bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive survey of scoring functions for protein docking models
Authors: Shirali Azam , Stebliankin Vitalii , Karki Ukesh , Shi Jimeng , Chapagain Prem , Narasimhan Giri 
Published: January 2025

Abstract

Background
While protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. Without accurate and efficient scoring functions to differentiate between native and non-native binding complexes, the accuracy of current docking tools cannot be guaranteed. Although many innovative scoring functions have been proposed, a good scoring function for docking remains elusive. Deep learning models offer alternatives to using explicit empirical or mathematical functions for scoring protein-protein complexes.

Results
In this study, we perform a comprehensive survey of the state-of-the-art scoring functions by considering the most popular and highly performant approaches, both classical and deep learning-based, for scoring protein-protein complexes. The methods were also compared based on their runtime as it directly impacts their use in large-scale docking applications.

Conclusions
We evaluate the strengths and weaknesses of classical and deep learning-based approaches across seven public and popular datasets to aid researchers in understanding the progress made in this field.
Joint embedding–classifier learning for interpretable collaborative filtering
Authors: Réda Clémence , Vie Jill-Jênn , Wolkenhauer Olaf 
Published: January 2025

Abstract

Background
Interpretability is a topical question in recommender systems, especially in healthcare applications. An interpretable classifier quantifies the importance of each input feature for the predicted item-user association in a non-ambiguous fashion.

Results
We introduce the novel Joint Embedding Learning-classifier for improved Interpretability (JELI). By combining the training of a structured collaborative-filtering classifier and an embedding learning task, JELI predicts new user-item associations based on jointly learned item and user embeddings while providing feature-wise importance scores. Therefore, JELI flexibly allows the introduction of priors on the connections between users, items, and features. In particular, JELI simultaneously (a) learns feature, item, and user embeddings; (b) predicts new item-user associations; (c) provides importance scores for each feature. Moreover, JELI instantiates a generic approach to training recommender systems by encoding generic graph-regularization constraints.

Conclusions
First, we show that the joint training approach yields a gain in the predictive power of the downstream classifier. Second, JELI can recover feature-association dependencies. Finally, JELI induces a restriction in the number of parameters compared to baselines in synthetic and drug-repurposing data sets.
The endoplasmic reticulum degradation-enhancing α-mannosidase-like protein 3 attenuates the unfolded protein response and has pro-survival and pro-viral roles in hepatoma cells and hepatocellular carcinoma patients
Authors: Ghionescu Alina-Veronica , Uta Mihaela , Sorop Andrei , Lazar Catalin , Flintoaca-Alexandru Petruta R. , Chiritoiu Gabriela , Sima Livia , Petrescu Stefana-Maria , Dima Simona Olimpia , Branza-Nichita Norica 
Published: January 2025

Abstract

Background
Chronic hepatitis B virus (HBV) infection is a major risk for development of hepatocellular carcinoma (HCC), a frequent malignancy with a poor survival rate. HBV infection results in significant endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR) signaling, a contributing factor to carcinogenesis. As part of the UPR, the ER-associated degradation (ERAD) pathway is responsible for removing the burden of misfolded secretory proteins, to re-establish cellular homeostasis. Emerging evidence indicates consistent upregulation of ERAD factors, including members of the ER degradation-enhancing alpha-mannosidase-like protein (EDEM) family in infection and various tumor types. However, the significance of this gene expression pattern in HBV-driven pathology is just beginning to be deciphered.

Methods
In this study we quantified the expression of the ERAD factor EDEM3, in a cohort of HCC patients with and without HBV infection, and validated our results by analysis of publically available transcriptomic and microarray data sets. We performed mechanistic studies in HepaRG cells with modulated EDEM3 expression to address UPR, ERAD, autophagy and apoptosis signaling, and their consequences on HBV infection.

Results
Our work revealed significantly elevated EDEM3 expression in HCC tissues irrespective of HBV infection, while the highest levels were observed in tissues from HBV-infected patients. Investigation of published transcriptomic data sets confirmed EDEM3 upregulation in independent HCC patient cohorts, associated with tumor progression, poor survival prognosis and resistance to therapy. EDEM3-overexpressing hepatic cells exhibited attenuated UPR and activated secretory autophagy, which promoted HBV production. Conversely, cell depletion of EDEM3 resulted in significant ER stress inducing pro-apoptotic mechanisms and cell death.

Conclusions
We provide evidence of major implications of the ERAD pathway in HBV infection and HCC development and progression. Our results suggest that ERAD activation in HBV-infected cells is a protective mechanism against prolonged ER stress, potentially contributing to establishment of chronic HBV infection and promoting tumorigenesis. Developing specific inhibitors for ERAD factors may be an attractive approach to improve efficiency of current antiviral and anticancer therapies.
Looking under the hood of a hybrid two-way texting intervention to improve early retention on antiretroviral therapy in Malawi: an implementation fidelity evaluation
Authors: Klabbers Robin E. , Feldacker Caryl , Huwa Jacqueline , Kiruthu-Kamamia Christine , Thawani Agness , Tweya Hannock 
Published: January 2025

Abstract

Background
While key to interpreting findings and assessing generalizability, implementation fidelity is underreported in mobile health (mHealth) literature. We evaluated implementation fidelity of an opt-in, hybrid, two-way texting (2wT) intervention previously demonstrated to improve 12-month retention on antiretroviral therapy (ART) among people living with HIV (PLHIV) in a quasi-experimental study in Lilongwe, Malawi.

Methods
Short message service (SMS) data and ART refill visit records were used to evaluate adherence to 2wT content, frequency and duration through the lens of the Conceptual Framework for Implementation Fidelity. Message delivery and 2wT participant interactions were considered across four core 2wT components: 1) weekly motivational SMS messages; 2) proactive SMS appointment reminders; 3) SMS reminders after missed appointments; and 4) interactive messaging with 2wT staff about transfers and appointment rescheduling. Using mixed-effects logistic regression models adjusted for participant demographics, we examined the effect of core 2wT component fidelity on a) on-time appointment attendance and b) timely return to care after a missed appointment, presenting adjusted odds ratios (aORs) and 95% confidence intervals (CIs).

Results
The 468 2wT participants had a median of 52 study weeks (interquartile range [IQR] 34 – 52) with 6 ART appointments (IQR 4—7) of which 2 (IQR 1 – 3) were missed. On average, participants received a motivation message for 75% (IQR 56%—83%) of enrolled weeks, a reminder before 83% (IQR 67%—100%) of appointments, and after 67% (IQR 0%—100%) of missed appointments. Participants reported 9 transfers and rescheduled 46 appointments through 2wT prompts; 196 appointments were changed via unprompted interaction. Participants with 10% higher expected motivation message delivery were more likely to attend clinic appointments on time (aOR: 1.08; 95%CI: 1.01 – 1.16, p = 0.03). Receiving and responding to an appointment reminder in any way were also associated with increased on-time appointment attendance (aOR: 1.35; 95%CI: 1.03 – 1.79, p = 0.03 and aOR: 1.47, 95%CI: 1.16 – 1.87, p = 0.001, respectively). No associations were found for 2wT messages and timely return to care following a missed appointment.

Conclusion
Greater 2wT implementation fidelity was associated with improved care outcomes. Although implementation fidelity monitoring of mHealth interventions is complex, it should be integrated into study design.
X-Mapper: fast and accurate sequence alignment via gapped x-mers
Authors: Gaston Jeffry M. , Alm Eric J. , Zhang An-Ni 
Published: January 2025

Abstract
Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aiming to offer high speed and accuracy via dynamic-length seeds containing gaps, called gapped x-mers. We observe 11–24-fold fewer suboptimal alignments analyzing a human reference and 3–579-fold lower inconsistency across bacterial references than other aligners, improving on 53% and 30% of reads aligned to non-target strains and species, respectively. Other seed-based analysis algorithms might benefit from gapped x-mers too.
Adherence to iron deficiency interventions among pregnant women attending antenatal clinics in Ubungo municipality, Dar es Salaam, Tanzania
Authors: Benjamin Glory , Mrema Ezra J. , Nhumba Nchang’wa , Wakoli Albert Burudi , Mwanga Hussein H. 
Published: January 2025

Abstract

Background
Iron deficiency anemia in pregnant women remains a public health concern despite iron deficiency interventions that have been implemented. This study investigated adherence to iron deficiency interventions and the associated factors among pregnant women attending antenatal clinics in Ubungo Municipality.

Methods
This cross-sectional study used a systematic random sampling technique to obtain 503 participants from the surveyed clinics. Interviews were conducted by using interviewer-administered questionnaires. Data were analyzed using Stata version 17. The study employed binary and multivariable logistic regression analysis to determine factors associated with adherence to iron deficiency interventions.

Results
In this study, 72% of participants were non-adherent and 28% were adherent to the interventions. In multivariable regression analysis, participants who forgot to take their iron tables on most days (AOR 2.35; 95% CI 1.23–4.48) and those who reported that not enough time was spent on education and counseling during antenatal clinic visits (AOR 3.87; 95% CI 1.08–13.84) were more likely to be non-adherent to iron deficiency interventions.

Conclusions
Majority of pregnant women in Ubungo Municipality were non-adherent to iron deficiency interventions. Non-adherence was associated with a tendency to forget taking iron tablets, and lack of enough time in providing health education and counseling. Improving the quality of health education and counseling could increase adherence to iron deficiency interventions and reduce maternal–child morbidity and mortality rates.
Ensuring representative sample volume predictions in microplastic monitoring
Authors: Cross Richard K. , Roberts Sarah L. , Jürgens Monika D. , Johnson Andrew C. , Davis Craig W. , Gouin Todd 
Published: January 2025

Abstract
A large body of literature is available quantifying microplastic contamination in freshwater and marine systems across the globe. “Microplastics” do not represent a single analyte. Rather, they are usually operationally defined based on their size, polymer and shape, dependent on the sample collection method and the analytical range of the measurement technique. In the absence of standardised methods, significant variability and uncertainty remains as to how to compare data from different sources, and so consider exposure correctly. To examine this issue, a previously compiled database containing 1603 marine observations and 208 freshwater observations of microplastic concentrations from across the globe between 1971 and 2020 was analysed. Reported concentrations span nine orders of magnitude. Investigating the relationship between sampling methods and reported concentrations, a striking correlation between smaller sample unit volumes and higher microplastic concentrations was observed. Close to half of the studies reviewed scored poorly in quality scoring protocols according to the sample volume taken. It is critical that sufficient particles are measured in a sample to reduce the errors from random chance. Given the inverse relationship with particle size and abundance, the volume required for a representative sample should be calculated case-by-case, based on what size microplastics are under investigation and where they are being measured. We have developed the Representative Sample Volume Predictor (RSVP) tool, which standardises statistical prediction of sufficient sample volumes, to ensure microplastics are detected with a given level of confidence. Reviewing reports in freshwater, we found ~ 12% of observations reported sample volumes which would have a false negative error rate > 5%. Such sample volumes run the risk of wrongly concluding that microplastics are absent in samples and are not sufficient to be quantitative. The RSVP tool also provides a harmonised Poisson point process estimation of confidence intervals to test whether two observations are likely to be significantly different, even in the absence of replication. In this way, we demonstrate application of the tool to evaluate historic data, but also to assist in new study designs to ensure that environmental microplastic exposure data is relevant and reliable. The tool can also be applied to other data for randomly dispersed events in space or time, and so has potential for transdisciplinary use.

Graphical Abstract
Excess costs of post-traumatic stress disorder related to child maltreatment in Germany
Authors: Grochtdreis Thomas , König Hans-Helmut , Leichsenring Falk , Beutel Manfred E. , Feix Lila , Gündel Harald , Hermann Andrea , Hitzler Melissa , Knaevelsrud Christine , Kolassa Iris-Tatjana , Kruse Johannes , Niemeyer Helen , Nöske Fatima , Salzer Simone , Sauer Karoline Sophie , Schuster Patrick , Steinert Christiane , Weidner Kerstin , von Wietersheim Jörn , Hoyer Jürgen , Dams Judith 
Published: January 2025

Abstract

Background
Childhood maltreatment (CM) significantly increases the risk of developing post-traumatic stress disorder (PTSD) for which the prevalence in Europe is higher than initially assumed. While the high economic burden of PTSD is well-documented, little is known about the health care cost differences between individuals with PTSD-CM and those without PTSD in Germany. This study aimed to determine the excess health care and absenteeism costs associated with PTSD-CM in Germany.

Methods
Baseline data from a multi-center randomized controlled trial on individuals with PTSD-CM (n = 361) were combined with data from individuals without PTSD (n = 4760). Entropy balancing was used to balance the data sets with regard to sociodemographic characteristics. Six-month excess health care costs from a societal perspective were calculated for 2022, using two-part models with logit specification for the first part and a generalized linear model for the second part.

Results
The total six-month excess costs associated with PTSD-CM were €8864 (95% CI: €6855 to €10,873) per person. Of this, the excess health care costs accounted for €4647 (95% CI €3296 to €5997) and the excess costs of absenteeism for €4217 (95% CI: €3121 to €5314). Individuals with mild to moderate PTSD symptoms incurred total excess costs of €6038 (95% CI: €3879 to €8197), while those with severe to extreme symptoms faced €11,433 (95% CI: €8220 to €14,646).

Conclusions
Excess health care and absenteeism costs associated with PTSD-CM were substantial, with absenteeism accounting for roughly half of the total excess costs.
Novel Use and Value of Contrast-Enhanced Susceptibility-Weighted Imaging Morphologic and Radiomic Features in Predicting Extremity Soft Tissue Undifferentiated Pleomorphic Sarcoma Treatment Response
Authors: Valenzuela Raul F. , Duran Sierra Elvis de Jesus , Canjirathinkal Mathew A. , Amini Behrang , Hwang Ken-Pin , Ma Jingfei , Torres Keila E. , Stafford R. Jason , Wang Wei-Lien , Benjamin Robert S. , Bishop Andrew J. , Madewell John E. , Murphy William A. , Costelloe Colleen M. 
Published: January 2025

PURPOSE
Undifferentiated pleomorphic sarcomas (UPSs) demonstrate therapy-induced hemosiderin deposition, granulation tissue formation, fibrosis, and calcification. We aimed to determine the treatment-assessment value of morphologic tumoral hemorrhage patterns and first- and high-order radiomic features extracted from contrast-enhanced susceptibility-weighted imaging (CE-SWI).

MATERIALS AND METHODS
This retrospective institutional review board–authorized study included 33 patients with extremity UPS with magnetic resonance imaging and resection performed from February 2021 to May 2023. Volumetric tumor segmentation was obtained at baseline, postsystemic chemotherapy (PC), and postradiation therapy (PRT). The pathology-assessed treatment effect (PATE) in surgical specimens separated patients into responders (R; ≥90%, n = 16), partial responders (PR; 89%-31%, n = 10), and nonresponders (NR; ≤30%, n = 7). RECIST, WHO, and volume were assessed for all time points. CE-SWI T2* morphologic patterns and 107 radiomic features were analyzed.

RESULTS

A Complete-Ring (CR) pattern was observed in PRT in 71.4% of R (
P
= 7.71 × 10
–6
), an Incomplete-Ring pattern in 33.3% of PR (
P
= .2751), and a Globular pattern in 50% of NR (
P
= .1562). The first-order radiomic analysis from the CE-SWI intensity histogram outlined the values of the 10th and 90th percentiles and their skewness. R showed a 280% increase in 10th percentile voxels (
P
= .061) and a 241% increase in skewness (
P
= .0449) at PC. PR/NR showed a 690% increase in the 90th percentile voxels (
P
= .03) at PC. Multiple high-order radiomic texture features observed at PRT discriminated better R versus PR/NR than the first-order features.

CONCLUSION
CE-SWI morphologic patterns strongly correlate with PATE. The CR morphology pattern was the most frequent in R and had the highest statistical association predicting response at PRT, easily recognized by a radiologist not requiring postprocessing software. It can potentially outperform size-based metrics, such as RECIST. The first- and high-order radiomic analysis found several features separating R versus PR/NR.
Interpretation of Viscoelastic Hemostatic Assays in Cardiac Surgery Patients: Importance of Clinical Context
Authors: Noteboom Sijm H. , Kho Eline , Veelo Denise P. , van der Ster Björn J.P. , van Haeren Maite M.T. , Viersen Victor A. , Müller Marcella C.A. , Hermanns Henning , Vlaar Alexander P.J. , Schenk Jimmy ,   the VHALID Expert Panel
Published: January 2025

BACKGROUND:
Rotational thromboelastometry (ROTEM) is widely used for point-of-care coagulation testing to reduce blood transfusions. Accurate interpretation of ROTEM data is crucial and requires substantial training. This study investigates the inter- and intrarater reliability of ROTEM interpretation among experts and compares their interpretations with a ROTEM-guided algorithm.

METHODS:
This study was conducted at Amsterdam University Medical Center and included 90 cardiac surgery patients. ROTEM data were collected at 4 surgical stages: before induction, after aortic declamping, postcoagulation correction, and within 2 hours of intensive care unit (ICU) admission. An international panel of 7 cardiovascular anesthesiologists and one intensivist interpreted the data. Interrater reliability was assessed using Fleiss’ kappa for binary decisions and the simple matching coefficient (SMC) for multiple-choice questions. Intrarater reliability with the ROTEM-guided algorithm was also evaluated.

RESULTS:
Three hundred forty-three ROTEM measurements were analyzed. The interrater reliability for binary decisions was substantial to almost perfect, except after declamping (Fleiss’ kappa = 0.34). The SMC for determining type of abnormality and interventions ranged from good to excellent across all ROTEM measuring moments (SMC ≥0.75). Intrarater reliability was almost perfect for binary questions (intraclass correlation coefficient [ICC] ≥0.81) and showed excellent agreement for multiple-choice questions. Comparing expert recommendations with the algorithm resulted in an average SMC of 0.70 indicating differences in intervention recommendations, with experts frequently recommending fibrinogen and protamine over the algorithm’s suggestions of plasma and PCC.

CONCLUSIONS:
This study demonstrates high inter- and intrarater reliability in ROTEM interpretation among trained professionals in cardiac surgery, with almost perfect agreement on abnormalities and interventions. However, differences between expert evaluations and the ROTEM-guided algorithm underscore the need for advanced clinical decision-making tools. Future efforts should focus on developing personalized, data-driven algorithms without predefined cutoff values to improve accuracy and patient outcomes.
Dynamic mechanisms for membrane skeleton transitions
Authors: Bonilla-Quintana Mayte , Ghisleni Andrea , Gauthier Nils C. , Rangamani Padmini 
Published: January 2025

ABSTRACT
The plasma membrane and the underlying skeleton form a protective barrier for eukaryotic cells. The molecular players forming this complex composite material constantly rearrange under mechanical stress. One of those molecules, spectrin, is ubiquitous in the membrane skeleton and linked by short actin filaments. In this work, we developed a generalized network model for the membrane skeleton integrating myosin contractility and membrane mechanics to investigate the response of the spectrin meshwork to mechanical loading. We observed that the force generated by membrane bending is important in maintaining a regular skeletal structure, suggesting that the membrane is not just supported by the skeleton, but actively contributes towards the stability of the cell structure. We found that spectrin and myosin turnover are necessary for the transition between stress and rest states in the skeleton. Simulations of a fully connected network representing a whole cell show that the surface area constraint of the plasma membrane and volume restriction of the cytoplasm enhance the stability of the membrane skeleton. Furthermore, we showed that cell attachment through adhesions promotes cell shape stabilization.