bluuebunny/crossref_metadata_2025_split huggingface dataset:
GlycoMaple: recent updates and applications in visualization and analysis of glycosylation pathways
Authors: Kong Wei-Ze , Fujita Morihisa 
Published: October 2024

Abstract
Post-translational modifications including glycosylation, phosphorylation, and lipidation expand the functionality and diversity of proteins. Protein glycosylation is one of the most abundant post-translational modifications in mammalian cells. The glycosylation process is regulated at multiple steps, including transcription, translation, protein folding, intracellular transport, and localization, and activity of glycosyltransferases and glycoside hydrolases. The glycosylation process is also affected by the concentration of sugar nucleotides in the lumen of the Golgi apparatus. Unlike the synthesis of other biological macromolecules, such as nucleic acids and proteins, glycan biosynthesis is not a template-driven process. In addition, the chemical complexity of glycan structures makes the glycosylation network extraordinarily intricate. We previously developed a web-based tool specially focused on glycan metabolic pathways known as GlycoMaple, which is able to easily visualize and estimate glycosylation pathways based on gene expression data. We recently updated GlycoMaple to incorporate the new genes and glycosylation pathways. Here, we introduce and discuss the uses and upgrades of GlycoMaple.
Quantification of the prevalence of harms in healthcare related to drug treatment: reflections regarding the use of definitions developed for other settings to estimate the magnitude of the problem
Authors: Wallerstedt Susanna M. , Hoffmann Mikael 
Published: October 2024

AbstractThe prevalence of harms in healthcare related to drug treatment is often quantified using terms developed for pharmacovigilance and pharmaceutical care. In this overview, we guide through the definitions and the settings for which they were developed, with the underlying intention to facilitate the interpretation of hitherto available research intended to contribute information regarding the magnitude of the problem in healthcare and to provide guidance for future research. To start, the regulatory/academic definitions of an adverse drug reaction (ADR) and a drug-related problem (DRP) are considerably broader than a literal interpretation would suggest. ADRs are defined for the pharmacovigilance setting, and for drug safety reasons the opposite of the benefit of the doubt rules; if it cannot be excluded that the medication has caused or contributed to an event, it will be a suspected ADR. DRPs represent the pharmaceutical care setting where every aspect is included that could potentially be problematic; a manifested problem is not required. When quantifying the prevalence of harms related to drug treatment in the healthcare setting, however, it may not be considered reasonable to count every circumstance that could possibly be an ADR or everything that could potentially be problematic. Therefore, definitions developed for the pharmacovigilance and the pharmaceutical care settings are not fully applicable to estimate the magnitude of drug treatment problems in healthcare. Proposed guidance for the future includes cautious interpretation of research results, as well as a conscious choice of definitions according to purpose and tempered reporting in research.
Confidence intervals estimator of the kinetic parameters: do its reliability depend on the assembling method of the oxygen uptakes?
Authors: Francescato Maria Pia , Cettolo Valentina 
Published: October 2024

AbstractGas exchange data acquired repeatedly under the same exercise conditions are assembled together to improve the kinetic parameters of breath-by-breath oxygen uptake. The latter are provided by the non-linear regression procedure, together with the corresponding estimators of the width of the Confidence Intervals (i.e., the Asymptotic Standard Errors; ASEs). We tested, for two different assembling procedures, whether the range of values identified by the ASE actually correspond to the 95% Confidence Interval. Ten O2 uptake responses were acquired on 10 healthy volunteers performing a square-wave moderate-intensity exercise. Kinetic parameters were estimated running the non-linear regression with a mono-exponential model on an increasingly greater number of responses (Nr, from 1 to 10), assembled together using the “stacking” and the “1-s-bins” procedures. Kinetic values obtained assembling together the 10 repetitions were assumed as “true” values. The time constant was not affected by Nr or by the assembling procedure (ANOVA; p>0.54 and p>0.16, respectively). The corresponding ASE decreased according to Nr (ANOVA; p=0.000), being significantly smaller for the “1-s-bins” procedure compared to the “stacking” one (ANOVA; p<0.001). Excluding 20s at the start of the fitting window, the range of values identified with the ASE provided by the “1-s-bins” and the “stacking” procedures included the “true” value in 85% and in 95% of cases, respectively. The “stacking” procedure should be preferred since it yielded ASEs for the time constant that provided a range of values satisfying the statistical meaning of the width of the Confidence Intervals, at the given degree of probability.
Online Paging with Heterogeneous Cache Slots
Authors: Chrobak Marek , Haney Samuel , Liaee Mehraneh , Panigrahi Debmalya , Rajaraman Rajmohan , Sundaram Ravi , Young Neal E. 
Published: October 2024

Abstract
It is natural to generalize the online

$$k$$

k

-Server problem by allowing each request to specify not only a point p, but also a subset S of servers that may serve it. To date, only a few special cases of this problem have been studied. The objective of the work presented in this paper has been to more systematically explore this generalization in the case of uniform and star metrics. For uniform metrics, the problem is equivalent to a generalization of Paging in which each request specifies not only a page p, but also a subset S of cache slots, and is satisfied by having a copy of p in some slot in S. We call this problem Slot-Heterogenous Paging. In realistic settings only certain subsets of cache slots or servers would appear in requests. Therefore we parameterize the problem by specifying a family

$${\mathcal {S}}\subseteq 2^{[k]}$$

S
⊆

2

[
k
]

of requestable slot sets, and we establish bounds on the competitive ratio as a function of the cache size k and family

$${\mathcal {S}}$$

S

:

If all request sets are allowed (

$${\mathcal {S}}=2^{[k]}\setminus \{\emptyset \}$$

S
=

2

[
k
]

\

{
∅
}

), the optimal deterministic and randomized competitive ratios are exponentially worse than for standard Paging (

$${\mathcal {S}}=\{[k]\}$$

S
=
{
[
k
]
}

).

As a function of

$$|{\mathcal {S}}|$$

|
S
|

and k, the optimal deterministic ratio is polynomial: at most

$$O(k^2|{\mathcal {S}}|)$$

O
(

k
2

|
S
|
)

and at least

$$\Omega (\sqrt{|{\mathcal {S}}|})$$

Ω
(

|
S
|

)

.

For any laminar family

$${\mathcal {S}}$$

S

of height h, the optimal ratios are O(hk) (deterministic) and

$$O(h^2\log k)$$

O
(

h
2

log
k
)

(randomized).

The special case of laminar

$${\mathcal {S}}$$

S

that we call All-or-One Paging extends standard Paging by allowing each request to specify a specific slot to put the requested page in. The optimal deterministic ratio for weighted All-or-One Paging is

$$\Theta (k)$$

Θ
(
k
)

. Offline All-or-One Paging is

$$\mathbb{N}\mathbb{P}$$

N
P

-hard.

Some results for the laminar case are shown via a reduction to the generalization of Paging in which each request specifies a set

$$P$$

P

of pages, and is satisfied by fetching any page from

$$P$$

P

into the cache. The optimal ratios for the latter problem (with laminar family of height h) are at most hk (deterministic) and

$$hH_k$$

h

H
k

(randomized).
Is body composition important in the context of renal function in pediatric neurogenic bladder?
Authors: Bagińska-Chyży Joanna , Błahuszewska Adrianna , Korzeniecka-Kozerska Agata 
Published: October 2024

Abstract
Background
Neurogenic bladder due to myelomeningocele (MMC) is a significant risk factor for chronic kidney disease in children. Cystatin C (CysC) is a more accurate GFR marker than creatinine as it is unaffected by muscle mass but may be influenced by fat mass and BMI. This study evaluates: (1) GFR measurement accuracy using CysC and creatinine in MMC-related neurogenic bladder, (2) the relationship between body composition via bioelectrical impedance analysis (BIA) and renal parameters, and (3) the use of BIA for non-invasive GFR and body composition assessment.

Methods
Forty children (median age 9.96 years) underwent serum creatinine, CysC testing, and BIA measurements. We assessed age, sex, spinal lesion level, anthropometric measurements, BMI, and activity using Hoffer’s scale. GFR was calculated using five creatinine-based formulas, three CysC-based, and three combining CysC and creatinine, including BIA GFR as an alternative approach.

Results
Creatinine-based GFR estimates were significantly higher than CysC-based GFR. Although only 30% of MMC patients met the traditional BMI criteria for overweight/obesity, 62.5% were obese based on BIA-measured body fat percentage. Significant differences were found in CysC and CysC-based GFR equations within BMI and fat mass groups. Positive correlations were observed between CysC and body weight, BMI percentiles, body fat mass and fat-to-muscle ratio. Muscle mass positively correlated with creatinine.

Conclusions
BIA-determined fat mass percentage is a more sensitive obesity indicator than BMI in MMC patients. CysC levels and CysC-based GFR equations are influenced by body fat mass, requiring consideration of adiposity to avoid misestimating renal impairment.

Graphical abstract
Effects of APOE isoforms in diabetic nephropathy patients of South India
Authors: Basavaraju Preethi , Moorthi Puthamohan Vinayaga , Meyyazhagan Arun , Devaraj Ilakkiyapavai , Babu Kavipriya , Panza Emanuele , Orlacchio Antonio 
Published: October 2024

Abstract
Background
Diabetic nephropathy (DN) is a grave complication and the most common renal dysfunction of diabetes mellitus. Genetic factors, including Apolipoprotein E (APOE) isoforms, have been implicated in the pathogenesis of DN.

Methods
A total of 577 type 2 Diabetes mellitus subjects were categorized into diabetes non-nephropathic (Controls: n = 321), diabetes nephropathic (DN: n = 256) groups. Demographic, clinical, and biochemical parameters including age, BMI, lipid profiles (TC, LDL-C, HDL-C, TG), glucose metabolism (plasma glucose, HbA1c, serum insulin), renal function (UACR, PCR), and blood pressure (SBP, DBP) were assessed. APOE variant frequencies were determined using restriction fragment length polymorphism (RFLP) analysis, validated against Hardy-Weinberg equilibrium (HWE), and statistically correlated with each clinical and biochemical parameter.

Results
The DN group had an increased prevalence of hypertension, fatty liver, and dyslipidemia compared to the Control group. Biochemical analyses revealed elevated levels of TC (213.41 mg/dL vs. 189.32 mg/dL), LDL-C (134.46 mg/dL vs. 107.56 mg/dL), and reduced HDL-C (58.13 mg/dL vs. 65.32 mg/dL) in DN cases compared to Controls (all p < 0.0001). The APOE variants distribution showed a significant increase in E2 allele frequency (69.1% vs. 15.3%) and corresponding homozygous genotype (E2/2: 42.2% vs. 5.6%) in DN cohorts.

Conclusion
The study found a higher frequency of E2 allele in the DN group compared to Controls, though no statistically significant risk of DN was linked to this allele. The results suggest a potential association for APOE polymorphisms, requiring broader studies to clarify the role of APOE polymorphisms in DN susceptibility.
Breaking barriers in Parkinson’s care: the multidisciplinary team approach
Authors: Pirtošek Zvezdan 
Published: October 2024

AbstractParkinson’s disease is a complex neurodegenerative disorder presenting a range of motor and non-motor symptoms that greatly impact both patients and caregivers. The diverse needs arising from these symptoms make a multidisciplinary team (MDT) approach crucial for effective management. This article explores the role and benefits of MDTs in Parkinson’s care, highlighting how collaborative models improve clinical outcomes and quality of life. MDTs integrate neurologists, nurse specialists, therapists, and other professionals to deliver comprehensive, patient-centered care. The inclusion of patients and caregivers fosters shared decision-making, enhancing health outcomes. However, challenges like limited controlled trials, lack of comprehensive guidelines, and under-referral remain. Innovative models, such as telehealth and community-based care, offer promising solutions, especially in underserved regions. The article advocates for further research and standardized guidelines to optimize the MDT approach for Parkinson’s disease.
Comparing the measurement properties of the EQ-5D-5 L, SF-6Dv2, QLU-C10D and FACT-8D among survivors of classical Hodgkin’s lymphoma
Authors: Xu Richard Huan , Zhao Zuyi , Pan Tianxin , Monteiro Andrea , Gu Hongfei , Dong Dong 
Published: October 2024

Abstract
Objective
This study aimed to evaluate the measurement properties of EQ-5D-5 L, SF-6Dv2, QLU-C10D, and FACT-8D in survivors of Classical Hodgkin’s Lymphoma (CHL).

Methods
A cross-sectional, web-based survey was conducted from May to August 2022 to collect data. Chinese value sets were used to estimate the utility scores for EQ-5D-5 L, SF-6Dv2, and QLU-C10D, while the Australian value set was used for FACT-8D. The measurement properties assessed included ceiling and floor effects, convergent validity (assessing associations between similar dimensions/utility scores using Spearman’s rank correlation and intraclass correlation coefficient), and known-group validity (measures could differentiate health-related quality of life (HRQoL) between risk groups).

Results
A total of 534 CHL survivors participated in the survey and completed the questionnaire. All dimensions of EQ-5D-5 L, SF-6D (except for vitality), QLU-C10D, and FACT-8D showed ceiling effects, ranging from 18 to 91.6%. The EQ-5D-5 L demonstrated the higher ceiling effects compared to other measures, with 33% of patients reporting full health on this scale. All 30 pairs of associations between similar dimensions from the four measures were statistically significant, with correlation coefficients ranging from 0.29 to 0.77. Regarding utility scores, the EQ-5D-5 L utility score showed a stronger correlation with SF-6Dv2 than with the other two measures. Statistically significant correlations of utility scores between the four measures were observed. EQ-5D-5 L can significantly differentiate HRQoL among all known-groups, while SF-6Dv2, QLU-C10D, and FACT-8D showed a less strong discriminant ability.

Conclusions
EQ-5D-5 L outperformed SF-6Dv2 in terms of agreement with cancer-specific PRMs and discriminant ability. However, SF-6Dv2 showed stronger associations with similar dimensions of QLU-C10D and FACT-8D, indicating high convergent validity. The generic PBMs are sensitive enough to measure HRQoL in survivors of CHL.
Multiscale homogenized constrained mixture model of the bio-chemo-mechanics of soft tissue growth and remodeling
Authors: Paukner Daniel , Humphrey Jay D. , Cyron Christian J. 
Published: October 2024

AbstractConstrained mixture models have successfully simulated many cases of growth and remodeling in soft biological tissues. So far, extensions of these models have been proposed to include either intracellular signaling or chemo-mechanical coupling on the organ-scale. However, no version of constrained mixture models currently exists that includes both aspects. Here, we propose such a version that resolves cellular signal processing by a set of logic-gated ordinary differential equations and captures chemo-mechanical interactions between cells by coupling a reaction-diffusion equation with the equations of nonlinear continuum mechanics. To demonstrate the potential of the model, we present 2 case studies within vascular solid mechanics: (i) the influence of angiotensin II on aortic growth and remodeling and (ii) the effect of communication between endothelial and intramural arterial cells via nitric oxide and endothelin-1.
A concurrent learning approach to monocular vision range regulation of leader/follower systems
Authors: Fairfax Luisa , Vela Patricio 
Published: October 2024

AbstractThis paper explores range and bearing angle regulation of a leader–follower using monocular vision. The main challenge is that monocular vision does not directly provide a range measurement. The contribution is a novel concurrent learning (CL) approach, called CL Subtended Angle and Bearing Estimator for Relative pose (CL-SABER), which achieves range regulation without communication, persistency of excitation or known geometry and is demonstrated on a physical, robot platform. A history stack estimates target size which augments the Kalman filter (KF) with a range pseudomeasurement. The target is followed to scale without drift, persistency of excitation requirements, prior knowledge, or additional measurements. Finite excitation is required to achieve parameter convergence and perform steady-state regulation using CL-SABER. Evaluation using simulation and mobile robot experiments in special Euclidean planar space (SE(2)) show that the new method provides stable and consistent range regulation, as demonstrated by the inter-rater reliability, including in noisy and high leader acceleration environments.
Limiting the memory consumption of caching for detecting subproblem dominance in constraint problems
Authors: Medema Michel , Breeman Luc , Lazovik Alexander 
Published: October 2024

AbstractSolving constraint satisfaction problems often involves a large amount of redundant exploration stemming from the existence of subproblems whose information can be reused for other subproblems. Subproblem dominance is a general notion of reusability that arises when one subproblem imposes more constraints on the remaining part of the search than another subproblem and allows the search to reuse the solutions of the dominating subproblem for the dominated subproblem. The search can exploit subproblem dominance by storing the subproblems that have been explored in a cache and abandoning the current subproblem whenever the cache contains a subproblem that dominates it. While using caching makes it possible to solve problems where subproblem dominance arises orders of magnitude faster, storing all of these subproblems can require a substantial amount of memory, making it impractical in many cases. This paper analyses the dominance between different subproblems for various constraint problems, revealing that only a relatively small number of subproblems dominate other subproblems. Based on these findings, two types of strategies are proposed for reducing the number of subproblems stored in the cache: limiting the number of subproblems that can be stored in the cache and periodically cleaning up the cache. An experimental evaluation demonstrates that these strategies provide an effective instrument for reducing the memory consumption of caching, allowing it to be used on a larger scale. However, there is a trade-off between saving memory and reducing redundant exploration, as removing subproblems from the cache may prevent dominance from being detected for certain subproblems.
An affordable operational oil spill monitoring system in action: A diachronic multiplatform analysis of recent incidents in the southern Gulf of Mexico
Authors: Uribe-Martínez Abigail , Espinoza-Tenorio Alejandro , Cruz-Pech Johnny Bryan , Cupido-Santamaría Deysi Guadalupe , Trujillo-Córdova Jorge Alfredo , García-Nava Héctor , Flores-Vidal Xavier , Gudiño-Elizondo Napoleón , Herguera Juan Carlos , Appendini Christian Mario , Cuevas Eduardo 
Published: October 2024

AbstractThe coexistence of marine sensitive areas with the oil industry requires robust preparedness and rapid response capabilities for monitoring and mitigating oil spill events. Scientifically proven satellite-based methods for the visual detection of oil spills are widely recognized as effective, low-cost, transferable, scalable, and operational solutions, particularly in developing economies. Following meticulous design and implementation, we adopted and executed a relatively low-cost operational monitoring and alert system for oil spill detection over the ocean surface and alert issuance. We analyzed over 1500 satellite images, issuing over 70 warning reports on oil slicks and spills in the southern Gulf of Mexico. To assess the system’s efficiency and performance, we leveraged data from three major oil spill incidents in the study region during June and July of 2023 in the study region, covering a maximum area of 669 km2 and tracked for 12 to 24 days. We documented the evolution of these oil spills by integrating satellite sensing data with on-site Lagrangian drifting buoys, a network of high-frequency radars, and citizen reports to validate the outcomes of this system. We generated timely technical information on the spill’s evolution, informing decision-makers and local community leaders to strengthen their mitigation response capabilities. Additionally, we developed a robust database with spectral and spatiotemporal features of satellite-detected oil, thereby contributing to advancing the scientific understanding of sea surface dynamics related to natural and anthropogenic oil sources. This study also highlights immediate-, medium-, and long-term research agendas and establishes a reference for a sustained, transferable, and operational oil spill monitoring system.
The upper bound of information diffusion in code review
Authors: Dorner Michael , Mendez Daniel , Wnuk Krzysztof , Zabardast Ehsan , Czerwonka Jacek 
Published: October 2024

Abstract

Background
Code review, the discussion around a code change among humans, forms a communication network that enables its participants to exchange and spread information. Although reported by qualitative studies, our understanding of the capability of code review as a communication network is still limited.

Objective
In this article, we report on a first step towards understanding and evaluating the capability of code review as a communication network by quantifying how fast and how far information can spread through code review: the upper bound of information diffusion in code review.

Method
In an in-silico experiment, we simulate an artificial information diffusion within large (Microsoft), mid-sized (Spotify), and small code review systems (Trivago) modelled as communication networks. We then measure the minimal topological and temporal distances between the participants to quantify how far and how fast information can spread in code review.

Results
An average code review participants in the small and mid-sized code review systems can spread information to between 72 % and 85 % of all code review participants within four weeks independently of network size and tooling; for the large code review systems, we found an absolute boundary of about 11 000 reachable participants. On average (median), information can spread between two participants in code review in less than five hops and less than five days.

Conclusion
We found evidence that the communication network emerging from code review scales well and spreads information fast and broadly, corroborating the findings of prior qualitative work. The study lays the foundation for understanding and improving code review as a communication network.