bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copper(II) invigorated EHU-30 for continuous electroreduction of CO2 into value-added chemicals
Authors: Landaluce Nerea , Perfecto-Irigaray Maite , Albo Jonathan , Beobide Garikoitz , Castillo Oscar , Irabien Angel , Luque Antonio , Méndez Alba S. J. , Platero-Prats Ana E. , Pérez-Yáñez Sonia 
Published: May 2022

AbstractThe doping of zirconium based EHU-30 and EHU-30-NH2 metal–organic frameworks with copper(II) yielded a homogeneous distribution of the dopant with a copper/zirconium ratio of 0.04–0.05. The doping mechanism is analysed by chemical analysis, microstructural analysis and pair distribution function (PDF) analysis of synchrotron total scattering data in order to get deeper insight into the local structure. According to these data, the Cu(II) atoms are assembled within the secondary building unit by a transmetalation reaction, contrarily to UiO-66 series in which the post-synthetic metalation of the MOF takes place through chemical anchorage. The resulting materials doubled the overall performance of the parent compounds for the CO2 electroreduction, while retained stable the performance during continuous transformation reaction.
Nitrate respiration occurs throughout the depth of mucoid and non-mucoid Pseudomonas aeruginosa submerged agar colony biofilms including the oxic zone
Authors: Schwermer Carsten Ulrich , de Beer Dirk , Stoodley Paul 
Published: May 2022

AbstractPseudomonas aeruginosa is an opportunistic pathogen and well characterized biofilm former. P. aeruginosa forms strong oxygen gradients inside biofilms due to rapid oxygen respiration in the top layers and the poor solubility of oxygen coupled with diffusion limited transport. Transcriptomic evidence from in vitro and ex vivo sampling suggests that denitrification is occurring in biofilms in ostensibly oxic environments. It is hypothesized that in the presence of nitrate there is stratification with aerobic respiration occurring in the outer oxic layer and denitrification in the lower anoxic zone. We used submerged agar colony biofilms grown from mucoid (FRD1) and non-mucoid (PAO1) strains to simultaneously measure depth microprofiles of oxygen and nitrous oxide in the same colony with microelectrodes. Oxygen respiration occurred at the top of the colony as expected but denitrification occurred throughout the entire depth, even in the oxic region. Local denitrification rates were highly variable suggesting heterogenous metabolic activity within the colony. We also assessed the short-term influence of tobramycin on aerobic respiration within a PAO1 colony. Although there was an immediate reduction in respiration it was never completely arrested over a 2 h period. On tobramycin removal the oxygen gradient steadily reestablished, demonstrating immediate recovery of metabolic activity.
Efficient capture of circulating tumor cells with low molecular weight folate receptor-specific ligands
Authors: Hu Yingwen , Chen Danyang , Napoleon John V. , Srinivasarao Madduri , Singhal Sunil , Savran Cagri A. , Low Philip S. 
Published: May 2022

AbstractRetrieval of circulating tumor cells (CTC) has proven valuable for assessing a patient's cancer burden, evaluating response to therapy, and analyzing which drug might treat a cancer best. Although most isolation methods retrieve CTCs based on size, shape, or capture by tumor-specific antibodies, we explore here the use of small molecule tumor-specific ligands linked to magnetic beads for CTC capture. We have designed folic acid-biotin conjugates with different linkers for the capture of folate receptor (FR) + tumor cells spiked into whole blood, and application of the same technology to isolate FR + CTCs from the peripheral blood of both tumor-bearing mice and non-small cell lung patients. We demonstrate that folic acid linked via a rigid linker to a flexible PEG spacer that is in turn tethered to a magnetic bead enables optimal CTC retrieval, reaching nearly 100% capture when 100 cancer cells are spiked into 1 mL of aqueous buffer and ~ 90% capture when the same quantity of cells is diluted into whole blood. In a live animal model, the same methodology is shown to efficiently retrieve CTCs from tumor-bearing mice, yielding cancer cell counts that are proportional to total tumor burden. More importantly, the same method is shown to collect ~ 29 CTCs/8 mL peripheral blood from patients with non-small cell lung cancer. Since the ligand-presentation strategy optimized here should also prove useful in targeting other nanoparticles to other cells, the methods described below should have general applicability in the design of nanoparticles for cell-specific targeting.
The influence of sea ice on the detection of bowhead whale calls
Authors: Jones Joshua M. , Hildebrand John A. , Thayre Bruce J. , Jameson Ellen , Small Robert J. , Wiggins Sean M. 
Published: May 2022

AbstractBowhead whales (Balaena mysticetus) face threats from diminishing sea ice and increasing anthropogenic activities in the Arctic. Passive acoustic monitoring is the most effective means for monitoring their distribution and population trends, based on the detection of their calls. Passive acoustic monitoring, however, is influenced by the sound propagation environment and ambient noise levels, which impact call detection probability. Modeling and simulations were used to estimate detection probability for bowhead whale frequency-modulated calls in the 80–180 Hz frequency band with and without sea ice cover and under various noise conditions. Sound transmission loss for bowhead calls is substantially greater during ice-covered conditions than during open-water conditions, making call detection ~ 3 times more likely in open-water. Estimates of daily acoustic detection probability were used to compensate acoustic detections for sound propagation and noise effects in two recording datasets in the northeast Chukchi Sea, on the outer shelf and continental slope, collected between 2012 and 2013. The compensated acoustic density suggests a decrease in whale presence with the retreat of sea ice at these recording sites. These results highlight the importance of accounting for effects of the environment on ambient noise and acoustic propagation when interpreting results of passive acoustic monitoring.
D-galactose-induced aging aggravates obesity-induced bone dyshomeostasis
Authors: Imerb Napatsorn , Thonusin Chanisa , Pratchayasakul Wasana , Arunsak Busarin , Nawara Wichwara , Ongnok Benjamin , Aeimlapa Ratchaneevan , Charoenphandhu Narattaphol , Chattipakorn Nipon , Chattipakorn Siriporn C. 
Published: May 2022

AbstractWe aimed to compare the time-course effect of D-galactose (D-gal)-induced aging, obesity, and their combined effects on bone homeostasis. Male Wistar rats were fed with either a normal diet (ND; n = 24) or a high-fat diet (HFD; n = 24) for 12 weeks. All rats were then injected with either vehicle or 150 mg/kg/day of D-gal for 4 or 8 weeks. Blood was collected to measure metabolic, aging, oxidative stress, and bone turnover parameters. Bone oxidative stress and inflammatory markers, as well as bone histomorphometry were also evaluated. Additionally, RAW 264.7 cells were incubated with either D-gal, insulin, or D-gal plus insulin to identify osteoclast differentiation capacity under the stimulation of receptor activator of nuclear factor κB ligand. At week 4, D-gal-induced aging significantly elevated serum malondialdehyde level and decreased trabecular thickness in ND- and HFD-fed rats, when compared to the control group. At week 8, D-gal-induced aging further elevated advanced glycation end products, increased bone inflammation and resorption, and significantly impaired bone microarchitecture in HFD-fed rats. The osteoclast number in vitro were increased in the D-gal, insulin, and combined groups to a similar extent. These findings suggest that aging aggravates bone dyshomeostasis in the obese condition in a time-dependent manner.
A generalization of the standard map and its statistical characterization
Authors: Cetin Kivanc , Tirnakli Ugur , Boghosian Bruce M. 
Published: May 2022

AbstractFrom the statistical mechanical point of view, area-preserving maps have great potential and importance. These maps exhibit chaotic and regular behavior separately or together in the available phase space as the control parameter changes. Several works on these maps, e.g., the standard map and the web map, have shown that ergodicity breakdown causes the statistical mechanical framework that describes the dynamics of the system to change. In this paper, for a novel generalization of the standard map, which we define by generalizing the periodic function used in its definition, we verify that a q-Gaussian with $$q\simeq 1.935$$

q
≃
1.935

for the probability distribution of sum of the iterates of the system with initial conditions chosen from the nonergodic stability islands is robust. We also show that the probability distributions become more complicated and unexpected limiting behavior occurs for some parameter regimes.
Evaluating machine learning classifiers for glaucoma referral decision support in primary care settings
Authors: Kaskar Omkar G. , Wells-Gray Elaine , Fleischman David , Grace Landon 
Published: May 2022

AbstractSeveral artificial intelligence algorithms have been proposed to help diagnose glaucoma by analyzing the functional and/or structural changes in the eye. These algorithms require carefully curated datasets with access to ocular images. In the current study, we have modeled and evaluated classifiers to predict self-reported glaucoma using a single, easily obtained ocular feature (intraocular pressure (IOP)) and non-ocular features (age, gender, race, body mass index, systolic and diastolic blood pressure, and comorbidities). The classifiers were trained on publicly available data of 3015 subjects without a glaucoma diagnosis at the time of enrollment. 337 subjects subsequently self-reported a glaucoma diagnosis in a span of 1–12 years after enrollment. The classifiers were evaluated on the ability to identify these subjects by only using their features recorded at the time of enrollment. Support vector machine, logistic regression, and adaptive boosting performed similarly on the dataset with F1 scores of 0.31, 0.30, and 0.28, respectively. Logistic regression had the highest sensitivity at 60% with a specificity of 69%. Predictive classifiers using primarily non-ocular features have the potential to be used for identifying suspected glaucoma in non-eye care settings, including primary care. Further research into finding additional features that improve the performance of predictive classifiers is warranted.
Mean-field theory of social laser
Authors: Alodjants Alexander P. , Bazhenov A. Yu. , Khrennikov A. Yu. , Bukhanovsky A. V. 
Published: May 2022

AbstractIn this work we suggest a novel paradigm of social laser (solaser), which can explain such Internet inspired social phenomena as echo chambers, reinforcement and growth of information cascades, enhancement of social actions under strong mass media operation. The solaser is based on a well-known in quantum physics laser model of coherent amplification of the optical field. Social networks are at the core of the solaser model; we define them by means of a network model possessing power–law degree distribution. In the solaser the network environment plays the same role as the gain medium has in a physical laser device. We consider social atoms as decision making agents (humans or even chat bots), which possess two (mental) states and occupy the nodes of a network. The solaser establishes communication between the agents as absorption and spontaneous or stimulated emission of socially actual information within echo chambers, which mimic an optical resonator of a convenient (physical) laser. We have demonstrated that social lasing represents the second order nonequilibrium phase transition, which evokes the release of coherent socially stimulated information field represented with the order parameter. The solaser implies the formation of macroscopic social polarization and results in a huge social impact, which is realized by viral information cascades occurring in the presence of population imbalance (social bias). We have shown that decision making agents follow an adiabatically time dependent mass media pump, which acts in the network community reproducing various reliable scenarios for information cascade evolution. We have also shown that in contrast to physical lasers, due to node degree peculiarities, the coupling strength of decision making agents with the network may be enhanced $$\sqrt{\langle k\rangle }$$

⟨
k
⟩

times. It leads to a large increase of speed, at which a viral message spreads through a social media. In this case, the mass media pump supports additional reinforcement and acceleration of cascade growth. We have revealed that the solaser model in some approximations possesses clear links with familiar Ising and SIS (susceptible-infected-susceptible) models typically used for evaluating a social impact and information growth, respectively. However, the solaser paradigm can serve as a new platform for modelling temporal social events, which originate from “microscopic” (quantum-like) processes occurring in the society. Our findings open new perspectives for interdisciplinary studies of distributed intelligence agents behavior associated with information exchange and social impact.
Quasinormal modes and shadow of noncommutative black hole
Authors: Campos J. A. V. , Anacleto M. A. , Brito F. A. , Passos E. 
Published: May 2022

AbstractIn this paper we investigate quasinormal modes (QNM) for a scalar field around a noncommutative Schwarzschild black hole. We verify the effect of noncommutativity on quasinormal frequencies by applying two procedures widely used in the literature. The first is the Wentzel–Kramers–Brillouin (WKB) approximation up to sixth order. In the second case we use the continuous fraction method developed by Leaver. Besides, we also show that due to noncommutativity, the shadow radius is reduced when we increase the noncommutative parameter. In addition, we find that the shadow radius is nonzero even at the zero mass limit for finite noncommutative parameter.
Orientation selective DBS of entorhinal cortex and medial septal nucleus modulates activity of rat brain areas involved in memory and cognition
Authors: Wu Lin , Canna Antonietta , Narvaez Omar , Ma Jun , Sang Sheng , Lehto Lauri J. , Sierra Alejandra , Tanila Heikki , Zhang Yuan , Gröhn Olli , Low Walter C. , Filip Pavel , Mangia Silvia , Michaeli Shalom 
Published: May 2022

AbstractThe recently introduced orientation selective deep brain stimulation (OS-DBS) technique freely controls the direction of the electric field’s spatial gradient by using multiple contacts with independent current sources within a multielectrode array. The goal of OS-DBS is to align the electrical field along the axonal track of interest passing through the stimulation site. Here we utilized OS-DBS with a planar 3-channel electrode for stimulating the rat entorhinal cortex (EC) and medial septal nucleus (MSN), two promising areas for DBS treatment of Alzheimer’s disease. The brain responses to OS-DBS were monitored by whole brain functional magnetic resonance imaging (fMRI) at 9.4 T with Multi-Band Sweep Imaging with Fourier Transformation (MB-SWIFT). Varying the in-plane OS-DBS stimulation angle in the EC resulted in activity modulation of multiple downstream brain areas involved in memory and cognition. Contrary to that, no angle dependence of brain activations was observed when stimulating the MSN, consistent with predictions based on the electrode configuration and on the main axonal directions of the targets derived from diffusion MRI tractography and histology. We conclude that tuning the OS-DBS stimulation angle modulates the activation of brain areas relevant to Alzheimer’s disease, thus holding great promise in the DBS treatment of the disease.
X-linked palindromic gene families 4930567H17Rik and Mageb5 are dispensable for male mouse fertility
Authors: Stark-Dykema Evan R. , Dulka Eden A. , Gerlinger Emma R. , Mueller Jacob L. 
Published: May 2022

AbstractMammalian sex chromosomes are enriched for large, nearly-identical, palindromic sequences harboring genes expressed predominately in testicular germ cells. Discerning if individual palindrome-associated gene families are essential for male reproduction is difficult due to challenges in disrupting all copies of a gene family. Here we generate precise, independent, deletions to assess the reproductive roles of two X-linked palindromic gene families with spermatid-predominant expression, 4930567H17Rik and Mageb5. Sequence analyses reveals mouse 4930567H17Rik and Mageb5 are orthologs of human HSFX3 and MAGEB5, respectively, where 4930567H17Rik/HSFX3 is harbored in a palindrome in humans and mice, while Mageb5 is not. Additional sequence analyses show 4930567H17Rik and HSFX3 are rapidly diverging in rodents and primates, respectively. Mice lacking either 4930567H17Rik or Mageb5 gene families do not have detectable defects in male fertility, fecundity, spermatogenesis, or in gene regulation, but do show differences in sperm head morphology, suggesting a potential role in sperm function. We conclude that while all palindrome-associated gene families are not essential for male fertility, large palindromes influence the evolution of their associated gene families.
A formal analysis method for composition protocol based on model checking
Authors: Xiao Meihua , Zhao Hanyu , Yang Ke , Ouyang Ri , Song Weiwei 
Published: May 2022

AbstractProtocol security in a composition protocol environment has always been an open problem in the field of formal analysis and verification of security protocols. As a well-known tool to analyze and verify the logical consistency of concurrent systems, SPIN (Simple Promela Interpreter) has been widely used in the analysis and verification of the security of a single protocol. There is no special research on the verification of protocol security in a composition protocol environment. To solve this problem, firstly, a formal analysis method for composition protocol based on SPIN is proposed, and a formal description of protocol operation semantics is given. Then the attacker model is formalized, and a message specification method based on field detection and component recognition is presented to alleviate the state explosion problem. Finally, the NSB protocol and the NSL protocol are used as examples for compositional analysis. It is demonstrated that the proposed method can effectively verify the security of the protocol in a composition protocol environment and enhance the efficiency of composition protocol verification.
Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants
Authors: da Costa Clauber Henrique Souza , de Freitas Camila Auad Beltrão , Alves Cláudio Nahum , Lameira Jerônimo 
Published: May 2022

AbstractThe severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) protein receptor-binding domain (RBD) are critical for the antibody resistance and infectivity of the SARS-CoV-2 variants. In this study, we have used accelerated molecular dynamics (aMD) simulations and free energy calculations to present a systematic analysis of the affinity and conformational dynamics along with the interactions that drive the binding between Spike protein RBD and human angiotensin-converting enzyme 2 (ACE2) receptor. We evaluate the impacts of the key mutation that occur in the RBDs Omicron and other variants in the binding with the human ACE2 receptor. The results show that S protein Omicron has stronger binding to the ACE2 than other variants. The evaluation of the decomposition energy per residue shows the mutations N440K, T478K, Q493R and Q498R observed in Spike protein of SARS-CoV-2 provided a stabilization effect for the interaction between the SARS-CoV-2 RBD and ACE2. Overall, the results demonstrate that faster spreading of SARS-CoV-2 Omicron may be correlated with binding affinity of S protein RBD to ACE2 and mutations of uncharged residues to positively charged residues such as Lys and Arg in key positions in the RBD.
Intra-regional classification of Codonopsis Radix produced in Gansu province (China) by multi-elemental analysis and chemometric tools
Authors: Bai Ruibin , Wang Yanping , Fan Jingmin , Zhang Jingjing , Li Wen , Zhang Yan , Hu Fangdi 
Published: May 2022

AbstractMulti-elemental analysis is widely used to identify the geographical origins of plants. The purpose of this study was to explore the feasibility of combining chemometrics with multi-element analysis for classification of Codonopsis Radix from different producing regions of Gansu province (China). A total of 117 Codonopsis Radix samples from 7 counties of Gansu province were collected. Inductively coupled plasma mass spectrometry (ICP-MS) was used for the determination of 28 elements (39 K, 24 Mg, 44Ca, 27Al, 137Ba, 57Fe, 23Na, 88Sr, 55Mn, 66Zn, 65Cu, 85Rb, 61Ni, 53Cr, 51 V, 7Li, 208Pb, 59Co, 75As, 133Cs, 71 Ga, 77Se, 205Tl, 114Cd, 238U, 107Ag, 4Be and 202Hg). Among macro elements, 39 K showed the highest level, whereas 23Na was found to have the lowest content value. Micro elements showed the concentrations order of: 88Sr > 55Mn > 66Zn > 85Rb > 65Cu. Among trace elements, 53Cr and 61Ni showed higher content and 4Be was not detected in all samples. Intra-regions differentiation was performed by principal component analysis (PCA), cluster analysis (CA) and supervised learning algorithms such as linear discriminant analysis (LDA), k-nearest neighbors (k-NN), support vector machines (SVM), and random forests (RF). Among them, the RF model performed the best with an accuracy rate of 78.79%. Multi-elemental analysis combined with RF was a reliable method to identify the origins of Codonopsis Radix in Gansu province.
Automatic worm detection to solve overlapping problems using a convolutional neural network
Authors: Mori Shinichiro , Tachibana Yasuhiko , Suzuki Michiyo , Harada Yoshinobu 
Published: May 2022

AbstractThe nematode Caenorhabditis elegans is a powerful experimental model to investigate vital functions of higher organisms. We recently established a novel method, named "pond assay for the sensory systems (PASS)”, that dramatically improves both the evaluation accuracy of sensory response of worms and the efficiency of experiments. This method uses many worms in numbers that are impractical to count manually. Although several automated detection systems have been introduced, detection of overlapped worms remains difficult. To overcome this problem, we developed an automated worm detection system based on a deep neural network (DNN). Our DNN was based on a “YOLOv4″ one-stage detector with one-class classification (OCC) and multi-class classification (MCC). The OCC defined a single class for worms, while the MCC defined four classes for the number of overlapped worms. For the training data, a total of 2000 model sub-images were prepared by manually drawing square worm bounding boxes from 150 images. To make simulated images, a total of 10–80 model images for each class were randomly selected and randomly placed on a simulated microscope field. A total of 19,000 training datasets and 1000 validation datasets with a ground-truth bounding-box were prepared. We evaluated detection accuracy using 150 images, which were different from the training data. Evaluation metrics were detection error, precision, recall, and average precision (AP). Precision values were 0.91 for both OCC and MCC. However, the recall value for MCC (= 0.93) was higher than that for OCC (= 0.79). The number of detection errors for OCC increased with increasing the ground truth; however, that for MCC was independent of the ground truth. AP values were 0.78 and 0.90 for the OCC and the MCC, respectively. Our worm detection system with MCC provided better detection accuracy for large numbers of worms with overlapping positions than that with the OCC.