Biomarker concentrations appeared to vary with age and to reflect age-specific collagen turnover. Moreover, their concentrations changed after GH administration.

Conclusions
Our method quantifies the proteins belonging to the family of P-III-CP and type III collagen degradation products in human serum, which could be used to detect GH administration in athletes and better understand diseases involving GH therapy or altered type III collagen turnover.
Prometheus in Russia: from revolution to dissidence
Authors: But Ekaterina 
Published: July 2022

AbstractThis essay examines the development of the image of Prometheus as a symbol of the revolutionary in Russia and the Soviet Union. After providing a historical overview of pre-Soviet and early-Soviet receptions of Prometheus’ image in Alexander Scriabin’s symphony Prometheus: The Poem of Fire (Prometei: Poema Ognia, 1908–10) and in the unfinished production of the ancient Greek tragic trilogy at the Moscow Art Theatre (1925–27), I focus on the analysis of Prometheus’ myth in three screen adaptations: the 1936 film Prometheus (Prometei) by Soviet Ukrainian director Ivan Kavaleridze and the animated films The Return from Olympus (Vozvrashchenie s Olimpa, 1969), and Prometheus (Prometei, 1974) by Alexandra Snezhko-Blotskaya. I demonstrate that, besides the animation films directed by Snezhko-Blotskaya, the rest of the receptions were not successful at the time of their production. I examine how the creative programs of these projects did not fit the contemporary context, institutional framework, or official ideology because of technical, aesthetical, and political reasons. I argue that the screen receptions of Prometheus’ myth employed Prometheus’ image to reflect on and to address the changing political and cultural climate of the Soviet Union during critical periods of its history.
Alcohol consumption and subclinical and clinical coronary heart disease: a Mendelian randomization analysis
Authors: Hisamatsu Takashi , Miura Katsuyuki , Tabara Yasuharu , Sawayama Yuichi , Kadowaki Takashi , Kadota Aya , Torii Sayuki , Kondo Keiko , Yano Yuichiro , Fujiyoshi Akira , Yamamoto Takashi , Nakagawa Yoshihisa , Horie Minoru , Kimura Takeshi , Okamura Tomonori , Ueshima Hirotsugu ,   for the SESSA and ACCESS Research Groups
Published: July 2022

Abstract

Aims
The potential effect of alcohol consumption on coronary heart disease (CHD) remains unclear. We used the variant rs671 in the aldehyde dehydrogenase 2 gene (ALDH2) as an instrument to investigate the causal role of alcohol intake in subclinical and clinical CHD.

Methods
We conducted two Mendelian randomization studies: a cross-sectional study of coronary artery calcification (CAC) on computed tomography of 1029 healthy men (mean age, 63.8 years) and a case–control study of 421 men with CHD [acute coronary syndrome (ACS) or stable angina pectoris] who underwent coronary revascularization and 842 age-matched male controls.

Results
In the CAC study, medians (25%tiles, 75%tiles) of alcohol consumption by ALDH2-rs671 *2 homozygotes [n = 86 (8.4%)], *1*2 heterozygotes [n = 397 (38.5%)], and *1 homozygotes [n = 546 (53.1%)] were 0.0 (0.0, 0.0), 28.0 (0.0, 129.0), and 224.0 (84.0, 350.0) g/week, respectively. In age-adjusted Poisson regression with robust error variance, compared with *2 homozygotes, relative risks for prevalent CAC score &gt;0, ≥100, and ≥300 in *1 homozygotes were 1.29 (95% confidence interval, 1.06–1.57), 1.76 (1.05–2.96), and 1.81 (0.80–4.09), respectively. In age-adjusted ordinal logistic regression for CAC distributions, we observed higher odds among *1 homozygotes [odds ratio, 2.19 (1.39–3.46)] and even among *1*2 heterozygotes [1.77 (1.11–2.82)] compared with *2 homozygotes. In the case–control study, conditional logistic regression revealed lower prevalence of *1 homozygotes among men with CHD [odds ratio, 0.54 (0.35–0.82)], especially ACS [0.46 (0.27–0.77)], than controls.

Conclusion
Our findings indicate a positive association of alcohol consumption with CAC burden but an inverse association with clinical CHD, especially ACS.
An entropy method for geodynamic modelling of phase transitions: capturing sharp and broad transitions in a multiphase assemblage
Authors: Dannberg Juliane , Gassmöller Rene , Li Ranpeng , Lithgow-Bertelloni Carolina , Stixrude Lars 
Published: July 2022

SUMMARY
Phase transitions play an important role for the style of mantle convection. While observations and theory agree that a substantial fraction of subducted slabs and rising plumes can move through the whole mantle at present day conditions, this behaviour may have been different throughout Earth’s history. Higher temperatures, such as in the early Earth, cause different phase transitions to be dominant, and also reduce mantle viscosity, favouring a more layered style of convection induced by phase transitions. A period of layered mantle convection in Earth’s past would have significant implications for the secular evolution of the mantle temperature and the mixing of mantle heterogeneities. The transition from layered to whole mantle convection could lead to a period of mantle avalanches associated with a dramatic increase in magmatic activity. Consequently, it is important to accurately model the influence of phase transitions on mantle convection. However, existing numerical methods generally preclude modelling phase transitions that are only present in a particular range of pressures, temperatures or compositions, and they impose an artificial lower limit on the thickness of phase transitions. To overcome these limitations, we have developed a new numerical method that solves the energy equation for entropy instead of temperature. This technique allows for robust coupling between thermodynamic and geodynamic models and makes it possible to model realistically sharp phase transitions with a wide range of properties and dynamic effects on mantle processes. We demonstrate the utility of our method by applying it in regional and global convection models, investigating the effect of individual phase transitions in the Earth’s mantle with regard to their potential for layering flow. We find that the thickness of the phase transition has a bigger influence on the style of convection than previously thought: with all other parameters being the same, a thin phase transition can induce fully layered convection where a broad phase transition would lead to whole-mantle convection. Our application of the method to convection in the early Earth illustrates that endothermic phase transitions may have induced layering for higher mantle temperatures in the Earth’s past.
Long-Term Outcomes After Ustekinumab Dose Intensification for Inflammatory Bowel Diseases
Authors: Dalal Rahul S , Pruce Jordan C , Allegretti Jessica R 
Published: July 2022

Lay Summary
In this retrospective cohort study, we demonstrated that dose intensification of ustekinumab to every 4 or every 6 weeks was effective in both achieving and maintaining clinical remission for &gt;40% of inflammatory bowel disease patients for up to 24 months.
Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program
Authors: Gray Rachel , Fusco Nicole , Miller Joshua M , Tapia Washington , Mariani Carol , Caccone Adalgisa , Jensen Evelyn L 
Published: July 2022

Abstract
Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017–2020) of the genetically informed captive breeding program for the Floreana Island Galapagos giant tortoise, Chelonoidis niger. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, C. becki. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding.
Flexible exchange rates in emerging markets: shock absorbers or drivers of endogenous cycles?
Authors: Kohler Karsten , Stockhammer Engelbert 
Published: July 2022

AbstractWhile flexible exchange rates are commonly regarded as shock absorbers, heterodox views suggest that they can play a pro-cyclical role in emerging markets. This article provides theoretical and empirical support for this view. Drawing on post-Keynesian and structuralist theories, we propose a simple model in which flexible exchange rates in conjunction with external shocks become endogenous drivers of boom-bust cycles, once financial effects from foreign-currency debt are accounted for. We present empirical evidence for regular cycles in nominal US-dollar exchange rates in several emerging markets that are closely aligned with cycles in economic activity. An econometric analysis suggests the presence of a cyclical interaction mechanism between exchange rates and output, in line with the theoretical model, in Chile, South Africa, and partly the Philippines. Further evidence indicates that such exchange rate cycles cannot exclusively be attributed to external factors, such as commodity prices, US monetary policy or the global financial cycle. We therefore argue that exchange rate cycles in emerging markets are driven by the interplay of external shocks and endogenous cycle mechanisms.
Correlation Between Postvaccination Anti-Spike Antibody Titers and Protection Against Breakthrough Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Population-Based Longitudinal Study
Authors: Vivaldi Giulia , Jolliffe David A , Faustini Sian , Shields Adrian M , Holt Hayley , Perdek Natalia , Talaei Mohammad , Tydeman Florence , Chambers Emma S , Cai Weigang , Li Wenhao , Gibbons Joseph M , Pade Corinna , McKnight Áine , Shaheen Seif O , Richter Alex G , Martineau Adrian R 
Published: July 2022

Abstract
In this population-based cohort of 7538 adults, combined immunoglobulin (Ig) G, IgA, and IgM (IgG/A/M) anti-spike titers measured after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination were predictive of protection against breakthrough SARS-CoV-2 infection. Discrimination was significantly improved by adjustment for factors influencing risk of SARS-CoV-2 exposure, including household overcrowding, public transport use, and visits to indoor public places. Anti-spike IgG/A/M titers showed positive correlation with neutralizing antibody titers (rs = 0.80 [95% confidence interval, .72–.86]; P &lt; .001) and S peptide–stimulated interferon-γ concentrations (rs = 0.31 [.13–.47]; P &lt; .001).
A Tunable, Simplified Model for Biological Latch Mediated Spring Actuated Systems
Authors: Cook Andrés , Pandhigunta Kaanthi , Acevedo Mason A , Walker Adam , Didcock Rosalie L , Castro Jackson T , O’Neill Declan , Acharya Raghav , Bhamla M Saad , Anderson Philip S L , Ilton Mark 
Published: July 2022

Synopsis
We develop a model of latch-mediated spring actuated (LaMSA) systems relevant to comparative biomechanics and bioinspired design. The model contains five components: two motors (muscles), a spring, a latch, and a load mass. One motor loads the spring to store elastic energy and the second motor subsequently removes the latch, which releases the spring and causes movement of the load mass. We develop freely available software to accompany the model, which provides an extensible framework for simulating LaMSA systems. Output from the simulation includes information from the loading and release phases of motion, which can be used to calculate kinematic performance metrics that are important for biomechanical function. In parallel, we simulate a comparable, directly actuated system that uses the same motor and mass combinations as the LaMSA simulations. By rapidly iterating through biologically relevant input parameters to the model, simulated kinematic performance differences between LaMSA and directly actuated systems can be used to explore the evolutionary dynamics of biological LaMSA systems and uncover design principles for bioinspired LaMSA systems. As proof of principle of this concept, we compare a LaMSA simulation to a directly actuated simulation that includes either a Hill-type force-velocity trade-off or muscle activation dynamics, or both. For the biologically-relevant range of parameters explored, we find that the muscle force-velocity trade-off and muscle activation have similar effects on directly actuated performance. Including both of these dynamic muscle properties increases the accelerated mass range where a LaMSA system outperforms a directly actuated one.