bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physics-Guided, Physics-Informed, and Physics-Encoded Neural Networks and Operators in Scientific Computing: Fluid and Solid Mechanics
Authors: Faroughi Salah A. , Pawar Nikhil M. , Fernandes Célio , Raissi Maziar , Das Subasish , Kalantari Nima K. , Kourosh Mahjour Seyed 
Published: January 2024

Abstract
Advancements in computing power have recently made it possible to utilize machine learning and deep learning to push scientific computing forward in a range of disciplines, such as fluid mechanics, solid mechanics, materials science, etc. The incorporation of neural networks is particularly crucial in this hybridization process. Due to their intrinsic architecture, conventional neural networks cannot be successfully trained and scoped when data are sparse, which is the case in many scientific and engineering domains. Nonetheless, neural networks provide a solid foundation to respect physics-driven or knowledge-based constraints during training. Generally speaking, there are three distinct neural network frameworks to enforce the underlying physics: (i) physics-guided neural networks (PgNNs), (ii) physics-informed neural networks (PiNNs), and (iii) physics-encoded neural networks (PeNNs). These methods provide distinct advantages for accelerating the numerical modeling of complex multiscale multiphysics phenomena. In addition, the recent developments in neural operators (NOs) add another dimension to these new simulation paradigms, especially when the real-time prediction of complex multiphysics systems is required. All these models also come with their own unique drawbacks and limitations that call for further fundamental research. This study aims to present a review of the four neural network frameworks (i.e., PgNNs, PiNNs, PeNNs, and NOs) used in scientific computing research. The state-of-the-art architectures and their applications are reviewed, limitations are discussed, and future research opportunities are presented in terms of improving algorithms, considering causalities, expanding applications, and coupling scientific and deep learning solvers.
Use of CRISPR interference for efficient and rapid gene inactivation in
Fusobacterium nucleatum
Authors: Zhou Peng , G. C. Bibek , Stolte Flynn , Wu Chenggang 
Published: January 2024

ABSTRACT

Gene inactivation by creating in-frame deletion mutations in
Fusobacterium nucleatum
is time consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPR interference (CRISPRi) system. This system employs the nuclease-inactive
Streptococcus pyogenes
Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single-guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes,
ftsX
and
radD
, which are pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline,
ftsX
suppression caused filamentous cell formation akin to chromosomal
ftsX
deletion, while targeting
radD
significantly reduced RadD protein levels, abolishing RadD-mediated coaggregation. The system was then extended to probe essential genes
bamA
and
ftsZ
, which are vital for outer membrane biogenesis and cell division. Impressively,
bamA
suppression disrupted membrane integrity and bacterial separation, stalling growth, while
ftsZ
targeting yielded elongated cells in broth with compromised agar growth. Further studies on
F. nucleatum
clinical strain CTI-2 and
Fusobacterium periodonticum
revealed reduced indole synthesis when targeting
tnaA
. Moreover, silencing
clpB
in
F. periodonticum
decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains.

IMPORTANCE

How can we effectively investigate the gene functions in
Fusobacterium nucleatum
, given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPR interference (CRISPRi) system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and single-guide RNA expression is driven by the robust, constitutive
rpsJ
promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered genetically intractable strains like CTI-2 and
Fusobacterium periodonticum
. With CRISPRi’s potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
Direct Reprogramming of Somatic Skin Cells from a Patient with Huntington’s Disease into Striatal Neurons to Create Models of Pathology
Authors: Kraskovskaya N. A. , Khotin M. G. , Tomilin A. N. , Mikhailova N. A. 
Published: January 2024

Abstract
A new in vitro model of Huntington’s disease (HD) was developed via a direct reprogramming of dermal fibroblasts from HD patients into striatal neurons. A reprogramming into induced pluripotent stem (iPS) cells is obviated in the case of direct reprogramming, which thus yields neurons that preserve the epigenetic information inherent in cells of a particular donor and, consequently, the age-associated disease phenotype. A main histopathological feature of HD was reproduced in the new model; i.e., aggregates of mutant huntingtin accumulated in striatal neurons derived from a patient’s fibroblasts. Experiments with cultured neurons obtained via direct reprogramming make it possible to individually assess the progression of neuropathology and to implement a personalized approach to choosing the treatment strategy and drugs for therapy. The in vitro model of HD can be used in preclinical drug studies.
Application of Bayesian statistics to the sector of decay constants in three-flavour $$\chi $$PT
Authors: Kolesár Marián , Říha Jaroslav 
Published: January 2024

AbstractThe sector of decay constants of the octet of light pseudoscalar mesons in the framework of ‘resummed’ SU(3) chiral perturbation theory is investigated. A theoretical prediction for the decay constant of $$\eta $$
η
-meson is compared to a range of available determinations. Compatibility of these determinations with the latest fits of the SU(3) low energy coupling constants is discussed. Using a Bayesian statistical approach, constraints on the low energy coupling constants $$L_4^r$$

L
4
r

and $$L_5^r$$

L
5
r

, as well as higher order remainders to the decay constants $$F_K$$

F
K

and $$F_\eta $$

F
η

, are extracted from the most recent experimental and lattice QCD inputs for the values of the decay constants.
Backdozer: A Backdoor Detection Methodology for DRL-based Traffic Controllers
Authors: Wang Yue , Li Wenqing , Alam Manaar , Maniatakos Michail , Jabari Saif Eddin 
Published: January 2024

While the advent of Deep Reinforcement Learning (DRL) has substantially improved the efficiency of Autonomous Vehicles (AVs), it makes them vulnerable to
backdoor attacks
that can potentially cause traffic congestion or even collisions. Backdoor functionality is typically implanted by poisoning training datasets with stealthy malicious data, designed to preserve high accuracy on legitimate inputs while inducing desired misclassifications for specific adversary-selected inputs. Existing countermeasures against backdoors predominantly concentrate on image classification, utilizing image-based properties, rendering these methods inapplicable to the regression tasks of DRL-based AV controllers that rely on continuous sensor data as inputs. In this article, we introduce the first-ever defense against backdoors on regression tasks of DRL-based models, called
Backdozer
. Our method systematically extracts more abstract features from representations of training data by projecting them into a specific
latent subspace
and segregating them into several disjoint groups based on the distribution of legitimate outputs. The key observation of
Backdozer
is that authentic representations for each group reside in one latent subspace, whereas the incorporation of malicious data impacts that subspace.
Backdozer
optimizes a sample-wise weight vector for the representations capturing the disparities in projections originating from different groups. We experimentally demonstrate that
Backdozer
can attain 100% accuracy in detecting backdoors. We also evaluate its effectiveness against three closely related state-of-the-art defenses.
Approval, Evidence, and “Off-Label” Device Utilization: The Patent Foramen Ovale Closure Story
Authors: Goldsweig Andrew M. , Deng Yihong , Yao Xiaoxi , Desai Nihar R. , Cohen David J. , Aronow Herbert D. , Messé Steven R. , Ross Joseph S. , Lansky Alexandra J. , Savitz Samuel T. 
Published: January 2024

BACKGROUND:
Following regulatory approval, medical devices may be used “off-label.” Patent foramen ovale (PFO) closure is indicated to reduce recurrent stroke but has been proposed for other indications, including migraine, transient ischemic attack, and diving decompression illness. We sought to evaluate PFO closure rates and indications relative to the timing of regulatory approval and publication of key randomized trials.

METHODS:
We performed a retrospective cohort study using the OptumLabs Data Warehouse of US commercial insurance enrollees from 2006 to 2019. We quantified PFO closure among individuals with ≥2 years of preprocedure coverage to establish indications, classified hierarchically as stroke/systemic embolism, migraine, transient ischemia attack, or other.

RESULTS:
We identified 5315 patients undergoing PFO closure (51.8% female, 29.2%≥60 years old), which increased from 4.75 per 100 000 person-years in 2006 to 6.60 per 100 000 person-years in 2019. Patients aged ≥60 years accounted for 29.2% of closures. Procedure volumes corresponded weakly with supportive clinical publications and device approval. Among patients with PFO closure, 58.6% underwent closure for stroke/systemic embolism, 10.2% for transient ischemia attack, 8.8% for migraine, and 22.4% for other indications; 17.6% of patients had atrial fibrillation at baseline; and 11.9% developed atrial fibrillation postprocedure. Those aged ≥60 years and male were less likely to undergo closure for migraine than stroke/systemic embolism.

CONCLUSIONS:
From 2006 to 2019, PFO closure use was consistently low and corresponded weakly with clinical trial publications and regulatory status. Nearly half of patients underwent PFO closure for indications unapproved by the Food and Drug Administration. Regulators and payers should coordinate mechanisms to promote utilization for approved indications to ensure patient safety and should facilitate clinical trials for other possible indications.
Self-Measured Blood Pressure–Guided Pharmacotherapy: A Systematic Review and Meta-Analysis of United States-Based Telemedicine Trials
Authors: Acharya Sameer , Neupane Gagan , Seals Austin , KC Madhav , Giustini Dean , Sharma Sharan , Taylor Yhenneko J. , Palakshappa Deepak , Williamson Jeff D. , Moore Justin B. , Bosworth Hayden B. , Pokharel Yashashwi 
Published: January 2024

BACKGROUND:
The optimal approach to implementing telemedicine hypertension management in the United States is unknown.

METHODS:
We examined telemedicine hypertension management versus the effect of usual clinic-based care on blood pressure (BP) and patient/clinician-related heterogeneity in a systematic review/meta-analysis. We searched United States-based randomized trials from Medline, Embase, CENTRAL, CINAHL, PsycINFO, Compendex, Web of Science Core Collection, Scopus, and 2 trial registries. We used trial-level differences in BP and its control rate at ≥6 months using random-effects models. We examined heterogeneity in univariable metaregression and in prespecified subgroups (clinicians leading pharmacotherapy [physician/nonphysician], self-management support [pharmacist/nurse], White versus non-White patient predominant trials [>50% patients/trial], diabetes predominant trials [≥25% patients/trial], and White patient predominant but not diabetes predominant trials versus both non-White and diabetes patient predominant trials].

RESULTS:
Thirteen, 11, and 7 trials were eligible for systolic and diastolic BP difference and BP control, respectively. Differences in systolic and diastolic BP and BP control rate were −7.3 mm Hg (95% CI, −9.4 to −5.2), −2.7 mm Hg (−4.0 to −1.5), and 10.1% (0.4%–19.9%), respectively, favoring telemedicine. Greater BP reduction occurred in trials where nonphysicians led pharmacotherapy, pharmacists provided self-management support, White patient predominant trials, and White patient predominant but not diabetes predominant trials, with no difference by diabetes predominant trials.

CONCLUSIONS:
Telemedicine hypertension management is more effective than clinic-based care in the United States, particularly when nonphysicians lead pharmacotherapy and pharmacists provide self-management support. Non-White patient predominant trials achieved less BP reduction. Equity-conscious, locally informed adaptation of telemedicine interventions is needed before wider implementation.
Navigating the New Normal: The European Union's Changing Stance on Globalization in the Era of  Trade Conflicts
Authors: Sjöholm Fredrik 
Published: January 2024

Abstract
The EU is becoming more inward-looking and more hesitant toward globalization. This paper examines recent transformations in the EU's economic policies, with a focus on international trade and industrial policy. It argues that these changes reflect the EU's response to the evolving global economic and political landscape, driven by factors such as China's rise and the United States’ protectionist policies. By analyzing the potential consequences of these policy adjustments on EU industries’ competitiveness and trade relations, the paper offers insights into the future prospects of EU economic policies and their role in shaping the global economy.
A Bayesian Approach to Uncertainty in Word Embedding Bias
Estimation
Authors: Dobrzeniecka Alicja , Urbaniak Rafal 
Published: January 2024

Abstract
Multiple measures, such as WEAT or MAC, attempt to quantify the magnitude of bias present in word embeddings in terms of a single-number metric. However, such metrics and the related statistical significance calculations rely on treating pre-averaged data as individual data points and utilizing bootstrapping techniques with low sample sizes. We show that similar results can be easily obtained using such methods even if the data are generated by a null model lacking the intended bias. Consequently, we argue that this approach generates false confidence. To address this issue, we propose a Bayesian alternative: hierarchical Bayesian modeling, which enables a more uncertainty-sensitive inspection of bias in word embeddings at different levels of granularity. To showcase our method, we apply it to Religion, Gender, and Race word lists from the original research, together with our control neutral word lists. We deploy the method using Google, GloVe, and Reddit embeddings. Further, we utilize our approach to evaluate a debiasing technique applied to the Reddit word embedding. Our findings reveal a more complex landscape than suggested by the proponents of single-number metrics. The datasets and source code for the paper are publicly available.1
Collaborative Exploration of Storm-Scale Probabilistic Guidance for NWS Forecast Operations
Authors: Wilson Katie A. , Burke Patrick C. , Gallo Burkely T. , Skinner Patrick S. , Lindley T. Todd , Gravelle Chad , Bieda Stephen W. , Madden Jonathan G. , Monroe Justin W. , Guerra Jorge E. , Morris Dale A. 
Published: January 2024

Abstract
The operational utility of the NOAA National Severe Storm Laboratory’s storm-scale probabilistic Warn-on-Forecast System (WoFS) was examined across the watch-to-warning time frame in a virtual NOAA Hazardous Weather Testbed (HWT) experiment. Over four weeks, 16 NWS forecasters from local Weather Forecast Offices, the Storm Prediction Center, and the Weather Prediction Center participated in simulated forecasting tasks and focus groups. Bringing together multiple NWS entities to explore new guidance impacts on the broader forecast process is atypical of prior NOAA HWT experiments. This study therefore provides a framework for designing such a testbed experiment, including methodological and logistical considerations necessary to meet the needs of both local office and national center NWS participants. Furthermore, this study investigated two research questions: 1) How do forecasters envision WoFS guidance fitting into their existing forecast process? and 2) How could WoFS guidance be used most effectively across the current watch-to-warning forecast process? Content and thematic analyses were completed on flowcharts of operational workflows, real-time simulation interactions, and focus group activities and discussions. Participants reported numerous potential applications of WoFS, including improved coordination and consistency between local offices and national centers, enhanced hazard messaging, and improved operations planning. Challenges were also reported, including the knowledge and training required to incorporate WoFS guidance effectively and forecasters’ trust in new guidance and openness to change. The solutions identified to these challenges will take WoFS one step closer to transition, and in the meantime, improve the capabilities of WoFS for experimental use within the operational community.

Significance Statement
A first-of-its-kind experiment brought together forecasters from local weather forecast offices and national centers to examine the experimental Warn-on-Forecast System’s (WoFS’s) potential applications across watch-to-warning scales. This experiment demonstrated that WoFS can provide great benefit to forecasters, though a few challenges remain. Benefits provided by WoFS frequently overlap roles and responsibilities at local and national scales, suggesting the potential for enhanced cross-office collaboration. The challenges anticipated for WoFS operational use are far fewer than the benefits, and some solutions to these challenges are now being implemented. Finally, the mixed-methods experimental framework described herein also provides guidance for future collaborative experiments in testbed research that examine impacts of new technologies across NWS entities.
Association Between Remnant Cholesterol and Contrast-Induced Nephropathy in Patients Undergoing Coronary Angiography and/or Percutaneous Coronary Intervention
Authors: Luo Baolin , Huang Xizhen , Peng Yanchun , Luo Hanbin , Chen Liangwan , Lin Yanjuan 
Published: January 2024

Contrast-induced nephropathy (CIN) is an acute renal complication that can occur after the use of iodinated contrast media. Remnant cholesterol (RC) is one of the markers of atherosclerotic cardiovascular disease risk. We evaluated the impact of RC on CIN and clinical outcomes after coronary angiography (CAG) and/or percutaneous coronary intervention (PCI). Consecutive patients ( n = 3332) undergoing CAG and/or PCI were assessed in this retrospective study. Patients were divided into four groups based on baseline RC levels. In the quartile analysis, RC were associated with a higher risk of CIN, especially when RC ≤0.20 or ≥0.38 mmol/L ( P < .05). However, after adjustment, the association of RC with CIN was not significant. There was a significant correlation between RC and repeated revascularization in patients undergoing PCI ( P < .001) and driven primarily by the highest quartile level. After adjustment, this remained statistically significant (adjusted odds ratio (aOR) 4.06; 95% CI 2.10–7.87; P < .001). This is the first large study to show a possible association between RC and the risk of CIN after CAG and/or PCI; however, this finding was not further confirmed after adjustment. The complex clinical risk profile of patients, rather than RC itself, may contribute to the risk of CIN in this high-risk subgroup.
The Effect of Gender on Triple Heart Valve Surgery Outcomes; Reinforcing Women’s Health
Authors: Alhijab Fatimah A. , Ismail Huda , Albabtain Monirah , Alfonso Juan , Algarni Khaled D. , Pragliola Claudio , Adam Adam I. , Arafat Amr A. 
Published: January 2024

Female gender is a risk factor in several cardiac surgery risk stratification systems. This study explored the differences in the outcomes following triple heart valve surgery in men vs women. The study included 250 patients (males n = 101; females n = 149) who underwent triple valve surgery from 2009 to 2020. BMI (body mass index) was higher in females (29.6 vs 26.5 kg/m2, P < .001), and diabetes was more common in males (44 vs 42%, P = .012). The ejection fraction was higher in females (55 vs 50%, P < .001). The severity of mitral valve stenosis and tricuspid valve regurgitation was significantly greater in females (33.11 vs 27.72%, P = .003 and 44.30 vs 19.8%, P < .001, respectively). Mitral valve replacement was more common in females ( P < .001), and they had lower concomitant coronary artery bypass grafting ( P = .001). Bleeding and renal failure were lower in females ( P = .021 and <0.001, respectively). Hospital mortality, readmission, and reintervention were not significantly different between genders. By multivariable analysis, male gender was a risk factor for lower survival [HR (hazard ratio): 2.18; P = .024]. Triple valve surgery can be performed safely in both genders, with better long-term survival in females. Female gender was not a risk factor in patients undergoing triple valve surgery.
Normal Weight Central Obesity is a Poor Prognostic Factor for Sudden Sensorineural Hearing Loss
Authors: Wang Shih-Wei , Tai Shu-Yu , Chen Chin-Kuo , Li Kuan-Hui , Chang Ning-Chia , Wang Ling-Feng , Liu Hui-Li , Ho Kuen-Yao , Chien Chen-Yu 
Published: January 2024

Objectives: To investigate the role of normal weight central obesity (NWCO) in the prognosis of sudden sensorineural hearing loss (SSNHL). Methods: We retrospectively investigated 807 cases of SSNHL from January of 2008 to August of 2019 from the Department of Otorhinolaryngology at Kaohsiung Medical University Hospital in southern Taiwan. We analyzed the association between overweight and obesity, NWCO, and the prognosis of SSNHL. The demographic and clinical characteristics, audiometry results, and outcomes were also reviewed. Results: The nonobese (body mass index [BMI] < 24 kg/m2) and overweight and obese groups (BMI ≥ 24 kg/m2) comprised 343 (42.50%) and 464 (57.50%) patients, respectively. The favorable prognosis rates in the nonobese and the overweight and obese groups were 45.48% and 45.91%, respectively, without a significant difference ( P = .9048). Multivariate logistic regression revealed that BMI (adjusted odds ratio [aOR] = 1.00, 95% CI = 0.948-1.062, P = .9165) was not significantly associated with SSNHL recovery. The normal weight noncentral obesity (NWNCO) and NWCO groups comprised 266 (77.55%) and 77 (22.45%) patients, respectively, and had favorable prognosis rates of 48.50% and 35.06%, respectively. The difference between the groups was significant ( P = .0371). Multivariate logistic regression analysis revealed that NWCO (aOR = 2.51, 95% CI = 1.292-5.019, P = .0075) was significantly associated with SSNHL recovery. Conclusions: NWCO may significantly affect the prognosis of SSNHL.