bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depositional age models in lacustrine systems from zircon and carbonate U‐Pb geochronology
Authors: Montano Damaris , Gasparrini Marta , Rohais Sébastien , Albert Richard , Gerdes Axel 
Published: April 2022

AbstractThe Yacoraite Formation (Salta rift, Argentina) consists of Maastrichtian–Danian lacustrine carbonate and siliciclastic deposits with interbedded volcanic ash layers, organized in four third‐order stratigraphic sequences. It offers the exceptional opportunity to jointly apply in situ zircon and carbonate U‐Pb geochronology that resulted in two distinct depositional age depth models. Ages of the youngest zircon population from ash layers were linearly interpolated to derive a zircon depositional age depth model. A carbonate depositional age depth model was instead obtained from dated carbonate phases including microbialites, ooids, oncoids of calcitic and dolomitic mineralogy as well as early lacustrine calcite cements. Mean ages were defined from different carbonate phases belonging to the same layer and then linearly interpolated. Sedimentation rates were calculated from both depth models between pairs of dated samples and used to estimate the age of sequence boundaries, as well as the duration of the four stratigraphic sequences. The zircon and carbonate depositional age depth models agree with biostratigraphic constraints and exhibit excellent consistency. The onset and end of sedimentation were estimated at 68.2 ± 0.9 Ma and 62.3 ± 0.6 Ma (duration ca 5.7 Ma) via zircon geochronology and at 67.9 ± 1.7 Ma and 61.9 ± 1.3 Ma (duration ca 6.0 Ma) via carbonate geochronology. Results from this study show that with suitable samples and a newly implemented working strategy, in situ U‐Pb dating of depositional and early diagenetic carbonates represent a valuable chronostratigraphic tool for estimating sedimentation rate and duration in poorly time‐framed depositional systems.
Study on Flow and Cavitation Characteristics of an Energy Storage Chamber Type Common-Rail Injector
Authors: Wentai Wang , Bolan Liu , Yaohui Han , Junwei Zhang , Fanshuo Liu , Ben Li , Peng Wan 
Published: April 2022

Abstract
The high-pressure common-rail fuel injection system is one of the key technologies of diesel engines, which directly affects engine combustion. An energy storage chamber type common rail injector was studied in this paper. The injector is considered to have good control of pressure fluctuation by utilizing a special chamber inside its body. To investigate the flow and cavitation characteristics of the injector, a computational fluid dynamic model was built and validated by experimental data. The flow performance of the energy storage chamber, control valve, and SAC was conducted. The results show that the flow inside the energy storage cavity is smooth, and there is almost no cavitation phenomenon. Although the eccentric valve needle of the control valve will accelerate the flow rate, it will cause a serious cavitation phenomenon, which should be avoided. Increasing the diameter of the injector needle will weaken the cavitation, but it will cause the injector needle valve outlet flow rate to decrease. Finally, for the SAC cavity, increasing the cavity radius, increasing the nozzle inlet angle, and reducing the nozzle length can improve the discharge coefficient and optimize the flow characteristics of the injector.
Effects of Bilateral Dorsolateral Prefrontal Cortex High-Definition Transcranial Direct-Current Stimulation on Physiological and Performance Responses at Severe-Intensity Exercise Domain in Elite Road Cyclists
Authors: Gallo Gabriele , Geda Elisabetta , Codella Roberto , Faelli Emanuela , Panascì Marco , Ranieri Luis Eduardo , Pollastri Luca , Brighenti Stefania , Molino Luigi , Riba Ugo , Luzi Livio , Ruggeri Piero , Filipas Luca 
Published: April 2022

Purpose: To investigate the effects of bilateral dorsolateral prefrontal cortex high-definition transcranial direct-current stimulation (HD-tDCS) on physiological and performance responses during exercise at the upper limit of the severe-intensity exercise domain in elite-level road cyclists. Methods: Eleven elite-level road cyclists (VO2peak: 71.8 [3.1] mL·kg−1·min−1) underwent the HD-tDCS or SHAM condition in a double-blind, counterbalanced, and randomized order. After 20 minutes of receiving either HD-tDCS on dorsolateral prefrontal cortex (F3 and F4) or SHAM stimulation, participants completed a 10-minute constant-load trial (CLT1) at 90% of the first ventilatory threshold and a 2-minute CLT (CLT2) at peak power output. Thereafter, they performed a simulated 2-km time trial (TT). Maximal oxygen uptake, respiratory exchange ratio, heart rate, and rating of perceived exertion were recorded during CLT1 and CLT2, whereas performance parameters were recorded during the TT. Results: In 6 out of 11 cyclists, the total time to complete the TT was 3.0% faster in HD-tDCS compared to SHAM. Physiological and perceptual variables measured during CLT1 and CLT2 did not change between HD‐tDCS and SHAM. Conclusions: HD-tDCS over the dorsolateral prefrontal cortex seemed to improve cycling TT performance within the upper limit of the severe-intensity exercise domain, suggesting that an upregulation of the prefrontal cortex could be critical even in this exercise intensity domain. However, the limited dimension and the high interindividual variability require further studies to test these putative ergogenic effects.
Effectiveness of Ultrasound-Guided Corticosteroid Injections, Prolotherapy, and Exercise Therapy on Partial-Thickness Supraspinatus Tears
Authors: Eroglu Ali , Yargic Melda Pelin 
Published: April 2022

Context: To investigate the effects of steroid injection (STE), prolotherapy (PRO), and exercise therapy in the treatment of partial tears of the supraspinatus. Design: A retrospective cohort study. Methods: A total of 64 patients with clinically and radiologically diagnosed partial-thickness supraspinatus tear who received either a cortisone injection (STE), dextrose PRO, or physical therapy combined with home-based exercise therapy were included. Main outcome measures were patients’ visual analog scale scores, Western Ontario Rotator Cuff (WORC) Index scores, and the Shoulder Pain and Disability Index scores at the baseline, 3 weeks, and 3 months. Results: The effect of group, time, and group–time interaction on visual analog scale, WORC, and Shoulder Pain and Disability Index scores was statistically significant (P < .001). Visual analog scale and Shoulder Pain and Disability Index scores were the lowest in the STE group at week 3, and the lowest in the PRO group at month 3 (P < .001). WORC scores of the STE group were the highest at week 3 (P < .001). At month 3, WORC scores of STE and PRO groups were similar (P = .089), but significantly higher than exercise therapy. Conclusions: Corticosteroids provide a fast pain-relieving effect and improvement in function in partial-thickness rotator cuff tears, but these effects diminish over time, whereas PRO provides a long-lasting effect.
Comparison of neonatal morbidity and mortality between single-room and open-bay care: a retrospective cohort study
Authors: Jansen Sophie , Berkhout Romy J M , te Pas Arjan B , Steggerda Sylke J , de Vries Linda S , Schalij-Delfos Nicoline , van der Hoeven Alieke , Lopriore Enrico , Bekker Vincent 
Published: April 2022

ObjectiveIn response to the increasing focus on family-centred care, neonatal intensive care unit (NICU) environments have gradually shifted towards the single-room design. However, the assumed benefits of this emerging design remain a subject of debate. Our goal was to evaluate the impact of single-room versus open-bay care on the risk of neonatal morbidity and mortality in preterm neonates.DesignRetrospective cohort study.SettingLevel III NICU.PatientsNeonates born <32 weeks’ gestation between 15 May 2015 and 15 May 2019.Main outcome measuresMortality and morbidities of a cohort of neonates admitted to a new, single-room unit (SRU) were compared with a historical cohort of neonates admitted to an open-bay unit (OBU). Group differences were evaluated and multivariable logistic regression analyses were performed.ResultsThree-hundred and fifty-six and 343 neonates were admitted to the SRU and OBU, respectively. No difference in neonatal morbidities and mortality were observed between cohorts (bronchopulmonary dysplasia: OR 1.08, 95% CI 0.73 to 1.58, p=0.44; retinopathy of the prematurity stage ≥2: OR 1.36, 95% CI 0.84 to 2.22, p=0.10; intraventricular haemorrhage: OR 0.89, 95% CI 0.59 to 1.34, p=0.86; mortality: OR 1.55, 95% CI 0.75 to 3.20, p=0.28). In adjusted regression models, single-room care was independently associated with a decreased risk of symptomatic patent ductus arteriosus (adjusted OR 0.54, 95% CI 0.31 to 0.95). No independent association between single-room care and any of the other investigated outcomes was observed.ConclusionsImplementation of single-rooms in our NICU did not lead to a significant reduction in neonatal morbidity and mortality outcomes.
Progression through return-to-sport and return-to-academics guidelines for concussion management and recovery in collegiate student athletes: findings from the Ivy League–Big Ten Epidemiology of Concussion Study
Authors: Wiebe Douglas J , Bretzin Abigail C , D'Alonzo Bernadette A 
Published: April 2022

ObjectiveTo examine the progression of collegiate student athletes through five stages of a return-to-activity protocol following sport-related concussion (SRC).MethodsIn a multisite prospective cohort study, we identified the frequency of initial 24–48 hours physical and cognitive rest, and the sequence of (1) symptom resolution and return to (2) exertion activity, (3) limited sport, (4) full sport and (5) full academics. In resulting profiles we estimated the likelihood of return to full sport ≤14 days or prolonged >28 days and tested for variability based on timing of the stages.ResultsAmong 1715 athletes with SRC (31.6% females), 67.9% had 24–48 hours initial physical and cognitive rest. The median was 6 days to return to full academics, 8 days to symptom resolution and 9 days to exertion. Three profiles emerged; all had the same sport-specific return progression, but varied in the relative timing of full academics. In unadjusted analyses, full academics as the first stage corresponded to the longest time to return to full sport, and initiating exertion the same day as symptom resolution resulted in the shortest time. In adjusted regression analyses, athletes initiating full academics while still symptomatic were 21.5% less likely (95% CI −27.4% to −15.5%) to return to full sport ≤14 days and, analogously, 19.1% more likely (95% CI 13.4% to 24.7%) to have prolonged return >28 days. While additionally controlling for initial rest, sex, symptom count and concussion history, the likelihood of prolonged return >28 days was 37.0% (95% CI 25.2% to 48.8%) in athletes initiating exertion considerably before symptoms resolved (ie, 7+ days), but only 3.6% (95% CI −1.4% to 8.6%) in athletes initiating exertion shortly before achieving symptom resolution (ie, 3–4 days).ConclusionWe found evidence that sequential progressions were consistent with current recommendations including brief initial rest, and the initiation and relative timing of each stage impacted the final return-to-sport outcome.
FOXA2 prevents hyperbilirubinaemia in acute liver failure by maintaining apical MRP2 expression
Authors: Wang Sai , Feng Rilu , Wang Shan Shan , Liu Hui , Shao Chen , Li Yujia , Link Frederik , Munker Stefan , Liebe Roman , Meyer Christoph , Burgermeister Elke , Ebert Matthias , Dooley Steven , Ding Huiguo , Weng Honglei 
Published: April 2022

ObjectiveMultidrug resistance protein 2 (MRP2) is a bottleneck in bilirubin excretion. Its loss is sufficient to induce hyperbilirubinaemia, a prevailing characteristic of acute liver failure (ALF) that is closely associated with clinical outcome. This study scrutinises the transcriptional regulation of MRP2 under different pathophysiological conditions.DesignHepatic MRP2, farnesoid X receptor (FXR) and Forkhead box A2 (FOXA2) expression and clinicopathologic associations were examined by immunohistochemistry in 14 patients with cirrhosis and 22 patients with ALF. MRP2 regulatory mechanisms were investigated in primary hepatocytes,Fxr−/−mice and lipopolysaccharide (LPS)-treated mice.ResultsPhysiologically, homeostatic MRP2 transcription is mediated by the nuclear receptor FXR/retinoid X receptor complex.Fxr−/−mice lack apical MRP2 expression and rapidly progress into hyperbilirubinaemia. In patients with ALF, hepatic FXR expression is undetectable, however, patients without infection maintain apical MRP2 expression and do not suffer from hyperbilirubinaemia. These patients express FOXA2 in hepatocytes. FOXA2 upregulates MRP2 transcription through binding to its promoter. Physiologically, nuclear FOXA2 translocation is inhibited by insulin. In ALF, high levels of glucagon and tumour necrosis factor α induce FOXA2 expression and nuclear translocation in hepatocytes. Impressively, ALF patients with sepsis express low levels of FOXA2, lose MRP2 expression and develop severe hyperbilirubinaemia. In this case, LPS inhibits FXR expression, induces FOXA2 nuclear exclusion and thus abrogates the compensatory MRP2 upregulation. In bothFxr−/−and LPS-treated mice, ectopic FOXA2 expression restored apical MRP2 expression and normalised serum bilirubin levels.ConclusionFOXA2 replaces FXR to maintain MRP2 expression in ALF without sepsis. Ectopic FOXA2 expression to maintain MRP2 represents a potential strategy to prevent hyperbilirubinaemia in septic ALF.
Structural geology of the Cadillac Group along the Malartic segment of the Larder Lake Cadillac deformation zone, Quebec, and implications for gold mineralization
Authors: Samson B. , Lafrance B. , Zhou X. , Hamilton M. , Quesnel B. , Scheffer C. , Beaudoin G. , Perrouty S. 
Published: April 2022

The gold-endowed Larder Lake Cadillac deformation zone (LLCDZ) in the Abitibi greenstone belt of the Archean Superior Province generally trends east but swings to the southeast along the Malartic segment in Quebec. Immediately north of the LLCDZ along this segment, deformation of the less than ca. 2687 Ma metasedimentary Cadillac Group began with the formation of isoclinal F1 folds, which are overprinted by post-2676 ± 2.0 Ma regional F2 folds with an axial planar S2 cleavage oriented parallel to the trend of the Malartic segment. Auriferous quartz veins strike east–west (085°) anticlockwise to bedding and S2. They are folded into sigmoidal S-shaped folds due to sinistral shear parallel to bedding. Later dextral shearing segmented the veins and folded the F2 folds into Z-shaped F3 folds. The veins are similar in structural chronology, fluid isotopic composition (calculated [Formula: see text] value between –9.5‰ and –3.4‰ and [Formula: see text] values of 12‰), and isotopic re-equilibration temperatures (469 and 498 °C, quartz–biotite oxygen thermometer) to the veins at the nearby Canadian Malartic deposit to the east. They possess comparable Au–As–Sb association and sericite-arsenopyrite alteration halo, as other Cadillac-Group-hosted veins at the Lapa mine to the west. Collectively, they constitute a vein field that extends across the entire length of the Malartic segment. Contrary to recent interpretations of the Malartic segment as an early accretionary structure that controlled the emplacement of gold deposits, its southeast trend is interpreted as the short limb of a broad Z-shaped flexure that formed during later F3 folding of the LLCDZ.
Are Two Binary Operators Necessary to Obtain a Finite Axiomatisation of Parallel Composition?
Authors: Aceto Luca , Castiglioni Valentina , Fokkink Wan , Ingólfsdóttir Anna , Luttik Bas 
Published: April 2022

Bergstra and Klop have shown thatbisimilarityhas afiniteequational axiomatisation over ACP/CCS extended with the binaryleftandcommunication mergeoperators. Moller proved that auxiliary operators arenecessaryto obtain a finite axiomatisation of bisimilarity over CCS, and Aceto et al. showed that this remains true whenHennessy’s mergeis added to that language. These results raise the question of whether there isoneauxiliarybinaryoperator whose addition to CCS leads to a finite axiomatisation of bisimilarity. We contribute to answering this question in the simplified setting of the recursion-, relabelling-, and restriction-free fragment of CCS. We formulate three natural assumptions pertaining to the operational semantics of auxiliary operators and their relationship to parallel composition and prove that an auxiliary binary operator facilitating a finite axiomatisation of bisimilarity in the simplified setting cannot satisfy all three assumptions.
The Oncogenic PI3K-Induced Transcriptomic Landscape Reveals Key Functions in Splicing and Gene Expression Regulation
Authors: Ladewig Erik , Michelini Flavia , Jhaveri Komal , Castel Pau , Carmona Javier , Fairchild Lauren , Zuniga Adler G. , Arruabarrena-Aristorena Amaia , Cocco Emiliano , Blawski Ryan , Kittane Srushti , Zhang Yuhan , Sallaku Mirna , Baldino Laura , Hristidis Vasilis , Chandarlapaty Sarat , Abdel-Wahab Omar , Leslie Christina , Scaltriti Maurizio , Toska Eneda 
Published: April 2022

Abstract

The phosphoinositide 3–kinase (PI3K) pathway regulates proliferation, survival, and metabolism and is frequently activated across human cancers. A comprehensive elucidation of how this signaling pathway controls transcriptional and cotranscriptional processes could provide new insights into the key functions of PI3K signaling in cancer. Here, we undertook a transcriptomic approach to investigate genome-wide gene expression and transcription factor activity changes, as well as splicing and isoform usage dynamics, downstream of PI3K. These analyses uncovered widespread alternatively spliced isoforms linked to proliferation, metabolism, and splicing in PIK3CA-mutant cells, which were reversed by inhibition of PI3Kα. Analysis of paired tumor biopsies from patients with PIK3CA-mutated breast cancer undergoing treatment with PI3Kα inhibitors identified widespread splicing alterations that affect specific isoforms in common with the preclinical models, and these alterations, namely PTK2/FRNK and AFMID isoforms, were validated as functional drivers of cancer cell growth or migration. Mechanistically, isoform-specific splicing factors mediated PI3K-dependent RNA splicing. Treatment with splicing inhibitors rendered breast cancer cells more sensitive to the PI3Kα inhibitor alpelisib, resulting in greater growth inhibition than alpelisib alone. This study provides the first comprehensive analysis of widespread splicing alterations driven by oncogenic PI3K in breast cancer. The atlas of PI3K-mediated splicing programs establishes a key role for the PI3K pathway in regulating splicing, opening new avenues for exploiting PI3K signaling as a therapeutic vulnerability in breast cancer.

Significance:
Transcriptomic analysis reveals a key role for the PI3K pathway in regulating RNA splicing, uncovering new mechanisms by which PI3K regulates proliferation and metabolism in breast cancer.
See related commentary by Claridge and Hopkins, p. 2216
Watch the interview with Eneda Toska, PhD, recipient of the 2023 Cancer Research Early Career Award: https://vimeo.com/847434965
Melancholic Redemption and the Hopelessness of Hope
Authors: Wolfson Elliot R. 
Published: April 2022

Abstract
Since late antiquity, a connection was made between Jews and the psychological state of despondency based, in part, on the link between melancholy and Saturn, and the further association of the Hebrew name of that planet, Shabbetai, and the Sabbath. The melancholic predisposition has had important anthropological, cosmological, and theological repercussions. In this essay, I focus on various perspectives on melancholia in thinkers as diverse as Kafka, Levinas, Blanchot, Rosenzweig, Benjamin, Bloch, Scholem, and Derrida. A common thread that links these thinkers is the hopelessness of hope imparted by the messianic belief in a future that must be perpetually deferred.
Induction of compression wood inhibits development of spiral grain in radiata pine
Authors: Thomas Jimmy , Dijkstra Stephanie M. , Harrington Jonathan J. , Collings David A. 
Published: April 2022

Summary
Spiral grain refers to the helical patterns formed by the wood grain in the trunks of many tree species. In most gymnosperms, grain near the pith is vertical but wood formed after several years of growth has a slight to pronounced left-handed twist. Grain changes presumably involve the slow rotation of cells within the vascular cambium, but the mechanisms that allow this reorientation to occur remain unclear. Understanding this process is, however, important as the presence of strong spiral grain within the corewood of gymnosperms is a major wood quality issue devaluing cut timber. In this study, we measured wood grain in stems of Pinus radiata (radiata pine) saplings through reconstructions of resin canals that follow the grain, visualised by serial sectioning and scanning with circularly polarised light, and through X-ray computed microtomography (μCT) and image analysis in ImageJ. Vertical trees retained a symmetrical grain pattern that was weakly right-handed near the pith, but which became progressively more left-handed during the first eight months of growth. In tilted trees, however, the development of left-handed grain was inhibited by the formation of compression wood on the lower side of the tree whereas the wood on the upper side of the tree developed increasingly more left-handed grain as in the vertical controls. These results demonstrate that a previously unidentified link exists between compression wood formation and the inhibition of grain development.
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment
Authors: Hersch Micha , Biasini Adriano , Marques Ana C. , Bergmann Sven 
Published: April 2022

Abstract
Background
Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measurements. Several computational methods to estimate RNA synthesis, processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate those three rates from a single sample.

Methods
Our method relies on the analytical solution to the Zeisel model of RNA dynamics. It was validated on metabolic labeling experiments performed on mouse embryonic stem cells. Resulting degradation rates were compared both to previously published rates on the same system and to a state-of-the-art method applied to the same data.

Results
Our method is computationally efficient and outputs rates that correlate well with previously published data sets. Using it on a single sample, we were able to reproduce the observation that dynamic biological processes tend to involve genes with higher metabolic rates, while stable processes involve genes with lower rates. This supports the hypothesis that cells control not only the mRNA steady-state abundance, but also its responsiveness, i.e., how fast steady state is reached. Moreover, degradation rates obtained with our method compare favourably with the other tested method.

Conclusions
In addition to saving experimental work and computational time, estimating rates for a single sample has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and assess sample quality. Finally the method and theoretical results described here are general enough to be useful in other contexts such as nucleotide conversion methods and single cell metabolic labeling experiments.