bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation
Authors: Ren Ying-Ying , Liu Zhen 
Published: November 2024

Abstract
Cis-regulatory elements govern the specific patterns and dynamics of gene expression in cells during development, which are the fundamental mechanisms behind cell differentiation. However, the genomic characteristics of single-cell cis-regulatory elements closely linked to cell differentiation during development remain unclear. To explore this, we systematically analyzed ∼250,000 putative single-cell cis-regulatory elements obtained from snATAC-seq analysis of the developing mouse cerebellum. We found that over 80% of these single-cell cis-regulatory elements show pleiotropic effects, being active in 2 or more cell types. The pleiotropic degrees of proximal and distal single-cell cis-regulatory elements are positively correlated with the density and diversity of transcription factor binding motifs and GC content. There is a negative correlation between the pleiotropic degrees of single-cell cis-regulatory elements and their distances to the nearest transcription start sites, and proximal single-cell cis-regulatory elements display higher relevance strengths than distal ones. Furthermore, both proximal and distal single-cell cis-regulatory elements related to cell differentiation exhibit enhanced sequence-level evolutionary conservation, increased density and diversity of transcription factor binding motifs, elevated GC content, and greater distances from their nearest genes. Together, our findings reveal the general genomic characteristics of putative single-cell cis-regulatory elements and provide insights into the genomic and evolutionary mechanisms by which single-cell cis-regulatory elements regulate cell differentiation during development.
Effect of protease supplementation on amino acid digestibility of soybean meal fed to growing-finishing pigs in two different ages
Authors: Galli Gabriela M , Levesque Crystal L , Cantarelli Vinicius S , Chaves Rhuan F , Silva Claudia C , Fascina Vitor B , Perez-Palencia Jorge Y 
Published: November 2024

Abstract
This study was conducted to investigate the effect of protease inclusion level in two different ages on the apparent (AID) and standardized (SID) ileal digestibility of crude protein (CP) and amino acids (AAs) in soybean meal (SBM) fed to growing-finishing pigs. Ten cannulated pigs (21 ± 2 kg) were assigned to experimental diets in a duplicate 5 × 5 Latin square design. In phase I (23 to 30 kg-pigs, 90 ± 17 d of age), ileal digesta was collected in five periods of 7 d (5 d adaptation and 2 d ileal digesta collection). In phase II, (50 to 65 kg-pigs, 140 ± 17 d of age), ileal digesta was collected in 5 more periods of 7 d. For both phases, a corn starch–based diet was formulated with SBM as the sole source of CP and AA and containing titanium as an indigestible marker. Protease was supplemented at 0, 15,000, 30,000, and 45,000 NFP/kg of feed (0, 25, 50, and 75 g/ton of ProAct 360). A nitrogen-free diet was used to estimate basal ileal endogenous AA losses. Pigs were fed at 4% of their body weight, which was adjusted at the end of each period. Orthogonal polynomial contrasts were used to determine the linear and quadratic effects of dietary protease supplementation in each phase. In phase I, increasing levels of protease resulted in a linear increase (P &lt; 0.10) in SID for the 7/11 indispensable AA (Except Arg, His, Met + Cys, and Trp) and the average of all dispensable AA. In phase II, the SID of Ile, Leu, Met, Met + Cys, Val, the average of all indispensable AA, and 4/7 dispensable AA were quadratically increased (P &lt; 0.10). In most cases, supplementation with 30,000 NFP/kg of feed (50 g/ton) resulted in the greatest increase in AA digestibility. However, the linear response in phase I for some AA suggests that diets for younger pigs could be supplemented with a greater level (45,000 NFP/kg or 75 g/ton of feed). Interestingly, younger pigs had consistently increased (P &lt; 0.10) SID of CP and 15/18 AA (Except Arg, Cys, and Ser), being ~5.6% greater for indispensable AA when compared to older pigs. In conclusion, dietary protease supplementation can increase the SID of AA in SBM in both growing and finishing periods. Pig age can potentially influence AA digestibility, possibly related to a greater ileal endogenous AA flow in younger pigs. However, this fact warrants further investigation.
Increasing Discharges Prior to 11:00 am in Patients with Burn Injuries
Authors: Leonard Clint , Sigel Matthew , Wagner Anne , Graham Richelle , Hargis Denise , Troche Maria , Slater Elizabeth Dale 
Published: November 2024

Abstract
This study describes a quality improvement project to increase the number of discharges prior to 11am in a high-volume Burn Center. A limited supply of staffed inpatient beds creates capacity constraints and can adversely affect patient flow.1 Discharging patients earlier may help promote throughput, improve length of stay (LOS) as well as patient satisfaction, and decrease costs.2 Burn injured patients face unique barriers to discharge prior to 11am compared to other inpatient groups. We used the Four Disciplines of Execution (4DX) quality improvement framework, which focuses on identifying key drivers to achieve a specific, time-delimited goal. Our primary target was increasing discharges prior to 11am to 30% over the span of 6 months. Four additional months were measured to assess for process drift. Interventions included (a) designation of “priority discharge” patients, (b) discharge order entry prior to 0930, and (c) decreasing time between discharge order entry and actual patient discharge. Baseline data was gathered from July 1st until Nov 30th 2022 and compared to the intervention period December 1st, 2022 through Sept 30th, 2023. Discharges prior to 11am increased from 10.0% to 27.1% over the course of the project. Median discharge time improved by 72 minutes. Discharge order entry time improved by 83 minutes. Potential special-cause variation was identified in December 2022. Despite not meeting our initial target, discharges prior to 11am were significantly increased after implementing a multidisciplinary approach between nursing, providers, case management and social work.
Macrophage foam cell-derived mediator promotes spontaneous fat lipolysis in atherosclerosis models
Authors: Banerjee Dipanjan , Patra Debarun , Sinha Archana , Chakrabarty Dwaipayan , Patra Aparup , Sarmah Raktim , Dey Upalabdha , Dutta Rajdeep , Bhagabati Sarada K , Mukherjee Ashis K , Kumar Aditya , Pal Durba , Dasgupta Suman 
Published: November 2024

Abstract
Ectopic lipid accumulation in macrophages is responsible for the formation of macrophage foam cells (MFCs) which are involved in the crosstalk with the perivascular adipose tissue (PVAT) of the vascular wall that plays a pivotal role in the progression of atherosclerosis. However, the interrelationship between MFCs and PVAT implementing adipocyte dysfunction during atherosclerosis has not yet been established. We hypothesized that MFC-secreted mediator(s) is causally linked with PVAT dysfunction and the succession of atherosclerosis. To test this hypothesis, MFCs were cocultured with adipocytes, or the conditional media of MFCs (MFC-CM) were exposed to adipocytes and found a significant induction of fat lipolysis in adipocytes. The molecular filtration followed by the high-performance liquid chromatography (HPLC) fractionation and liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS) analysis of MFC-CM revealed a novel mediator fetuin-A (FetA) that significantly augments toll-like receptor 4 (TLR4)-dependent fat lipolysis in adipocytes. Mechanistically, MFC-derived FetA markedly increased TLR4-dependent c-Jun N-terminal kinases (JNK)/extracellular signal-regulated kinases (ERK) activation that causes spontaneous fat lipolysis implementing adipocyte dysfunction. Thus, the present study provides the first evidence of MFC-derived FetA that induces adipocyte dysfunction by the stimulation of spontaneous fat lipolysis. Therefore, targeting the crosstalk between MFCs and adipocytes could be a newer approach to counter the progression of atherosclerosis.
Orbital motion of gold heterodimer driven by optical force of circularly polarized light and reactive drag of medium
Authors: Ku Yun-Cheng , Yang Yao-Sheng , Kuo Mao-Kuen , Liaw Jiunn-Woei 
Published: November 2024

Abstract
This theoretical study explores the two-dimensional orbital motion of an optically bound heterodimer consisting of two gold nanoparticles (NPs) of different sizes, driven by circularly polarized (CP) light. Although a CP light possesses only spin angular momentum without orbital angular momentum, it can still induce orbital revolution in the plasmonic heterodimer. This phenomenon arises from the interaction between the optical force and torque generated by the CP light and the reactive drag force and torque from the surrounding medium. We calculate the optical forces acting on each NP by analyzing the Maxwell stress tensor at their surfaces, and we account for the reactive drag force using Stokes’ law. These forces are used to simulate the trajectories of the NPs through dynamic equations of motion. Our results demonstrate that, regardless of the initial conditions of the two NPs, they will become optically bound together, exhibiting rigid-body translation and rotation. Notably, the center of mass of the heterodimer undergoes an orbital revolution around a fixed point eventually. The CP light-manipulated heterodimer behaves like a boomerang, acting as a spinning rotor on a circular path. The heterodimer's orbital radius and direction of revolution are influenced by the size disparity between the two NPs. Additionally, each NP experiences spin motion, with the spin direction determined by the handedness of the CP light. The optically bound gold heterodimer functions as a light-driven microrotor, with potential applications in microfluidic channels. These findings offer valuable insights into the optomechanical manipulation of non-monodisperse NP clusters using CP light.
Legged robot locomotion on viscoelastic terrain using a reduced-order dynamic model with rolling contact and energy input and dissipation
Authors: Wang Tso-Kang , Lin Pei-Chun 
Published: November 2024

ABSTRACT
In recent decades, robots have gradually taken on more tasks that require mobility. However, unlike animals that are capable of coordinating complex sensing organs and muscles to achieve dynamic motion on all kinds of terrains, robots have difficulties traversing rough terrains at high speeds due to limitations of computational resources, actuator strength, etc. This research aims to build a new model that captures the essence of how animals achieve dynamic motion and traverse rough terrains. Based on the previously developed dynamic model running on the rigid ground, this model incorporates the interaction between the leg and the ground, which is described by a combination of linear springs and dampers that can model a wide range of terrains. Simulation results show chaotic behavior under certain conditions, and an experiment verified such behavior. This work underscores the urgency and significance of understanding and replicating the capabilities of animals in robot locomotion, and its relevance to the field of robotics is significant.
Stellar surface information from the Ca ii H&K lines – II. Defining better activity proxies
Authors: Cretignier M , Hara N C , Pietrow A G M , Zhao Y , Yu H , Dumusque X , Sozzetti A , Lovis C , Aigrain S 
Published: November 2024

ABSTRACT
In our former paper I, we showed on the Sun that different active regions possess unique intensity profiles on the Ca ii H & K lines. We now extend the analysis by showing how those properties can be used on real stellar observations, delivering more powerful activity proxies for radial velocity correction. More information can be extracted on rotational time-scale from the Ca ii  H & K lines than the classical indicators: S-index and $\log (R^{^{\prime }}_{\text{HK}})$. For high-resolution HARPS observations of $\alpha$ Cen B, we apply a principal and independent component analysis on the Ca ii  H & K spectra time-series to disentangle the different sources that contribute to the disc-integrated line profiles. While the first component can be understood as a denoised version of the Mount-Wilson S-index, the second component appears as powerful activity proxies to correct the radial velocities induced by the inhibition of the convective blueshift in stellar active regions. However, we failed to interpret the extracted component into a physical framework. We conclude that a more complex kernel or bandpass than the classical triangular of the Mount Wilson convention should be used to extract activity proxies. To this regard, we provide the first principal component activity profile obtained across the spectral type sequence between M1V to F9V type stars.
Conjugation Mediates Large-Scale Chromosomal Transfer in Streptomyces Driving Diversification of Antibiotic Biosynthetic Gene Clusters
Authors: Choufa Caroline , Gascht Pauline , Leblond Hugo , Gauthier Anthony , Vos Michiel , Bontemps Cyril , Leblond Pierre 
Published: November 2024

Abstract
Streptomyces are ubiquitous soil-dwelling bacteria with large, linear genomes that are of special importance as a source of metabolites used in human and veterinary medicine, agronomy, and industry. Conjugative elements (actinomycetes integrative and conjugative elements, AICEs) are the main drivers of Streptomyces Horizontal Gene Transfer. AICE transfer has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains of Streptomyces result in the large-scale, genome-wide distributed replacement of up to one-third of the recipient chromosome, a phenomenon for which we propose the name “Streptomyces Chromosomal Transfer” (SCT). Such chromosome blending results in the acquisition, loss, and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated specialized metabolite biosynthesis gene cluster diversification holds great promise in the discovery of new bioactive compounds including antibiotics.
Industrial reform policies: does marketization enhance productivity more than privatization?
Authors: Chen Yang , He Ming , Rudkin Simon , Webber Don J 
Published: November 2024

Abstract
Placing state-owned firms into the private sector is understood to yield productivity gains, but this effect is seldom decomposed into changes in ownership (privatization) and changes in firm characteristics to match privately owned firms without changing ownership (marketization). This article presents an empirical assessment of Chinese firm-level data using a counterfactual design approach to identify if the Chinese ‘grasp the large and let go of the small’ industrial policy reform initiative reduced the efficiency gap between state-owned and non-state-owned enterprises and whether any gains were associated with privatization or marketization. Our empirical results show that marketization was associated with stronger increases in productivity than was privatization, suggesting that industrial reforms should consolidate assets, enhance cash flows, and reduce the need for external liquidity rather than focusing on changing ownership.
Vonoprazan
Authors: Provenza Delaney , Provenza John Michael 
Published: November 2024

ABSTRACT

Helicobacter pylori is the most common chronic bacterial infection worldwide. Because of the risk for chronic gastritis, peptic ulcer disease, and gastric malignancy, all patients with H. pylori should be treated. Unfortunately, eradication rates remain low, and barriers to successful treatment include inadequate acid suppression, locoregional antibiotic resistance, and patient nonadherence to complicated treatment regimens. Vonoprazan, a new medication for the treatment of H. pylori infections, provides more potent acid suppression and is simpler to dose than proton pump inhibitors. This article provides a data-driven algorithm for incorporating vonoprazan into the treatment of patients with H. pylori infections.
Postoperative Opioid Consumption After Discharge: An Update From the Michigan Surgical Quality Collaborative Registry
Authors: Kulkarni Ashwin J. , Gunaseelan Vidhya , Brummett Chad M. , Waljee Jennifer , Englesbe Michael , Bicket Mark C. 
Published: November 2024

Objective:
To evaluate opioid consumption for 21 procedures over 4 years from the Michigan Surgical Quality Collaborative (MSQC) registry and update post-discharge prescribing guidelines.

Background:
Opioids remain a common treatment for postoperative pain of moderate-to-severe intensity not adequately addressed by nonopioid analgesics, but excessive prescribing correlates with increased usage. This analysis provides updates and compares patient-reported consumption in response to new guidelines.

Methods:
We examined data from the MSQC registry for opioid-naive adult patients undergoing surgery between January 1, 2018, and October 31, 2021. The primary outcome was patient-reported opioid consumption in oxycodone 5 mg equivalents. Guidelines were anchored to the 75th percentile of consumption, updating previous guidelines from January 2020 based on data from January 1, 2018, to May 31, 2019.

Results:
39,493 opioid-naive surgical patients (average age 53.8 years [SD 16.4], 56.3% female, 19.1% non-White, 43.9% with public insurance) were included. Guidelines did not change for 7 of the 16 procedures including the most common procedures: minor hernia, laparoscopic cholecystectomy, laparoscopic appendectomy, and laparoscopic hysterectomy. Recommended prescribing ranges were lower for 9 procedures, with most (8) procedures having a reduction of 5 pills. Prescribing guidelines were developed for 5 new procedures. All procedures had upper-limit guidelines of 10 pills or less.

Conclusions:
For most procedures, patient-reported opioid consumption decreased between 2018 and 2021 when compared to the period between 2018 and 2019. New guidelines were established for a dozen procedures to balance maximizing pain control with reducing harms from inappropriate prescribing.
Heterogeneous Treatment Effects of High-Frequency Oscillatory Ventilation for Acute Respiratory Distress Syndrome: A Post Hoc Analysis of the Oscillation for Acute Respiratory Distress Syndrome Treated Early (OSCILLATE) Trial
Authors: Kobayashi Hirotada , Angriman Federico , Ferguson Niall D. , Adhikari Neill K. J. 
Published: November 2024

OBJECTIVES:
We sought to evaluate whether different subgroups of adults with acute respiratory distress syndrome (ARDS) respond differently to high-frequency oscillatory ventilation (HFOV).

DESIGN:
The Oscillation for ARDS Treated Early (OSCILLATE) trial was a randomized controlled trial of HFOV vs. conventional ventilation that found an increased risk of in-hospital mortality (primary outcome) with HFOV. In a post hoc analysis, we applied three different approaches to evaluate heterogeneity of treatment effect for in-hospital mortality: 1) subgroup analyses based on baseline Pao
2:Fio
2 ratio and oxygenation index (OI); 2) a risk-based approach using a multivariable outcome prediction model; and 3) a clustering approach via multivariable latent class analysis. We used multivariable logistic regression models to assess for interaction.

SETTING:
Thirty-nine ICUs, five countries.

SUBJECTS:
Five hundred forty-eight adults with moderate to severe ARDS.

INTERVENTIONS:
HFOV vs. conventional mechanical ventilation with low tidal volume and higher positive end-expiratory pressure.

MEASUREMENTS AND MAIN RESULTS:
The effect of HFOV on in-hospital mortality was consistent across categories of Pao
2:Fio
2 ratio (adjusted odds ratio [aOR], 2.04; 95% CI, 1.32–3.17 and aOR, 1.16; 95% CI, 0.49–2.75 for groups with Pao
2:Fio
2 above or equal to 80, vs. below 80, respectively; interaction p = 0.23) and OI (aOR, 1.78; 95% CI, 0.67–4.70; aOR, 3.19; 95% CI, 1.44–7.09; aOR, 1.73; 95% CI, 0.82–3.65; and aOR, 1.33; 95% CI, 0.61–2.90 for quartiles of baseline OI, respectively; interaction p = 0.44). Point estimates for the effect of HFOV were consistent across risk categories (aOR, 2.44; 95% CI, 0.40–14.83; aOR, 1.69; 95% CI, 0.75–3.85; and aOR, 2.10; 95% CI, 0.59–7.54 for the lowest, moderate, and highest risk categories, respectively; interaction p = 0.32). Using a clustering approach, point estimates for HFOV were also consistent (cluster 1: aOR, 1.85; 95% CI, 1.15–3.00 and cluster 2: aOR, 1.75; 95% CI, 0.91–3.38; interaction p = 0.75).

CONCLUSIONS:
We did not identify heterogeneity in the effect of HFOV across different subgroups of patients with ARDS.
Comparison of associations between proximity to major roads and all-cause mortality across a spectrum of cardiovascular diseases
Authors: Raab Henry , Breen Miyuki , Weaver Anne M. , Moyer Joshua , Cascio Wayne E. , Diaz-Sanchez David , Ward-Caviness Cavin K. 
Published: November 2024

Background:
Global urbanization is leading to increased exposure to traffic-related air pollution (TRAP), which is associated with adverse health events. While individuals with cardiovascular disease (CVD) are known to have elevated susceptibility to air pollution exposure, no studies have evaluated how mortality risks associated with TRAP exposure differ based on the presence of CVD.

Methods:
We used three electronic health record-based cohorts to examine associations between proximity to major roadways and all-cause mortality. The three cohorts were a random sample of the hospital population, individuals with a prior myocardial infarction, and individuals with diagnosed heart failure (HF). We used Cox proportional hazards models to evaluate associations while adjusting for age, race, sex, and census block group socioeconomic status.

Results:
Residing <250 m from a major roadway was associated with a hazard ratio (HR) of 1.13 (95% confidence interval = 1.05, 1.23) for individuals with HF, an HR of 1.07 (95% confidence interval = 0.96, 1.20) for those with a prior myocardial infarction, and an HR of 1.03 (95% confidence interval = 0.89, 1.20) for a random sample of hospital patients. This pattern persisted across several sensitivity analyses including alternative definitions of proximity to major roadways and matching the cohorts on demographics.

Conclusion:
These results highlight the differences in air quality-related health risks based on underlying CVD. Individuals with HF consistently had the highest environmental health risks. These results may better inform risks related to TRAP exposure in populations with differing underlying CVD.