bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safe Shelter: A Case for Prioritizing Housing Quality in Climate Adaptation Policy by Remotely Sensing Roof Tarps in the San Francisco Bay Area
Authors: Velterop Emma , Uzkent Burak , Suckale Jenny 
Published: August 2022

AbstractThe number and intensity of climate‐related hazards are increasing globally, but some communities are much more heavily impacted than others by the same event. One factor among many is housing quality because an intact house is a household's first line of defense against the wrath of nature. By taking the San Francisco Bay Area as a proof‐of‐concept, we develop a deep‐learning algorithm to show that blue roof tarps, used in the area as semipermanent fixtures to reduce roof leakage, can serve as a proxy for poor‐quality housing. Our cascading structure of Convolutional Neural Networks (CNNs) operates in a coarse‐to‐fine manner by first identifying buildings and then classifying them as containing a blue roof tarp or not, achieving a recall of 89.6% and a precision of 34.3% in our study area. Our work suggests that up to 5% of houses are of poor quality in some low‐to‐intermediate income communities in the San Francisco Bay Area. However, the percentage of poor‐quality houses varies by an order of magnitude even in communities with a comparable median income or social vulnerability index, suggesting that prioritizing climate adaptation investments based on these common indicators could be ineffective. Our work emphasizes the value of a community‐centric approach to improving housing quality and reducing the disproportional impacts of not only one but multiple climate hazards.
Functional antagonism between CagA and DLC1 in gastric cancer
Authors: Hinsenkamp Isabel , Köhler Jan P. , Flächsenhaar Christoph , Hitkova Ivana , Meessen Sabine Eberhart , Gaiser Timo , Wieland Thomas , Weiss Christel , Röcken Christoph , Mowat Michael , Quante Michael , Taxauer Karin , Mejias-Luque Raquel , Gerhard Markus , Vogelmann Roger , Meindl-Beinker Nadja , Ebert Matthias , Burgermeister Elke 
Published: August 2022

AbstractHelicobacter (H.) pylori-induced gastritis is a risk factor for gastric cancer (GC). Deleted-in-liver-cancer-1 (DLC1/ARHGAP7) inhibits RHOA, a downstream mediator of virulence factor cytotoxin-A (CagA) signalling and driver of consensus-molecular-subtype-2 diffuse GC. DLC1 located to enterochromaffin-like and MIST1+ stem/chief cells in the stomach. DLC1+ cells were reduced in H. pylori gastritis and GC, and in mice infected with H. pylori. DLC1 positivity inversely correlated with tumour progression in patients. GC cells retained an N-terminal truncation variant DLC1v4 in contrast to full-length DLC1v1 in non-neoplastic tissues. H. pylori and CagA downregulated DLC1v1/4 promoter activities. DLC1v1/4 inhibited cell migration and counteracted CagA-driven stress phenotypes enforcing focal adhesion. CagA and DLC1 interacted via their N- and C-terminal domains, proposing that DLC1 protects against H. pylori by neutralising CagA. H. pylori-induced DLC1 loss is an early molecular event, which makes it a potential marker or target for subtype-aware cancer prevention or therapy.
A mid-infrared lab-on-a-chip for dynamic reaction monitoring
Authors: Hinkov Borislav , Pilat Florian , Lux Laurin , Souza Patricia L. , David Mauro , Schwaighofer Andreas , Ristanić Daniela , Schwarz Benedikt , Detz Hermann , Andrews Aaron M. , Lendl Bernhard , Strasser Gottfried 
Published: August 2022

AbstractMid-infrared spectroscopy is a sensitive and selective technique for probing molecules in the gas or liquid phase. Investigating chemical reactions in bio-medical applications such as drug production is recently gaining particular interest. However, monitoring dynamic processes in liquids is commonly limited to bulky systems and thus requires time-consuming offline analytics. In this work, we show a next-generation, fully-integrated and robust chip-scale sensor for online measurements of molecule dynamics in a liquid solution. Our fingertip-sized device utilizes quantum cascade technology, combining the emitter, sensing section and detector on a single chip. This enables real-time measurements probing only microliter amounts of analyte in an in situ configuration. We demonstrate time-resolved device operation by analyzing temperature-induced conformational changes of the model protein bovine serum albumin in heavy water. Quantitative measurements reveal excellent performance characteristics in terms of sensor linearity, wide coverage of concentrations, extending from 0.075 mg ml−1 to 92 mg ml−1 and a 55-times higher absorbance than state-of-the-art bulky and offline reference systems.
Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits
Authors: Nucci Amandine , Rocha Eduardo P. C. , Rendueles Olaya 
Published: August 2022

AbstractThe extracellular capsule is a major virulence factor, but its ubiquity in free-living bacteria with large environmental breadths suggests that it shapes adaptation to novel niches. Yet, how it does so, remains unexplored. Here, we evolve threeKlebsiellastrains and their capsule mutants in parallel. Their comparison reveals different phenotypic and genotypic evolutionary changes that alter virulence-associated traits. Non-capsulated populations accumulate mutations that reduce exopolysaccharide production and increase biofilm formation and yield, whereas most capsulated populations become hypermucoviscous, a signature of hypervirulence. Hence, adaptation to novel environments primarily occurs by fine-tuning expression of the capsular locus. The same evolutionary conditions selecting for mutations in the capsular genewzcleading to hypermucoviscosity also result in increased susceptibility to antibiotics by mutations in theramAregulon. This implies that general adaptive processes outside the host can affect capsule evolution and its role in virulence and infection outcomes may be a by-product of such adaptation.
Diverse synthesis of α-tertiary amines and tertiary alcohols via desymmetric reduction of malonic esters
Authors: Liu Haichao , Lau Vincent Ho Man , Xu Pan , Chan Tsz Hin , Huang Zhongxing 
Published: August 2022

AbstractAmines and alcohols with a fully substituted α-carbon are structures of great value in organic synthesis and drug discovery. While conventional methods towards these motifs often rely on enantioselective carbon-carbon or carbon-heteroatom bond formation reactions, a desymmetric method is developed here by selectively hydrosilylating one of the esters of easily accessible α-substituted α-amino- and -oxymalonic esters. The desymmetrization is enabled by a suite of dinuclear zinc catalysts with pipecolinol-derived tetradentate ligands and can accommodate a diverse panel of heteroatom substituents, including secondary amides, tertiary amines, and ethers of different sizes. The polyfunctionalized reduction products, in return, have provided expeditious approaches to enantioenriched nitrogen- and oxygen-containing molecules, including dipeptides, vitamin analogs, and natural metabolites.
A high-resolution Orbitrap Mass spectral library for trace volatile compounds in fruit wines
Authors: Liu Yaran , Li Na , Li Xiaoyao , Qian Wenchao , Liu Jiani , Su Qingyu , Chen Yixin , Zhang Bolin , Zhu Baoqing , Cheng Jinxin 
Published: August 2022

AbstractThe overall aroma is an important factor of the sensory quality of fruit wines, which attributed to hundreds of volatile compounds. However, the qualitative determination of trace volatile compounds is considered to be very challenging work. GC-Orbitrap-MS with high resolution and high sensitivity provided more possibilities for the determination of volatile compounds, but without the high-resolution mass spectral library. For accuracy of qualitative determination in fruit wines by GC-Orbitrap-MS, a high-resolution mass spectral library, including 76 volatile compounds, was developed in this study. Not only the HRMS spectrum but also the exact ion fragment, relative abundance, retention indices (RI), CAS number, chemical structure diagram, aroma description and aroma threshold (ortho-nasally) were provided and were shown in a database website (Food Flavor Laboratory, http://foodflavorlab.cn/). HRMS library was used to successfully identify the volatile compounds mentioned above in 16 fruit wines (5 blueberry wines, 6 goji berry wines and 5 hawthorn wines). The library was developed as an important basis for further understanding of trace volatile compounds in fruit wines.
A global dataset for prevalence of Salmonella Gallinarum between 1945 and 2021
Authors: Zhou Xiao , Kang Xiamei , Zhou Kun , Yue Min 
Published: August 2022

AbstractPullorum disease and fowl typhoid are among the most significant poultry diseases worldwide. However, the global burden of these diseases remains unknown. Most importantly, the parameters contributing to the prevalence of Salmonella Gallinarum variants are not well documented. Therefore, in this study, we present a systematic review and meta-analysis of the global prevalence of Salmonella Gallinarum during 1945–2021. In total, 201 studies were identified for qualitative analysis (>900 million samples). The meta-analysis was subjected to over 183 screened studies. The global prevalence of S. Gallinarum (percentage of positive samples in total samples) was 8.54% (95% CI: 8.43–8.65) and showed a V-shaped recovery over time. Pullorum disease is most common in Asia, particularly in eastern China. Further investigations on chicken origin samples revealed significant differences in S. Gallinarum prevalence by gender, breed, raising mode, economic use, and growth stage, indicating a critical role of vertical transmission. Together, this study offered an updated, evidence-based dataset and knowledge regarding S. Gallinarum epidemics, which might significantly impact decision-making policy with targeted interventions.
The gill transcriptome of threatened European freshwater mussels
Authors: Gomes-dos-Santos André , Machado André M. , Castro L. Filipe C. , Prié Vincent , Teixeira Amílcar , Lopes-Lima Manuel , Froufe Elsa 
Published: August 2022

AbstractGenomic tools applied to non-model organisms are critical to design successful conservation strategies of particularly threatened groups. Freshwater mussels of the Unionida order are among the most vulnerable taxa and yet almost no genetic resources are available. Here, we present the gill transcriptomes of five European freshwater mussels with high conservation concern:Margaritifera margaritifera,Unio crassus,Unio pictorum,Unio mancusandUnio delphinus. The final assemblies, with N50 values ranging from 1069–1895 bp and total BUSCO scores above 90% (Eukaryote and Metazoan databases), were structurally and functionally annotated, and made available. The transcriptomes here produced represent a valuable resource for future studies on these species’ biology and ultimately guide their conservation.
Measurement of foliar H2O2 concentration can be an indicator of riparian vegetation management
Authors: Asaeda Takashi , Rahman Mizanur , Vamsi-Krishna Lekkala , Schoelynck Jonas , Rashid Md Harun 
Published: August 2022

AbstractRiparian vegetation is frequently exposed to abiotic stress, which generates reactive oxygen species (ROS) caused by strong differences in a river’s hydrological conditions. Among different ROS, hydrogen peroxide (H2O2) is relatively steady and can be measured appropriately. Thus, the quantification of plant H2O2can be used as a stress indicator for riparian vegetation management. The current study examines the spatial distribution of plants by riparian vegetation communities across the elevation gradient of riparian zones through quantification of environmental stress using foliar H2O2concentration. The treesSalixspp.,Robinia pseudoacacia,Ailanthus altissimawithJuglans mandshurica, and the herbsPhragmites australis,Phragmites japonica, andMiscanthus saccharifloruswere selected for this study. Leaf tissues were collected to analyze H2O2concentration, meanwhile riparian soil was sampled to measure total nitrogen (TN), total phosphorus (TP), and moisture content. The H2O2concentration of tree species increased with higher soil moisture content, which was negatively correlated forSalixand herb spp., in which H2O2concentration always decreased with high soil moisture. In this study, we found a unique significant interaction between soil moisture content and H2O2concentration, both positively or negatively correlated relationships, when compared with other parameters, such as TN or TP concentrations or TN: TP in riparian soil. The species-specific distribution zones can be explained by the H2O2concentration in the plant for gravelly and sandy channels on a theoretical range of soil moisture. Each species’ H2O2concentration was estimated through derived equations and is directly related to an elevation above the channel. The comparison with the observed distribution of plant elevations in the field indicated that all species showed a spatial distribution that acts as species-specific elevations where H2O2concentrations stayed below 40 μmol/gFW. Hence, the present study suggests that foliar H2O2concentration can be a useful benchmark for the distribution potentiality of riparian vegetation.
Multi-stage optimal dynamic treatment regimes for survival outcomes with dependent censoring
Authors: Cho Hunyong , Holloway Shannon T , Couper David J , Kosorok Michael R 
Published: August 2022

Summary
We propose a reinforcement learning method for estimating an optimal dynamic treatment regime for survival outcomes with dependent censoring. The estimator allows the failure time to be conditionally independent of censoring and dependent on the treatment decision times, supports a flexible number of treatment arms and treatment stages, and can maximize either the mean survival time or the survival probability at a certain time-point. The estimator is constructed using generalized random survival forests and can have polynomial rates of convergence. Simulations and analysis of the Atherosclerosis Risk in Communities study data suggest that the new estimator brings higher expected outcomes than existing methods in various settings.
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification
Authors: Erdengasileng Arslan , Han Qing , Zhao Tingting , Tian Shubo , Sui Xin , Li Keqiao , Wang Wanjing , Wang Jian , Hu Ting , Pan Feng , Zhang Yuan , Zhang Jinfeng 
Published: August 2022

Abstract
Large volumes of publications are being produced in biomedical sciences nowadays with ever-increasing speed. To deal with the large amount of unstructured text data, effective natural language processing (NLP) methods need to be developed for various tasks such as document classification and information extraction. BioCreative Challenge was established to evaluate the effectiveness of information extraction methods in biomedical domain and facilitate their development as a community-wide effort. In this paper, we summarize our work and what we have learned from the latest round, BioCreative Challenge VII, where we participated in all five tracks. Overall, we found three key components for achieving high performance across a variety of NLP tasks: (1) pre-trained NLP models; (2) data augmentation strategies and (3) ensemble modelling. These three strategies need to be tailored towards the specific tasks at hands to achieve high-performing baseline models, which are usually good enough for practical applications. When further combined with task-specific methods, additional improvements (usually rather small) can be achieved, which might be critical for winning competitions.
Database URL: https://doi.org/10.1093/database/baac066
To Be, or Not to Be … Original Under Copyright Law, That Is (One of) the Main Questions Concerning AI-Produced Works
Authors: Iaia Vincenzo 
Published: August 2022

Abstract
This paper will examine whether different types of AI-produced works, namely AI-assisted, AI-generated, and AI-genassisted works, are able to satisfy the originality requirement, as established within the EU copyright acquis. It will argue that even assuming that the choices of AIs can be deemed free, they could not be considered creative due to the anthropological footprint of copyright law which traditionally covers only human creativity. This implies that copyright protection can be granted only to outputs that display a sufficient level of original human intervention, which is most likely present in AI-assisted works and, depending on the case, in AI-genassisted works, too. The desirability of stretching copyright further to accommodate artificial creativity is also lessened by the risk that it could saturate the creative market due to an overexpansion of monopoly rights. Thus, the copyright solution will be evaluated together with some existing alternative legal tools, such as neighbouring rights, sui generis rights, patents, or even the absence of protection over AI-generated works to preserve a robust public domain.
A case of papillary thyroid carcinoma with renal and pulmonary metastases
Authors: Aoyama Mariko , Inui Tomohiro , Miyamoto Naoki , Sakamoto Shinichi , Inoue Seiya , Fujiwara Satoshi , Goto Masakazu , Toba Hiroaki , Takizawa Hiromitsu 
Published: August 2022

Abstract
Distant metastases derived from papillary carcinoma are generally detected in the lungs and bones. However, renal metastasis is rare. We herein report a case of papillary thyroid carcinoma with renal and pulmonary metastases that had been initially diagnosed as primary renal carcinoma with pulmonary metastases. The lesions showed response to immune checkpoint inhibitors and tyrosine kinase inhibitor but not to radioactive iodine therapy.
Seronegative Mediastinal Coccidioidomycosis as a Novel Presentation of CTPS1 Combined Immunodeficiency
Authors: Krase Ifat Z , Woodward James , Bauer Cindy S , Miller Holly , Sacco Keith 
Published: August 2022

Abstract
Inborn errors of immunity may present with susceptibility to coccidioidomycosis. This is especially so in disorders impairing the interferon-γ and interleukin 12 signaling axis. We describe the first case of cytidine nucleotide triphosphate synthetase 1 (CTPS1) deficiency, a combined immunodeficiency impairing lymphocyte proliferation, presenting with coccidioidomycosis.
From the Ivory Tower to the Courtroom: Cooperative Federalism in the Supreme Court of Canada
Authors: Harding Mark S , Snow Dave 
Published: August 2022

AbstractThis article provides the first exhaustive quantitative account of the Supreme Court of Canada’s use of the term “cooperative federalism.” We find that cooperative federalism has appeared in twenty-four Supreme Court decisions from 1976 to 2019, and that these decisions have been more likely to favor the federal government than the provinces. Moreover, the Court’s use of the term can be divided between two distinct periods. During the formative period (1976–2009), the Court used the term fairly consistently. From 2010 to 2019, the Court has entered a contested period characterized by split decisions in which the Court is divided over differing conceptions of federalism. As cooperative federalism has transformed from a relatively vague concept into a more substantive constitutional principle, fissures over the term’s application have developed. This article shows how scholarly terminology can have an unexpected and even dispositive effect on judicial decisions, which can reflect uncertainty over how judges understand their institutional role.
Variants Of the Selberg Sieve and Almost PrimeK-tuples
Authors: Lewulis Paweł 
Published: August 2022

AbstractLet $k\geqslant 2$ and $\mathcal{P} (n) = (A_1 n + B_1 ) \cdots (A_k n + B_k)$ where all the $A_i, B_i$ are integers. Suppose that $\mathcal{P} (n)$ has no fixed prime divisors. For each choice of k it is known that there exists an integer ϱk such that $\mathcal{P} (n)$ has at most ϱk prime factors infinitely often. We used a new weighted sieve setup combined with a device called ɛ-trick to improve the possible values of ϱk for $k\geqslant 7$. As a by-product of our approach, we improve the conditional possible values of ϱk for $k\geqslant 4$, assuming the generalized Elliott–Halberstam conjecture.
Data-intensive Innovation and the State: Evidence from AI Firms in China
Authors: Beraja Martin , Yang David Y , Yuchtman Noam 
Published: August 2022

Abstract
Developing artificial intelligence (AI) technology requires data. In many domains, government data far exceed in magnitude and scope data collected by the private sector, and AI firms often gain access to such data when providing services to the state. We argue that such access can stimulate commercial AI innovation in part because data and trained algorithms are shareable across government and commercial uses. We gather comprehensive information on firms and public security procurement contracts in China’s facial recognition AI industry. We quantify the data accessible through contracts by measuring public security agencies’ capacity to collect surveillance video. Using a triple-differences strategy, we find that data-rich contracts, compared to data-scarce ones, lead recipient firms to develop significantly and substantially more commercial AI software. Our analysis suggests a contribution of government data to the rise of China’s facial recognition AI firms, and that states’ data collection and provision policies could shape AI innovation.
THE IMPACT OF THE VITREOMACULAR INTERFACE ON FUNCTIONAL AND ANATOMICAL OUTCOMES IN DIABETIC MACULAR EDEMA TREATED WITH THREE DIFFERENT ANTI-VEGF AGENTS
Authors: Mylonas Georgios , Najeeb Bilal Haj , Goldbach Felix , Deak Gabor G. , Michl Martin , Brugger Jonas , Schmidt-Erfurth Ursula , Gerendas Bianca S. 
Published: August 2022

Purpose:
To investigate the impact of baseline vitreomacular interface status on treatment outcomes in patients treated with three different anti–vascular endothelial growth factors for diabetic macular edema.

Methods:
Post hoc analysis from patients enrolled in the DRCR.net Protocol T study. Optical coherence tomography images were analyzed at baseline and at the end of follow-up to identify the presence of complete vitreomacular adhesion, partial vitreomacular adhesion, vitreomacular traction syndrome, and complete posterior vitreous detachment.

Results:
Six hundred and twenty-nine eyes were eligible for the study based on the study criteria. Complete adhesion eyes gained on average +3.7 more ETDRS letters compared with the complete posterior vitreous detachment group at the end of the 12 months follow-up (P < 0.001). Baseline vitreomacular interface status had no significant influence on central subfield thickness at 12 months (P = 0.144). There was no difference between the treatment arms based on effect of baseline vitreomacular interface status on best-corrected visual acuity gain.

Conclusion:
This study provides evidence that vitreomacular interface status affects functional outcomes in diabetic macular edema patients treated with anti–vascular endothelial growth factor injections. The presence of complete or partial vitreomacular adhesion at baseline may be associated with a larger treatment benefit than those with complete posterior vitreous detachment.