bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water-soluble saponins accumulate in drought-stressed switchgrass and may inhibit yeast growth during bioethanol production
Authors: Chipkar Sarvada , Smith Katherine , Whelan Elizabeth M. , Debrauske Derek J. , Jen Annie , Overmyer Katherine A. , Senyk Andrea , Hooker-Moericke Larkin , Gallmeyer Marissa , Coon Joshua J. , Jones A. Daniel , Sato Trey K. , Ong Rebecca G. 
Published: October 2022

Abstract
Background
Developing economically viable pathways to produce renewable energy has become an important research theme in recent years. Lignocellulosic biomass is a promising feedstock that can be converted into second-generation biofuels and bioproducts. Global warming has adversely affected climate change causing many environmental changes that have impacted earth surface temperature and rainfall patterns. Recent research has shown that environmental growth conditions altered the composition of drought-stressed switchgrass and directly influenced the extent of biomass conversion to fuels by completely inhibiting yeast growth during fermentation. Our goal in this project was to find a way to overcome the microbial inhibition and characterize specific compounds that led to this inhibition. Additionally, we also determined if these microbial inhibitors were plant-generated compounds, by-products of the pretreatment process, or a combination of both.

Results
Switchgrass harvested in drought (2012) and non-drought (2010) years were pretreated using Ammonia Fiber Expansion (AFEX). Untreated and AFEX processed samples were then extracted using solvents (i.e., water, ethanol, and ethyl acetate) to selectively remove potential inhibitory compounds and determine whether pretreatment affects the inhibition. High solids loading enzymatic hydrolysis was performed on all samples, followed by fermentation using engineered Saccharomyces cerevisiae. Fermentation rate, cell growth, sugar consumption, and ethanol production were used to evaluate fermentation performance. We found that water extraction of drought-year switchgrass before AFEX pretreatment reduced the inhibition of yeast fermentation. The extracts were analyzed using liquid chromatography–mass spectrometry (LC–MS) to detect compounds enriched in the extracted fractions. Saponins, a class of plant-generated triterpene or steroidal glycosides, were found to be significantly more abundant in the water extracts from drought-year (inhibitory) switchgrass. The inhibitory nature of the saponins in switchgrass hydrolysate was validated by spiking commercially available saponin standard (protodioscin) in non-inhibitory switchgrass hydrolysate harvested in normal year.

Conclusions
Adding a water extraction step prior to AFEX-pretreatment of drought-stressed switchgrass effectively overcame inhibition of yeast growth during bioethanol production. Saponins appear to be generated by the plant as a response to drought as they were significantly more abundant in the drought-stressed switchgrass water extracts and may contribute toward yeast inhibition in drought-stressed switchgrass hydrolysates.
Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis
Authors: Xu Zhangyang , Peng Bo , Kitata Reta Birhanu , Nicora Carrie D. , Weitz Karl K. , Pu Yunqiao , Shi Tujin , Cort John R. , Ragauskas Arthur J. , Yang Bin 
Published: October 2022

Abstract
Background
Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process.

Results
This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn2+-peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn2+-peroxidase. Gas chromatography–mass spectrometry (GC–MS) and two-dimensional 1H–13C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C–C bond (β-β, β-5, and β-1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C–O bond (β-O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process.

Conclusions
Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion.

Graphical Abstract
Establishing a framework for privacy-preserving record linkage among electronic health record and administrative claims databases within PCORnet®, the National Patient-Centered Clinical Research Network
Authors: Kiernan Daniel , Carton Thomas , Toh Sengwee , Phua Jasmin , Zirkle Maryan , Louzao Darcy , Haynes Kevin , Weiner Mark , Angulo Francisco , Bailey Charles , Bian Jiang , Fort Daniel , Grannis Shaun , Krishnamurthy Ashok Kumar , Nair Vinit , Rivera Pedro , Silverstein Jonathan , Marsolo Keith 
Published: October 2022

Abstract
Objective
The aim of this study was to determine whether a secure, privacy-preserving record linkage (PPRL) methodology can be implemented in a scalable manner for use in a large national clinical research network.

Results
We established the governance and technical capacity to support the use of PPRL across the National Patient-Centered Clinical Research Network (PCORnet®). As a pilot, four sites used the Datavant software to transform patient personally identifiable information (PII) into de-identified tokens. We queried the sites for patients with a clinical encounter in 2018 or 2019 and matched their tokens to determine whether overlap existed. We described patient overlap among the sites and generated a “deduplicated” table of patient demographic characteristics. Overlapping patients were found in 3 of the 6 site-pairs. Following deduplication, the total patient count was 3,108,515 (0.11% reduction), with the largest reduction in count for patients with an “Other/Missing” value for Sex; from 198 to 163 (17.6% reduction). The PPRL solution successfully links patients across data sources using distributed queries without directly accessing patient PII. The overlap queries and analysis performed in this pilot is being replicated across the full network to provide additional insight into patient linkages among a distributed research network.
Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information
Authors: Hamamoto Ryuji , Koyama Takafumi , Kouno Nobuji , Yasuda Tomohiro , Yui Shuntaro , Sudo Kazuki , Hirata Makoto , Sunami Kuniko , Kubo Takashi , Takasawa Ken , Takahashi Satoshi , Machino Hidenori , Kobayashi Kazuma , Asada Ken , Komatsu Masaaki , Kaneko Syuzo , Yatabe Yasushi , Yamamoto Noboru 
Published: October 2022

AbstractSince U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year’s State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of oncology. With the advent of next-generation sequencers specifically, genome analysis technology has made remarkable progress, and there are active efforts to apply genome information to diagnosis and treatment. Generally, in the process of feeding back the results of next-generation sequencing analysis to patients, a molecular tumor board (MTB), consisting of experts in clinical oncology, genetic medicine, etc., is established to discuss the results. On the other hand, an MTB currently involves a large amount of work, with humans searching through vast databases and literature, selecting the best drug candidates, and manually confirming the status of available clinical trials. In addition, as personalized medicine advances, the burden on MTB members is expected to increase in the future. Under these circumstances, introducing cutting-edge artificial intelligence (AI) technology and information and communication technology to MTBs while reducing the burden on MTB members and building a platform that enables more accurate and personalized medical care would be of great benefit to patients. In this review, we introduced the latest status of elemental technologies that have potential for AI utilization in MTB, and discussed issues that may arise in the future as we progress with AI implementation.
New finding of Trichoderma asperellum in decreasing soil N2O emission
Authors: Wu Hong-sheng , Chen Su-yun , Ding Jun , Tian Wei , Wang Ti-jian , Shen Li-dong , Li Yan-hui , Liu Zheng , Li Ji 
Published: October 2022

Abstract
Background
Global warming caused by greenhouse gas emissions affects sustainable human development. Agricultural practices are important source of greenhouse gases (GHG). Nitrous oxide (N2O) contributes greatly to farming GHG. It is important to find a potential and practical biological technique that mitigate N2O emissions in an environment friendly way.

Methods
N2O-inhibiting fungi were isolated and identified in the lab. The fungi were added into the soil and placed in the incubator and interval gas sampling was analyzed by gas chromatograph.

Results
Fungus coding Z17 was identified molecularly with the same evolutionary branch on the phylogenetic tree with Trichoderma asperellum by BLAST comparison on NCBI GenBank. In the lab simulation, the N2O emission flux was decreased by 28.18–47.16% by inoculating Trichoderma asperellum with 106 cfu·g−1, 5 × 106 cfu·g−1 and 107 cfu·g−1 fungal spores in the soil compared to the control.

Conclusions
The N2O-inhibiting fungus Z17 was identified as Trichoderma asperellum, capable of suppressing N2O emissions from soil with at least 106 CFU·g−1 soil. The best N2O-inhibiting effect was on day 9 of inoculation into soil because most of the fungal numbers were present in soil.

Graphical Abstract
Fitness of the fall armyworm Spodoptera frugiperda to a new host plant, banana (Musa nana Lour.)
Authors: Zhou Shangchao , Qin Yanxiang , Wang Xiaoyun , Zheng Xialin , Lu Wen 
Published: October 2022

Abstract
Background
The fall armyworm Spodoptera frugiperda is a highly destructive agricultural pest that primarily damages maize in China. However, there were no reports of S. frugiperda damage to banana until it was observed on bananas in the wild. This suggested that banana crops may be potential hosts of the pest. To clarify the fitness and potential impact of S. frugiperda on banana, this study analysed the survival and development of S. frugiperda fed on bananas in the laboratory and constructed age-stage and two-sex life tables.

Results
Larvae of S. frugiperda fed on bananas completed their life cycles and produced fertile offspring, but the larvae had eight instars and presented longer developmental duration, slower population growth, and lower body weight than maize-fed larvae. Furthermore, the banana-fed S. frugiperda had longer adult longevity and preoviposition periods than the maize-fed larvae, while the opposite tendency was observed for oviposition days and egg production. Based on age-stage and two-sex life tables, the survival probability at each stage of S. frugiperda fed on bananas was lower than that of maize-fed larvae, and banana-fed S. frugiperda showed lower reproductive capacity.

Conclusions
Although banana is not an ideal host for the fall armyworm, it may be colonized by the species in situations in which the population density is high or the preferred host is scarce. Therefore, it is essential to prevent the pest from transferring to bananas and thereby increasing the number of sources of outbreaks.

Graphical Abstract
Measurement properties of the Brazilian online version of the Fibromyalgia Rapid Screening Tool (FiRST)
Authors: de Sousa Ana Paula , de Arruda Guilherme Tavares , Pontes-Silva André , de Souza Marcelo Cardoso , Driusso Patricia , Avila Mariana Arias 
Published: October 2022

Abstract
Objective
The Fibromyalgia Rapid Screening Tool (FiRST) was developed to screen people with chronic pain for Fibromyalgia (FM), especially in primary health care settings. This study aimed to translate the FiRST into Brazilian Portuguese and evaluate its measurement properties for an online application.

Methods
After the process of translation and backtranslation, the FiRST was applied online in 483 adults with chronic pain (FM group n = 395; Chronic pain group n = 88), along with the Numerical Rating Scale for pain and fatigue, the Brief Pain Inventory, and the Fibromyalgia Impact Questionnaire-Revised. A Receiver Operating Characteristics (ROC) curve was computed and the area under the curve (AUC) was used to determine the sensibility, specificity, and cut-off score for the FiRST. The Mann-Whitney test was used for quantitative variables and the Chi-square and the Fisher’s exact test, for the categorical variables with level of significance of 5%. Fleiss’ Kappa, Gwet’s AC1 and percentage of agreement were also calculated between test and retest.

Results
For all the questionnaires, the FM group presented higher scores, which mean a worst condition. The FiRST presented a sensitivity of 92.3%, and a specificity of 61.6% with 5 as the cut-off score. AUC, Fleiss’ Kappa, Gwet’s AC1 and percentage of agreement were, respectively, 0.82, 0.38, 0.63 and 71.8%.

Conclusion
The FiRST was translated into Brazilian Portuguese and the online version presented a good content validity and adequate measurement errors that allow FM patients to be screened among people with chronic pain.
Promoting spatial cognition in hospital buildings using space syntax analyses
Authors: Youssef Khaled Ali , Youssef Amr Mamdoh Ali 
Published: October 2022

AbstractSpatial cognition is a pivotal consideration in hospital buildings. Potential circulation configuration alternatives in hospitals have been filtered to 59 significant alternatives, to be simulated using space syntax analyses for measuring connectivity, visual integration, and visual step depth. Best alternatives have been determined via comparison and correlation analysis. A survey has been conducted, comparing the preferences of professional architects with simulation outcomes. Results show that best and worst alternatives exist in triangular and circular buildings, respectively. Also, cul-de-sac corridors are argued to promote spatial cognition better than looped corridors. Notably, cognition is inversely proportional to the curvature of the circulation spaces, number of nodes, and the number of branches. The survey showed a weak perception of the best alternatives, while respondents have a better perception of highly visible locations in these alternatives.
Skeletal Effects of Sleeve Gastrectomy in Adolescents and Young Adults: A 2-Year Longitudinal Study
Authors: Mitchell Deborah M , Singhal Vibha , Animashaun Abisayo , Bose Amita , Carmine Brian , Stanford Fatima C , Inge Thomas H , Kelsey Megan M , Lee Hang , Bouxsein Mary L , Yu Elaine W , Bredella Miriam A , Misra Madhusmita 
Published: October 2022

Abstract

Context
Vertical sleeve gastrectomy (VSG) is an increasingly common tool to achieve weight loss and improve metabolic health in adolescents and young adults with obesity, although it may adversely affect bone health.

Objective
This work aimed to evaluate the effect of VSG on bone health in youth.

Methods
An observational 2-year study was conducted at a tertiary care center of 66 patients aged 13 to 24 years with moderate-to-severe obesity meeting criteria for VSG. The patients underwent VSG (n = 30) or nonsurgical (n = 36) management per the decision of patient and clinical team. Main outcome measures included dual-energy x-ray absorptiometry (DXA) and high-resolution peripheral quantitative computed tomography (HRpQCT) measures of bone mineral density (BMD), geometry, and microarchitecture.

Results
VSG patients achieved 25.3 ± 2.0% weight loss at 2 years (P &lt; .001) while control subjects gained 4.0 ± 2.0% (P = .026). Total hip BMD declined 8.5 ± 1.0% following VSG compared with 0.1 ± 1.0% gain in controls (P &lt; .001), with similar results at the femoral neck (P &lt; .001). Total volumetric BMD (vBMD) decreased both at the distal radius and tibia following VSG (P &lt; .001) driven primarily by trabecular vBMD loss (P &lt; .001). Two-year changes in cortical vBMD did not differ between groups, though cortical porosity decreased following VSG both at the radius and tibia (P = .048 and P &lt; .001). Cortical thickness increased in controls but not in VSG (P = .022 and P = .002 for between-group comparisons at the radius and tibia, respectively). Following VSG, estimated failure load decreased at the radius and did not demonstrate the physiologic increases at the tibia observed in controls.

Conclusion
VSG leads to progressive changes in bone health over 2 years, and may lead to increased skeletal fragility in adolescents and young adults.
Women’s perceptions and attitudes to the use of AI in breast cancer screening: a survey in a cancer referral centre
Authors: Pesapane Filippo , Rotili Anna , Valconi Elena , Agazzi Giorgio Maria , Montesano Marta , Penco Silvia , Nicosia Luca , Bozzini Anna , Meneghetti Lorenza , Latronico Antuono , Pizzamiglio Maria , Rossero Eleonora , Gaeta Aurora , Raimondi Sara , Pizzoli Silvia Francesca Maria , Grasso Roberto , Carrafiello Gianpaolo , Pravettoni Gabriella , Cassano Enrico 
Published: October 2022

Objective:
Although breast cancer screening can benefit from Artificial Intelligence (AI), it is still unknown whether, to which extent or under which conditions, the use of AI is going to be accepted by the general population. The aim of our study is to evaluate what the females who are eligible for breast cancer screening know about AI and how they perceive such innovation.

Methods:
We used a prospective survey consisting of a 11-multiple-choice questionnaire evaluating statistical associations with Chi-Square-test or Fisher-exact-test. Multinomial-logistic-regression was performed on items with more than two response categories. Odds ratio (OR) with 95% CI were computed to estimate the probability of a specific response according to patient’s characteristics.

Results:
In the 800 analysed questionnaires, 51% of respondents confirmed to have knowledge of AI. Of these, 88% expressed a positive opinion about its use in medicine. Non-Italian respondents were associated with the belief of having a deep awareness about AI more often than Italian respondents (OR = 1.91;95% CI[1.10–3.33]). Higher education level was associated with better opinions on the use of AI in medicine (OR = 4.69;95% CI[1.36–16.12]). According to 94% of respondents, the radiologists should always produce their own report on mammograms, whilst 77% agreed that AI should be used as a second reader. Most respondents (52%) considered that both the software developer and the radiologist should be held accountable for AI errors.

Conclusions:
Most of the females undergoing screening in our Institute approve the introduction of AI, although only as a support to radiologist, and not in substitution thereof. Yet, accountability in case of AI errors is still unsolved. advances in knowledge:
This survey may be considered as a pilot-study for the development of large-scale studies to understand females’s demands and concerns about AI applications in breast cancer screening.
On the Disclosure of Half-Truths and the Duty to Update
Authors: Beyer Anne , Dye Ronald A. 
Published: October 2022

We develop a model of a manager’s equilibrium voluntary disclosure policy to study how that policy changes depending on whether the manager is prohibited from disclosing, or allowed to disclose, a half-truth; we also examine how the disclosure policy changes depending on whether the manager has a duty to update past disclosures. Among our results, we show that if a manager is prohibited from issuing half-truths, the manager discloses a wider array of information than if the manager is allowed to issue half-truths, and investors view the absence of disclosure more skeptically; we also show that imposing a duty to update on the manager does not affect the manager’s initial disclosures, but it results in the manager disclosing uniformly more information over time. This paper was accepted by Brian Bushee, accounting.
Risk-Averse Optimal Control in Continuous Time by Nesting Risk Measures
Authors: Pichler Alois , Schlotter Ruben 
Published: October 2022

This paper extends dynamic control problems from a risk-neutral to a risk-averse setting. We establish a limit for consecutive risk-averse decision making by consistently and adequately nesting coherent risk measures. This approach provides a new perspective on multistage optimal control problems in continuous time. For the limiting case, we elaborate a new dynamic programming principle, which is risk averse, and give risk-averse Hamilton–Jacobi–Bellman equations by generalizing the infinitesimal generator. In doing so, we provide a constructive explanation of the driver g in g-expectation, a dynamic risk measure based on backward stochastic differential equations. Funding: This work was supported by Deutsche Forschungsgemeinschaft [Project-ID 416228727 – SFB 1410].
Türkiye’s Climate Policies in the Context of Sustainable Security
Authors: ATVUR Senem , VURAL Çağla 
Published: October 2022

Climate change is becoming one of the most crucial problems threatening the integrity of the global system. The impacts of climate change have been posing new threats to the states’
interests, human prosperity and environmental sustainability. This article aims to analyze Türkiye’s climate policies within the context of the sustainable security approach, which focuses on
the balance between national, human and environmental security. The study argues that Türkiye’s economic priorities prevail over its climate strategies. Moreover, Türkiye becomes more vulnerable
and less resilient to the impacts of climate change as long as the country’s carbon emissions continue to rise. Therefore, this article argues that if Türkiye considers the risks of climate change with
a sustainable security approach; economic advantages, social prosperity and environmental protection for both present and future generations could be equivalently guaranteed.
Multiple microwave frequency measurement system based on a sawtooth-wave-modulated non-flat optical frequency comb
Authors: Zhu Wei , Li Jing , Yan Miaoxia , Pei Li , Ning Tigang , Zheng Jingjing , Wang Jianshuai 
Published: October 2022

A photonic-assisted instantaneous microwave measurement system, capable of measuring multiple frequency signals, is demonstrated and analyzed. The principle lies in the combination of a channelizer and frequency-to-power mapping. An effective generation method of a non-flat optical frequency comb is proposed based on sawtooth wave modulation, which has more comb lines and adjustable comb spacing. Under this method, two low-speed post-processing devices are utilized to realize frequency measurements up to 32 GHz. The scheme is verified by simulation, and factors affecting system performance are also studied.