bluuebunny/crossref_metadata_2025_split huggingface dataset:
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions
Authors: Wu Yifan , Gao Min , Zeng Min , Zhang Jie , Li Min 
Published: March 2022

AbstractMotivationExploring drug–protein interactions (DPIs) provides a rapid and precise approach to assist in laboratory experiments for discovering new drugs. Network-based methods usually utilize a drug–protein association network and predict DPIs by the information of its associated proteins or drugs, called ‘guilt-by-association’ principle. However, the ‘guilt-by-association’ principle is not always true because sometimes similar proteins cannot interact with similar drugs. Recently, learning-based methods learn molecule properties underlying DPIs by utilizing existing databases of characterized interactions but neglect the network-level information.ResultsWe propose a novel method, namely BridgeDPI. We devise a class of virtual nodes to bridge the gap between drugs and proteins and construct a learnable drug–protein association network. The network is optimized based on the supervised signals from the downstream task—the DPI prediction. Through information passing on this drug–protein association network, a Graph Neural Network can capture the network-level information among diverse drugs and proteins. By combining the network-level information and the learning-based method, BridgeDPI achieves significant improvement in three real-world DPI datasets. Moreover, the case study further verifies the effectiveness and reliability of BridgeDPI.Availability and implementationThe source code of BridgeDPI can be accessed at https://github.com/SenseTime-Knowledge-Mining/BridgeDPI. The source data used in this study is available on the https://github.com/IBM/InterpretableDTIP (for the BindingDB dataset), https://github.com/masashitsubaki/CPI_prediction (for the C.ELEGANS and HUMAN) datasets, http://dude.docking.org/ (for the DUD-E dataset), repectively.
Clinical Risk Factors Associated With Late-Onset Invasive Group B Streptococcal Disease: Systematic Review and Meta-Analyses
Authors: Karampatsas Konstantinos , Davies Hannah , Mynarek Maren , Andrews Nick , Heath Paul T , Le Doare Kirsty 
Published: March 2022

Abstract

Background
Group B streptococcal (GBS) infection remains one of the most significant causes of late-onset sepsis and meningitis (LOGBS) among young infants. However, transmission routes and risk factors for LOGBS are not yet fully understood.

Methods
We conducted systematic reviews on clinical risk factors previously reported in the literature (prematurity, low birth weight [&lt;2500 g], antenatal colonization, multiple-gestation pregnancy, maternal age &lt;20 years, male infant sex, intrapartum fever, prolonged rupture of membranes) and meta-analyses to determine pooled estimates of risk.

Results
We included 27 articles, reporting 5315 cases. Prematurity (odds ratio [OR] 5.66; 95% confidence interval [CI]: 4.43–7.22), low birth weight (OR 6.73; 95% CI: 4.68–9.67), maternal colonization (2.67; [2.07–3.45]), and multiple-gestation pregnancies (OR 8.01; 95% CI: 5.19–12.38) were associated with an increased risk of LOGBS.

Conclusions
Prematurity/low birth weight and maternal colonization are major risk factors for LOGBS. Future GBS vaccine studies should try to establish the optimal time for vaccination during pregnancy to protect preterm infants.
Remote ECG monitoring to reduce complications following transcatheter aortic valve implantations: the Redirect TAVI study
Authors: Natarajan Madhu Kailash , Sheth Tej Narendra , Wijeysundera Harindra Channa , Chavarria Jorge , Rodes-Cabau Josep , Velianou James Louis , Radhakrishnan Sam , Newman Toni , Smith Amanda , Wong Jorge Alfredo , Schwalm Jon David , Duong Monica , Mian Rajibul Islam , Bishop Marsella Giuliana , Healey Jeffrey Sean 
Published: March 2022

Abstract

Aims
The optimal strategy of monitoring for conduction disturbances in patients undergoing transcatheter aortic valve implantation (TAVI) is uncertain. We evaluated a pre- and post-TAVI remote ambulatory cardiac monitoring (rACM) strategy for identification of conduction disturbances and to reduce unplanned pre-discharge post-TAVI permanent pacemaker implantation (PPMI).

Methods and results
REdireCT TAVI (NCT0381820) was a prospective cohort study of patients referred for outpatient TAVI. Patients with prior PPMI were excluded. Remote ambulatory cardiac monitoring consisted of 2 weeks of continuous electrocardiogram (ECG) monitoring (Pocket-ECGTM) both before and after TAVI. Compliance to monitoring, frequency of notifications, unplanned PPMI post-TAVI, and length of hospitalization were measured. Between June 2018 and March 2020, in 192 undergoing TAVI (mean age: 81.8 years; female sex 46%; balloon-expandable valve 95.3%), compliance to rACM was 91.7% pre-TAVI (mean duration: 12.8 days), and 87.5% post-TAVI (mean duration: 12.9 days). There were 24 (12.5%) rACM notifications (13 pre-TAVI; 11 post-TAVI) resulting in 14 (7.3%) planned PPMI: seven pre-TAVI [due to sinus pauses n = 2 or atrio-ventricular block (AVB) n = 5] and seven post-TAVI [due to sinus pauses n = 1 or AVB n = 5 or ventricular tachycardia (VT) n = 1]. In addition, nine (4.7%) patients received pre-TAVI PPMI due to high-risk baseline ECG (right bundle branch block with hemi-block or prolonged PR interval). Unplanned PPMI post-TAVI during index hospitalization occurred in six (3.1%) patients due to AVB and in one patient readmitted with AVB. The median length of stay post-TAVI was 1 day.

Conclusion
A strategy of routine rACM was feasible and frequently led to PPMI. Our approach of 2-week rACM both pre- and post-TAVI achieves both high patient compliance and sufficient surveillance.

Clinical trial registration
Clinical Trial Registration: https://clinicaltrials.gov/ct2/show/NCT03810820
Imaging the Kanto Basin seismic basement with earthquake and noise autocorrelation functions
Authors: Viens Loïc , Jiang Chengxin , Denolle Marine A 
Published: March 2022

SUMMARYSedimentary basins can strongly amplify seismic waves from earthquakes. To better predict future ground motions, detailed knowledge of the sediment thickness and internal structure of basins is required. We image the sediment-to-bedrock interface of the Kanto Basin in Japan using the P-wave reflectivity response from earthquake and ambient seismic noise autocorrelation functions (ACFs) at 286 shallow borehole stations. Earthquake ACFs are computed using P-wave records from 50 Mw 6+ teleseismic events. Noise ACFs are obtained using 1 month of continuous data. Both methods are used to retrieve P-wave traveltimes between the surface and the bedrock interface and map the basin basement geometry. Our prediction of the basement depth agrees generally well with that from a reference velocity model, except for smoother variations in the central part of the basin. Using full-wavefield simulations, we show that the nature of the autocorrelated wavefield has a significant impact on the shape of the ACF waveforms and that earthquake ACFs yield more accurate results in the Kanto Basin.
Abelianization of Matrix Orthogonal Polynomials
Authors: Bertola M 
Published: March 2022

Abstract
The main goal of the paper is to connect matrix polynomial biorthogonality on a contour in the plane with a suitable notion of scalar, multi-point Padé approximation on an arbitrary Riemann surface endowed with a rational map to the Riemann sphere. To this end we introduce an appropriate notion of (scalar) multi-point Padé approximation on a Riemann surface and corresponding notion of biorthogonality of sections of the semi-canonical bundle (half-differentials). Several examples are offered in illustration of the new notions.
Finite axiomatizability of logics of distributive lattices with negation
Authors: Marcelino Sérgio , Rivieccio Umberto 
Published: March 2022

Abstract
This paper focuses on order-preserving logics defined from varieties of distributive lattices with negation, and in particular on the problem of whether these can be axiomatized by means Hilbert-style calculi that are finite (i.e. that contain a finite number of finitary rule schemata). On the negative side, we provide a syntactic condition on the equational presentation of a variety that entails failure of finite axiomatizability for the corresponding logic. An application of this result is that the logic of all distributive lattices with negation is not finitely axiomatizable; we likewise establish that the order-preserving logic of the variety of all Ockham algebras is also not finitely axiomatizable. On the positive side, we show that an arbitrary subvariety of semi-De Morgan algebras is axiomatized by a finite number of equations if and only if the corresponding order-preserving logic is axiomatized by a finite Hilbert-style calculus. This equivalence also holds for every subvariety of a Berman variety of Ockham algebras. We obtain, as a corollary, a new proof that the implication-free fragment of intuitionistic logic is finitely axiomatizable, as well as a new corresponding Hilbert-style calculus. Our proofs are constructive in that they allow us to effectively convert an equational presentation of a variety of algebras into a Hilbert-style calculus for the corresponding order-preserving logic, and vice versa. We also consider the assertional logics associated to the above-mentioned varieties, showing in particular that the assertional logics of finitely axiomatizable subvarieties of semi-De Morgan algebras are finitely axiomatizable as well.
CD4/CD8 Ratio and Cancer Risk Among Adults With HIV
Authors: Castilho Jessica L , Bian Aihua , Jenkins Cathy A , Shepherd Bryan E , Sigel Keith , Gill M John , Kitahata Mari M , Silverberg Michael J , Mayor Angel M , Coburn Sally B , Wiley Dorothy , Achenbach Chad J , Marconi Vincent C , Bosch Ronald J , Horberg Michael A , Rabkin Charles S , Napravnik Sonia , Novak Richard M , Mathews W Christopher , Thorne Jennifer E , Sun Jing , Althoff Keri N , Moore Richard D , Sterling Timothy R , Sudenga Staci L ,   the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epidemiology Databases to Evaluate AIDS (IeDEA), Castilho Jessica L , Bian Aihua , Jenkins Cathy A , Shepherd Bryan E , Sigel Keith , John Gill M , Kitahata Mari M , Silverberg Michael J , Mayor Angel M , Coburn Sally B , Wiley Dorothy , Achenbach Chad J , Marconi Vincent C , Bosch Ronald J , Horberg Michael A , Rabkin Charles S , Napravnik Sonia , Novak Richard M , Christopher Mathews W , Thorne Jennifer E , Sun Jing , Althoff Keri N , Moore Richard D , Sterling Timothy R , Sudenga Staci L 
Published: March 2022

Abstract

Background
Independent of CD4 cell count, a low CD4/CD8 ratio in people with HIV (PWH) is associated with deleterious immune senescence, activation, and inflammation, which may contribute to carcinogenesis and excess cancer risk. We examined whether low CD4/CD8 ratios predicted cancer among PWH in the United States and Canada.

Methods
We examined all cancer-free PWH with 1 or more CD4/CD8 values from North American AIDS Cohort Collaboration on Research and Design observational cohorts with validated cancer diagnoses between 1998 and 2016. We evaluated the association between time-lagged CD4/CD8 ratio and risk of specific cancers in multivariable, time-updated Cox proportional hazard models using restricted cubic spines. Models were adjusted for age, sex, race and ethnicity, hepatitis C virus, and time-updated CD4 cell count, HIV RNA, and history of AIDS-defining illness.

Results
Among 83 893 PWH, there were 5628 incident cancers, including lung cancer (n = 755), Kaposi sarcoma (n = 501), non-Hodgkin lymphoma (n = 497), and anal cancer (n = 439). The median age at cohort entry was 43 years. The overall median 6-month lagged CD4/CD8 ratio was 0.52 (interquartile range = 0.30-0.82). Compared with a 6-month lagged CD4/CD8 of 0.80, a CD4/CD8 of 0.30 was associated with increased risk of any incident cancer (adjusted hazard ratio = 1.24 [95% confidence interval = 1.14 to 1.35]). The CD4/CD8 ratio was also inversely associated with non-Hodgkin lymphoma, Kaposi sarcoma, lung cancer, anal cancer, and colorectal cancer in adjusted analyses (all 2-sided P &lt; .05). Results were similar using 12-, 18-, and 24-month lagged CD4/CD8 values.

Conclusions
A low CD4/CD8 ratio up to 24 months before cancer diagnosis was independently associated with increased cancer risk in PWH and may serve as a clinical biomarker.
A rare case of a large low-grade appendicular mucinous neoplasm causing compressive symptoms
Authors: Ekblad John R , Bhuller Sidra B , Weaver John , Bertocchi Michael E 
Published: March 2022

Abstract
Primary neoplasm of the appendix is often diagnosed incidentally after an appendectomy. Low-grade appendiceal mucinous neoplasms (LAMNs) make up a small portion of these neoplasms. We present a rare case of a patient with a slow-growing LAMN causing urinary retention and constipation. The mass was initially found incidentally 25 years prior, but the patient declined further workup since he was asymptomatic at that time. The patient experienced progressively worsening abdominal discomfort related to urinary retention and difficulty in evacuating his bowels. Imaging identified a large abdominal mass (19.3 × 8.7 × 13.5 cm). The mass was surgically resected. Pathology was consistent with a LAMN. In general, an incidental finding of an abdominal mass should be further investigated regardless of symptomology. Patients should be educated about the potential of malignancy and the need for a major abdominal surgery in the future if they choose not to have a mass further evaluated.
Two Nineteenth-Century Copies of Joseph Prémare’s Notitia linguæ sinicæ
Authors: Kua Paul 
Published: March 2022

Abstract
French Jesuit Joseph Prémare, a missionary to Qing Dynasty China, had completed by the end of 1728 the draft of a book entitled Notitia linguæ sinicæ, intended to assist aspiring Catholic missionaries from Europe in learning the Chinese language. One of the original manuscripts sent from Canton to Paris, now held in the Bibliothæque nationale de France in Paris, was rediscovered in the 1810s by the French sinologist Jean-Pierre Abel-Rémusat, and became the source for some manuscript copies, made mostly before the work’s eventual publication in 1831. This paper examines two of these manuscript copies dated between 1825 and 1830, held respectively in the Archive of the School of Oriental and African Studies in London and the the Bayerische Staatsbibliothek in Munich, both important in their own ways, and both somewhat misunderstood and largely neglected by recent studies.
Avalanches of magnetic flux rope in the state of self-organized criticality
Authors: Wang W B , Li C , Tu Z L , Guo J H , Chen P F , Wang F Y 
Published: March 2022

ABSTRACT
The self-organized criticality (SOC) is a universal theory to explain the ubiquitous power-law size distributions of astrophysical instabilities such as solar eruptions. One way to understand the dynamical processes of an SOC system is through cellular automaton (CA) simulations. Here, we develop a three-dimensional solar CA model that assumes a twisted magnetic flux rope (MFR), in which the avalanche takes place when a local magnetic vector potential exceeds a Gaussian distributed instability criterion, triggered by a global and space-dependent energy driving mechanism. To avoid non-physical released energies, an energy screening mechanism is applied to calculate the avalanche energies of each time-step. Our results show that the statistics of the CA simulated flaring events are comparable to the frequency distributions of observed solar flares originating from an individual active region. Due to the fact of the universality of MFRs, the CA model can be applied to many other astrophysical SOC systems.
Wide binaries from the H3 survey: the thick disc and halo have similar wide binary fractions
Authors: Hwang Hsiang-Chih , Ting Yuan-Sen , Conroy Charlie , Zakamska Nadia L , El-Badry Kareem , Cargile Phillip , Zaritsky Dennis , Chandra Vedant , Han Jiwon Jesse , Speagle Joshua S , Bonaca Ana 
Published: March 2022

ABSTRACTDue to the different environments in the Milky Way’s disc and halo, comparing wide binaries in the disc and halo is key to understanding wide binary formation and evolution. By using Gaia Early Data Release 3, we search for resolved wide binary companions in the H3 survey, a spectroscopic survey that has compiled ∼150 000 spectra for thick-disc and halo stars to date. We identify 800 high-confidence (a contamination rate of 4 per cent) wide binaries and two resolved triples, with binary separations mostly between 103 and 105 au and a lowest [Fe/H] of −2.7. Based on their Galactic kinematics, 33 of them are halo wide binaries, and most of those are associated with the accreted Gaia-Sausage-Enceladus galaxy. The wide binary fraction in the thick disc decreases toward the low metallicity end, consistent with the previous findings for the thin disc. Our key finding is that the halo wide binary fraction is consistent with the thick-disc stars at a fixed [Fe/H]. There is no significant dependence of the wide binary fraction on the α-captured abundance. Therefore, the wide binary fraction is mainly determined by the iron abundance, not their disc or halo origin nor the α-captured abundance. Our results suggest that the formation environments play a major role for the wide binary fraction, instead of other processes like radial migration that only apply to disc stars.
Explosive instability of dust settling in a protoplanetary disc
Authors: Zhuravlev V V 
Published: March 2022

ABSTRACT
It is shown that gas-dust perturbations in a disc with dust settling to the disc mid-plane exhibit the non-linear three-wave resonant interactions between streaming dust wave (SDW) and two inertial waves (IW). In the particular case considered in this paper, SDW at the wavenumber k• = 2κ/(g$z$ts), where κ, g$z$, and ts are, respectively, epicyclic frequency, vertical gravitational acceleration, and particle’s stopping time, interacts with two IW at the lower wavenumbers k′ and k″ such that k′ &lt; kDSI &lt; k″ &lt; k•, where kDSI = κ/(g$z$ts) is the wavenumber of the linear resonance between SDW and IW associated with the previously discovered linear dust settling instability. The problem is solved analytically in the limit of the small dust fraction. As soon as the dynamical dust back reaction on gas is taken into account, k•, k′, and k″ become slightly non-collinear and the emerging interaction of waves leads to simultaneous explosive growth of their amplitudes. This growth is explained by the conservative exchange with energy between the waves. The amplitudes of all three waves grow because the negative energy SDW transfers its energy to the positive energy IW. The product of the dimension-less amplitude of initially dominant wave and the time of explosion can be less than Keplerian time in a disc. It is shown that, generally, the three-wave resonance of an explosive type exists in a wide range of wavenumbers 0 &lt; k• ≤ 2κ/(g$z$ts). An explosive instability of gas-dust mixture may facilitate the dust clumping and the subsequent formation of planetesimals in young protoplanetary discs.
The THOR + HELIOS general circulation model: multiwavelength radiative transfer with accurate scattering by clouds/hazes
Authors: Deitrick Russell , Heng Kevin , Schroffenegger Urs , Kitzmann Daniel , Grimm Simon L , Malik Matej , Mendonça João M , Morris Brett M 
Published: March 2022

ABSTRACT
General circulation models (GCMs) provide context for interpreting multiwavelength, multiphase data of the atmospheres of tidally locked exoplanets. In the current study, the non-hydrostatic THOR GCM is coupled with the HELIOS radiative transfer solver for the first time, supported by an equilibrium chemistry solver (FastChem), opacity calculator (HELIOS-K), and Mie scattering code (LX-MIE). To accurately treat the scattering of radiation by medium-sized to large aerosols/condensates, improved two-stream radiative transfer is implemented within a GCM for the first time. Multiple scattering is implemented using a Thomas algorithm formulation of the two-stream flux solutions, which decreases the computational time by about 2 orders of magnitude compared to the iterative method used in past versions of HELIOS. As a case study, we present four GCMs of the hot Jupiter WASP-43b, where we compare the temperature, velocity, entropy, and streamfunction, as well as the synthetic spectra and phase curves, of runs using regular versus improved two-stream radiative transfer and isothermal versus non-isothermal layers. While the global climate is qualitatively robust, the synthetic spectra and phase curves are sensitive to these details. A THOR + HELIOS WASP-43b GCM (horizontal resolution of about 4 deg on the sphere and with 40 radial points) with multiwavelength radiative transfer (30 k-table bins) running for 3000 Earth days (864 000 time-steps) takes about 19–26 d to complete depending on the type of GPU.
Measuring weak lensing masses on individual clusters
Authors: Murray Calum , Bartlett James G , Artis Emmanuel , Melin Jean-Baptiste 
Published: March 2022

ABSTRACT
We present weak lensing mass estimates for a sample of 458 galaxy clusters from the redMaPPer Sloan Digital Sky Survey DR8 catalogue using Hyper Suprime-Cam weak lensing data. We develop a method to quickly estimate cluster masses from weak lensing shear and use this method to estimate weak lensing masses for each of the galaxy clusters in our sample. Subsequently, we constrain the mass–richness relation as well as the intrinsic scatter between the cluster richness and the measured weak lensing masses. When calculating the mass–richness relation for all clusters with a richness λ &gt; 20, we find a tension in the slope of the mass–richness relation with the Dark Energy Survey Year 1 stacked weak lensing analysis. For a reduced sample of clusters with a richness λ &gt; 40, our results are consistent with the Dark Energy Survey Year 1 analysis.
Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach
Authors: Liang Mindong , Liu Leshi , Xu Fei , Zeng Xiaoqian , Wang Ruijun , Yang Jinling , Wang Weishan , Karthik Loganathan , Liu Jiakun , Yang Zhiheng , Zhu Guoliang , Wang Shuliu , Bai Linquan , Tong Yaojun , Liu Xueting , Wu Min , Zhang Li-Xin , Tan Gao-Yi 
Published: March 2022

Abstract
Direct cloning of biosynthetic gene clusters (BGCs) from microbial genomes facilitates natural product-based drug discovery. Here, by combining Cas12a and the advanced features of bacterial artificial chromosome library construction, we developed a fast yet efficient in vitro platform for directly capturing large BGCs, named CAT-FISHING (CRISPR/Cas12a-mediated fast direct biosynthetic gene cluster cloning). As demonstrations, several large BGCs from different actinomycetal genomic DNA samples were efficiently captured by CAT-FISHING, the largest of which was 145 kb with 75% GC content. Furthermore, the directly cloned, 110 kb long, cryptic polyketide encoding BGC from Micromonospora sp. 181 was then heterologously expressed in a Streptomyces chassis. It turned out to be a new macrolactam compound, marinolactam A, which showed promising anticancer activity. Our results indicate that CAT-FISHING is a powerful method for complicated BGC cloning, and we believe that it would be an important asset to the entire community of natural product-based drug discovery.