bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of replicative and translesion DNA polymerases to mutagenic bypass of canonical and atypical UV photoproducts
Authors: Vandenberg Brittany N. , Laughery Marian F. , Cordero Cameron , Plummer Dalton , Mitchell Debra , Kreyenhagen Jordan , Albaqshi Fatimah , Brown Alexander J. , Mieczkowski Piotr A. , Wyrick John J. , Roberts Steven A. 
Published: May 2023

AbstractUV exposure induces a mutation signature of C > T substitutions at dipyrimidines in skin cancers. We recently identified additional UV-induced AC > TT and A > T substitutions that could respectively cause BRAF V600K and V600E oncogenic mutations. The mutagenic bypass mechanism past these atypical lesions, however, is unknown. Here, we whole genome sequenced UV-irradiated yeast and used reversion reporters to delineate the roles of replicative and translesion DNA polymerases in mutagenic bypass of UV-lesions. Our data indicates that yeast DNA polymerase eta (pol η) has varied impact on UV-induced mutations: protecting against C > T substitutions, promoting T > C and AC > TT substitutions, and not impacting A > T substitutions. Surprisingly, deletion rad30Δ increased novel UV-induced C > A substitutions at CA dinucleotides. In contrast, DNA polymerases zeta (pol ζ) and epsilon (pol ε) participated in AC > TT and A > T mutations. These results uncover lesion-specific accurate and mutagenic bypass of UV lesions, which likely contribute to key driver mutations in melanoma.
Extensive characterization and implementation of a family of three-qubit gates at the coherence limit
Authors: Warren Christopher W. , Fernández-Pendás Jorge , Ahmed Shahnawaz , Abad Tahereh , Bengtsson Andreas , Biznárová Janka , Debnath Kamanasish , Gu Xiu , Križan Christian , Osman Amr , Fadavi Roudsari Anita , Delsing Per , Johansson Göran , Frisk Kockum Anton , Tancredi Giovanna , Bylander Jonas 
Published: May 2023

AbstractWhile all quantum algorithms can be expressed in terms of single-qubit and two-qubit gates, more expressive gate sets can help reduce the algorithmic depth. This is important in the presence of gate errors, especially those due to decoherence. Using superconducting qubits, we have implemented a three-qubit gate by simultaneously applying two-qubit operations, thereby realizing a three-body interaction. This method straightforwardly extends to other quantum hardware architectures, requires only a firmware upgrade to implement, and is faster than its constituent two-qubit gates. The three-qubit gate represents an entire family of operations, creating flexibility in the quantum-circuit compilation. We demonstrate a process fidelity of 97.90%, which is near the coherence limit of our device. We then generate two classes of entangled states, the Greenberger–Horne–Zeilinger and Dicke states, by applying the new gate only once; in comparison, decompositions into the standard gate set would have a two-qubit gate depth of two and three, respectively. Finally, we combine characterization methods and analyze the experimental and statistical errors in the fidelity of the gates and of the target states.
Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice
Authors: Gencay Yilmaz Emre , Jasinskytė Džiuginta , Robert Camille , Semsey Szabolcs , Martínez Virginia , Petersen Anders Østergaard , Brunner Katja , de Santiago Torio Ana , Salazar Alex , Turcu Iszabela Cristiana , Eriksen Melissa Kviesgaard , Koval Lev , Takos Adam , Pascal Ricardo , Schou Thea Staffeldt , Bayer Lone , Bryde Tina , Johansen Katja Chandelle , Bak Emilie Glad , Smrekar Frenk , Doyle Timothy B. , Satlin Michael J. , Gram Aurelie , Carvalho Joana , Jessen Lene , Hallström Björn , Hink Jonas , Damholt Birgitte , Troy Alice , Grove Mette , Clube Jasper , Grøndahl Christian , Haaber Jakob Krause , van der Helm Eric , Zdravkovic Milan , Sommer Morten Otto Alexander 
Published: May 2023

AbstractAntibiotic treatments have detrimental effects on the microbiome and lead to antibiotic resistance. To develop a phage therapy against a diverse range of clinically relevant Escherichia coli, we screened a library of 162 wild-type (WT) phages, identifying eight phages with broad coverage of E. coli, complementary binding to bacterial surface receptors, and the capability to stably carry inserted cargo. Selected phages were engineered with tail fibers and CRISPR–Cas machinery to specifically target E. coli. We show that engineered phages target bacteria in biofilms, reduce the emergence of phage-tolerant E. coli and out-compete their ancestral WT phages in coculture experiments. A combination of the four most complementary bacteriophages, called SNIPR001, is well tolerated in both mouse models and minipigs and reduces E. coli load in the mouse gut better than its constituent components separately. SNIPR001 is in clinical development to selectively kill E. coli, which may cause fatal infections in hematological cancer patients.
Dupilumab in patients with prurigo nodularis: two randomized, double-blind, placebo-controlled phase 3 trials
Authors: Yosipovitch Gil , Mollanazar Nicholas , Ständer Sonja , Kwatra Shawn G. , Kim Brian S. , Laws Elizabeth , Mannent Leda P. , Amin Nikhil , Akinlade Bolanle , Staudinger Heribert W. , Patel Naimish , Yancopoulos George D. , Weinreich David M. , Wang Sheldon , Shi Genming , Bansal Ashish , O’Malley John T. 
Published: May 2023

AbstractPrurigo nodularis (PN) is a chronic inflammatory skin disease with intensely pruritic nodules. The LIBERTY-PN PRIME and PRIME2 phase 3 trials enrolled adults with PN with ≥20 nodules and severe itch uncontrolled with topical therapies. Dupilumab, a fully human monoclonal antibody, blocks the shared receptor component for interleukin (IL)-4 and IL-13. Patients were randomized 1:1 to 300 mg dupilumab or placebo subcutaneously every 2 weeks for 24 weeks. The primary endpoint was pruritus improvement, measured by proportion of patients with a ≥4-point reduction in Worst Itch Numeric Rating Scale (WI-NRS) from baseline at week 24 (PRIME) or week 12 (PRIME2). Key secondary endpoints included nodule number reduction to ≤5 at week 24. PRIME and PRIME2 enrolled 151 and 160 patients, respectively. Both trials met all the pre-specified primary and key secondary endpoints. A ≥4-point WI-NRS reduction at week 24 in the dupilumab and placebo arms was achieved by 60.0% and 18.4% of patients, respectively, in PRIME (95% confidence interval (CI), 27.8–57.7 for the difference, P < 0.001) and at week 12 by 37.2% and 22.0% of patients, respectively, in PRIME2 (95% CI, 2.3–31.2; P = 0.022). Dupilumab demonstrated clinically meaningful and statistically significant improvements in itch and skin lesions versus placebo in PN. Safety was consistent with the known dupilumab safety profile.ClinicalTrials.gov identifiers: NCT04183335 and NCT04202679.
Design of electromagnetic metasurface using two dimensional crystal nets
Authors: Hou Jie , Zhang Xiaohong , Guo Ying , Zhang Rui-Zhi , Guo Meng 
Published: May 2023

AbstractMetasurfaces are of great interest as they exhibit unique electromagnetic properties. Currently, metasurface design focuses on generating new meta-atoms and their combinations. Here a topological database, reticular chemistry structure resource (RCSR), is introduced to bring a new dimension and more possibilities for metasurface design. RCSR has over 200 two-dimensional crystal nets, among which 72 are identified as suitable for metasurface design. Using a simple metallic cross as the metaatom, 72 metasurfaces are constructed from the atom positions and lattice vectors of the crystal nets templates. The transmission curves of all the metasurfaces are calculated using the finite-difference time-domain method. The calculated transmission curves have good diversity, showing that the crystal nets approach is a new engineering dimension for metasurface design. Three clusters are found for the calculated curves using the K-means algorithm and principal component analysis. The structure–property relationship between metasurface topology and transmission curve is investigated, but no simple descriptor has been found, indicating that further work is still needed. The crystal net design approach developed in this work can be extended to three-dimensional design and other types of metamaterials like mechanical materials.
Continued fractions and the Thomson problem
Authors: Moscato Pablo , Haque Mohammad Nazmul , Moscato Anna 
Published: May 2023

AbstractWe introduce new analytical approximations of the minimum electrostatic energy configuration of n electrons, E(n), when they are constrained to be on the surface of a unit sphere. Using 453 putative optimal configurations, we searched for approximations of the form $$E(n) = (n^2/2) \, e^{g(n)}$$

E

(
n
)

=

(

n
2

/
2
)

e

g
(
n
)

where g(n) was obtained via a memetic algorithm that searched for truncated analytic continued fractions finally obtaining one with Mean Squared Error equal to $${5.5549 \times 10^{-8}}$$

5.5549
×

10

-
8

for the model of the normalized energy ($$E_n(n) \equiv e^{g(n)} \equiv 2E(n)/n^2$$

E
n

(
n
)

≡

e

g
(
n
)

≡
2
E

(
n
)

/

n
2

). Using the Online Encyclopedia of Integer Sequences, we searched over 350,000 sequences and, for small values of n, we identified a strong correlation of the highest residual of our best approximations with the sequence of integers n defined by the condition that $$n^2+12$$

n
2

+
12

is a prime. We also observed an interesting correlation with the behavior of the smallest angle $$\alpha (n)$$

α
(
n
)

, measured in radians, subtended by the vectors associated with the nearest pair of electrons in the optimal configuration. When using both $$\sqrt{n}$$

n

and $$\alpha (n)$$

α
(
n
)

as variables a very simple approximation formula for $$E_n(n)$$

E
n

(
n
)

was obtained with MSE= $$7.9963 \times 10^{-8}$$

7.9963
×

10

-
8

and MSE= 73.2349 for E(n). When expanded as a power series in infinity, we observe that an unknown constant of an expansion as a function of $$n^{-1/2}$$

n

-
1
/
2

of E(n) first proposed by Glasser and Every in 1992 as $$-1.1039$$

-
1.1039

, and later refined by Morris, Deaven and Ho as $$-1.104616$$

-
1.104616

in 1996, may actually be very close to −1.10462553440167 when the assumed optima for $$n\le 200$$

n
≤
200

are used.
Efficient MIR crosstalk reduction based on silicon-on-calcium fluoride platform with Ge/Si strip arrays
Authors: Elgammal Nayira M. , Younis B. M. , Gaafar Mahmoud A. , Elkholy M. M. , Hameed Mohamed Farhat O. , Obayya S. S. A. 
Published: May 2023

AbstractReduction of the crosstalk (CT) between contiguous photonic components is still a big challenge in fabricating high packing density photonic integrated circuits (PICs). Few techniques to accomplish that goal have been offered in recent years but all in the near-IR region. In this paper, we report a design for realizing a highly efficient CT reduction in the MIR regime, for the first time to the best of our knowledge. The reported structure is based on the silicon-on-calcium-fluoride (SOCF) platform with uniform Ge/Si strip arrays. Using Ge strips shows better CT reduction and longer coupling length (Lc) than the conventional Si based devices over a wide bandwidth in the MIR region. The effect of adding a different number of Ge and Si strips with different dimensions between two adjacent Si waveguides on the Lc and hence on the CT is analyzed using both full vectorial finite element method and 3D finite difference time domain method. An increase in the Lc by 4 orders of magnitude and 6.5 times are obtained using Ge and Si strips, respectively, compared to strips-free Si waveguides. Consequently, crosstalk suppression of − 35 dB and − 10 dB for the Ge and Si strips, respectively, is shown. The proposed structure is beneficial for high packing density nanophotonic devices in the MIR regime, such as switches, modulators, splitters, and wavelength division (de)multiplexers, which are important for MIR communication integrated circuits, spectrometers, and sensors.
A data-driven approach to quantify disparities in power outages
Authors: Bhattacharyya Arkaprabha , Hastak Makarand 
Published: May 2023

AbstractThis research proposes a data-driven approach to identify possible disparities in a utility’s outage management practices. The approach has been illustrated for an Investor-Owned Utility located in the Midwest region in the U.S. Power outage data for approximately 5 years between March 2017 and January 2022 was collected for 36 ZIP/postal codes located within the utility’s service territory. The collected data was used to calculate the total number of outages, customers affected, and the duration of outages during those 5 years for each ZIP code. Next, each variable was normalized with respect to the population density of the ZIP code. After normalizing, a K-means clustering algorithm was implemented that created five clusters out of those 36 ZIP codes. The difference in the outage parameters was found to be statistically significant. This indicated differential experience with power outages in different ZIP codes. Next, three Generalized Linear Models were developed to test if the presence of critical facilities such as hospitals, 911 centers, and fire stations, as socioeconomic and demographic characteristics of the ZIP codes, can explain their differential experience with the power outage. It was found that the annual duration of outages is lower in the ZIP codes where critical facilities are located. On the other hand, ZIP codes with lower median household income have experienced more power outages, i.e., higher outage counts in those 5 years. Lastly, the ZIP codes with a higher percentage of the White population have experienced more severe outages that have affected more customers.
Morphodynamical cell state description via live-cell imaging trajectory embedding
Authors: Copperman Jeremy , Gross Sean M. , Chang Young Hwan , Heiser Laura M. , Zuckerman Daniel M. 
Published: May 2023

AbstractTime-lapse imaging is a powerful approach to gain insight into the dynamic responses of cells, but the quantitative analysis of morphological changes over time remains challenging. Here, we exploit the concept of “trajectory embedding” to analyze cellular behavior using morphological feature trajectory histories—that is, multiple time points simultaneously, rather than the more common practice of examining morphological feature time courses in single timepoint (snapshot) morphological features. We apply this approach to analyze live-cell images of MCF10A mammary epithelial cells after treatment with a panel of microenvironmental perturbagens that strongly modulate cell motility, morphology, and cell cycle behavior. Our morphodynamical trajectory embedding analysis constructs a shared cell state landscape revealing ligand-specific regulation of cell state transitions and enables quantitative and descriptive models of single-cell trajectories. Additionally, we show that incorporation of trajectories into single-cell morphological analysis enables (i) systematic characterization of cell state trajectories, (ii) better separation of phenotypes, and (iii) more descriptive models of ligand-induced differences as compared to snapshot-based analysis. This morphodynamical trajectory embedding is broadly applicable to the quantitative analysis of cell responses via live-cell imaging across many biological and biomedical applications.
Cells sorted off hiPSC-derived kidney organoids coupled with immortalized cells reliably model the proximal tubule
Authors: Banan Sadeghian Ramin , Ueno Ryohei , Takata Yuji , Kawakami Akihiko , Ma Cheng , Araoka Toshikazu , Takasato Minoru , Yokokawa Ryuji 
Published: May 2023

AbstractOf late, numerous microphysiological systems have been employed to model the renal proximal tubule. Yet there is lack of research on refining the functions of the proximal tubule epithelial layer—selective filtration and reabsorption. In this report, pseudo proximal tubule cells extracted from human-induced pluripotent stem cell-derived kidney organoids are combined and cultured with immortalized proximal tubule cells. It is shown that the cocultured tissue is an impervious epithelium that offers improved levels of certain transporters, extracellular matrix proteins collagen and laminin, and superior glucose transport and P-glycoprotein activity. mRNA expression levels higher than those obtained from each cell type were detected, suggesting an anomalous synergistic crosstalk between the two. Alongside, the improvements in morphological characteristics and performance of the immortalized proximal tubule tissue layer exposed, upon maturation, to human umbilical vein endothelial cells are thoroughly quantified and compared. Glucose and albumin reabsorption, as well as xenobiotic efflux rates through P-glycoprotein were all improved. The data presented abreast highlight the advantages of the cocultured epithelial layer and the non-iPSC-based bilayer. The in vitro models presented herein can be helpful in personalized nephrotoxicity studies.
Knowledge graph-enhanced molecular contrastive learning with functional prompt
Authors: Fang Yin , Zhang Qiang , Zhang Ningyu , Chen Zhuo , Zhuang Xiang , Shao Xin , Fan Xiaohui , Chen Huajun 
Published: May 2023

AbstractDeep learning models can accurately predict molecular properties and help making the search for potential drug candidates faster and more efficient. Many existing methods are purely data driven, focusing on exploiting the intrinsic topology and construction rules of molecules without any chemical prior information. The high data dependency makes them difficult to generalize to a wider chemical space and leads to a lack of interpretability of predictions. Here, to address this issue, we introduce a chemical element-oriented knowledge graph to summarize the basic knowledge of elements and their closely related functional groups. We further propose a method for knowledge graph-enhanced molecular contrastive learning with functional prompt (KANO), exploiting external fundamental domain knowledge in both pre-training and fine-tuning. Specifically, with element-oriented knowledge graph as a prior, we first design an element-guided graph augmentation in contrastive-based pre-training to explore microscopic atomic associations without violating molecular semantics. Then, we learn functional prompts in fine-tuning to evoke the downstream task-related knowledge acquired by the pre-trained model. Extensive experiments show that KANO outperforms state-of-the-art baselines on 14 molecular property prediction datasets and provides chemically sound explanations for its predictions. This work contributes to more efficient drug design by offering a high-quality knowledge prior, interpretable molecular representation and superior prediction performance.
Study on Hopf bifurcation types and dominant parameters of grid‐connected voltage source converter considering non‐linear saturation elements
Authors: Xu Yanhui , Cheng Yundan , Liu Hui , Zheng Le 
Published: May 2023

AbstractSubsynchronous oscillation events of grid‐connected voltage source converter (VSC) pose a potential risk to the security and stability of power systems. It is particularly challenging to reveal the subsynchronous oscillation mechanism precisely because the grid‐connected VSC consists of non‐linear components such as saturation. The describing function and the generalized Nyquist criterion are used in this paper to investigate the bifurcation types and dominant parameters of grid‐connected VSC. First, the condition of a supercritical Hopf bifurcation is investigated, which generates subsynchronous oscillations. Then, the dominant parameters of supercritical Hopf bifurcation are deduced, including the grid strength, the active power reference, or the proportional coefficient of phase‐locked loop. Finally, it is examined how the saturation's limit value impacts the limit cycle's amplitude and stability. The findings demonstrate that a system's stability depends on whether its closed‐loop frequency characteristic curve intersects the describing function's negative reciprocal curve. When the two curves intersect, the supercritical Hopf bifurcation appears, and changing the limit value can affect the limit cycle's amplitude. However, if the two curves do not intersect, altering the limit value cannot cause the supercritical Hopf bifurcation, and the subsynchronous oscillation will not happen. Variations in grid strength, active power reference, or proportional coefficient of phase‐locked loop will significantly affect the Nyquist curve, determining if supercritical Hopf bifurcation appears.
A novel scheme based on information theory and transfer learning for multi classes motor imagery decoding
Authors: Parchami Jaber , Sarbishaei Ghazaleh 
Published: May 2023

AbstractThe most important challenges of classifying Motor Imagery tasks based on the EEG signal are low signal‐to‐noise ratio, non‐stationarity, and the high subject dependence of the EEG signal. In this study, a framework for multi‐class decoding of Motor Imagery signals is presented. This framework is based on information theory and hybrid deep learning along with transfer learning. In this study, the OVR‐FBDiv method, which is based on the symmetric Kullback—Leibler divergence, is used to differentiate between features of different classes and highlight them. Then, the mRMR algorithm is used to select the most distinctive features obtained from the filters of symmetric KL divergence. Finally, a hybrid deep neural network consisting of CNN and LSTM is used to learn the spatial and temporal features of the EEG signal along with the transfer learning technique to overcome the problem of subject dependence in EEG signals. The average value of Kappa for the classification of 4‐class Motor Imagery data on BCI competition IV dataset 2a by the proposed method is 0.84. Also, the proposed method is compared with other state‐of‐the‐art methods.