bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thrombin receptor PAR4 cross-activates the tyrosine kinase c-met in atrial cardiomyocytes
Authors: Mittendorff Claudia , Abu-Taha Issam , Kassler Lena , Hustedt Tobias , Wolf Stephanie , Bode Johannes G. , Kamler Markus , Dobrev Dobromir , Fender Anke C. 
Published: September 2024

AbstractThrombin supports coagulation-independent inflammation via protease-activated receptors (PAR). PAR4 is specifically increased in obese human atria, correlating with NLRP3 inflammasome activation. PAR4-mediated NLRP3 inflammasome activation in atrial cardiomyocytes is not known, nor have signaling partners been identified. Thrombin transactivates the hepatocyte growth factor receptor in some cancer cells, so we examined PAR4/c-met cross-talk in atrial cardiomyocytes and its possible significance in obesity. Cardiomyocytes from right atrial appendages (RAA) of obese patients expressed more PAR1 and PAR4 compared to non-obese. In HL-1 atrial cardiomyocytes, thrombin induced caspase-1 auto-activation and IL-1β maturation; IL-1β secretion was evoked by PAR4-activating peptide (AP), but not PAR1-AP. PAR4-AP additionally increased phosphorylated CaMKII-Thr287, mTOR-Ser2481, and Akt-Ser473 while suppressing AMPK-Thr172 phosphorylation. Total kinase levels were largely unaltered. PAR4AP rapidly increased phosphorylated c-met in HL-1 cells and over time also transcriptionally upregulated c-met. The c-met inhibitor SGX-523 abrogated the effects of PAR4-AP on CaMKII/AKT/mTOR phosphorylation but did not affect PAR4-stimulated IL-1β production. Obese human RAA contained more IL-1β, phospho-c-met, and phospho-mTOR than non-obese RAA; CamKII phosphorylation was not modified. Atria from high-fat diet (HFD) versus chow-fed mice also contained more IL-1β, together with higher myeloperoxidase activity, Acta2 mRNA total and phosphorylated c-met; these increases were blunted in PAR4-/- HFD-fed mice. Thrombin cross-activates c-met via PAR4 in atrial cardiomyocytes. Transactivated c-met contributes partially to PAR4-mediated signaling, but NLRP3 inflammasome activation appears to be largely independent of c-met. Abundance of PAR4 and activated c-met increases with obesity, providing therapeutic targets for management of adiposity-driven AF.
Tropical Refined Curve Counting with Descendants
Authors: Kennedy-Hunt Patrick , Shafi Qaasim , Urundolil Kumaran Ajith 
Published: September 2024

AbstractWe prove a q-refined tropical correspondence theorem for higher genus descendant logarithmic Gromov–Witten invariants with a $$\lambda _g$$

λ
g

class in toric surfaces. Specifically, a generating series of such logarithmic Gromov–Witten invariants agrees with a q-refined count of rational tropical curves satisfying higher valency conditions. As a corollary, we obtain a geometric proof of the deformation invariance of this tropical count. In particular, our results give an algebro-geometric meaning to the tropical count defined by Blechman and Shustin. Our strategy is to use the logarithmic degeneration formula, and the key new technique is to reduce to computing integrals against double ramification cycles and connect these integrals to the non-commutative KdV hierarchy.
Elastic-Degenerate String Matching with 1 Error or Mismatch
Authors: Bernardini Giulia , Gabory Esteban , Pissis Solon P. , Stougie Leen , Sweering Michelle , Zuba Wiktor 
Published: September 2024

AbstractAn elastic-degenerate (ED) string is a sequence of n finite sets of strings of total length N, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all occurrences of a pattern of length m in an ED text. The EDSM problem has recently received some attention by the combinatorial pattern matching community, culminating in an $$\mathcal {\tilde{O}}(nm^{\omega -1})+\mathcal {O}(N)$$

O
~

(
n

m

ω
-
1

)

+
O

(
N
)

-time algorithm [Bernardini et al., SIAM J. Comput. 2022], where $$\omega $$
ω
denotes the matrix multiplication exponent and the $$\mathcal {\tilde{O}}(\cdot )$$

O
~

(
·
)

notation suppresses polylog factors. In the k-EDSM problem, the approximate version of EDSM, we are asked to report all pattern occurrences with at most k errors. k-EDSM can be solved in $$\mathcal {O}(k^2mG+kN)$$

O
(

k
2

m
G
+
k
N
)

time, under edit distance, or $$\mathcal {O}(kmG+kN)$$

O
(
k
m
G
+
k
N
)

time, under Hamming distance, where G denotes the total number of strings in the ED text [Bernardini et al., Theor. Comput. Sci. 2020]. Unfortunately, G is only bounded by N, and so even for $$k=1$$

k
=
1

, the existing algorithms run in $$\varOmega (mN)$$

Ω
(
m
N
)

time in the worst case. In this paper we make progress in this direction. We show that 1-EDSM can be solved in $$\mathcal {O}((nm^2 + N)\log m)$$

O
(

(
n

m
2

+
N
)

log
m
)

or $$\mathcal {O}(nm^3 + N)$$

O
(
n

m
3

+
N
)

time under edit distance. For the decision version of the problem, we present a faster $$\mathcal {O}(nm^2\sqrt{\log m} + N\log \log m)$$

O
(
n

m
2

log
m

+
N
log
log
m
)

-time algorithm. We also show that 1-EDSM can be solved in $$\mathcal {O}(nm^2 + N\log m)$$

O
(
n

m
2

+
N
log
m
)

time under Hamming distance. Our algorithms for edit distance rely on non-trivial reductions from 1-EDSM to special instances of classic computational geometry problems (2d rectangle stabbing or 2d range emptiness), which we show how to solve efficiently. In order to obtain an even faster algorithm for Hamming distance, we rely on employing and adapting the k-errata trees for indexing with errors [Cole et al., STOC 2004]. This is an extended version of a paper presented at LATIN 2022.
Single and basal crop coefficients for temperate climate fruit trees, vines and shrubs with consideration of fraction of ground cover, height, and training system
Authors: López-Urrea Ramón , Oliveira Cristina M. , Montoya Francisco , Paredes Paula , Pereira Luis S. 
Published: September 2024

AbstractThe objective of the present review article was to update the standard single (Kc) and basal (Kcb) crop coefficients published in the FAO Irrigation and Drainage Paper No. 56 (FAO56), focusing on temperate climate fruit trees (pome, stone and nut fruit trees), vines and shrubs (kiwi, hop and blue- and blackberries). Standard conditions refer to crops grown in medium to large fields, having enough fetch for non-impeding accurate use of flux measuring equipment to represent non-limiting conditions of crop evapotranspiration, ETc. Moreover, the crop needs to be managed without soil water deficit, free of pests and diseases, and must be able to reach full production under the given environmental conditions. For this purpose, more than 150 articles published over the last 25 years were reviewed. Of these, we selected 76 that refer to case studies that reporting on appropriate yield conditions, describe adequate ETc measurement and adopt the FAO reference evapotranspiration or another method closely related to it. The selection of papers to be analysed followed the same methods as the companion papers on Mediterranean woody fruit crops (Pereira et al. 2023), and on tropical and subtropical ones (Paredes et al. 2024). The literature review focused on articles that are in line with the FAO56 methodology; that is, where the grass reference evapotranspiration (ETo) was computed with the FAO Penman–Monteith ETo, the ASCE Penman–Monteith ETo equations, or other equations whose results relate well to the former. In addition, where the crop evapotranspiration (ETc) and/or crop transpiration (Tc) were determined with sufficient accuracy from field observations in crops grown under standard, well-watered conditions, i.e., under pristine (i.e., non-stress cropping conditions) or eustress (i.e., “good stress”) conditions. Information collected from the selected studies included cultivar and rootstock, plant density and spacing, training system, fraction of ground cover or intercepted PAR radiation, crop height and age. Additional data were gathered on irrigation system and strategy for full or deficit irrigation. The Kc and Kcb values reported were recomputed and grouped according to the degree of ground cover, training system and plant density. Thus, the proposed tabulated standard Kc and Kcb values for initial, mid- and end-season are based on the values obtained from field observations reported in the selected papers, and on the ranges of Kc/Kcb values previously tabulated, mainly in FAO56. The currently tabulated values are updated, with the aim being their use in orchard management. They should consist of the upper limit of Kc/Kcb application, and take into account the general awareness of water scarcity and water conservation, thus helping improve the accuracy in estimating crop water requirements and optimizing irrigation scheduling.
Connecting high-resolution 3D chromatin maps with cell division and cell differentiation at the root apical meristem
Authors: Caballero Lara , Pasternak Taras , Riyazuddin Riyazuddin , Pérez-Pérez José Manuel 
Published: September 2024

Abstract
Key message
We used marker-free technologies to study chromatin at cellular resolution. Our results show asymmetric chromatin distribution, explore chromatin dynamics during mitosis, and reveal structural differences between trichoblast and atrichoblast cell.

Abstract
The shapes, sizes, and structural organizations of plant nuclei vary considerably among cell types, tissues, and species. This diversity is dependent on various factors, including cellular function, developmental stage, and environmental or physiological conditions. The differences in nuclear structure reflect the state of chromatin, which, in turn, controls gene expression and regulates cell fate. To examine the interrelationship between nuclear structure, cell morphology, and tissue-specific cell proliferation and differentiation processes, we conducted multiple visualizations of H3K4me1, H3K9me2, 4′,6-diamidino-2-phenylindole, 5-ethynyl 2′-deoxyuridine, and SCRI Renaissance 2200, followed by subsequent quantitative analysis of individual cells and nuclei. By assigning cylindrical coordinates to the nuclei in the iRoCS toolbox, we were able to construct in situ digital three-dimensional chromatin maps for all the tissue layers of individual roots. A detailed analysis of the nuclei features of H3K4me1 and H3K9me2 in the mitotic and the elongation zones in trichoblast and atrichoblast cells at the root apical meristem revealed cell type-specific chromatin dynamics with asymmetric distribution of euchromatin and heterochromatin marks that may be associated with cell cycle and cell differentiation characteristics of specific cells. Furthermore, the spatial distribution of nuclei stained with 5-ethynyl 2′-deoxyuridine in the epidermis and cortex tissues suggests short-range coordination of cell division and nuclear migration in a linear sequence through an unknown regulatory mechanism.
Improvement and Analysis of Peak Shift Demand Response Scenarios of Industrial Consumers Using an Electricity Market Model
Authors: Cheng Long , Izumi Kiyoshi , Hirano Masanori 
Published: September 2024

AbstractElectricity procurement of industrial consumers is becoming more and more complicated, involving a combination of various procurement methods due to electricity liberalization and decarbonization trends. This study analyzed and improved power procurement strategies for a factory to achieve carbon neutralization through a multi-agent model simulating the electricity market and introduced a factory agent using various procurement methods including PV, FC, storage batteries (SB), and DR. Firstly, we created a new procurement strategy utilizing all methods. Then, by using the simulation model, we assessed the effectiveness of the existing peak shift DR scenarios in terms of cost reduction efficiency. Results revealed that the introduction of PV has led to a counterproductive outcome for DR. Based on the results, we proposed two methods to improve the effectiveness of DR, namely considering the operation of PV in the DR scenario and expanding the range of optional time periods for DR activation. Finally, we made three new DR scenarios based on our proposal. Through experiment, the new scenarios were confirmed to be effective in cost-effectiveness for decarbonization.
Detailed analysis of learning phases and outcomes in robotic and endoscopic thyroidectomy
Authors: Yu Jia-Fan , Huang Wen-Yu , Wang Jun , Ao Wei , Wang Si-Si , Cai Shao-Jun , Lin Si-Ying , Zhou Chi-Peng , Li Meng-Yao , Cao Xiao-Shan , Cao Xiang-Mao , Tang Zi-Han , Wang Zhi-hong , Hua Surong , Zhao Wen-Xin , Wang Bo 
Published: September 2024

Abstract
Background
Thyroid surgery has undergone significant transformation with the introduction of minimally invasive techniques, particularly robotic and endoscopic thyroidectomy. These advancements offer improved precision and faster recovery but also present unique challenges. This study aims to compare the learning curves, operational efficiencies, and patient outcomes of robotic versus endoscopic thyroidectomy.

Methods
A retrospective cohort study was conducted, analyzing 258 robotic (da Vinci) and 214 endoscopic thyroidectomy cases. Key metrics such as operation duration, drainage volume, lymph node dissection outcomes, and hypoparathyroidism incidence were assessed to understand surgical learning curves and efficiency.

Results
Robotic thyroidectomy showed a longer learning curve with initially longer operation times and higher drainage volumes but superior lymph node dissection outcomes. Both techniques were safe, with no permanent hypoparathyroidism or recurrent laryngeal nerve damage reported. The study delineated four distinct stages in the robotic and endoscopic surgery learning curve, each marked by specific improvements in proficiency. Endoscopic thyroidectomy displayed a shorter learning curve, leading to quicker operational efficiency gains.

Conclusion
Robotic and endoscopic thyroidectomies are viable minimally invasive approaches, each with its learning curves and efficiency metrics. Despite initial challenges and a longer learning period for robotic surgery, its benefits in complex dissections may justify specialized training. Structured training programs tailored to each technique are crucial for improving outcomes and efficiency. Future research should focus on optimizing training protocols and increasing accessibility to these technologies, enhancing patient care in thyroid surgery.
Association of pancreatic atrophy patterns with intraductal extension of early pancreatic ductal adenocarcinoma: a multicenter retrospective study
Authors: Miki Mika , Masuda Atsuhiro , Takenaka Mamoru , Shiomi Hideyuki , Iemoto Takao , Tsumura Hidetaka , Tsujimae Masahiro , Toyama Hirochika , Sofue Keitaro , Ueshima Eisuke , Omoto Shunsuke , Yoshida Akihiro , Fukunaga Tomohiro , Tanaka Hidekazu , Nakano Ryota , Ota Shogo , Kobayashi Takashi , Sakai Arata , Kanzawa Maki , Itoh Tomoo , Kodama Yuzo ,   SMT Study Group in Japan
Published: September 2024

Abstract
Background
Focal pancreatic parenchymal atrophy (FPPA) and upstream pancreatic atrophy (UPA) may indicate the presence of early pancreatic cancer. In early pancreatic cancer, the tumor occasionally spreads laterally along the main pancreatic duct, presenting challenges in determining the extent of surgical resection. This study aimed to investigate the association of pancreatic atrophy pattern and intraductal cancer extension.

Methods
Thirty-two patients with early-stage pancreatic cancer who underwent surgery at five participating centers were enrolled. Pancreatic atrophy was defined as the narrowing of parenchyma compared to the surrounding parenchyma and was classified as either FPPA (partial atrophy surrounding the pancreatic duct stenosis) or UPA (global atrophy caudal to the site of duct stenosis). Intraductal cancer extension was defined as an extension exceeding 10 mm.

Results
Preoperative computed tomography revealed FPPA, UPA, and no parenchymal atrophy in 13, 13, and 6 patients. Cases with FPPA or UPA showed significantly longer cancer extensions than those without atrophy (P = 0.005 and P = 0.03, respectively). Intraductal cancer extension was present in all but one case of FPPA. 69% (9/13) of the cases with UPA showed intraductal cancer extension, whereas cases without atrophy showed no intraductal cancer extension. Importantly, two patients with FPPA or UPA showed positive resection margins during surgery and three patients with FPPA or UPA showed recurrence in the remnant pancreas.

Conclusions
The presence of FPPA and UPA indicates lateral cancer extension in early-stage pancreatic cancer. Preoperative assessment of the pancreatic parenchyma may provide valuable insights for determining the extent of surgical resection.
Mandibular overdentures retained by 1 or 2 implants: a 5-year randomized clinical trial on implant stability and peri-implant outcomes
Authors: Leles Cláudio Rodrigues , de Resende Gabriela Pereira , de Oliveira Martins Nilva , Nascimento Lays Noleto , Costa Nadia Lago , Srinivasan Murali , Schimmel Martin 
Published: September 2024

Abstract
Aim
This is a report of the 5-year results of a two-group parallel randomized clinical trial comparing longitudinal implant stability, and clinical and radiographic peri-implant outcomes of mandibular overdentures retained by one (1-IOD group) or two (2-IOD group) implants.

Methods
All participants received 4.1 mm diameter tissue-level implants (Straumann® Standard Plus – SLActive®, Institut Straumann AG), installed in the mandible midline (1-IOD; n = 23) or the lateral incisor-canine area bilaterally (2-IOD; n = 24), and loaded after 3 weeks. Implant Stability Quotient (ISQ) was measured using a resonance frequency device (Osstell® Mentor, Integration Diagnostics) at implant placement, after three weeks (loading), and at the 6-month, 1-, 3-, and 5-year follow-ups. Marginal bone loss and clinical implant outcomes (plaque, calculus, suppuration and bleeding) were assessed periodically up to 5 years after loading.

Results
Only minor changes in marginal bone level were observed after 5 years (mean = 0.37; SD = 0.44 mm), and satisfactory and stable peri-implant parameters were observed throughout the 5-year follow-up. No significant differences between groups were found. Overall, the mean primary implant stability was considered high (> 70) for the two groups (1-IOD = 78.1 ± 4.5; 2-IOD = 78.0 ± 5.8). No noticeable changes were observed between implant insertion and loading. A marked increase was observed from insertion to the 6-month follow-up – the mean difference for the 1-IOD group was + 5.5 ± 5.5 (Effect size = 1.00), while for the 2-IOD group, the mean difference was + 6.0 ± 5.6 (Effect size = 1.08). No relevant changes were observed throughout the follow-up periods up to 5 years. Linear mixed-effect model regression showed no influence of the bone-related variables (p > 0.05) and the number of implants (p = 0.087), and a significant effect of the time variable (p < 0.001).

Conclusion
Satisfactory peri-implant outcomes and stable secondary stability suggest good clinical performance and successful long-term osseointegration of the implants for single and two-implant mandibular overdentures. Using a single implant to retain a mandibular overdenture does not seem to result in detrimental implant loading over the five years of overdenture use.

Clinical relevance
This study corroborates the use of a single implant to retain a mandibular denture.
Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine
Authors: Bellankimath Anurag Basavaraj , Chapagain Crystal , Branders Sverre , Ali Jawad , Wilson Robert C , Johansen Truls E. Bjerklund , Ahmad Rafi 
Published: September 2024

Abstract
Purpose
Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150 million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2–4 days for pathogen identification and susceptibility testing.

Methods
This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 103-105 CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells.

Results
The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 105 CFU/ml, achieved after 10 min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 103 colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes.

Conclusion
This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72 h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.
Risk factors for infection after carbapenem-resistant Acinetobacter baumannii colonization
Authors: Peghin Maddalena , Givone Filippo , de Martino Maria , Ali Raja Waqar , Graziano Elena , Isola Miriam , Grossi Paolo Antonio 
Published: September 2024

Abstract
Purpose
Predicting infection risk in carbapenem-resistant Acinetobacter baumannii (CRAB) colonized patients may help in improving timely appropriate antibiotic therapy. This study aims to explore risk factors for developing infections in hospitalized patients with previous CRAB colonization.

Methods
We performed an observational retrospective cohort study at ASST Sette Laghi-Varese Hospital between January 2020 and December 2022. All consecutive adult (> 18 years old) hospitalized patients with documented colonization by CRAB at any anatomical site or with CRAB infections preceded by CRAB colonization were included. Univariate and multivariate analyses were performed to investigate infection risk factors.

Results
Overall, 144 patients were included in the study: 104 colonized only and 40 infected patients. Colonization and infection rates significantly changed over the years (2020–2022, p < 0.001). The incidence of infections in CRAB carriers was 27.8% (40/144). Median time from colonization to infection was 4 days (IQR 1-8.5). Overall, inhospital mortality was 32.7% and 55.0% in colonized only and infected patients, respectively. At the multivariable logistic regression cardiovascular disease (OR 5.83, 95% CI 1.12–30.43, p = 0.037), COVID-19 (OR 3.72, 95% CI 1.16–11.91, p = 0.027) and intensive care unit (ICU) admission (OR 8.83, 95% CI 2.94–26.51, p < 0.001) were risk factors independently associated with cardiovascular disease CRAB infection after colonization.

Conclusions
We observed an increased infection risk in patients colonized with CRAB with cardiovascular disease, COVID-19 and admitted in ICU setting. Additional evidence is needed to identify predictors of infection in colonized patients.