bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction and prevention of pandemics via graphical model inference and convex programming
Authors: Krechetov Mikhail , Esmaieeli Sikaroudi Amir Mohammad , Efrat Alon , Polishchuk Valentin , Chertkov Michael 
Published: May 2022

AbstractHard-to-predict bursts of COVID-19 pandemic revealed significance of statistical modeling which would resolve spatio-temporal correlations over geographical areas, for example spread of the infection over a city with census tract granularity. In this manuscript, we provide algorithmic answers to the following twointer-related public health challenges of immense social impact which have not been adequately addressed(1)Inference Challengeassuming that there areNcensus blocks (nodes) in the city, and given an initial infection at any set of nodes, e.g. anyNof possible single node infections, any$$N(N-1)/2$$N(N-1)/2of possible two node infections, etc, what is the probability for a subset of census blocks to become infected by the time the spread of the infection burst is stabilized? (2)Prevention ChallengeWhat is the minimal control action one can take to minimize the infected part of the stabilized state footprint? To answer the challenges, we build a Graphical Model of pandemic of the attractive Ising (pair-wise, binary) type, where each node represents a census tract and each edge factor represents the strength of the pairwise interaction between a pair of nodes, e.g. representing the inter-node travel, road closure and related, and each local bias/field represents the community level of immunization, acceptance of the social distance and mask wearing practice, etc.Resolving the Inference Challengerequires finding the Maximum-A-Posteriory (MAP), i.e. most probable, state of the Ising Model constrained to the set of initially infected nodes. (An infected node is in the$$+ \, 1$$+1state and a node which remained safe is in the$$- \, 1$$-1state.) We show that almost all attractive Ising Models on dense graphs result in either of the two possibilities (modes) for the MAP state: either all nodes which were not infected initially became infected, or all the initially uninfected nodes remain uninfected (susceptible). This bi-modal solution of the Inference Challenge allows us to re-state thePrevention Challengeas the followingtractable convex programming: for the bare Ising Model with pair-wise and bias factors representing the system without prevention measures, such that the MAP state is fully infected for at least one of the initial infection patterns, find the closest, for example in$$l_1$$l1,$$l_2$$l2or any other convexity-preserving norm, therefore prevention-optimal, set of factors resulting in all the MAP states of the Ising model, with the optimal prevention measures applied, to become safe. We have illustrated efficiency of the scheme on a quasi-realistic model of Seattle. Our experiments have also revealed useful features, such as sparsity of the prevention solution in the case of the$$l_1$$l1norm, and also somehow unexpected features, such as localization of the sparse prevention solution at pair-wise links which are NOT these which are most utilized/traveled.
Moroccan entomopathogenic nematodes as potential biocontrol agents against Dactylopius opuntiae (Hemiptera: Dactylopiidae)
Authors: El Aalaoui Mohamed , Mokrini Fouad , Dababat Abdelfattah A. , Lahlali Rachid , Sbaghi Mohamed 
Published: May 2022

AbstractDactylopius opuntiae(Cockerell) (Hemiptera: Dactylopiidae) or prickly pear cochineal, is the most damaging pest on cactus species with heavy economic losses worldwide. The efficacy of two Moroccan EPN isolates;Steinernema feltiae(Filipjev) (Rhabditida: Steinernematidae) andHeterorhabditis bacteriophora(Poinar) (Rhabditida: Heterorhabditidae) (applied at 25, 50, and 75 IJs cm−2) againstD. opuntiaenymphs and young females were evaluated under both laboratory bioassays and field conditions. Results showed thatS. feltiaewas more effective, causing higher mortality of nymphs and adult females (98.8% and 97.5%, respectively) after 8 days of exposure, resulting in an LT50value of 5.9 days (nymph) and 6.0 days (young female). While,H. bacteriophorahad lower mortalities (83.8% for nymph and 81.3% for adult females). For the cochineal nymphs and adult females, no significant difference was observed amongS. feltiaeat 25, 50, and 75 IJs cm−2, and the positive control,d-limonene applied at 0.5 g/L which was used due to its high effectiveness against nymphs and females ofD. opuntiae. In the field experiment,d-limonene at 0.5 g/L andS. feltiaeapplied at 75 IJs cm−2were effective in reducing nymph and adult female populations by 85.3–93.9% at 12 days of post exposure period. To our knowledge, this work is the first report on the use of EPNs to controlD. opuntiae. Thus, in addition tod-limonene, both Moroccan EPN isolatesS. feltiae, andH. bacteriophoracould be used as part of the integrated pest management strategy againstD. opuntiae. Many factors such as temperature can affect the establishment and effectiveness of EPNs under field conditions. Therefore, additional studies under field conditions are needed.
Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels
Authors: Kondapuram Mahesh , Frieg Benedikt , Yüksel Sezin , Schwabe Tina , Sattler Christian , Lelle Marco , Schweinitz Andrea , Schmauder Ralf , Benndorf Klaus , Gohlke Holger , Kusch Jana 
Published: May 2022

AbstractHyperpolarization-activated and cyclic nucleotide (HCN) modulated channels are tetrameric cation channels. In each of the four subunits, the intracellular cyclic nucleotide-binding domain (CNBD) is coupled to the transmembrane domain via a helical structure, the C-linker. High-resolution channel structures suggest that the C-linker enables functionally relevant interactions with the opposite subunit, which might be critical for coupling the conformational changes in the CNBD to the channel pore. We combined mutagenesis, patch-clamp technique, confocal patch-clamp fluorometry, and molecular dynamics (MD) simulations to show that residue K464 of the C-linker is relevant for stabilizing the closed state of the mHCN2 channel by forming interactions with the opposite subunit. MD simulations revealed that in the K464E channel, a rotation of the intracellular domain relative to the channel pore is induced, which is similar to the cAMP-induced rotation, weakening the autoinhibitory effect of the unoccupied CL-CNBD region. We suggest that this CL-CNBD rotation is considerably involved in activation-induced affinity increase but only indirectly involved in gate modulation. The adopted poses shown herein are in excellent agreement with previous structural results.
Speciation and population divergence in a mutualistic seed dispersing bird
Authors: de Raad Jordi , Päckert Martin , Irestedt Martin , Janke Axel , Kryukov Alexey P. , Martens Jochen , Red’kin Yaroslav A. , Sun Yuehua , Töpfer Till , Schleuning Matthias , Neuschulz Eike Lena , Nilsson Maria A. 
Published: May 2022

AbstractBird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds.
Optimized single-step optical clearing solution for 3D volume imaging of biological structures
Authors: Kim Kitae , Na Myeongsu , Oh Kyoungjoon , Cho Eunji , Han Seung Seok , Chang Sunghoe 
Published: May 2022

AbstractVarious optical clearing approaches have been introduced to meet the growing demand for 3D volume imaging of biological structures. Each has its own strengths but still suffers from low transparency, long incubation time, processing complexity, tissue deformation, or fluorescence quenching, and a single solution that best satisfies all aspects has yet been developed. Here, we develop OptiMuS, an optimized single-step solution that overcomes the shortcomings of the existing aqueous-based clearing methods and that provides the best performance in terms of transparency, clearing rate, and size retention. OptiMuS achieves rapid and high transparency of brain tissues and other intact organs while preserving the size and fluorescent signal of the tissues. Moreover, OptiMuS is compatible with the use of lipophilic dyes, revealing DiI-labeled vascular structures of the whole brain, kidney, spleen, and intestine, and is also applied to 3D quantitative and comparative analysis of DiI-labeled vascular structures of glomeruli turfs in normal and diseased kidneys. Together, OptiMuS provides a single-step solution for simple, fast, and versatile optical clearing method to obtain high tissue transparency with minimum structural changes and is widely applicable for 3D imaging of various whole biological structures.
Hypertension induces gonadal macrophage imbalance, inflammation, lymphangiogenesis, and dysfunction
Authors: Navaneethabalakrishnan Shobana , Wilcox Brooke K. , Goodlett Bethany L. , Murphy Malea M. , Mitchell Brett M. 
Published: May 2022

AbstractHypertension (HTN) is associated with gonadal dysfunction and impaired reproductive health in both men and women. An imbalance in the systemic and renal proinflammatory (M1)/anti-inflammatory (M2) macrophage ratio, increased inflammation, and inflammation-associated lymphangiogenesis have been observed in animals with HTN. However, the impact of HTN on gonadal macrophages, inflammation, and lymphatics remains obscure. We hypothesized that salt-sensitive HTN (SSHTN) and HTN alters gonadal macrophage polarization, which is associated with inflammation, inflammation-associated lymphangiogenesis, and reproductive dysfunction. Flow cytometry analyses revealed a significant increase in M1 macrophages in the testes of SSHTN and nitro-L-arginine methyl ester hydrochloride (L-NAME)-induced HTN (LHTN) mice, with a concurrent decrease in M2 macrophages in SSHTN mice yet an increase in M2 macrophages in LHTN mice. Ovaries from SSHTN mice exhibited an increase in M1 and a decrease in M2 macrophages, while ovaries from LHTN mice had a significant increase in M2 and a decrease in M1 macrophages. Gene expression patterns of proinflammatory cytokines revealed gonadal inflammation in all hypertensive mice. Increased lymphatic vessel density in the gonads of both male and female hypertensive mice was confirmed by immunofluorescence staining for lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1). HTN adversely affected the expression pattern of steroidogenic enzymes, hormone receptors, and secretory proteins in both the testes and ovaries. In line with these results, male hypertensive mice also presented with decreased sperm concentration, and increased percentage of sperm with abnormal morphology, damaged acrosome, and nonfunctional mitochondrial activity. These data demonstrate that HTN alters gonadal macrophage polarization, which is associated with gonadal inflammation, inflammation-associated lymphangiogenesis, and dysfunction.
Multi‐layer random walker image segmentation for overlapped cervical cells using probabilistic deep learning methods
Authors: Mahyari Tayebeh Lotfi , Dansereau Richard M. 
Published: May 2022

AbstractA method for overlapping cell image segmentation is presented with a focus on multi‐layer image processing in a three‐phase scheme. In the first phase, a convolutional neural network is developed to provide a coarse cell segmentation with multiple output layers to identify cell cytoplasm, locations of cell nuclei, and the background, all as probabilistic image maps for the layer outputs. In the second phase, the probabilistic image maps from the convolutional neural network are used to identify locations of cell nuclei and cell cytoplasm. Then, multi‐layer random walker image segmentation is used with cell nuclei as hard initial seeds and the cytoplasm estimates as soft seeds in a diffusion graph‐based segmentation of the cells. With rough cell segmentation from both the trained convolutional neural network and the multi‐layer random walker graph‐based technique, a third phase combines and refines the cell segmentation using the Hungarian algorithm to optimise the assignment of individual pixel locations for the final cell segmentation. We evaluate the proposed method on cervical cell images generated from the International Symposium on Biomedical Imaging 2014 dataset with results that give a Dice similarity coefficient of 97.2% (compared to 93.2% for competitors) when trained on the generated dataset.
Intelligent train operation based on deep learning from excellent driver manipulation patterns
Authors: Xu Kai , Tu Yongchao , Xu Wenxuan , Wu Shixun 
Published: May 2022

AbstractIn the application of deep learning to realize intelligent train operation, there are some problems, such as the single learning task. Especially when using the gradient descent approach to optimize the structure, weight and threshold of a deep network, it is easy in this task to fall into a local optimum. This leads to excessive reliance on manual tuning experience. Aiming at the above issues, this paper proposes a new approach of train manipulation and prediction based on a long short‐term memory (LSTM) deep network. From the perspective of automatic hyper‐parameter optimization, the gradient‐free intelligent search method is principally chosen to optimize the architecture and parameters of a LSTM deep network, so as to improve the manipulation accuracy based on learning from excellent drivers. This method first selects excellent driver data through the Pareto dominance principle and crowding distance calculation; on this basis, a step‐by‐step method is used to optimize the structure, weight and threshold of the LSTM network. Particularly, in the first step, we adopt a genetic algorithm to search for the optimal deep network structure, which overcomes the problem that the structure is difficult to determine. In the second step, we optimize the parameters of the deep network, a process that is divided into two stages of ‘rough learning’ and ‘precise learning’. In the ‘rough learning’ stage, we use the multi‐population chained multi‐agent (MPCMA) algorithm to preliminarily optimize the LSTM network parameters. In the ‘precise learning’ stage, the Adam algorithm is applied to further finely optimize the network parameters. Finally, through simulation experiments, it is verified that the proposed method improves the accuracy of train manipulation and prediction, and shows strong robustness in situations of multiple manipulation sequences and different temporary speed limits.
Validation of the German Inflammatory Bowel Disease Fatigue (IBD-F) Questionnaire
Authors: Scholz Karina Antonia Magdalena , Thomann Anne Kerstin , Teich Niels , Baumann Hartmut , Walldorf Jens , Büning Carsten , Rosania Rosa , Canbay Ali , Arnim Ulrike von 
Published: May 2022

Abstract
Introduction Fatigue is a common symptom in patients with inflammatory bowel diseases (IBD). To date, there is no instrument to assess IBD-specific fatigue in German. The aim of this study was to translate the IBD Fatigue (IBD-F) scale and to test its psychometric properties in a German IBD population.
Methods After completing the translation process, 20 IBD patients participated in a pilot testing phase. For further analyses, 180 IBD patients with fatigue answered the IBD-F (Sections I, II, III) and the IBD Questionnaire (IBDQ-D). Reliability was tested by using Cronbach's alpha and corrected item–total correlation. Exploratory factor analyses (EFA) were carried out. Spearman’s correlation was calculated between the IBD-F and IBDQ-D . 78 patients could be included to calculate the test–retest reliability.
Results The German version of the IBD-F shows high face and content validity. Internal consistency was excellent, with a Cronbach's alpha of 0.93–0.98. Corrected item–total correlations ranged from 0.51 to 0.89. The correlation between the IBD-F and the IBDQ-D was statistically significant for Section I (rs=-0.59; p<0.01) and Section II (rs=-0.76; p<0.01) of the IBD-F. The EFA identified one relevant factor for each section. Test-retest reliability was acceptable for Section I (intraclass correlation coefficient (ICC)=0.73) and Section II (ICC=0.84).
Conclusion The German version of the IBD-F is a reliable and valid tool to assess fatigue in IBD.
Exploration of Core Genes in ACTH-Independent Macronodular Adrenal
Hyperplasia
Authors: Li Junwu , Wang Yunhui , Li Qinke , Zhang Ronggui 
Published: May 2022

AbstractThis study explores the core genes involved in the pathogenesis of
ACTH-independent macronodular adrenal hyperplasia (AIMAH), so as to provide
robust biomarkers for the clinical diagnosis and treatment of this disease. Gene
Expression Omnibus (GEO) database was used to obtain GSE25031 microarray
dataset. R package “limma” was applied to identify
differentially expressed genes (DEGs) between AIMAH and normal samples. The
Database for Annotation, Visualization and Integrated Discovery (DAVID) was
employed to perform Gene Ontology (GO) annotation for the DEGs, and Kyoto
Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was
conducted. A protein-protein interaction network (PPI) was constructed using the
STRING online website and visualized using the Cytoscape software. The key
modules and hub genes were then identified. Finally, Gene Set Enrichment
Analysis (GSEA) enrichment analysis was carried out to find the signaling
pathways of significant clinical value in AIMAH. A total of 295 DEGs between
AIMAH and healthy samples were screened out, including 164 upregulated genes and
131 downregulated genes. Combining enrichment analysis and PPI network
construction, there were 5 signifiant pathways and 10 hub genes, among which 3
genes (FOS, FOSB, and DUSP1) were identified as potential core genes of clinical
significance in AIMAH. In conclusion, the 3 core genes, FOS, FOSB, and DUSP1,
identified here might be potential biomarkers for AIMAH, and the current study
is of guiding significance for clinical diagnosis and treatment of this
disease.
Adrenal Surgery in the Era of Multidisciplinary Endocrine Tumor
Boards
Authors: Chiapponi Costanza , Santos Daniel Pinto Dos , Hartmann Milan Janis Michael , Schmidt Matthias , Faust Michael , Wahba Roger , Bruns Christiane Josephine , Schultheis Anne Maria , Alakus Hakan 
Published: May 2022

AbstractWork up of adrenal masses includes assessment of endocrine activity and
malignancy risk. There is no indication for surgical removal of nonfunctional
adrenal adenomas, according to the guidelines. In the present study, we aimed at
evaluating the impact of a university endocrine tumor board on the quality of
the indications for adrenal surgery at our institution. One hundred consecutive
patients receiving primary adrenal surgery at the University Hospital of
Cologne, Germany were included. Their demographics, clinic-pathologic
characteristics, treatment and outcome were analyzed. In 55 (55%) cases,
indication for surgery consisted in functional benign tumors, including Conn,
Cushing adenomas and pheochromocytomas. Forty (40%) tumors were referred
to surgery for malignancy suspicion and 5 (5%) myelolipomas were removed
due to their size. Eighty-nine percent of surgeries were performed as minimally
invasive procedures. Overall morbidity included two (2%) self-limiting
pancreatic fistulas after left laparoscopic adrenalectomy for pheochromocytoma.
All functional tumors were confirmed benign by final histology. Only 33
(82.5%) of 40 suspicious cases turned out to be malignant. Consequently,
nonfunctional benign adenomas were “unnecessarily” removed in
only 7 (7%) patients, with 6 (85.7%) of them having a history of
extra-adrenal cancer and all of them fulfilling criteria for surgery, according
to the international guidelines. In conclusion, the endocrine tumor board
provided an excellent adherence to the guidelines with most surgeries being
performed either for functional or malignant tumors. In nonfunctional tumors
with history of extra adrenal cancer, CT guided biopsy might be considered for
obviating surgery.
Physiological Functions of FBW7 in Metabolism
Authors: Zhang Jianmei , Kong De-huan , Huang Xiaocheng , Yu Rongbo , Yang Yachao 
Published: May 2022

AbstractFBW7 is the recognition subunit of the SCF (Skp1-Cullin1-F-box proteins) E3
ubiquitin ligase complex, and it determines the specificity of the SCF
substrate. SCFFBW7 is a recognized tumor suppressor because of its ability to
degrade many proto-oncogenic substrates. Recent studies have shown that FBW7
plays a key role in metabolism by targeting the degradation of critical
regulators involved in cellular metabolism in a ubiquitin-dependent manner.
Here, we review recent studies, which highlight the important role of FBW7 in
metabolism.
Differences in Training Characteristics Between Junior, Under 23 and
Professional Cyclists
Authors: Gallo Gabriele , Leo Peter , March Manuel Mateo , Giorgi Andrea , Faelli Emanuela , Ruggeri Piero , Mujika Iñigo , Filipas Luca 
Published: May 2022

AbstractThe aim was to compare the training characteristics of junior, under 23 and
professional road cyclists. Training data collected during the 2019 competitive
season of thirty male cyclists, divided into three age-related categories (JUN;
U23; PRO), were retrospectively analyzed for training characteristics, external
and internal training load. Higher duration per training session were observed
in PRO (2.6±0.3 h) compared to both U23 (2.2±0.3 h;
P<0.001) and JUN (2.0±0.2 h; P<0.001).
Elevation gain per distance was higher in PRO (13.8±1.9
m·km−1) compared to U23 (10.6±0.9
m·km−1; P=0.001) and JUN
(6.7±0.3 m·km-1; P<0.001), and in U23
compared to JUN (P<0.001). Annual total work was lower in JUN
(3694±467 kJ·kg−1) compared to U23
(5268±746 kJ·kg−1; P=0.001)
and PRO (5759±1103 kJ·kg−1;
P<0.001). eTRIMP per hour was higher in JUN (151±40)
compared to both U23 (115±23; P=0.003) and PRO
(112±22; P=0.013). JUN spent more training time at medium
and high heart rate intensity zones compared to U23 and PRO
(P<0.05).
Acetylenic Esters in Organic Synthesis
Authors: Hajinasiri Rahimeh 
Published: May 2022

AbstractActivated acetylenic substrates such as acetylenic esters and alkyl propiolates are very important in organic synthesis. Due to their electron deficiency, these compounds are widely used in combinatorial and multicomponent reactions, enabling the synthesis of a large variety of novel compounds. In addition, these substrates are powerful Michael acceptors and convenient dienophiles and dipolarophiles in Diels–Alder and 1,3-dipolar cycloaddition reactions. The addition of different nucleophiles, primarily phosphorus, nitrogen or sulfur, to the triple bonds of these substrates produces key intermediates, such as Tebby and Huisgen zwitterions, which can lead to designing pathways toward the generation of spirocyclic and polycyclic compounds. This account highlights recent studies on the chemistry of acetylenic esters and their applications in organic synthesis.1 Introduction2 Synthesis of Acyclic and Monocyclic Compounds3 Synthesis of Spirocyclic Compounds4 Synthesis of Polycyclic Compounds5 Conclusion