bluuebunny/crossref_metadata_2025_split huggingface dataset:
EMES: Efficient Multi-Encoding Schemes for HEVC-based Adaptive Bitrate Streaming
Authors: Menon Vignesh V , Amirpour Hadi , Ghanbari Mohammad , Timmerer Christian 
Published: December 2022

In
HTTP Adaptive Streaming
(HAS), videos are encoded at multiple bitrates and spatial resolutions (
i.e.
,
representations
) to adapt to the heterogeneity of network conditions, device attributes, and end-user preferences. Encoding the same video segment at multiple representations increases costs for content providers. State-of-the-art multi-encoding schemes improve the encoding process by utilizing encoder analysis information from already encoded representation(s) to reduce the encoding time of the remaining representations. These schemes typically use the highest bitrate representation as the reference to accelerate the encoding of the remaining representations. Nowadays, most streaming services utilize cloud-based encoding techniques, enabling a fully parallel encoding process to reduce the overall encoding time. The highest bitrate representation has the highest encoding time than the other representations. Thus, utilizing it as the reference encoding is unfavorable in a parallel encoding setup as the overall encoding time is bound by its encoding time. This paper provides a comprehensive study of various multi-rate and multi-encoding schemes in both serial and parallel encoding scenarios. Furthermore, it introduces novel heuristics to limit the
Rate Distortion Optimization
(RDO) process across various representations. Based on these heuristics, three multi-encoding schemes are proposed, which rely on encoder analysis sharing across different representations:
(i)
optimized for the
highest compression efficiency
,
(ii)
optimized for the
best compression efficiency-encoding time savings trade-off
, and
(iii)
optimized for the
best encoding time savings
. Experimental results demonstrate that the proposed multi-encoding schemes
(i)
,
(ii)
, and
(iii)
reduce the overall serial encoding time by 34.71%, 45.27%, and 68.76% with a 2.3%, 3.1%, and 4.5% bitrate increase to maintain the same VMAF, respectively compared to stand-alone encodings. The overall parallel encoding time is reduced by 22.03%, 20.72%, and 76.82% compared to stand-alone encodings for schemes
(i)
,
(ii)
, and
(iii)
, respectively.
PINK1-Mediated Mitophagy Promotes Oxidative Phosphorylation and Redox Homeostasis to Induce Drug-Tolerant Persister Cancer Cells
Authors: Li Yun , Chen Hengxing , Xie Xuan , Yang Bing , Wang Xiaojuan , Zhang Jingyuan , Qiao Tian , Guan Jiao , Qiu Yuntan , Huang Yong-Xin , Tian Duanqing , Yao Xinyi , Lu Daning , Koeffler H. Phillip , Zhang Yin , Yin Dong 
Published: December 2022

Abstract

The drug-tolerant persister (DTP) state enables cancer cells to evade cytotoxic stress from anticancer therapy. However, the mechanisms governing DTP generation remain poorly understood. Here, we observed that lung adenocarcinoma (LUAD) cells and organoids entered a quiescent DTP state to survive MAPK inhibitor treatment. DTP cells following MAPK inhibition underwent a metabolic switch from glycolysis to oxidative phosphorylation (OXPHOS). PTEN-induced kinase 1 (PINK1), a serine/threonine kinase that initiates mitophagy, was upregulated to maintain mitochondrial homeostasis during DTP generation. PINK1-mediated mitophagy supported DTP cell survival and contributed to poor prognosis. Mechanistically, MAPK pathway inhibition resulted in MYC-dependent transcriptional upregulation of PINK1, leading to mitophagy activation. Mitophagy inhibition using either clinically applicable chloroquine or depletion of PINK1 eradicated drug tolerance and allowed complete response to MAPK inhibitors. This study uncovers PINK1-mediated mitophagy as a novel tumor protective mechanism for DTP generation, providing a therapeutic opportunity to eradicate DTP and achieve complete responses.

Significance:
DTP cancer cells that cause relapse after anticancer therapy critically depend on PINK1-mediated mitophagy and metabolic reprogramming, providing a therapeutic opportunity to eradicate persister cells to prolong treatment efficacy.
Smoking Cessation and Tobacco-related Risk Perceptions among People with and without a Diagnosis of Cancer
Authors: Land Stephanie R. , Baker Laura , Twesten Jenny , Reyes-Guzman Carolyn M. , Kaufman Annette R. 
Published: December 2022

Abstract

Background:
Little is known about how cancer diagnosis and tobacco-related risk perceptions are associated with smoking behavior.

Methods:
We used data from Waves (W) 1–3 (2013–2016) of the Population Assessment of Tobacco and Health Study to analyze longitudinal smoking behavior among adults who were current smokers and not previously diagnosed with cancer at baseline (W1; N = 7,829). The outcome was smoking cessation as of follow-up (W3). Explanatory variables were sociodemographics, other tobacco product use, adult at first cigarette, tobacco dependence, cancer diagnosis after baseline, and tobacco-related risk perceptions [cigarette harm perception, worry that tobacco products will damage one's health (“worry”), belief that smoking causes cancer (“belief”), and nondaily smoking harm perception].

Results:
Cessation was significantly associated with baseline worry (OR = 1.26; 95% confidence interval, 1.13–1.40), follow-up cigarette harm perception [OR = 2.01 (1.77–2.29)], and follow-up belief [OR = 1.40 (1.20–1.63)]. Cessation was inversely associated with follow-up (W3) worry, and this association was stronger among those without a cancer diagnosis (OR = 0.37 without cancer; OR = 0.76 among individuals diagnosed with cancer; interaction P = 0.001).

Conclusions:
Cessation is associated with tobacco-related risk perceptions, with different perceptions contributing in unique ways. Cessation is predicted by baseline worry but is inversely associated with worry at follow-up, suggesting that perhaps cessation has alleviated worry. The latter finding was stronger among respondents not diagnosed with cancer.

Impact:
Associations between cancer diagnosis, tobacco-related risk perceptions, and smoking behavior may inform the development of evidence-based smoking cessation interventions.
Impact of Brief Quality Improvement Coaching on Adolescent HPV Vaccination Coverage: A Pragmatic Cluster Randomized Trial
Authors: Gilkey Melissa B. , Heisler-MacKinnon Jennifer , Boynton Marcella H. , Calo William A. , Moss Jennifer L. , Brewer Noel T. 
Published: December 2022

Abstract

Background:
Health departments in the United States routinely conduct quality improvement (QI) coaching to help primary care providers optimize vaccine delivery. In a prior trial focusing on multiple adolescent vaccines, this light-touch intervention yielded only short-term improvements in HPV vaccination. We sought to evaluate the impact of an enhanced, HPV vaccine-specific QI coaching intervention when delivered in person or virtually.

Methods:
We partnered with health departments in three states to conduct a pragmatic cluster randomized trial in 2015 to 2016. We randomized 224 primary care clinics to receive no intervention (control), in-person coaching, or virtual coaching. Health department staff delivered the brief (45–60 minute) coaching interventions, including HPV vaccine-specific training with assessment and feedback on clinics’ vaccination coverage (i.e., proportion of patients vaccinated). States’ immunization information systems provided data to assess coverage change for HPV vaccine initiation (≥1 doses) at 12-month follow-up, among patients ages 11 to 12 (primary outcome) and 13 to 17 (secondary outcome) at baseline.

Results:
Clinics served 312,227 patients ages 11 to 17. For ages 11 to 12, coverage change for HPV vaccine initiation was higher in the in-person and virtual coaching arms than in the control arm at 12-month follow-up (1.2% and 0.7% point difference, both P &lt; 0.05). For ages 13 to 17, coverage change was higher for virtual coaching than control (1.4% point difference, P &lt; 0.001), but in-person coaching did not yield an intervention effect.

Conclusions:
Our brief QI coaching intervention produced small long-term improvements in HPV vaccination.

Impact:
Health departments may benefit from targeting QI coaching to specific vaccines, like HPV vaccine, that need them most.
Clinical Implications of APOBEC3-Mediated Mutagenesis in Breast Cancer
Authors: Roelofs Pieter A. , Martens John W.M. , Harris Reuben S. , Span Paul N. 
Published: December 2022

Abstract
Over recent years, members of the APOBEC3 family of cytosine deaminases have been implicated in increased cancer genome mutagenesis, thereby contributing to intratumor and intertumor genomic heterogeneity and therapy resistance in, among others, breast cancer. Understanding the available methods for clinical detection of these enzymes, the conditions required for their (dysregulated) expression, the clinical impact they have, and the clinical implications they may offer is crucial in understanding the current impact of APOBEC3-mediated mutagenesis in breast cancer. Here, we provide a comprehensive review of recent developments in the detection of APOBEC3-mediated mutagenesis and responsible APOBEC3 enzymes, summarize the pathways that control their expression, and explore the clinical ramifications and opportunities they pose. We propose that APOBEC3-mediated mutagenesis can function as a helpful predictive biomarker in several standard-of-care breast cancer treatment plans and may be a novel target for treatment.
Heparin Does Not Regulate Circulating Human PCSK9 (Proprotein Convertase Subtilisin-Kexin Type 9) in a General Population—Brief Report
Authors: Xia Vivian Q. , Ong Chui Mei , Zier Lucas S. , MacGregor John S. , Wu Alan H.B. , Chorba John S. 
Published: December 2022

Background:
PCSK9 (proprotein convertase subtilisin-kexin type 9) chaperones the hepatic LDLR (low-density lipoprotein receptor) for lysosomal degradation, elevating serum LDL (low-density lipoprotein) cholesterol and promoting atherosclerotic heart disease. Though the major effect on the hepatic LDLR comes from secreted PCSK9, the details of PCSK9 reuptake into the hepatocyte remain unclear. In both tissue culture and animal models, HSPGs (heparan sulfate proteoglycans) on hepatocytes act as co-receptors to promote PCSK9 reuptake. We hypothesized that if this PCSK9:HSPG interaction is important in humans, disrupting it with unfractionated heparin (UFH) would acutely displace PCSK9 from the liver and increase plasma PCSK9.

Methods:
We obtained remnant plasma samples from 160 subjects undergoing cardiac catheterization before and after administration of intravenous UFH. PCSK9 levels were determined using a commercial enzyme-linked immunosorbent assay.

Results:

Median plasma PCSK9 was 113 ng/mL prior to UFH and 119 ng/mL afterward. This difference was not significant (
P
=0.83 [95% CI, −6.23 to 6.31 ng/mL]). Equivalence testing provided 95% confidence that UFH would not raise plasma PCSK9 by > 4.7%. Among all subgroups, only subjects with the lowest baseline PCSK9 concentrations exhibited a response to UFH (8.8% increase, adj.
P
=0.044). A modest correlation was observed between baseline plasma PCSK9 and the change in plasma PCSK9 due to UFH (R
S
=−0.3634;
P
<0.0001).

Conclusions:
Administration of UFH does not result in a clinically meaningful effect on circulating PCSK9 among an unselected population of humans. The results cast doubt on the clinical utility of disrupting the PCSK9:HSPG interaction as a general therapeutic strategy for PCSK9 inhibition. However, the observations suggest that in selected populations, disrupting the PCSK9:HSPG interaction could still affect PCSK9 reuptake and offer a therapeutic benefit.
Control of system parameters by estimating screw withdrawal strength values of particleboards using artificial neural network-based statistical control charts
Authors: Kurt Rıfat 
Published: December 2022

AbstractIn this study, with data obtained from a particleboard factory, screw withdrawal strength (SWS) values of particleboards were estimated using artificial neural networks (ANNs). Predictive control charts were also created. A total of seven independent variables were used for the ANN model: modulus of elasticity (MoE), surface soundness (SS), internal bond strength (IBS), density, press time, press temperature, and press pressure. The results showed that the ANN-based individual moving range (I-MR) and cumulative sum (CUSUM) control charts created for SWS values detected out-of-control signal points close to those of the real-time control charts. Among the selected independent variables, IBS was the most important parameter affecting SWS. The most suitable press temperatures and times for high SWS values were determined as 198–201 °C and 165–175 s, respectively. Moreover, the boards with 2500–2800 N/mm2 MoE and 0.55 N/mm2 IBS values exhibited the best SWS.
Determination of biomarkers threshold values and illustration of their use for the diagnostic in large-scale freshwater biomonitoring surveys
Authors: Leprêtre Maxime , Geffard Alain , Palos Ladeiro Mélissa , Dedourge-Geffard Odile , David Elise , Delahaut Laurence , Bonnard Isabelle , Barjhoux Iris , Nicolaï Miguel , Noury Patrice , Espeyte Anabelle , Chaumot Arnaud , Degli-Esposti Davide , Geffard Olivier , Lopes Christelle 
Published: December 2022

Abstract
Background
Several biomarkers developed from freshwater sentinel species are used to complement chemical assessment of freshwater ecosystems and improve the evaluation of their contamination levels. While active biomonitoring strategies allow to compare biological data in the field, the lack of assessment criteria to interpret biomarkers modulations restricts their application in freshwater biomonitoring surveys. For this purpose, the determination of threshold values emerges as a relevant approach to support the biomarker-based diagnosis within biomonitoring surveys. Based on the distribution of contamination baselines, a statistical approach was proposed to define threshold values of bioaccumulated concentrations in the sentinel species Gammarus fossarum. Although this methodology is limited to chemical databases, this approach could be adapted for defining threshold values at the biological level. This study aims to demonstrate the possibility of defining threshold values for different classes of biomarkers monitored in two freshwater sentinel species (Dreissena polymorpha, G. fossarum) and evidence the added value of such an approach in biomarker-based diagnosis.

Results
For this purpose, the study benefited from exceptional environmental biomarker datasets acquired from mussels and gammarids caged in hundred environmental sites, representative of the diversity of French water bodies. Thanks to these environmental datasets, inhibition and/or induction thresholds could be defined for 8 biochemical, cellular, and molecular biomarkers of D. polymorpha and 25 peptide biomarkers of G. fossarum, not influenced by confounding factors. Threshold values were then applied to another biomarker dataset acquired from mussels and gammarids caged upstream and downstream four wastewater treatment plants (WWTPs). Several biomarkers were modulated both downstream and upstream of WWTPs, indicating a potential contamination not related to WWTPs. In contrast, some biomarkers were impacted exclusively downstream of the WWTPs, highlighting an impact of WWTP discharges on the aquatic fauna.

Conclusions
This study demonstrates the possibility to define threshold values for a wide range of biomarkers (cellular, biochemical and molecular) monitored on different sentinel species. The definition of threshold values constitutes an attractive solution to support the application of biomarkers in active biomonitoring surveys and improve the biomarker-based diagnosis without the need of “reference sites”.
Impacts of multiple anthropogenic stressors on the transcriptional response of Gammarus fossarum in a mesocosm field experiment
Authors: Brasseur Marie V. , Beermann Arne J. , Elbrecht Vasco , Grabner Daniel , Peinert-Voss Bianca , Salis Romana , Weiss Martina , Mayer Christoph , Leese Florian 
Published: December 2022

Abstract

Background
Freshwaters are exposed to multiple anthropogenic stressors, leading to habitat degradation and biodiversity decline. In particular, agricultural stressors are known to result in decreased abundances and community shifts towards more tolerant taxa. However, the combined effects of stressors are difficult to predict as they can interact in complex ways, leading to enhanced (synergistic) or decreased (antagonistic) response patterns. Furthermore, stress responses may remain undetected if only the abundance changes in ecological experiments are considered, as organisms may have physiological protective pathways to counteract stressor effects. Therefore, we here used transcriptome-wide sequencing data to quantify single and combined effects of elevated fine sediment deposition, increased salinity and reduced flow velocity on the gene expression of the amphipod Gammarus fossarum in a mesocosm field experiment.

Results
Stressor exposure resulted in a strong transcriptional suppression of genes involved in metabolic and energy consuming cellular processes, indicating that G. fossarum responds to stressor exposure by directing energy to vitally essential processes. Treatments involving increased salinity induced by far the strongest transcriptional response, contrasting the observed abundance patterns where no effect was detected. Specifically, increased salinity induced the expression of detoxification enzymes and ion transporter genes, which control the membrane permeability of sodium, potassium or chloride. Stressor interactions at the physiological level were mainly antagonistic, such as the combined effect of increased fine sediment and reduced flow velocity. The compensation of the fine sediment induced effect by reduced flow velocity is in line with observations based on specimen abundance data.

Conclusions
Our findings show that gene expression data provide new mechanistic insights in responses of freshwater organisms to multiple anthropogenic stressors. The assessment of stressor effects at the transcriptomic level and its integration with stressor effects at the level of specimen abundances significantly contribute to our understanding of multiple stressor effects in freshwater ecosystems.
Genome-wide identification and functional analysis of Dof transcription factor family in Camelina sativa
Authors: Luo Tao , Song Yanan , Gao Huiling , Wang Meng , Cui Hongli , Ji Chunli , Wang Jiping , Yuan Lixia , Li Runzhi 
Published: December 2022

Abstract
Background
Dof transcription factors (TFs) containing C2-C2 zinc finger domains are plant-specific regulatory proteins, playing crucial roles in a variety of biological processes. However, little is known about Dof in Camelina sativa, an important oil crop worldwide, with high stress tolerance. In this study, a genome-wide characterization of Dof proteins is performed to examine their basic structural characteristics, phylogenetics, expression patterns, and functions to identify the regulatory mechanism underlying lipid/oil accumulation and the candidate Dofs mediating stress resistance regulation in C. sativa.

Results
Total of 103 CsDof genes unevenly distributed on 20 chromosomes were identified from the C. sativa genome, and they were classified into four groups (A, B, C and D) based on the classification of Arabidopsis Dof gene family. All of the CsDof proteins contained the highly-conserved typic CX2C-X21-CX2C structure. Segmental duplication and purifying selection were detected for CsDof genes. 61 CsDof genes were expressed in multiple tissues, and 20 of them showed tissue-specific expression patterns, suggesting that CsDof genes functioned differentially in different tissues of C. sativa. Remarkably, a set of CsDof members were detected to be possible involved in regulation of oil/lipid biosynthesis in C. sativa. Six CsDof genes exhibited significant expression changes in seedlings under salt stress treatment.

Conclusions
The present data reveals that segmental duplication is the key force responsible for the expansion of CsDof gene family, and a strong purifying pressure plays a crucial role in CsDofs’ evolution. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Collectively, our findings provide a foundation for deep understanding the roles of CsDofs and genetic improvements of oil yield and salt stress tolerance in this species and the related crops.
Prevalence of sensory impairments in home care and long-term care using interRAI data from across Canada
Authors: Guthrie Dawn M. , Williams Nicole , Jaiswal Atul , Mick Paul , O’Rourke Hannah M. , Pichora-Fuller M. Kathleen , Wittich Walter , Sutradhar Rinku 
Published: December 2022

Abstract
Background
In the general population, sensory impairments increase markedly with age in adults over 60 years of age. We estimated the prevalence of hearing loss only (HL), vision loss only (VL), and a combined impairment (i.e., dual sensory loss or DSL) in Canadians receiving home care (HC) or long-term care (LTC).

Methods
Annual cross-sectional analyses were conducted using data collected with one of two interRAI assessments, one used for the HC setting (n = 2,667,199), and one for LTC (n = 1,538,691). Items in the assessments were used to measure three mutually exclusive outcomes: prevalence of VL only, HL only, or DSL. Trends over time for each outcome were examined using the Cochran-Armitage trend test. A negative binomial model was used to quantify the trends over time for each outcome while adjusting for age, sex and province.

Results
In HC, there was a significant trend in the rate for all three outcomes (p < 0.001), with a small increase (roughly 1%) each year. In HC, HL was the most prevalent sensory loss, with a rate of roughly 25% to 29%, while in LTC, DSL was the most prevalent impairment, at roughly 25% across multiple years of data. In both settings, roughly 60% of the sample was female. Males in both HC and LTC had a higher prevalence of HL compared to females, but the differences were very small (no more than 2% in any given year). The prevalence of HL differed by province after adjusting for year, age and sex. Compared to Ontario, Yukon Territory had a 26% higher rate of HL in HC (relative rate [RR] = 1.26; 95% confidence interval [CI]:1.11, 1.43), but LTC residents in Newfoundland and Labrador had a significantly lower rate of HL (RR: 0.57; CI: 0.43, 0.76).When combined, approximately 60% of LTC residents, or HC clients, had at least one sensory impairment.

Conclusions
Sensory impairments are highly prevalent in both HC and LTC, with small sex-related differences and some variation across Canadian provinces. The interRAI assessments provide clinicians with valuable information to inform care planning and can also be used to estimate the prevalence of these impairments in specific population sub-groups.