bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global and seasonal variation of marine phosphonate metabolism
Authors: Lockwood Scott , Greening Chris , Baltar Federico , Morales Sergio E 
Published: June 2022

Abstract
Marine microbial communities rely on dissolved organic phosphorus (DOP) remineralisation to meet phosphorus (P) requirements. We extensively surveyed the genomic and metagenomic distribution of genes directing phosphonate biosynthesis, substrate-specific catabolism of 2-aminoethylphosphonate (2-AEP, the most abundant phosphonate in the marine environment), and broad-specificity catabolism of phosphonates by the C-P lyase (including methylphosphonate, a major source of methane). We developed comprehensive enzyme databases by curating publicly available sequences and then screened metagenomes from TARA Oceans and Munida Microbial Observatory Time Series (MOTS) to assess spatial and seasonal variation in phosphonate metabolism pathways. Phosphonate cycling genes were encoded in diverse gene clusters by 35 marine bacterial and archaeal classes. More than 65% of marine phosphonate cycling genes mapped to Proteobacteria with production demonstrating wider taxonomic diversity than catabolism. Hydrolysis of 2-AEP was the dominant phosphonate catabolism strategy, enabling microbes to assimilate carbon and nitrogen alongside P. Genes for broad-specificity catabolism by the C-P lyase were far less widespread, though enriched in the extremely P-deplete environment of the Mediterranean Sea. Phosphonate cycling genes were abundant in marine metagenomes, particularly from the mesopelagic zone and winter sampling dates. Disparity between prevalence of substrate-specific and broad-specificity catabolism may be due to higher resource expenditure from the cell to build and retain the C-P lyase. This study is the most comprehensive metagenomic survey of marine microbial phosphonate cycling to date and provides curated databases for 14 genes involved in phosphonate cycling.
Advancing our understanding of genetic risk factors and potential personalized strategies for pelvic organ prolapse
Authors: Pujol-Gualdo Natàlia , Läll Kristi , Lepamets Maarja ,   Estonian Biobank Research Team, Metspalu Andres , Nelis Mari , Milani Lili , Esko Tõnu , Hudjashov Georgi , Rossi Henna-Riikka , Arffman Riikka K. , Piltonen Terhi T. , Mägi Reedik , Laisk Triin 
Published: June 2022

AbstractPelvic organ prolapse is a common gynecological condition with limited understanding of its genetic background. In this work, we perform a genome-wide association meta-analysis comprising 28,086 cases and 546,291 controls from European ancestry. We identify 19 novel genome-wide significant loci, highlighting connective tissue, urogenital and cardiometabolic as likely affected systems. Here, we prioritize many genes of potential interest and assess shared genetic and phenotypic links. Additionally, we present the first polygenic risk score, which shows similar predictive ability (Harrell C-statistic (C-stat) 0.583, standard deviation (sd) = 0.007) as five established clinical risk factors combined (number of children, body mass index, ever smoked, constipation and asthma) (C-stat = 0.588, sd = 0.007) and demonstrates a substantial incremental value in combination with these (C-stat = 0.630, sd = 0.007). These findings improve our understanding of genetic factors underlying pelvic organ prolapse and provide a solid start evaluating polygenic risk scores as a potential tool to enhance individual risk prediction.
Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation
Authors: Theilgaard-Mönch Kim , Pundhir Sachin , Reckzeh Kristian , Su Jinyu , Tapia Marta , Furtwängler Benjamin , Jendholm Johan , Jakobsen Janus Schou , Hasemann Marie Sigurd , Knudsen Kasper Jermiin , Cowland Jack Bernard , Fossum Anna , Schoof Erwin , Schuster Mikkel Bruhn , Porse Bo T. 
Published: June 2022

AbstractDifferentiation of multipotent stem cells into mature cells is fundamental for development and homeostasis of mammalian tissues, and requires the coordinated induction of lineage-specific transcriptional programs and cell cycle withdrawal. To understand the underlying regulatory mechanisms of this fundamental process, we investigated how the tissue-specific transcription factors, CEBPA and CEBPE, coordinate cell cycle exit and lineage-specification in vivo during granulocytic differentiation. We demonstrate that CEBPA promotes lineage-specification by launching an enhancer-primed differentiation program and direct activation of CEBPE expression. Subsequently, CEBPE confers promoter-driven cell cycle exit by sequential repression of MYC target gene expression at the G1/S transition and E2F-meditated G2/M gene expression, as well as by the up-regulation of Cdk1/2/4 inhibitors. Following cell cycle exit, CEBPE unleashes the CEBPA-primed differentiation program to generate mature granulocytes. These findings highlight how tissue-specific transcription factors coordinate cell cycle exit with differentiation through the use of distinct gene regulatory elements.
Impact of interannual and multidecadal trends on methane-climate feedbacks and sensitivity
Authors: Cheng Chin-Hsien , Redfern Simon A. T. 
Published: June 2022

AbstractWe estimate the causal contributions of spatiotemporal changes in temperature (T) and precipitation (Pr) to changes in Earth’s atmospheric methane concentration (CCH4) and its isotope ratio δ13CH4 over the last four decades. We identify oscillations between positive and negative feedbacks, showing that both contribute to increasing CCH4. Interannually, increased emissions via positive feedbacks (e.g. wetland emissions and wildfires) with higher land surface air temperature (LSAT) are often followed by increasing CCH4 due to weakened methane sink via atmospheric •OH, via negative feedbacks with lowered sea surface temperatures (SST), especially in the tropics. Over decadal time scales, we find alternating rate-limiting factors for methane oxidation: when CCH4 is limiting, positive methane-climate feedback via direct oceanic emissions dominates; when •OH is limiting, negative feedback is favoured. Incorporating the interannually increasing CCH4 via negative feedbacks gives historical methane-climate feedback sensitivity ≈ 0.08 W m−2 °C−1, much higher than the IPCC AR6 estimate.
Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing
Authors: Lainšček Duško , Forstnerič Vida , Mikolič Veronika , Malenšek Špela , Pečan Peter , Benčina Mojca , Sever Matjaž , Podgornik Helena , Jerala Roman 
Published: June 2022

AbstractThe CRISPR/Cas system has emerged as a powerful and versatile genome engineering tool, revolutionizing biological and biomedical sciences, where an improvement of efficiency could have a strong impact. Here we present a strategy to enhance gene editing based on the concerted action of Cas9 and an exonuclease. Non-covalent recruitment of exonuclease to Cas9/gRNA complex via genetically encoded coiled-coil based domains, termed CCExo, recruited the exonuclease to the cleavage site and robustly increased gene knock-out due to progressive DNA strand recession at the cleavage site, causing decreased re-ligation of the nonedited DNA. CCExo exhibited increased deletion size and enhanced gene inactivation efficiency in the context of several DNA targets, gRNA selection, Cas variants, tested cell lines and type of delivery. Targeting a sequence-specific oncogenic chromosomal translocation using CCExo in cells of chronic myelogenous leukemia patients and in an animal model led to the reduction or elimination of cancer, establishing it as a highly specific tool for treating CML and potentially other appropriate diseases with genetic etiology.
Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome
Authors: de Jonge Patrick A. , Wortelboer Koen , Scheithauer Torsten P. M. , van den Born Bert-Jan H. , Zwinderman Aeilko H. , Nobrega Franklin L. , Dutilh Bas E. , Nieuwdorp Max , Herrema Hilde 
Published: June 2022

AbstractThere is significant interest in altering the course of cardiometabolic disease development via gut microbiomes. Nevertheless, the highly abundant phage members of the complex gut ecosystem -which impact gut bacteria- remain understudied. Here, we show gut virome changes associated with metabolic syndrome (MetS), a highly prevalent clinical condition preceding cardiometabolic disease, in 196 participants by combined sequencing of bulk whole genome and virus like particle communities. MetS gut viromes exhibit decreased richness and diversity. They are enriched in phages infecting Streptococcaceae and Bacteroidaceae and depleted in those infecting Bifidobacteriaceae. Differential abundance analysis identifies eighteen viral clusters (VCs) as significantly associated with either MetS or healthy viromes. Among these are a MetS-associated Roseburia VC that is related to healthy control-associated Faecalibacterium and Oscillibacter VCs. Further analysis of these VCs revealed the Candidatus Heliusviridae, a highly widespread gut phage lineage found in 90+% of participants. The identification of the temperate Ca. Heliusviridae provides a starting point to studies of phage effects on gut bacteria and the role that this plays in MetS.
Online information analysis on pancreatic cancer in Korea using structural topic model
Authors: Jo Wonkwang , Kim Yeol , Seo Minji , Lee Nayoung , Park Junli 
Published: June 2022

AbstractInappropriate information on a deadly and rare disease can make people vulnerable to problematic decisions, leading to irreversible bad outcomes. This study explored online information exchanges on pancreatic cancer. We collected 35,596 questions and 83,888 answers related to pancreatic cancer from January 1, 2003 to May 31, 2020, from Naver, the most popular Korean web portal. We also collected 8495 news articles related to pancreatic cancer during the same period. The study methods employed were structural topic modeling, keyword frequency analysis, and qualitative coding of medical professionals. The number of questions and news articles increased over time. In Naver’s questions, topics on symptoms and diagnostic tests regarding pancreatic cancer increased in proportion. The news topics on new technologies related to pancreatic cancer from various companies increased as well. The use of words related to back pain—which is not an important early symptom in pancreatic cancer—and biomarker tests using blood increased over time in Naver’s questions. Based on 100 question samples related to symptoms and diagnostic tests and an analysis of the threaded answers’ appropriateness, there was considerable misinformation and commercialized information in both categories.
Comparison of early and late Pneumocystis jirovecii Pneumonia in kidney transplant patients: the Korean Organ Transplantation Registry (KOTRY) Study
Authors: Lee Gongmyung , Koo Tai Yeon , Kim Hyung Woo , Lee Dong Ryeol , Lee Dong Won , Oh Jieun , Kim Beom Seok , Kim Myoung Soo , Yang Jaeseok ,   KOTRY Study Group, Kim Myoung Soo , Yang Jaeseok , Kong Jin Min , Kwon Oh Jung , Kim Deok Gie , Jung Cheol Woong , Kim Yeong Hoon , Kim Joong Kyung , Kim Chan-Duck , Min Ji Won , Lee Sik , Park Yeon Ho , Park Jae Berm , Park Jung Hwan , Park Jong-Won , Ban Tae Hyun , Song Sang Heon , Song Seung Hwan , Shin Ho Sik , Yang Chul Woo , Yoon Hye Eun , Lee Kang Wook , Lee Dong Ryeol , Lee Dong Won , Oh Jieun , Lee Sang-Ho , Lee Su Hyung , Lee Yu Ho , Lee Jung Pyo , Lee Jeong-Hoon , Jeon Jin Seok , Jun Heungman , Jeong Kyung Hwan , Chung Ku Yong , Lee Jong Soo , Ki Ju Man , Chae Dong-Wan , Choi Soo Jin Na , Shin Sung , Han Seungyeup , Huh Kyu Ha 
Published: June 2022

AbstractLate Pneumocystis jirovecii pneumonia (PJP) is not rare in the era of universal prophylaxis after kidney transplantation. We aimed to determine the nationwide status of PJP prophylaxis in Korea and compare the incidence, risk factors, and outcomes of early and late PJP using data from the Korean Organ Transplantation Registry (KOTRY), a nationwide Korean transplant cohort. We conducted a retrospective analysis using data of 4,839 kidney transplant patients from KOTRY between 2014 and 2018, excluding patients who received multi-organ transplantation or were under 18 years old. Cox regression analysis was performed to determine risk factors for early and late PJP. A total of 50 patients developed PJP. The number of patients who developed PJP was same between onset before 6 months and onsets after 6 months. There were no differences in the rate, duration, or dose of PJP prophylaxis between early and late PJP. Desensitization, higher tacrolimus dose at discharge, and acute rejection were associated with early PJP. In late PJP, old age as well as acute rejection were significant risk factors. In conclusion late PJP is as common and risky as early PJP and requires individualized risk-based prophylaxis, such as prolonged prophylaxis for old patients with a history of rejection.
Effects of exercise initiation and smoking cessation after new-onset type 2 diabetes mellitus on risk of mortality and cardiovascular outcomes
Authors: Kim Mee Kyoung , Han Kyungdo , Kim Bongsung , Kim Jinyoung , Kwon Hyuk-Sang 
Published: June 2022

AbstractLifestyle changes after a diagnosis of type 2 diabetes mellitus (DM) can affect vascular health outcomes. The objective of this study was to investigate the effects of changes in smoking and exercise on the risk of cardiovascular disease (CVD) and mortality in patients with newly diagnosed DM. Data were analyzed for 181,591 people with newly diagnosed type 2 DM who underwent 2 serial health examinations within 2 years before and after DM diagnosis. The study population was followed from the baseline to the date of death or cardiovascular events, or until December 31, 2018 and median follow-up was 6.07 years. Based on the change in status from before to after the diagnosis, participants were grouped into smoking groups (continuous smokers, quitters, new smokers, and nonsmokers) and exercise groups (constant exercisers, new exercisers, exercise dropouts, and nonexercisers). Compared with the nonexercisers, those who initiated exercise after their DM diagnosis had a lower risk of myocardial infarction (MI), stroke, and all-cause mortality: the hazard ratio (HR; 95% confidence interval [CI]) was 0.85 (0.76–0.94) for MI, 0.86 (0.78–0.94) for stroke, and 0.84 (0.89–0.90) for all-cause mortality. Quitters had a higher risk of MI, stroke, and all-cause mortality than nonsmokers, but their risk level was much lower than that in continuous smokers. When the group of continuous smokers and nonexercisers was considered as the reference group, participants who quit smoking and remained nonexercisers had a 21% lower risk of CVD (HR 0.79; 95% CI 0.70–0.90). Those who quit smoking and started exercising had a 46% reduced risk of CVD (HR 0.54; 95% CI 0.41–0.71) and a 22% reduced risk in all-cause mortality (HR 0.78; 95% CI 0.63–0.96). Smoking cessation and exercise initiation after a diagnosis of new-onset type 2 DM was associated with a reduced risk of CVD and all-cause mortality.
Incidence density and factors associated with peripheral neuropathy among women with breast cancer during taxane-based chemotherapy
Authors: Rattanakrong Nida , Siriphorn Akkradate , Boonyong Sujitra 
Published: June 2022

AbstractThis work aimed to determine the incidence density of taxane-induced peripheral neuropathy (TIPN) and its risk factors among women with breast cancer. One hundred and forty-one women with breast cancer participated in this cohort study. TIPN symptoms were evaluated with the European Organization for Research and Treatment of Cancer CIPN specific self-report questionnaire (EORTC QOL-CIPN20) at five-time points throughout chemotherapy treatment. Over three months, 125 (89%) and 59 (44.03%) women with breast cancer were identified with sensory and motor neuropathy, respectively. The sensory neuropathy incidence density was 21 per 1000 person-days. The motor neuropathy incidence density was 6 per 1000 person-days. This study discovered a significant link between age and the incidence density of sensory neuropathy (HR = 1.02; 95% CI: 1.01–1.05) as well as motor neuropathy (HR = 1.05; 95% CI: 1.01–1.08). These findings imply that screening may be necessary to detect early TIPN symptoms and provide appropriate rehabilitation programs, particularly for elderly persons.
The landscape of facial processing applications in the context of the European AI Act and the development of trustworthy systems
Authors: Hupont Isabelle , Tolan Songül , Gunes Hatice , Gómez Emilia 
Published: June 2022

AbstractThis work focuses on facial processing, which refers to artificial intelligence (AI) systems that take facial images or videos as input data and perform some AI-driven processing to obtain higher-level information (e.g. a person’s identity, emotions, demographic attributes) or newly generated imagery (e.g. with modified facial attributes). Facial processing tasks, such as face detection, face identification, facial expression recognition or facial attribute manipulation, are generally studied as separate research fields and without considering a particular scenario, context of use or intended purpose. This paper studies the field of facial processing in a holistic manner. It establishes the landscape of key computational tasks, applications and industrial players in the field in order to identify the 60 most relevant applications adopted for real-world uses. These applications are analysed in the context of the new proposal of the European Commission for harmonised rules on AI (the AI Act) and the 7 requirements for Trustworthy AI defined by the European High Level Expert Group on AI. More particularly, we assess the risk level conveyed by each application according to the AI Act and reflect on current research, technical and societal challenges towards trustworthy facial processing systems.
Musical emotions affect memory for emotional pictures
Authors: Talamini Francesca , Eller Greta , Vigl Julia , Zentner Marcel 
Published: June 2022

AbstractMusic is widely known for its ability to evoke emotions. However, assessing specific music-evoked emotions other than through verbal self-reports has proven difficult. In the present study, we explored whether mood-congruency effects could be used as indirect measures of specific music-evoked emotions. First, participants listened to 15 music excerpts chosen to induce different emotions; after each excerpt, they were required to look at four different pictures. The pictures could either: (1) convey an emotion congruent with that conveyed by the music (i.e., congruent pictures); (2) convey a different emotion than that of the music, or convey no emotion (i.e., incongruent pictures). Second, participants completed a recognition task that includednewpictures as well asalready seencongruent and incongruent pictures. From previous findings about mood-congruency effects, we hypothesized that if music evokes a given emotion, this would facilitate memorization of pictures that convey the same emotion. Results revealed that accuracy in the recognition task was indeed higher for emotionally congruent pictures than for emotionally incongruent ones. The results suggest that music-evoked emotions have an influence on subsequent cognitive processing of emotional stimuli, suggesting a role of mood-congruency based recall tasks as non-verbal methods for the identification ofspecificmusic-evoked emotions.
Lead ferrite-activated carbon magnetic composite for efficient removal of phenol from aqueous solutions: synthesis, characterization, and adsorption studies
Authors: Allahkarami Esmaeil , Dehghan Monfared Abolfazl , Silva Luis Felipe Oliveira , Dotto Guilherme Luiz 
Published: June 2022

AbstractA novel lead ferrite-magnetic activated carbon (lead ferrite-MAC) composite was developed using the chemical co-precipitation method. Instrumental analyses such as X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), and Brunauer–Emmett–Teller (BET) analysis were performed to characterize adsorbent. The uptake of phenol from aqueous solutions using the developed adsorbent was compared to that of pristine activated carbon. The maximum adsorption capacity of lead ferrite-MAC composite (145.708 mg/g) was more than that of pristine activated carbon (116.606 mg/g) due to the metal hydroxides coated on activated carbon since they improve the retention of phenol on the available active sites of adsorbent and create an additional electrostatic interaction with the phenol adsorbate. Regarding the high value of the coefficient of determination (R2) and adjusted determination coefficient (R2adj), coupled with the lower values of average relative error (ARE) and minimum squared error (MSE), it can be found that the isothermal data for the lead ferrite-MAC adsorbent were in agreement with the isotherm models of Redlich-Peterson and Langmuir. From the kinetic viewpoint, pseudo-second-order and linear driving force models explained the phenol adsorption data for both adsorbents. The reusability tests for lead ferrite-MAC composite revealed that after six cycles, 85% of the initial adsorption capacity was maintained. The developed adsorbent can be successfully applied to uptake phenol from aqueous solutions.
A comprehensive study on the effect of carbonization temperature on the physical and chemical properties of carbon fibers
Authors: Shokrani Havigh Roya , Mahmoudi Chenari Hossein 
Published: June 2022

AbstractCarbon fibers were successfully fabricated via the electrospinning technique, followed by stabilizing and carbonizing electrospun PAN fibers. A wide range of analytical techniques such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), Diffuse reflectance spectroscopy (DRS), photoluminescence spectroscopy (PL), vibrating sample magnetometer (VSM) techniques, and Hall effect were performed to study of the effect of carbonization temperature on the physical and chemical characterization of carbon fibers. The SEM images of the PAN precursor exhibit a smooth outer surface, after the stabilization and carbonization process, along with a broken fiber at higher carbonization temperature about 1400 °C. Morphological characterization based on the recorded TEM images of carbonized fibers at 1000 °C and 1400 °C, showed that the obtained morphology can be classified as fiber structures, where their diameters ranged from 196 to 331 nm. The XRD patterns of PAN-based carbon fibers confirm the structural changes from linear structure into a graphite-like structure. The DRS study indicates the possible π–π*/σ–π* and n–π* transitions. The presence of the surface functional groups and different trapped radiative recombination on the emission bands is confirmed by the PL. VSM results shows the weak ferromagnetic nature of the carbon fibers.