bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of an improved self-consistent lower bound theory with Lehmann’s method for low-lying eigenvalues
Authors: Ronto Miklos , Pollak Eli , Martinazzo Rocco 
Published: December 2021

AbstractRitz eigenvalues only provide upper bounds for the energy levels, while obtaining lower bounds requires at least the calculation of the variances associated with these eigenvalues. The well-known Weinstein and Temple lower bounds based on the eigenvalues and variances converge very slowly and their quality is considerably worse than that of the Ritz upper bounds. Lehmann presented a method that in principle optimizes Temple’s lower bounds with significantly improved results. We have recently formulated a Self-Consistent Lower Bound Theory (SCLBT), which improves upon Temple’s results. In this paper, we further improve the SCLBT and compare its quality with Lehmann’s theory. The Lánczos algorithm for constructing the Hamiltonian matrix simplifies Lehmann’s theory and is essential for the SCLBT method. Using two lattice Hamiltonians, we compared the improved SCLBT (iSCLBT) with its previous implementation as well as with Lehmann’s lower bound theory. The novel iSCLBT exhibits a significant improvement over the previous version. Both Lehmann’s theory and the SCLBT variants provide significantly better lower bounds than those obtained from Weinstein’s and Temple’s methods. Compared to each other, the Lehmann and iSCLBT theories exhibit similar performance in terms of the quality and convergence of the lower bounds. By increasing the number of states included in the calculations, the lower bounds are tighter and their quality becomes comparable with that of the Ritz upper bounds. Both methods are suitable for providing lower bounds for low-lying excited states as well. Compared to Lehmann’s theory, one of the advantages of the iSCLBT method is that it does not necessarily require the Weinstein lower bound for its initial input, but Ritz eigenvalue estimates can also be used. Especially owing to this property the iSCLBT method sometimes exhibits improved convergence compared to that of Lehmann’s lower bounds
reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization
Authors: Manzini Stefano , Busnelli Marco , Colombo Alice , Franchi Elsa , Grossano Pasquale , Chiesa Giulia 
Published: December 2021

AbstractFunctional enrichment analysis is an analytical method to extract biological insights from gene expression data, popularized by the ever-growing application of high-throughput techniques. Typically, expression profiles are generated for hundreds to thousands of genes/proteins from samples belonging to two experimental groups, and after ad-hoc statistical tests, researchers are left with lists of statistically significant entities, possibly lacking any unifying biological theme. Functional enrichment tackles the problem of putting overall gene expression changes into a broader biological context, based on pre-existing knowledge bases of reference: database collections of known expression regulation, relationships and molecular interactions. STRING is among the most popular tools, providing both protein–protein interaction networks and functional enrichment analysis for any given set of identifiers. For complex experimental designs, manually retrieving, interpreting, analyzing and abridging functional enrichment results is a daunting task, usually performed by hand by the average wet-biology researcher. We have developed reString, a cross-platform software that seamlessly retrieves from STRING functional enrichments from multiple user-supplied gene sets, with just a few clicks, without any need for specific bioinformatics skills. Further, it aggregates all findings into human-readable table summaries, with built-in features to easily produce user-customizable publication-grade clustermaps and bubble plots. Herein, we outline a complete reString protocol, showcasing its features on a real use-case.
A proof of concept study on real-time LiMAx CYP1A2 liver function assessment of donor grafts during normothermic machine perfusion
Authors: Schurink Ivo J. , de Haan Jubi E. , Willemse Jorke , Mueller Matteo , Doukas Michael , Roest Henk , de Goeij Femke H. C. , Polak Wojciech G. , Ijzermans Jan N. M. , Dutkowski Philipp , van der Laan Luc J. W. , de Jonge Jeroen 
Published: December 2021

AbstractNo single reliable parameter exists to assess liver graft function of extended criteria donors during ex-vivo normothermic machine perfusion (NMP). The liver maximum capacity (LiMAx) test is a clinically validated cytochromal breath test, measuring liver function based on 13CO2 production. As an innovative concept, we aimed to integrate the LiMAx breath test with NMP to assess organ function. Eleven human livers were perfused using NMP. After one hour of stabilization, LiMAx testing was performed. Injury markers (ALT, AST, miR-122, FMN, and Suzuki-score) and lactate clearance were measured and related to LiMAx values. LiMAx values ranged between 111 and 1838 µg/kg/h, and performing consecutive LiMAx tests during longer NMP was feasible. No correlation was found between LiMAx value and miR-122 and FMN levels in the perfusate. However, a significant inverse correlation was found between LiMAx value and histological injury (Suzuki-score, R = − 0.874, P < 0.001), AST (R = − 0.812, P = 0.004) and ALT (R = − 0.687, P = 0.028). Furthermore, a significant correlation was found with lactate clearance (R = 0.683, P = 0.043). We demonstrate, as proof of principle, that liver function during NMP can be quantified using the LiMAx test, illustrating a positive correlation with traditional injury markers. This new breath-test application separates livers with adequate cytochromal liver function from inadequate ones and may support decision-making in the safe utilization of extended criteria donor grafts.
iTRAQ-based quantitative proteome analysis insights into cold stress of Winter Rapeseed (Brassica rapa L.) grown in the field
Authors: Niu Zaoxia , Liu Lijun , Pu Yuanyuan , Ma Li , Wu Junyan , Hu Fangdi , Fang Yan , Li Xuecai , Sun Wancang , Wang Wangtian , Bai Chunsheng 
Published: December 2021

AbstractWinter rapeseed (Brassica rapaL.) is a major oilseed crop in Northern China, where its production was severely affected by chilling and freezing stress. However, not much is known about the role of differentially accumulated proteins (DAPs) during the chilling and freezing stress. In this study, isobaric tag for relative and absolute quantification (iTRAQ) technology was performed to identify DAPs under freezing stress. To explore the molecular mechanisms of cold stress tolerance at the cellular and protein levels, the morphological and physiological differences in the shoot apical meristem (SAM) of two winter rapeseed varieties, Longyou 7 (cold-tolerant) and Lenox (cold-sensitive), were explored in field-grown plants. Compared to Lenox, Longyou 7 had a lower SAM height and higher collar diameter. The level of malondialdehyde (MDA) and indole-3-acetic acid (IAA) content was also decreased. Simultaneously, the soluble sugars (SS) content, superoxide dismutase (SOD) activity, peroxidase (POD) activity, soluble protein (SP) content, and collar diameter were increased in Longyou 7 as compared to Lenox. A total of 6330 proteins were identified. Among this, 98, 107, 183 and 111 DAPs were expressed in L7 CK/Le CK, L7 d/Le d, Le d/Le CK and L7 d/L7 CK, respectively. Quantitative real-time PCR (RT-qPCR) analysis of the coding genes for seventeen randomly selected DAPs was performed for validation. These DAPs were identified based on gene ontology enrichment analysis, which revealed that glutathione transferase activity, carbohydrate-binding, glutathione binding, metabolic process, and IAA response were closely associated with the cold stress response. In addition, some cold-induced proteins, such as glutathione S-transferase phi 2(GSTF2), might play an essential role during cold acclimation in the SAM ofBrassica rapa. The present study provides valuable information on the involvement of DAPs during cold stress responses inBrassica rapaL, and hence could be used for breeding experiments.
Adaptive value of foot-and-mouth disease virus capsid substitutions with opposite effects on particle acid stability
Authors: Caridi Flavia , Cañas-Arranz Rodrigo , Vázquez-Calvo Ángela , de León Patricia , Calderón Katherine I. , Domingo Esteban , Sobrino Francisco , Martín-Acebes Miguel A. 
Published: December 2021

AbstractFoot-and-mouth disease virus (FMDV) is a picornavirus that exhibits an extremely acid sensitive capsid. This acid lability is directly related to its mechanism of uncoating triggered by acidification inside cellular endosomes. Using a collection of FMDV mutants we have systematically analyzed the relationship between acid stability and the requirement for acidic endosomes using ammonium chloride (NH4Cl), an inhibitor of endosome acidification. A FMDV mutant carrying two substitutions with opposite effects on acid-stability (VP3 A116V that reduces acid stability, and VP1 N17D that increases acid stability) displayed a rapid shift towards acid lability that resulted in increased resistance to NH4Cl as well as to concanamicyn A, a different lysosomotropic agent. This resistance could be explained by a higher ability of the mutant populations to produce NH4Cl-resistant variants, as supported by their tendency to accumulate mutations related to NH4Cl-resistance that was higher than that of the WT populations. Competition experiments also indicated that the combination of both amino acid substitutions promoted an increase of viral fitness that likely contributed to NH4Cl resistance. This study provides novel evidences supporting that the combination of mutations in a viral capsid can result in compensatory effects that lead to fitness gain, and facilitate space to an inhibitor of acid-dependent uncoating. Thus, although drug-resistant variants usually exhibit a reduction in viral fitness, our results indicate that compensatory mutations that restore this reduction in fitness can promote emergence of resistance mutants.
Power efficient refined seizure prediction algorithm based on an enhanced benchmarking
Authors: Wang Ziyu , Yang Jie , Wu Hemmings , Zhu Junming , Sawan Mohamad 
Published: December 2021

AbstractDeep learning techniques have led to significant advancements in seizure prediction research. However, corresponding used benchmarks are not uniform in published results. Moreover, inappropriate training and evaluation processes used in various work create overfitted models, making prediction performance fluctuate or unreliable. In this study, we analyzed the various data preparation methods, dataset partition methods in related works, and explained the corresponding impacts to the prediction algorithms. Then we applied a robust processing procedure that considers the appropriate sampling parameters and the leave-one-out cross-validation method to avoid possible overfitting and provide prerequisites for ease benchmarking. Moreover, a deep learning architecture takes advantage of a one-dimension convolutional neural network and a bi-directional long short-term memory network is proposed for seizure prediction. The architecture achieves 77.6% accuracy, 82.7% sensitivity, and 72.4% specificity, and it outperforms the indicators of other prior-art works. The proposed model is also hardware friendly; it has 6.274 k parameters and requires only 12.825 M floating-point operations, which is advantageous for memory and power constrained device implementations.
Effect of public corruption on the COVID-19 immunization progress
Authors: Farzanegan Mohammad Reza , Hofmann Hans Philipp 
Published: December 2021

AbstractThe coronavirus disease (COVID-19) outbreak has resulted in the death of over four million people since late 2019. To reduce the human and economic costs of COVID-19, different vaccines have been developed and distributed across countries. There has been significant cross-country variation in the vaccination of people against COVID-19. In this study, we focus on public corruption to explain the significant cause of cross-country variation in immunization progress. We suggest that countries with a higher degree of public corruption have been less successful in the vaccination of their population, controlling for other important determinants of immunization progress.
Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers
Authors: Grant Adam , Xicola Rosa M. , Nguyen Vivian , Lim James , Thorne Curtis , Salhia Bodour , Llor Xavier , Ellis Nathan , Padi Megha 
Published: December 2021

AbstractThe tumor suppressor gene adenomatous polyposis coli (APC) is the initiating mutation in approximately 80% of all colorectal cancers (CRC), underscoring the importance of aberrant regulation of intracellular WNT signaling in CRC development. Recent studies have found that early-onset CRC exhibits an increased proportion of tumors lacking an APC mutation. We set out to identify mechanisms underlying APC mutation-negative (APCmut–) CRCs. We analyzed data from The Cancer Genome Atlas to compare clinical phenotypes, somatic mutations, copy number variations, gene fusions, RNA expression, and DNA methylation profiles between APCmut– and APC mutation-positive (APCmut+) microsatellite stable CRCs. Transcriptionally, APCmut– CRCs clustered into two approximately equal groups. Cluster One was associated with enhanced mitochondrial activation. Cluster Two was strikingly associated with genetic inactivation or decreased RNA expression of the WNT antagonist RNF43, increased expression of the WNT agonist RSPO3, activating mutation of BRAF, or increased methylation and decreased expression of AXIN2. APCmut– CRCs exhibited evidence of increased immune cell infiltration, with significant correlation between M2 macrophages and RSPO3. APCmut– CRCs comprise two groups of tumors characterized by enhanced mitochondrial activation or increased sensitivity to extracellular WNT, suggesting that they could be respectively susceptible to inhibition of these pathways.
A 1-minute blood test detects decreased immune function and increased clinical risk in COVID-19 patients
Authors: Deb Chirajyoti , Salinas Allan N. , Zheng Tianyu , Middleton Aurea , Kern Katelyn , Penoyer Daleen , Borsadia Rahul , Hunley Charles , Abomoelak Bassam , Mehta Vijay , Irastorza Laura , Mehta Devendra I. , Huo Qun 
Published: December 2021

AbstractUpon infection with SARS-CoV-2, the virus that causes COVID-19, most people will develop no or mild symptoms. However, a small percentage of the population will become severely ill, and some will succumb to death. The clinical severity of COVID-19 has a close connection to the dysregulation of the patient’s immune functions. We previously developed a simple, nanoparticle-enabled blood test that can determine the humoral immune status in animals. In this study, we applied this new test to analyze the immune function in relation to disease severity in COVID-19 patients. From the testing of 153 COVID-19 patient samples and 142 negative controls, we detected a drastic decrease of humoral immunity in COVID-19 patients who developed moderate to severe symptoms, but not in patients with no or mild symptoms. The new test may be potentially used to monitor the immunity change and predict the clinical risk of patients with COVID-19.
Resistance training induces similar adaptations of upper and lower-body muscles between sexes
Authors: Kojić Filip , Mandić Danimir , Ilić Vladimir 
Published: December 2021

AbstractThe purpose of the study was to compare sex adaptations in hypertrophy, strength and contractile properties of upper and lower-body muscles induced by resistance training (RT). Eighteen RT untrained male (MG) and female (FG) students (aged 24.1 ± 1.7 years, height: 1.75 ± 0.08 m, weight: 70.4 ± 12.3 kg) undervent 7 weeks of biceps curl and squat training (2 days/week, 60–70% repetition maximum, 3–4 sets, 120 s rest intervals, reps until muscular failure). At baseline and final measurement, thickness and cross-section area, one-repetition maximum and tensiomyography parameters (contraction time − Tc and radial displacement − Dm) of elbow flexors (biceps brachii) and knee extensors (4 quadriceps muscles) were evaluated. Although MG tends to display greater absolute strength gains for upper- (p = 0.055) and lower-body (p = 0.098), for relative changes ANCOVA revealed no sex-specific differences for either of the tested variables. Significant hypertrophy was observed for all tested muscles, except for vastus intermedius in FG (p = 0.076). The Dm significantly decreased for biceps brachii (MG by 12%, p < 0.01 and FG by 13.1%, p < 0.01) and rectus femoris (MG by19.2%, p < 0.01 and FG by 12.3%, p < 0.05), while Tc values remain unchanged. These results indicate that initial morphological, functional and contractile alterations following RT are similar for males and females, and that there are no specific sex adaptations either for the upper- or lower-body muscles. The study was registered with ClinicalTrials.gov (NCT04845295).
Effects of process factors on performances of liquid membrane-based transfer of indole-3-acetic acid
Authors: Diaconu Ioana , Pârvulescu Oana Cristina , Topală Sorina Laura , Dobre Tănase 
Published: December 2021

AbstractThe paper has aimed at studying the transfer of indole 3-acetic acid (IAA) from a feed aqueous solution to a stripping aqueous solution of NaOH using a chloroform bulk liquid membrane and trioctylamine (TOA) as a ligand (L). Initial molar concentrations of IAA in the feed phase, cIAA,F0 (10–4–10–3 kmol/m3), of TOA in the membrane phase, cL,M0 (10–2 and 10–1 kmol/m3), and of NaOH in the stripping phase, cNaOH,S0 (10–2 and 1 kmol/m3), were selected as process factors. Their effects on the final values of IAA concentration in the feed phase (cIAA,Ff) and stripping solution (cIAA,Sf), extraction efficiency (EF), distribution coefficient (KD), and recovery efficiency (ER) were quantified using multiple regression equations. Regression coefficients were determined from experimental data, i.e., cIAA,Ff,ex = 0.02–1 × 10–4 kmol/m3, cIAA,Sf,ex = 0.22–2.58 × 10–3 kmol/m3, EF,ex = 90.0–97.9%, KD,ex = 9.0–46.6, and ER,ex = 66.5–94.2%. It was found that cIAA,F0 had the most significant positive effect on cIAA,Ff and cIAA,Sf, whereas cNaOH,S0 had a major positive effect on EF, KD, and ER. A deterministic model based on mass transfer of IAA was developed and its parameters, i.e., mass transfer coefficient of IAA-L complex in the liquid membrane (0.82–11.5 × 10–7 m/s) and extraction constant (1033.9–1779.7 m3/kmol), were regressed from experimental data. The effect of cL,M0 on both parameters was significant.
Application of droplet digital polymerase chain reaction of plasma methylated septin 9 on detection and early monitoring of colorectal cancer
Authors: Ma Zhi Yao , Chan Cherry Sze Yan , Lau Kam Shing , Ng Lui , Cheng Yuen Yee , Leung Wai K. 
Published: December 2021

AbstractMethylated septin 9 (SEPT9) has been approved for non-invasive screening of colorectal cancer (CRC), but data on monitoring of CRC is sparse. Droplet digital polymerase chain reaction (ddPCR), with higher detection precision and simpler quantification than conventional PCR, has not been applied in SEPT9 detection. We explored the role of SEPT9 ddPCR for CRC detection and to measure serial SEPT9 levels in blood samples of CRC patients before and 3-month after surgery. SEPT9 methylated ratio, methylated abundance, and CEA levels were all higher in CRC patients than normal controls (all P < 0.05). The area under the curve (AUC) for methylated ratio and abundance to detect CRC was 0.707 and 0.710, respectively. There was an increasing trend for SEPT9 methylated abundance from proximal to distal cancers (P = 0.017). At 3-month after surgery, both methylated abundance and ratio decreased (P = 0.005 and 0.053, respectively), especially methylated abundance in stage III and distal cancer (both P < 0.01). We have developed a ddPCR platform for the quantitative detection of plasma SEPT9 in CRC patients. SEPT9 methylated abundance had an early post-operative decline, which may be useful in monitoring of treatment response.
Pilot imaging study of o-BMVC foci for discrimination of indeterminate cytology in diagnosing fine-needle aspiration of thyroid nodules
Authors: Tseng Ting-Yuan , Shih Shyang-Rong , Wang Cheng-Ping , Lin Shang-Jyun , Jan I.-Shiow , Wang Chiung-Lin , Liu Shin-Ya , Chang Cheng-Chung , Lou Pei-Jen , Chang Ta-Chau 
Published: December 2021

AbstractFluorescence lifetime imaging microscopy of a fluorescence probe, 3,6-bis(1-methyl-2-vinylpyridinium) carbazole diiodide (o-BMVC), provides an objective method for preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. The key of this o-BMVC test of FNA smears is the measurement of the digital number of o-BMVC foci in the nucleus. Thus, there are three categories classified in the o-BMVC test, which are nondiagnostic for unsatisfactory samples, benign for less numbers of o-BMVC foci, and malignant for more numbers of o-BMVC foci. The discrimination of indeterminate (including atypia, follicular neoplasm, suspicious) cytology into benign or malignant cases can reduce diagnostic uncertainty and benefit clinical decision making. This pilot study strongly suggests that the o-BMVC test is an invaluable method for diagnosing FNA samples. Particularly, the combination of FNA cytology and the o-BMVC test holds great promise to improve the efficacy of diagnosis and reduce the healthcare costs.
Peptides derived from gp43, the most antigenic protein from Paracoccidioides brasiliensis, form amyloid fibrils in vitro: implications for vaccine development
Authors: Cardim-Pires Thyago R. , Sant’Anna Ricardo , Foguel Debora 
Published: December 2021

AbstractFungal infection is an important health problem in Latin America, and in Brazil in particular. Paracoccidioides (mainly P. brasiliensis and P. lutzii) is responsible for paracoccidioidomycosis, a disease that affects mainly the lungs. The glycoprotein gp43 is involved in fungi adhesion to epithelial cells, which makes this protein an interesting target of study. A specific stretch of 15 amino acids that spans the region 181–195 (named P10) of gp43 is an important epitope of gp43 that is being envisioned as a vaccine candidate. Here we show that synthetic P10 forms typical amyloid aggregates in solution in very short times, a property that could hamper vaccine development. Seeds obtained by fragmentation of P10 fibrils were able to induce the aggregation of P4, but not P23, two other peptides derived from gp43. In silico analysis revealed several regions within the P10 sequence that can form amyloid with steric zipper architecture. Besides, in-silico proteolysis studies with gp43 revealed that aggregation-prone, P10-like peptides could be generated by several proteases, which suggests that P10 could be formed under physiological conditions. Considering our data in the context of a potential vaccine development, we redesigned the sequence of P10, maintaining the antigenic region (HTLAIR), but drastically reducing its aggregation propensity.