bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting lymph node metastasis from primary tumor histology and clinicopathologic factors in colorectal cancer using deep learning
Authors: Krogue Justin D. , Azizi Shekoofeh , Tan Fraser , Flament-Auvigne Isabelle , Brown Trissia , Plass Markus , Reihs Robert , Müller Heimo , Zatloukal Kurt , Richeson Pema , Corrado Greg S. , Peng Lily H. , Mermel Craig H. , Liu Yun , Chen Po-Hsuan Cameron , Gombar Saurabh , Montine Thomas , Shen Jeanne , Steiner David F. , Wulczyn Ellery 
Published: April 2023

Abstract
Background
Presence of lymph node metastasis (LNM) influences prognosis and clinical decision-making in colorectal cancer. However, detection of LNM is variable and depends on a number of external factors. Deep learning has shown success in computational pathology, but has struggled to boost performance when combined with known predictors.

Methods
Machine-learned features are created by clustering deep learning embeddings of small patches of tumor in colorectal cancer via k-means, and then selecting the top clusters that add predictive value to a logistic regression model when combined with known baseline clinicopathological variables. We then analyze performance of logistic regression models trained with and without these machine-learned features in combination with the baseline variables.

Results
The machine-learned extracted features provide independent signal for the presence of LNM (AUROC: 0.638, 95% CI: [0.590, 0.683]). Furthermore, the machine-learned features add predictive value to the set of 6 clinicopathologic variables in an external validation set (likelihood ratio test, p < 0.00032; AUROC: 0.740, 95% CI: [0.701, 0.780]). A model incorporating these features can also further risk-stratify patients with and without identified metastasis (p < 0.001 for both stage II and stage III).

Conclusion
This work demonstrates an effective approach to combine deep learning with established clinicopathologic factors in order to identify independently informative features associated with LNM. Further work building on these specific results may have important impact in prognostication and therapeutic decision making for LNM. Additionally, this general computational approach may prove useful in other contexts.
Adaptive spectroscopic visible-light optical coherence tomography for clinical retinal oximetry
Authors: Rubinoff Ian , Kuranov Roman V. , Fang Raymond , Ghassabi Zeinab , Wang Yuanbo , Beckmann Lisa , Miller David A. , Wollstein Gadi , Ishikawa Hiroshi , Schuman Joel S. , Zhang Hao F. 
Published: April 2023

Abstract
Background
Retinal oxygen saturation (sO2) provides essential information about the eye’s response to pathological changes that can result in vision loss. Visible-light optical coherence tomography (vis-OCT) is a noninvasive tool that has the potential to measure retinal sO2 in a clinical setting. However, its reliability is currently limited by unwanted signals referred to as spectral contaminants (SCs), and a comprehensive strategy to isolate true oxygen-dependent signals from SCs in vis-OCT is lacking.

Methods
We develop an adaptive spectroscopic vis-OCT (ADS-vis-OCT) technique that can adaptively remove SCs and accurately measure sO2 under the unique conditions of each vessel. We also validate the accuracy of ADS-vis-OCT using ex vivo blood phantoms and assess its repeatability in the retina of healthy volunteers.

Results
In ex vivo blood phantoms, ADS-vis-OCT agrees with a blood gas machine with only a 1% bias in samples with sO2 ranging from 0% to 100%. In the human retina, the root mean squared error between sO2 values in major arteries measured by ADS-vis-OCT and a pulse oximeter is 2.1% across 18 research participants. Additionally, the standard deviations of repeated ADS-vis-OCT measurements of sO2 values in smaller arteries and veins are 2.5% and 2.3%, respectively. Non-adaptive methods do not achieve comparable repeatabilities from healthy volunteers.

Conclusions
ADS-vis-OCT effectively removes SCs from human images, yielding accurate and repeatable sO2 measurements in retinal arteries and veins with varying diameters. This work could have important implications for the clinical use of vis-OCT to manage eye diseases.
Adaptive p‐norm weighted cyclic algorithm‐new algorithm for designing unimodular multiple input multiple output radar waveforms with good correlations
Authors: Liu Tianqu , Sun Jinping , Wang Guohua , Du Xiaoyong , Hu Weidong 
Published: April 2023

AbstractThis letter formulates a high‐dimensional multi‐objective optimization model to minimize all correlation function values for multiple input multiple output (MIMO) radar waveforms. Then, to solve this problem, this letter proposes an adaptive weighted cyclic algorithm‐new (CAN), named p‐norm weighted cyclic algorithm‐new (p‐WeCAN). Specifically, the adaptive weight updating function is constructed using p‐norm to minimize peak side‐lobe level (PSL) and integrated side‐lobe level (ISL) simultaneously. Numerical results show that the p‐norm weighted cyclic algorithm‐new obtains similar PSL values as the best PSL minimization algorithm and low integrated side‐lobe level values close to its lower bound at the same time.
Multiregression spatially variant blur kernel estimation based on inter‐kernel consistency
Authors: Kim Min Hyuk , Yun Jun‐Seok , Yoo Seok Bong 
Published: April 2023

AbstractMost single‐image super‐resolution (SR) models suffer from the degradation of image restoration performance when restoring a high‐resolution (HR) image from a low‐resolution (LR) image downscaled using an unknown blur kernel. The spatially invariant blur kernel estimators have been proposed to predict the blur kernel to address this issue. Nevertheless, the spatially variant blur exists in the real‐world; thus, these blur kernel estimators are unsuitable for real‐world applications. Although the spatially variant blur kernel estimators have been proposed, SR models still suffer from performance degradation because these estimators do neither consider the consistency between surrounding blur kernels nor refine non‐parametric blur kernels as parameters. To address this problem, the authors propose a multiregression spatially variant blur kernel estimation based on inter‐kernel consistency. The proposed estimator consists of three parts: non‐parametric regression, an inter‐kernel consistency block, and parametric regression. Specifically, it predicts spatially variant blur kernels while considering the inter‐kernel consistency between nearby blur kernels. Our source codes with pretrained models are available on https://github.com/alsgur0720/multiregression.
A mode switching based transient ride‐through phase‐locked loop
Authors: Fan Yiwen , Han Minxiao , Zhang Li , Wang Shuozhe , Sun Tiankui 
Published: April 2023

AbstractIn the case of grid voltage quality problems, the traditional phase‐locked loop (PLL) is hard to detect the accurate grid frequency and phase during the transient response, which will be detrimental to the transient synchronous stability of grid‐connected inverters. This paper proposes a mode switching based transient ride‐through PLL (TRT‐PLL), aiming to improve the transient phase‐locking performance through detection technique and mode switching. The TRT‐PLL incorporates a hybrid filter (HF), a dual‐speed detection module, and a state switch into the traditional synchronous reference frame PLL (SRF‐PLL) structure. The theoretical analysis and paradigm design of TRT‐PLL is presented in detail. Digital simulations and physical experiments are carried out for the comparisons with other existed PLL techniques. The results demonstrate that the satisfied transient performance of the TRT‐PLL has significant advantages, especially in the event of phase jumps.
Population study on MHD wind-driven disc evolution
Authors: Weder Jesse , Mordasini Christoph , Emsenhuber Alexandre 
Published: April 2023

Context. Current research has established magnetised disc winds as a promising way of driving accretion in protoplanetary discs.
Aims. We investigate the evolution of large protoplanetary disc populations under the influence of magnetically driven disc winds as well as internal and external photoevaporation. We aim to constrain magnetic disc wind models through comparisons with observations.
Methods. We ran 1D vertically integrated evolutionary simulations for low-viscosity discs, including magnetic braking and various outflows. The initial conditions were varied and chosen to produce populations that are representative of actual disc populations inferred from observations. We then compared the observables from the simulations (e.g. stellar accretion rate, disc mass evolution, disc lifetime, etc.) with observational data.
Results. Our simulations show that to reach stellar accretion rates comparable to those found by observations (~10−8 M⊙ yr−1), it is necessary to have access not only to strong magnetic torques, but weak magnetic winds as well. The presence of a strong magnetic disc wind, in combination with internal photoevaporation, leads to the rapid opening of an inner cavity early on, allowing the stellar accretion rate to drop while the disc is still massive. Furthermore, our model supports the notion that external photoevaporation via the ambient far-ultraviolet radiation of surrounding stars is a driving force in disc evolution and could potentially exert a strong influence on planetary formation.
Conclusions. Our disc population syntheses show that for a subset of magnetohydrodynamic wind models (weak disc wind, strong torque), it is possible to reproduce important statistical observational constraints. The magnetic disc wind paradigm thus represents a novel and appealing alternative to the classical α-viscosity scenario.
Self-Complementary Dimer of Zinc(II) Porphyrins through Coordination with Oxygen Ligands
Authors: Ke Yuanzhen , Liu Zhichang , Luh Tien-Yau , Wang Hsian-Wen 
Published: April 2023

AbstractOxygen ligands have been shown to play a critical role in the formation and organization of metalloporphyrin assemblies and natural chlorosomes. In this work, mutually complementary head-to-tail dimers of zinc(II) porphyrins were synthesized through the coordination of zinc with the imide group and 7-oxanorbornene oxygen ligands. UV/Vis absorption and emission, 1H NMR as well as FT-IR analyses were used to determine the structure. The dimerization association constant K has been determined to be 5.6 M–1 and 29 M–1, respectively, by the dilution experiment.
Negative Pressure Pulmonary Edema after Bilateral Nasal Packing following Transsphenoidal Pituitary Surgery for Nonfunctioning Pituitary Tumor
Authors: Singh Apoorva , Mahajan Shalvi , Aghi Shweta , Kumar Sanjay 
Published: April 2023

AbstractNegative pressure pulmonary edema (NPPE) is a well-known, albeit infrequent complication caused by upper airway obstruction. It may be seen after extubation following general anesthesia due to excessive negative intrathoracic pressure exerted against an obstructed upper airway. This leads to fluid extravasation from the pulmonary capillaries into the alveolar spaces and lung parenchyma. We report a case of NPPE after endoscopic transsphenoidal resection of the nonfunctional pituitary tumor, which occurred secondary to bilateral nasal packing. Reintubation and positive pressure ventilation were used to manage the patient, who was later extubated after the resolution of features of NPPE.
Dental Professionals' Awareness on Updated Guidelines for Basic Life Support in COVID-19 Patients
Authors: Abhilasha Kumari , Jayanthi D. , Vivekananda Lalith 
Published: April 2023

Abstract
Background Members of dental fraternity have a duty of care to provide safe services to the patients. The satisfactory performance in a medical emergency in dental practice has wide-range implications. But, in the current scenario, the challenge is to ensure that patients with or without coronavirus disease 2019 (COVID-19), who undergo any medical emergency, get the best possible chance of survival without compromising the safety of rescuers, who will be needed to take care for future patients.
Aim This article assesses the awareness and knowledge on interim guidelines for Basic Life Support in adults with suspected or confirmed COVID-19 among various dental health care professionals.
Materials and Methods An online questionnaire-based survey was conducted; framed in Google Forms and sent to various dental health care professionals through WhatsApp, email, and other means. Results were then analyzed and are presented in the form of frequency and percentage.
Results In the study, 224 responders were included comprising undergraduates, postgraduates, and dental practitioners. Dismally, none of them had complete knowledge on the interim guidance for Basic Life Support for suspected or confirmed COVID-19 patients.
Conclusion The study suggests that updated interim guidelines were unknown to maximum percentage of dental professionals which implies that there is need to keep ourselves up-to-date to provide safe services.
Structures of Vac8-containing protein complexes reveal the underlying mechanism by which Vac8 regulates multiple cellular processes
Authors: Kim Hyejin , Park Jihyeon , Kim Hyunwoo , Ko Naho , Park Jumi , Jang Eunhong , Yoon So Young , Diaz Joyce Anne R. , Lee Changwook , Jun Youngsoo 
Published: April 2023

Vac8, a yeast vacuolar protein with armadillo repeats, mediates various cellular processes by changing its binding partners; however, the mechanism by which Vac8 differentially regulates these processes remains poorly understood. Vac8 interacts with Nvj1 to form the nuclear–vacuole junction (NVJ) and with Atg13 to mediate cytoplasm-to-vacuole targeting (Cvt), a selective autophagy-like pathway that delivers cytoplasmic aminopeptidase I directly to the vacuole. In addition, Vac8 associates with Myo2, a yeast class V myosin, through its interaction with Vac17 for vacuolar inheritance from the mother cell to the emerging daughter cell during cell divisions. Here, we determined the X-ray crystal structure of the Vac8–Vac17 complex and found that its interaction interfaces are bipartite, unlike those of the Vac8–Nvj1 and Vac8–Atg13 complexes. When the key amino acids present in the interface between Vac8 and Vac17 were mutated, vacuole inheritance was severely impaired in vivo. Furthermore, binding of Vac17 to Vac8 prevented dimerization of Vac8, which is required for its interactions with Nvj1 and Atg13, by clamping the H1 helix to the ARM1 domain of Vac8 and thereby preventing exposure of the binding interface for Vac8 dimerization. Consistently, the binding affinity of Vac17-bound Vac8 for Nvj1 or Atg13 was markedly lower than that of free Vac8. Likewise, free Vac17 had no affinity for the Vac8–Nvj1 and Vac8–Atg13 complexes. These results provide insights into how vacuole inheritance and other Vac8-mediated processes, such as NVJ formation and Cvt, occur independently of one another.
Consequences of poly(ethylene oxide) and poloxamer P188 on transcription in healthy and stressed myoblasts
Authors: Crabtree Adelyn A. , Boehnke Natalie , Bates Frank S. , Hackel Benjamin J. 
Published: April 2023

Poly(ethylene oxide) (PEO) and poloxamers, a class of poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers, have many personal and medical care applications, including the stabilization of stressed cellular membranes. Despite the widespread use, the cellular transcriptional response to these molecules is relatively unknown. C2C12 myoblasts, a model muscle cell, were subjected to short-term Poloxamer 188 (P188) and PEO181(8,000 g/mol) treatment in culture. RNA was extracted and sequenced to quantify transcriptomic impact. The addition of moderate concentrations (14 µM) of either polymer to unstressed cells caused substantial differential gene expression, including at least twofold modulation of 357 and 588 genes, respectively. In addition, evaluation of the transcriptome response to osmotic stress without polymer treatment revealed dramatic change in RNA expression. Interestingly, the addition of polymer to stressed cells—at concentrations that provide physiological protection—did not yield a significant difference in expression of any gene relative to stress alone. Genome-scale expression analysis was corroborated by single-gene quantitative real-time PCR. Changes in protein expression were measured via western blot, which revealed partial alignment with the RNA results. Collectively, the significant changes to expression of multiple genes and resultant protein translation demonstrates an unexpectedly broad biochemical response to these polymers in healthy myoblasts in vitro. Meanwhile, the lack of substantial transcriptional response to polymer treatment in stressed cells highlights the physical nature of that protective mechanism.
The origin of blinking in both mudskippers and tetrapods is linked to life on land
Authors: Aiello Brett R. , Bhamla M. Saad , Gau Jeff , Morris John G. L. , Bomar Kenji , da Cunha Shashwati , Fu Harrison , Laws Julia , Minoguchi Hajime , Sripathi Manognya , Washington Kendra , Wong Gabriella , Shubin Neil H. , Sponberg Simon , Stewart Thomas A. 
Published: April 2023

Blinking, the transient occlusion of the eye by one or more membranes, serves several functions including wetting, protecting, and cleaning the eye. This behavior is seen in nearly all living tetrapods and absent in other extant sarcopterygian lineages suggesting that it might have arisen during the water-to-land transition. Unfortunately, our understanding of the origin of blinking has been limited by a lack of known anatomical correlates of the behavior in the fossil record and a paucity of comparative functional studies. To understand how and why blinking originates, we leverage mudskippers (Oxudercinae), a clade of amphibious fishes that have convergently evolved blinking. Using microcomputed tomography and histology, we analyzed two mudskipper species,
Periophthalmus barbarus
and
Periophthalmodon septemradiatus
, and compared them to the fully aquatic round goby,
Neogobius melanostomus
. Study of gross anatomy and epithelial microstructure shows that mudskippers have not evolved novel musculature or glands to blink. Behavioral analyses show the blinks of mudskippers are functionally convergent with those of tetrapods:
P. barbarus
blinks more often under high-evaporation conditions to wet the eye, a blink reflex protects the eye from physical insult, and a single blink can fully clean the cornea of particulates. Thus, eye retraction in concert with a passive occlusal membrane can achieve functions associated with life on land. Osteological correlates of eye retraction are present in the earliest limbed vertebrates, suggesting blinking capability. In both mudskippers and tetrapods, therefore, the origin of this multifunctional innovation is likely explained by selection for increasingly terrestrial lifestyles.
Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM
Authors: Highland Carolyn M. , Tan Aaron , Ricaña Clifton L. , Briggs John A. G. , Dick Robert A. 
Published: April 2023

The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but detailed structural information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryoelectron tomography and single particle analysis (SPA) cryoelectron microscopy to determine structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a method of liposome scaffold-based in vitro lattice assembly (“lattice templating”) that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (lenacapavir). Our work reveals key structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and SPA as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds.
Noun phrases in mixed Martinican Creole and French
Authors: Vaillant Pascal 
Published: April 2023

AbstractContact between French and Martinican Creole (MC) takes place in a society where bilingualism is the standard, in a situation of constant language mixing. French and MC, although related, show significant typological divergences on some specific features, e.g. the order between noun and definite determiner in the noun phrase, or the use of a linker to mark a possessive embedded noun phrase. In this paper, I explore the possible combination of the different values of these features in mixed noun phrases occurring in corpora. I inquire about the possible parameters which may influence the outcome and explain the relative frequencies of these different combinations. It appears that there is a partially common pool of elementary structures. Many utterances fall into the category termed byMuysken (2000)‘congruent lexicalization’. I also observe that apparent complex double embeddings have an internal logic, as they result from adjunction of multi-word modifiers. Finally I propose a model which accounts for the observed occurrences by postulating a level in the speech generation process where language itself is underspecified, and where it is in a position to be specified on the fly by contextual factors, coming either from the lexicon or from the constructional frame.
Exploring the structural, optoelectronic, elastic, and thermoelectric properties of cubic ternary fluoro-perovskites sodium based NaMF3 (M = Si and Ge) compounds for heterojunction solar cells applications
Authors: Rahman Nasir , Husain Mudasser , Sohail Mohammad , Khan Rajwali , Zaman Tahir , Neffati Riadh , Murtaza Ghulam , Khan Aurangzeb , Khan Abid Ali , Iqbal Zaffar 
Published: April 2023

Abstract
In the current research, the structural, optoelectronic, elastic, and thermoelectric properties of NaMF3 (M = Si and Ge) ternary halide perovskites compounds are computed within the DFT framework using first-principle modeling. The obtained results of phonons dispersion curves and the tolerance factor is calculated for NaSiF3 and NaGeF3 and is found to be 1.001 and 1.004 respectively, which reveals that these compounds are structurally and thermodynamically stable in the cubic phase. The elastic constants and other mechanical parameters demonstrate that these compounds are mechanically stable, hard to scratch, ductile, anisotropic, and possess resistance to plastic distortion. The band structure and density of states (DOS) demonstrate that NaSiF3 and NaGeF3 compounds are semiconductors and possess a direct band gap of 1.15 eV and 3.31 eV respectively from ‘R-R’ symmetries points. The optical properties are investigated and it is observed that the selected compounds possesses strong optical conduction and absorption coefficients and are transparent at low incident photons energy ranges. This led us to the conclusion that for high-fRequency UV devices, these compounds possess suitable applications. The thermoelectric properties indicate that both materials possess notable power factors and figures of merit (ZT), due to which their applications in solar cells can be deemed. To our knowledge, this is the first theoretical computational systematic study of structural, optoelectronic, elastic, and thermoelectric properties for NaMF3 (M = Si and Ge), which will be experimentally validated. Our findings add comprehensive insight into predicting high-performance Heterojunction Solar Cells.