bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico design and evaluation of multi-epitope dengue virus vaccines: a promising approach to combat global dengue burden
Authors: Saha Otun , Razzak Abdur , Sarker Nikkon , Rahman Nymur , Zahid Abdullah bin , Sultana Afroza , Shishir Tushar Ahmed , Bahadur Newaz Mohammed , Rahaman Md. Mizanur , Hossen Foysal , Amin Mohammad Ruhul , Akter Mir Salma 
Published: April 2024

AbstractDengue virus, a pervasive mosquito-borne pathogen, imposes a substantial global health burden and is responsible for numerous fatalities annually globally, with tropical and sub-tropical regions particularly susceptible to dengue outbreaks. Despite decades of efforts, there has been no effective treatment or prevention for dengue, which makes it a life-threatening disease. Hence, this study proposes an innovative bioinformatics-driven approach to construct a vaccine targeting the dengue virus. The study involved a comprehensive analysis of conserved regions of dengue virus serotypes 1–4's non-structural proteins (NS1, NS3, and NS5) and structural protein (E) to predict the potential B & T-cell epitopes which were linked with appropriate adjuvants and linkers to generate four distinct vaccine candidates. The constructed vaccine models underwent rigorous evaluation, considering physicochemical attributes, structural integrity, population coverage, and immune system response through simulation. The results confirm that these vaccine candidates are non-allergenic, non-toxic, antigenic, and immunogenic. Additionally, they exhibit 99.70% world population coverage and 100% conservation across all dengue strains, which is crucial for vaccine efficacy. A Ramachandran plot showed that 95.6% of the amino acid residues of the candidates belong to the optimal zone, while around 4% are in additional allowed regions. Further, molecular docking and dynamic simulation of interaction with the human toll-like receptor 4, a fundamental component of innate immunity, was carried out to gain more insight into interaction dynamics. As a result of these analyses, the candidates' binding dynamics and structural stability were revealed. Overall, this study presents promising vaccine candidates for addressing dengue's global health burden. Their robust design and demonstrated immunogenicity make them attractive candidates for further experimental testing and development as potential vaccines against current strains and future variants.
Contributions of Tropical Cyclones and Atmospheric Rivers to Extreme Precipitation Trends Over the Northeast US
Authors: Jong Bor‐Ting , Murakami Hiroyuki , Delworth Thomas L. , Cooke William F. 
Published: April 2024

AbstractThe Northeast United States (NEUS) has faced the most rapidly increasing occurrences of extreme precipitation within the US in the past few decades. Understanding the physics leading to long‐term trends in regional extreme precipitation is essential but the progress is limited partially by the horizontal resolution of climate models. The latest fully coupled 25‐km GFDL (Geophysical Fluid Dynamics Laboratory) SPEAR (Seamless system for Prediction and EArth system Research) simulations provide a good opportunity to study changes in regional extreme precipitation and the relevant physical processes. Here, we focus on the contributions of changes in synoptic‐scale events, including atmospheric rivers (AR) and tropical cyclone (TC)‐related events, to the trend of extreme precipitation in the fall season over the Northeast US in both the recent past and future projections using the 25‐km GFDL‐SPEAR. In observations, increasing extreme precipitation over the NEUS since the 1990s is mainly linked to TC‐related events, especially those undergoing extratropical transitions. In the future, both AR‐related and TC‐related extreme precipitation over the NEUS are projected to increase, even though the numbers of TCs in the North Atlantic are projected to decrease in the SPEAR simulations using the SSP5‐8.5 projection of future radiative forcing. Factors such as enhancing TC intensity, strengthening TC‐related precipitation, and/or westward shift in Atlantic TC tracks may offset the influence of declining Atlantic TC numbers in the model projections, leading to more frequent TC‐related extreme precipitation over the NEUS.
Surface oxidation/spin state determines oxygen evolution reaction activity of cobalt-based catalysts in acidic environment
Authors: Huang Jinzhen , Borca Camelia Nicoleta , Huthwelker Thomas , Yüzbasi Nur Sena , Baster Dominika , El Kazzi Mario , Schneider Christof W. , Schmidt Thomas J. , Fabbri Emiliana 
Published: April 2024

AbstractCo-based catalysts are promising candidates to replace Ir/Ru-based oxides for oxygen evolution reaction (OER) catalysis in an acidic environment. However, both the reaction mechanism and the active species under acidic conditions remain unclear. In this study, by combining surface-sensitive soft X-ray absorption spectroscopy characterization with electrochemical analysis, we discover that the acidic OER activity of Co-based catalysts are determined by their surface oxidation/spin state. Surfaces composed of only high-spin CoII are found to be not active due to their unfavorable water dissociation to form CoIII-OH species. By contrast, the presence of low-spin CoIII is essential, as it promotes surface reconstruction of Co oxides and, hence, OER catalysis. The correlation between OER activity and Co oxidation/spin state signifies a breakthrough in defining the structure-activity relationship of Co-based catalysts for acidic OER, though, interestingly, such a relationship does not hold in alkaline and neutral environments. These findings not only help to design efficient acidic OER catalysts, but also deepen the understanding of the reaction mechanism.
Molecular patterns of resistance to immune checkpoint blockade in melanoma
Authors: Lauss Martin , Phung Bengt , Borch Troels Holz , Harbst Katja , Kaminska Kamila , Ebbesson Anna , Hedenfalk Ingrid , Yuan Joan , Nielsen Kari , Ingvar Christian , Carneiro Ana , Isaksson Karolin , Pietras Kristian , Svane Inge Marie , Donia Marco , Jönsson Göran 
Published: April 2024

AbstractImmune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB naïve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.
Viability leads to the emergence of gait transitions in learning agile quadrupedal locomotion on challenging terrains
Authors: Shafiee Milad , Bellegarda Guillaume , Ijspeert Auke 
Published: April 2024

AbstractQuadruped animals are capable of seamless transitions between different gaits. While energy efficiency appears to be one of the reasons for changing gaits, other determinant factors likely play a role too, including terrain properties. In this article, we propose that viability, i.e., the avoidance of falls, represents an important criterion for gait transitions. We investigate the emergence of gait transitions through the interaction between supraspinal drive (brain), the central pattern generator in the spinal cord, the body, and exteroceptive sensing by leveraging deep reinforcement learning and robotics tools. Consistent with quadruped animal data, we show that the walk-trot gait transition for quadruped robots on flat terrain improves both viability and energy efficiency. Furthermore, we investigate the effects of discrete terrain (i.e., crossing successive gaps) on imposing gait transitions, and find the emergence of trot-pronk transitions to avoid non-viable states. Viability is the only improved factor after gait transitions on both flat and discrete gap terrains, suggesting that viability could be a primary and universal objective of gait transitions, while other criteria are secondary objectives and/or a consequence of viability. Moreover, our experiments demonstrate state-of-the-art quadruped robot agility in challenging scenarios.
Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases
Authors: Brunderová Mária , Havlíček Vojtěch , Matyašovský Ján , Pohl Radek , Poštová Slavětínská Lenka , Krömer Matouš , Hocek Michal 
Published: April 2024

AbstractInnovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases – SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.
Anderson critical metal phase in trivial states protected by average magnetic crystalline symmetry
Authors: Wang Fa-Jie , Xiao Zhen-Yu , Queiroz Raquel , Bernevig B. Andrei , Stern Ady , Song Zhi-Da 
Published: April 2024

AbstractTransitions between distinct obstructed atomic insulators (OAIs) protected by crystalline symmetries, where electrons form molecular orbitals centering away from the atom positions, must go through an intermediate metallic phase. In this work, we find that the intermediate metals will become a scale-invariant critical metal phase (CMP) under certain types of quenched disorder that respect the magnetic crystalline symmetries on average. We explicitly construct models respecting average C2zT, m, and C4zT and show their scale-invariance under chemical potential disorder by the finite-size scaling method. Conventional theories, such as weak anti-localization and topological phase transition, cannot explain the underlying mechanism. A quantitative mapping between lattice and network models shows that the CMP can be understood through a semi-classical percolation problem. Ultimately, we systematically classify all the OAI transitions protected by (magnetic) groups $$Pm,P{2}^{{\prime} },P{4}^{{\prime} }$$
P
m
,
P

2

′

,
P

4

′

, and $$P{6}^{{\prime} }$$
P

6

′

with and without spin-orbit coupling, most of which can support CMP.
Upcycling of polyethylene to gasoline through a self-supplied hydrogen strategy in a layered self-pillared zeolite
Authors: Cen Ziyu , Han Xue , Lin Longfei , Yang Sihai , Han Wanying , Wen Weilong , Yuan Wenli , Dong Minghua , Ma Zhiye , Li Fang , Ke Yubin , Dong Juncai , Zhang Jin , Liu Shuhu , Li Jialiang , Li Qian , Wu Ningning , Xiang Junfeng , Wu Hao , Cai Lile , Hou Yanbo , Cheng Yongqiang , Daemen Luke L. , Ramirez-Cuesta Anibal J. , Ferrer Pilar , Grinter David C. , Held Georg , Liu Yueming , Han Buxing 
Published: April 2024

AbstractConversion of plastic wastes to valuable carbon resources without using noble metal catalysts or external hydrogen remains a challenging task. Here we report a layered self-pillared zeolite that enables the conversion of polyethylene to gasoline with a remarkable selectivity of 99% and yields of >80% in 4 h at 240 °C. The liquid product is primarily composed of branched alkanes (selectivity of 72%), affording a high research octane number of 88.0 that is comparable to commercial gasoline (86.6). In situ inelastic neutron scattering, small-angle neutron scattering, solid-state nuclear magnetic resonance, X-ray absorption spectroscopy and isotope-labelling experiments reveal that the activation of polyethylene is promoted by the open framework tri-coordinated Al sites of the zeolite, followed by β-scission and isomerization on Brönsted acids sites, accompanied by hydride transfer over open framework tri-coordinated Al sites through a self-supplied hydrogen pathway to yield selectivity to branched alkanes. This study shows the potential of layered zeolite materials in enabling the upcycling of plastic wastes.
Late presentations and missed opportunities among newly diagnosed HIV patients presenting to a specialty clinic in Lebanon
Authors: Mahmoud Maya , Ballouz Tala , Lahoud Chloe , Adnan Jana , Habib Paola Abi , Saab Reem , Farhat Haya , Hussein Mohammad El , Rizk Nesrine 
Published: April 2024

AbstractLate presentation to medical care of individuals infected with the human immunodeficiency virus (HIV) is linked to poor outcomes and increased morbidity and mortality. Missed opportunities for a prompt diagnosis are frequently reported among late presenters. We aimed to estimate the proportion of late presenters and missed opportunities in diagnosis among newly diagnosed HIV-positive subjects presenting to a specialty clinic in Lebanon. This is a retrospective chart review of all newly diagnosed adult HIV-positive subjects presenting to clinic from 2012 to 2022. Demographic, laboratory, and clinical data were collected at initial HIV diagnosis or presentation to medical care. We defined late presentation as having a CD4 count < 350 or AIDS-defining event regardless of CD4 count. Advanced disease is defined as having a CD4 count below 200 cells/μL or the presence of an AIDS-defining illness, regardless of the CD4 count. A missed opportunity was defined as the presence of an indicator condition (IC) that suggests infection with HIV/AIDS during 3 years preceding the actual HIV diagnosis and not followed by a recommendation for HIV testing. The proportions for demographic, epidemiological, and clinical characteristics are calculated by excluding cases with missing information from the denominator. Our cohort included 150 subjects (92.7% males; 63.6% men who have sex with men (MSM); 33.3% heterosexuals; median age 30.5 years at diagnosis). 77 (51.3%) were late presenters and 53 (35.3% of all subjects, 68.8% of late presenters) had advanced HIV on presentation. Up to 76.5% of late presenters had a presentation with an HIV-related condition at a healthcare provider without getting HIV test within the previous 3 years. The most frequent ICs were weight loss, generalized lymphadenopathy, constitutional symptoms, and chronic idiopathic diarrhea. Overall mortality rate was 4% (6/150 individuals). All-cause mortality among those who presented with AIDS was 15.4% (6/39 subjects). In our setting, late presentations and missed opportunities for HIV diagnosis are common. In the Middle East, AIDS mortality remains high with a large gap in HIV testing. To effectively influence policies, comprehensive analyses should focus on estimating the preventable health and financial burdens of late HIV presentations. Another concern pertains to healthcare providers’ attitudes and competencies.
A mathematical model to assess the effects of COVID-19 on the cardiocirculatory system
Authors: Tonini Andrea , Vergara Christian , Regazzoni Francesco , Dede’ Luca , Scrofani Roberto , Cogliati Chiara , Quarteroni Alfio 
Published: April 2024

AbstractImpaired cardiac function has been described as a frequent complication of COVID-19-related pneumonia. To investigate possible underlying mechanisms, we represented the cardiovascular system by means of a lumped-parameter 0D mathematical model. The model was calibrated using clinical data, recorded in 58 patients hospitalized for COVID-19-related pneumonia, to make it patient-specific and to compute model outputs of clinical interest related to the cardiocirculatory system. We assessed, for each patient with a successful calibration, the statistical reliability of model outputs estimating the uncertainty intervals. Then, we performed a statistical analysis to compare healthy ranges and mean values (over patients) of reliable model outputs to determine which were significantly altered in COVID-19-related pneumonia. Our results showed significant increases in right ventricular systolic pressure, diastolic and mean pulmonary arterial pressure, and capillary wedge pressure. Instead, physical quantities related to the systemic circulation were not significantly altered. Remarkably, statistical analyses made on raw clinical data, without the support of a mathematical model, were unable to detect the effects of COVID-19-related pneumonia in pulmonary circulation, thus suggesting that the use of a calibrated 0D mathematical model to describe the cardiocirculatory system is an effective tool to investigate the impairments of the cardiocirculatory system associated with COVID-19.
Flexion contracture can cause component mismatch in the Prophecy® preoperative patient-specific instrumentation for Evolution® medial-pivot knee system
Authors: Hiyama Shuhei , Takahashi Tsuneari , Handa Mikiko , Takeshita Katsushi 
Published: April 2024

Introduction: Patient-specific instrumentation (PSI) systems are used to conduct total knee arthroplasty. PSI reduces operative time, is less invasive and easier to use, and minimizes the risk of errors by providing precise measurements and reducing operating room turnover time. However, a study on the accuracy of Prophecy Evolution PSI (Microport Inc., Arlington, TN, USA) reported that 94% were below the error margin of 1.5 mm and 90% had error margins of 1 mm. This study aimed to evaluate the accuracy of the Prophecy Evolution PSI system in terms of the thickness of “total” bony resection required to achieve adequate extension/flexion gaps and the component match ratio between preoperative planning and actual component size inserted. Methods: Comparisons were made between the sizes of femoral and tibial components planned with PSI and those inserted. The primary outcome was the average preoperative range of motion with and without matched femoral/tibial components. The study further analyzed the proportions of cases in which both the femoral and tibial components matched, neither matched, and only one of the femoral or tibial components matched. Results: The ratio of the same sizes between the PSI planning and those inserted was 50.8% (33 patients) for both the femoral and tibial components. For the femoral component alone, the ratio was 84.6% (55 patients), and for the tibial component, it was 58.4% (38 patients). A receiver-operating characteristic curve analysis indicated that flexion contracture greater than 20° was a significant prognostic factor for the PSI component match group versus the mismatch group. Discussion: Flexion contracture may cause PSI mismatch. Notably, flexion contracture greater than 20° was a significant risk factor for the PSI component match group versus the mismatch group. During preoperative planning for a patient with flexion contracture, surgeons should prepare for the possibility of inserting an undersized tibial component.
Artificial intelligence for ultrasound microflow imaging in breast cancer diagnosis
Authors: Eun Na Lae , Lee Eunjung , Park Ah Young , Son Eun Ju , Kim Jeong-Ah , Youk Ji Hyun 
Published: April 2024

Abstract
Purpose To develop and evaluate artificial intelligence (AI) algorithms for ultrasound (US) microflow imaging (MFI) in breast cancer diagnosis.
Materials and Methods We retrospectively collected a dataset consisting of 516 breast lesions (364 benign and 152 malignant) in 471 women who underwent B-mode US and MFI. The internal dataset was split into training (n = 410) and test datasets (n = 106) for developing AI algorithms from deep convolutional neural networks from MFI. AI algorithms were trained to provide malignancy risk (0–100%). The developed AI algorithms were further validated with an independent external dataset of 264 lesions (229 benign and 35 malignant). The diagnostic performance of B-mode US, AI algorithms, or their combinations was evaluated by calculating the area under the receiver operating characteristic curve (AUROC).
Results The AUROC of the developed three AI algorithms (0.955–0.966) was higher than that of B-mode US (0.842, P < 0.0001). The AUROC of the AI algorithms on the external validation dataset (0.892–0.920) was similar to that of the test dataset. Among the AI algorithms, no significant difference was found in all performance metrics combined with or without B-mode US. Combined B-mode US and AI algorithms had a higher AUROC (0.963–0.972) than that of B-mode US (P < 0.0001). Combining B-mode US and AI algorithms significantly decreased the false-positive rate of BI-RADS category 4A lesions from 87% to 13% (P < 0.0001).
Conclusion AI-based MFI diagnosed breast cancers with better performance than B-mode US, eliminating 74% of false-positive diagnoses in BI-RADS category 4A lesions.
Sleep Status and Chronotype in University Athletes with and without Chronic Low Back Pain: A Cross-Sectional Study
Authors: Ansari Sumbul , Sharma Saurabh 
Published: April 2024

Abstract
Objective This study aimed to evaluate the status of sleep, chronotype, and related variables of university athletes with and without chronic low back pain (CLBP), to find the correlation between CLBP, sleep difficulty score (SDS), and chronotype, and to determine if SDS and chronotype predict CLBP.
Methods Ninety-two university athletes [46 with CLBP (Age: 22.08±2.74 years) and 46 healthy athletes (Age: 22.32±3.11 years) completed the athlete sleep screening questionnaire (ASSQ), also, their demographic, anxiety, depression, and sports-related details were collected. A Pearson correlation and logistic regression models (univariate and multivariate) were used for the statistical analysis.
Results The results demonstrated a higher SDS and evening type preference in CLBP athletes, a significant negative correlation between CLBP and chronotype (r = −0.40, p<0.01), a significant correlation between SDS and CLBP (r = 0.25, p = 0.01). SDS and chronotype were not found to be significant independent predictors of CLBP.
Conclusion This study concludes that there exists a correlation of CLBP, SDS, and chronotype However, despite the relationship, SDS and chronotype cannot predict CLBP.