bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysregulation of HNF1B/Clusterin axis enhances disease progression in a highly aggressive subset of pancreatic cancer patients
Authors: Yang Shouhui , Tang Wei , Azizian Azadeh , Gaedcke Jochen , Ströbel Philipp , Wang Limin , Cawley Helen , Ohara Yuuki , Valenzuela Paloma , Zhang Lin , Lal Trisha , Sinha Sanju , Rupin Eythan , Hanna Nader , Ghadimi B Michael , Hussain S Perwez 
Published: November 2022

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy and is largely refractory to available treatments. Identifying key pathways associated with disease aggressiveness and therapeutic resistance may characterize candidate targets to improve patient outcomes. We used a strategy of examining the tumors from a subset of PDAC patient cohorts with the worst survival to understand the underlying mechanisms of aggressive disease progression and to identify candidate molecular targets with potential therapeutic significance. Non-negative matrix factorization (NMF) clustering, using gene expression profile, revealed three patient subsets. A 142-gene signature specific to the subset with the worst patient survival, predicted prognosis and stratified patients with significantly different survival in the test and validation cohorts. Gene-network and pathway analysis of the 142-gene signature revealed dysregulation of Clusterin (CLU) in the most aggressive patient subset in our patient cohort. Hepatocyte nuclear factor 1 b (HNF1B) positively regulated CLU, and a lower expression of HNF1B and CLU was associated with poor patient survival. Mechanistic and functional analyses revealed that CLU inhibits proliferation, 3D spheroid growth, invasiveness and epithelial-to-mesenchymal transition (EMT) in pancreatic cancer cell lines. Mechanistically, CLU enhanced proteasomal degradation of EMT-regulator, ZEB1. In addition, orthotopic transplant of CLU-expressing pancreatic cancer cells reduced tumor growth in mice. Furthermore, CLU enhanced sensitivity of pancreatic cancer cells representing aggressive patient subset, to the chemotherapeutic drug gemcitabine. Taken together, HNF1B/CLU axis negatively regulates pancreatic cancer progression and may potentially be useful in designing novel strategies to attenuate disease progression in PDAC patients.
Clinical features, diagnosis, and management of pembrolizumab-induced myasthenia gravis
Authors: Zhao Shaoli , Zhou Yulu , Sun Wei , Li Zuojun , Wang Chunjiang 
Published: November 2022

Abstract
Myasthenia gravis (MG) is a rare but life-threatening adverse event with pembrolizumab. What is known about pembrolizumab-induced MG is largely based on case reports. This analysis collected pembrolizumab-induced MG cases from Chinese and English databases published from September 1, 2014, to June 30, 2022. Demographic and clinical information of the patients, management, and outcome data were collected and analyzed. Sixty-five patients with a median age of 73 years (range 30–86), including 43 male patients (66.2%), were included. Eight patients (12.3%) with prior MG experienced worsening symptoms after receiving pembrolizumab. The median time to the onset of MG was four weeks (range 0.7–27). The most common symptoms were ptosis (81.5%, 53 patients), diplopia (50.8%, 33 patients), dyspnea (44.6%, 29 patients), trunk or peripheral weakness (43.1%, 28 patients), and dysphagia (30.8%, 20 patients). Concurrent myositis and myocarditis occurred in 13 (20.0%) and 17 patients (26.2%). Pembrolizumab was discontinued in 63 patients (96.9%). Forty-four patients (67.7%) received combination therapies based on steroids (intravenous immune globulin, plasmapheresis, or immunosuppressants). Twenty-seven patients (41.5%) had symptoms completely recovered. Fourteen patients (21.5%) died from immunotoxicity or primary cancers. Clinicians should consider the possibility of pembrolizumab-induced MG, especially during the first eight weeks of therapy. Patients should be treated as early as possible, regardless of the severity of the initial symptoms.
Assemblage of Ceutorhynchinae Weevils Associated With Brassicaceae in Quebec (Canada) Agroecosystems
Authors: Desroches Claudine , Bouchard Patrice , Labrie Geneviève , Lucas Eric 
Published: November 2022

AbstractCeutorhynchinae Gistel (Coleoptera: Curculionidae) are a highly diverse phytophagous group of weevils in which the most species rich genus, Ceutorhynchus Germar (Coleoptera: Curculionidae), is mainly associated with Brassicaceae. Some Ceutorhynchinae, such as the invasive cabbage seedpod weevil (CSW), Ceutorhynchus obstrictus (Marsham), are important pests of cultivated Brassicaceae, and others are natural enemies of weeds and potential biological control agents. This study aims to characterize Ceutorhynchinae assemblages in canola growing regions of Quebec. Ceutorhynchinae were sampled in areas adjacent to canola fields or other crops in six administrative regions of Quebec during the summers of 2019 and 2020. A total of 25 Ceutorhynchinae species were collected and identified. Canonical analysis and multivariate regression tree analysis revealed that the assemblage of Ceutorhynchinae varied regionally and was either dominated by the invasive canola pest CSW or by the native weevil Ceutorhynchus neglectus Blatchley. Our results also highlighted new biological associations between weevils and Brassicaceae like the CSW with the yellow rocket, Barbarea vulgaris R. Br., native Ceutorhynchus pauxillus Dietz with common pepper grass, Lepidium densiflorum, and native Ceutorhynchus semirufus LeConte with Pennsylvania bittercress, Cardamine pensylvanica Muhl. This study also provides a useful tool to find new biological control agents against Brassicaceae weeds and to monitor the abundance and diversity of this taxon and provide baseline data to assess future impacts of exotic parasitoids of CSW on native weevils.
Mitochondrial genome maintenance—the kinetoplast story
Authors: Amodeo Simona , Bregy Irina , Ochsenreiter Torsten 
Published: November 2022

Abstract
Mitochondrial DNA replication is an essential process in most eukaryotes. Similar to the diversity in mitochondrial genome size and organization in the different eukaryotic supergroups, there is considerable diversity in the replication process of the mitochondrial DNA. In this review, we summarize the current knowledge of mitochondrial DNA replication and the associated factors in trypanosomes with a focus on Trypanosoma brucei, and provide a new model of minicircle replication for this protozoan parasite. The model assumes the mitochondrial DNA (kinetoplast DNA, kDNA) of T. brucei to be loosely diploid in nature and the replication of the genome to occur at two replication centers at the opposing ends of the kDNA disc (also known as antipodal sites, APS). The new model is consistent with the localization of most replication factors and in contrast to the current model, it does not require the assumption of an unknown sorting and transport complex moving freshly replicated DNA to the APS. In combination with the previously proposed sexual stages of the parasite in the insect vector, the new model provides a mechanism for maintenance of the mitochondrial genetic diversity.
Full-waveform inversion method for tunnel seismic forward prospecting
Authors: Liu Bin , Gong Zhifei , Zhang Fengkai , Xu Xinji , Zhao Yang , Chen Lei 
Published: November 2022

SUMMARY
During tunnel construction, accurately ascertaining the adverse geological condition in front of the tunnel face is essential to ensure construction safety and decrease economic loss. As an accurate wave velocity modelling method, seismic full-waveform inversion (FWI) still faces many difficulties when applied in a tunnel observation environment because of fewer observation data and smaller offset than ground seismic detection. This paper analysed the FWI for tunnel active seismic forward prospecting with a single shot. We adopted the N-order time integral wavefield and normalized integration objective function method to improve the stability and reduce the dependence of FWI on the initial model. Based on two assumptions on the wave velocity distribution in the tunnel, we proposed a 1-D velocity structure correction method to reduce the multiplicity of inversion. Then the improved tunnel FWI method based on these two inversion strategies was applied to a synthetic model with a rectangular anomaly and a lithology interface, verifying the method's effectiveness. Based on typical adverse geological bodies during tunnelling, three additional adverse geological models were built and verified the reliability of the methods in tunnel detection environments. There are still some false anomalies interference in the inversion results of the synthetic models from the inversion results. However, these problems are acceptable in limited tunnel observation space. Then the method was applied in a field example in the Yinsong water supply project in Jilin Province, China, and verified the effect on field data. Finally, the influence of the shot number on the inversion effect and the method's robustness are discussed.
Broad-band ocean bottom seismometer noise properties
Authors: Janiszewski Helen A , Eilon Z , Russell J B , Brunsvik B , Gaherty J B , Mosher S G , Hawley W B , Coats S 
Published: November 2022

SUMMARY
We present a new compilation and analysis of broad-band ocean bottom seismometer noise properties from 15 yr of seismic deployments. We compile a comprehensive data set of representative four-component (seismometer and pressure gauge) noise spectra and cross-spectral properties (coherence, phase and admittance) for 551 unique stations spanning 18 U.S.-led experiments. This is matched with a comprehensive compilation of metadata parameters related to instrumentation and environmental properties for each station. We systematically investigate the similarity of noise spectra by grouping them according to these metadata parameters to determine which factors are the most important in determining noise characteristics. We find evidence for improvements in similarity of noise properties when grouped across parameters, with groupings by seismometer type and deployment water depth yielding the most significant and interpretable results. Instrument design, that is the entire deployed package, also plays an important role, although it strongly covaries with seismometer and water depth. We assess the presence of traditional sources of tilt, compliance, and microseismic noise to characterize their relative role across a variety of commonly used seismic frequency bands. We find that the presence of tilt noise is primarily dependent on the type of seismometer used (covariant with a particular subset of instrument design), that compliance noise follows anticipated relationships with water depth, and that shallow, oceanic shelf environments have systematically different microseism noise properties (which are, in turn, different from instruments deployed in shallow lake environments). These observations have important implications for the viability of commonly used seismic analysis techniques. Finally, we compare spectra and coherences before and after vertical channel tilt and compliance noise removal to evaluate the efficacy and limitations of these now standard processing techniques. These findings may assist in future experiment planning and instrument development, and our newly compiled noise data set serves as a building block for more targeted future investigations by the marine seismology community.
A deep learning-based network for the simulation of airborne electromagnetic responses
Authors: Wu Sihong , Huang Qinghua , Zhao Li 
Published: November 2022

SUMMARYAirborne electromagnetic (AEM) method detects the subsurface electrical resistivity structure by inverting the measured electromagnetic field. AEM data inversion is extremely time-consuming when huge volumes of observational data are involved. Forward modelling is an essential part and represents a large proportion of computational cost in the inversion process. In this study, we develop an AEM simulator using deep learning as a computationally efficient alternative to accelerate 1-D forward modelling. Inspired by Google's neural machine translation, our AEM simulator adopts the long short-term memory (LSTM) modules with an encoder–decoder structure, combining the advantages in time-series regression and feature extraction. The well-trained LSTM network describes directly the mapping relationship between resistivity models with transceiver altitudes and time-domain AEM signals. The prediction results of the test set show that 95 per cent of the relative errors at most sampling points fall in the range of ±5 per cent, with average values within the range of ±0.5 per cent, indicating an overall prediction accuracy. We investigate the effects of the distributions of both resistivity and transceiver altitude in the training set on the prediction accuracy. The LSTM-based AEM simulator can effectively handle the resistivity characteristics involved in the training set and yields great sensitivity to the variations of transceiver altitudes. We also examine the adaptability of our AEM simulator for discontinuous resistivity variations. Synthetic tests indicate that the application effect of the AEM simulator relies on the completeness of the training samples and suggest that enriching the sample diversity is necessary to ensure the prediction accuracy, in cases of observation environments dominated by extreme transceiver altitudes or under-represented geological features. Furthermore, we discuss the influence of network configuration on its accuracy and computational efficiency. Our simulator can deliver ∼13 600 1-D forward modelling calculations within 1 s, which significantly improves the simulation efficiency of AEM data.
Spectral induced polarization of heterogeneous non-consolidated clays
Authors: Mendieta A , Maineult A , Leroy P , Jougnot D 
Published: November 2022

SUMMARY
Clays are ubiquitously located in the Earth’s near surface and have a high impact on the subsurface permeability. Most geo-electrical characterizations of clays do not take into account the heterogeneous nature of clay geological media. We want to better understand the influence of heterogeneities on the geo-electrical signature, thus we collected a data set of spectral induced polarization (SIP) of artificial heterogeneous non-consolidated clay samples. The samples are made of illite and red montmorillonite in a parallel and perpendicular disposition (with respect to the applied electric field). Another sample is a homogeneous mixture composed of the same volumetric fraction of illite and red montmorillonite. For all the samples, the polarization is dominated by the red montmorillonite, given by the shape of the spectra (presence or lack of a peak at a particular frequency). We compared the experimental data with classical mixing laws and complex conductance network models to test how to better predict the SIP signature of such mixtures when the SIP spectra of the two components are known. The real conductivity is better predicted by the mixing laws, but the shape of the spectra (presence of polarization peaks at particular frequencies) is best predicted by the conductance network models. This study is a step forward towards a better characterization of heterogeneous clay systems using SIP.
Quantifying and Predicting Ongoing Human Immunodeficiency Virus Type 1 Transmission Dynamics in Switzerland Using a Distance-Based Clustering Approach
Authors: Labarile Marco , Loosli Tom , Zeeb Marius , Kusejko Katharina , Huber Michael , Hirsch Hans H , Perreau Matthieu , Ramette Alban , Yerly Sabine , Cavassini Matthias , Battegay Manuel , Rauch Andri , Calmy Alexandra , Notter Julia , Bernasconi Enos , Fux Christoph , Günthard Huldrych F , Pasin Chloé , Kouyos Roger D ,   the Swiss HIV Cohort Study, Abela I , Aebi-Popp K , Anagnostopoulos A , Battegay M , Bernasconi E , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H F , Hachfeld A , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Kahlert C R , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Kusejko K , Martinetti G , de Tejada B Martinez , Marzolini C , Metzner K J , Müller N , Nemeth J , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Wandeler G , Yerly S 
Published: November 2022

Abstract

Background
Despite effective prevention approaches, ongoing human immunodeficiency virus 1 (HIV-1) transmission remains a public health concern indicating a need for identifying its drivers.

Methods
We combined a network-based clustering method using evolutionary distances between viral sequences with statistical learning approaches to investigate the dynamics of HIV transmission in the Swiss HIV Cohort Study and to predict the drivers of ongoing transmission.

Results
We found that only a minority of clusters and patients acquired links to new infections between 2007 and 2020. While the growth of clusters and the probability of individual patients acquiring new links in the transmission network was associated with epidemiological, behavioral, and virological predictors, the strength of these associations decreased substantially when adjusting for network characteristics. Thus, these network characteristics can capture major heterogeneities beyond classical epidemiological parameters. When modeling the probability of a newly diagnosed patient being linked with future infections, we found that the best predictive performance (median area under the curve receiver operating characteristic AUCROC = 0.77) was achieved by models including characteristics of the network as predictors and that models excluding them performed substantially worse (median AUCROC = 0.54).

Conclusions
These results highlight the utility of molecular epidemiology-based network approaches for analyzing and predicting ongoing HIV transmission dynamics. This approach may serve for real-time prospective assessment of HIV transmission.
Amalgamation and Robinson property in universal algebraic logic
Authors: Gyenis Zalán , Öztürk Övge 
Published: November 2022

Abstract
There is a well-established correspondence between interpolation and amalgamation for algebraizable logics that satisfy certain additional assumptions. In this paper, we introduce the Robinson property of a logic and show that a conditionally algebraizable logic without any additional assumptions has the Robinson property if and only if the corresponding class of Lindenbaum–Tarski algebras has the amalgamation property. Moreover, we give the logical characterization of the strong amalgamation property, solving an open problem of Andréka–Németi–Sain. It is also shown that given the mentioned extra assumptions the Robinson property implies the interpolation property. As conditionally algebraizable logics cover algebraizable logics as well as various quantifier logics such as classical first order logic, our results yield a generalization of some of the results concerning interpolation and amalgamation.
The European Restructuring Directive
Authors: Olivares-Caminal Rodrigo , Guynn Randall D , Kornberg Alan W , Paterson Sarah , Singh Dalvinder 
Published: November 2022

Abstract
Chapter 2 provides an overview and analysis of the European Restructuring Directive. It starts with an analysis of the motivations for the Directive and of criticisms which have been advanced in the scholarship. The chapter then continues with an analysis of the provisions of the Directive. There is a particular focus on difficult issues which arise in interpreting the language of the Directive, and on the optionality which the Directive provides Member States. Examples of implementation from Germany and the Netherlands are also included. The chapter concludes with a brief analysis of avenues for cross-border recognition of European restructuring plans.
Resolution of US Banks and Other Financial Institutions
Authors: Olivares-Caminal Rodrigo , Guynn Randall D , Kornberg Alan W , Paterson Sarah , Singh Dalvinder 
Published: November 2022

Abstract
Chapter 8 provides an overview of the resolution regimes under US law applicable to (i) banks; (ii) Fannie Mae, Freddie Mac, and the Federal Home Loan Banks (government-sponsored enterprises or GSEs); and (iii) systemically important financial institutions. This chapter includes a detailed summary of the applicable resolution regimes, as well as a summary of the development of US resolution authority over time, from the establishment of the Federal Deposit Insurance Corporation (FDIC) in the early twentieth century to the creation in the early twenty-first century of a resolution statute for GSEs, to the post-financial crisis establishment of the orderly liquidation authority and resolution planning requirements in the Dodd-Frank Act. The chapter also provides overviews of the supervisory tools that banking regulators use to prevent the failure of banks, the single-point-of-entry recapitalization in resolution strategy that has been adopted by all the US global systemically important banking groups (G-SIBs), and international efforts to coordinate on cross-border resolutions.
Litigation Aspects of Sovereign Debt
Authors: Olivares-Caminal Rodrigo , Guynn Randall D , Kornberg Alan W , Paterson Sarah , Singh Dalvinder 
Published: November 2022

Abstract
Chapter 11 presents the options and obstacles that a creditor faces has when pursuing a claim against a debtor, mainly in New York and English courts. It presents a practical step-by-step guide covering the issues that need to be addressed to evaluated prior to and in the process of obtaining a court order. In doing so, it looks at pre-action issues such as the applicable contractual and post judgment interests (the economic analysis prior to action) and different considerations on which courts to use. Then, it moves into more procedural aspects such as immunity from suit, personal and subject matter jurisdiction, the doctrines of act of state and comity, etc. Then, this chapter looks at the other side of the coin, enforcement. It is one thing obtaining a judgment and quite another enforcing it. Within the enforcement analysis the chapter focuses on the pari passu litigation and other key legal precedents in the US, UK, and other jurisdictions to illustrate the different challenges that may arise.
Transactional Aspects of Sovereign Debt Restructuring
Authors: Olivares-Caminal Rodrigo , Guynn Randall D , Kornberg Alan W , Paterson Sarah , Singh Dalvinder 
Published: November 2022

Abstract
Chapter 12 provides an overview of the transactional aspects of sovereign debt restructuring, looking at the procedures and methods to conduct a successful restructuring, addressing this from the perspective of borrowers/debtors and lenders/creditors. This chapter looks at both (1) policy approaches towards conducting a debt restructuring (ie, the theoretical Sovereign Debt Restructuring Mechanism (SDRM), the use of the European Financial Stability Facility (EFSF) and the European Stability Mechanism (ESM) in the Greek restructuring, and the more novel Debt Service Suspension Initiative (DSSI) and the Common Framework developed to tackle the distress situations resulting from the COVID-19 pandemic) and (2) the transactional aspects, the imbedded clauses that can facilitate a restructuring (ie the industry-wide collective action clauses (CACs) and the recent challenges posed to them by re-designation and the Pac-man technique) as well as the fallback option of voluntary exchange offers combined with contractual sweeteners and exit consents.