bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying mild traumatic brain injury using measures of frequency-specified networks
Authors: Salsabilian Shiva , Bibineyshvili Yelena , Margolis David J , Najafizadeh Laleh
Published: September 2022

Objective. Early diagnosis of mild traumatic brain injury (mTBI) is challenging, yet crucial for providing patients with timely treatments and minimizing the risks of developing injury-related disorders. To tackle this problem, this paper presents a framework based on measures of frequency-specified brain functional networks identifying mTBI. Approach. Cortical activity of 15 control and 15 injury Thy1-GCaMP6s mice are recorded, using widefield calcium imaging, prior to and 20 minutes after inducing injury. Power spectral distribution (PSD) of the recorded cortical activities is examined, and the frequency bands with significant difference in PSD between the injury and control groups are identified. Frequency-specified functional networks are then constructed. Employing graph theoretical analysis, various network measures from the constructed frequency-specified functional networks are extracted and used as features. Several classifiers are utilized to evaluate the performance of the computed network measures, either individually or collectively as features, to classify mTBI from control. Main results. Spectral analysis reveals the presence of two dominant frequency bands (low:

<

1

Hz) and high: [1–8] Hz) in the cortical activities recorded via calcium imaging. Comparison of the brain networks of control and injury groups shows significant reduction (p < 0.05) in global functional connectivity following injury, specially for the high frequency band network. Interestingly, graph measures of the high frequency band network provided higher classification accuracy results, compared to those computed from the low frequency band network, suggesting that mTBI network-based features are frequency dependent. Using all network measures collectively as a multi-measure feature vector and a convolutional neural networks classifier, a model for identifying mTBI is developed, offering an average classification accuracy of 97.28%. Significance. Results signifies the importance of considering frequency-specific analysis in functional networks for mTBI identification, and demonstrate the possibility of using network measures for early mTBI diagnosis.
Kinematic fitting of neutral current events in deep inelastic ep collisions.
Authors: Aggarwal Ritu , Caldwell Allen
Published: September 2022

In this paper we present a technique to reconstruct the
scaling variables defining ep deep inelastic scattering by
performing a kinematic fit. This reconstruction technique makes use
of the full potential of the data collected. It is based on Bayes'
Theorem and involves the use of informative priors. The kinematic
fit method has been tested using a simulated sample of ep neutral
current events at a center of mass energy of 318 GeV with 
Q
2 > 400 GeV2. In addition to the scaling variables, this
method is able to estimate the energy of possible initial state
radiation (Eγ
) which otherwise goes undetected. A better
resolution than standard electron and double angle techniques in the
reconstruction of scaling variables is achieved using a kinematic
fit.
Compact phase comparison system for the synthetic HCOOH laser diagnostic system in HL-2A
Authors: Zhang W. , Wu T.Y. , Li Y.G. , Zhang Y.P.
Published: September 2022

Recently, a synthetic formic-acid laser diagnostic system
has been deployed in HL-2A tokamak. However, the main electronics of
the subsystems were discrete devices, and multimodal data analysis
remained out of reach. In this work, we developed a novel compact
high sensitivity Phasemeter (CHSP) system to integrate
interferometer, far-forward collective scattering diagnostic (FCS),
and Faraday effect polarimeter. It provides a framework for
real-time intelligent diagnosis such as plasma disruptions
prediction. We also propose a Synchronous Fast Fourier Transform
(SFFT) method for suppression of spectral leakage and noise
reduction. Experimental results indicate that the electronics system
accuracy is about 1.0× 1015/m-3, which fully meets
the requirements of HL-2A. This work represents a crucial step
toward a high-performance intelligent diagnosis in HL-2A.
Seismic Analysis of Diagrid Structure on Sloping Ground
Authors: Shylaja N , Ashwini R M , Babu E R
Published: September 2022

Lateral efficiency of a building is very important in high-rise buildings, when it comes to building them on sloping ground it is highly required to design the structure for wind load and earthquake loads. The diagrid structure thus provides very high lateral stability and reduces the lateral displacement of the building. In recent years the diagrid structure has attracted many researchers and scholars due to this greater structural efficiency. Diagrid structural system has evolved to be structurally the most efficient, aesthetically pleasant and highly economical. The present paper involves the study of diagrid structure on sloping ground and comparing it with the conventional system and finding the optimum angle of diagrid on different slopes of ground. A 12- storey building is used for comparing diagrid structure and conventional structure on sloping ground, a 48 storey building is used to find out the optimum angle of diagrid on sloping ground, ETABS software Is used for modelling and analysis, response spectrum method is used for analysis, the results show that diagrid structure is more efficient than conventional structure on sloping ground, and the optimum angle of diagrid lies between 60-75° on sloping ground.
Compressive strength of recron fibred cement mortar by replacement of cement with alccofine
Authors: Deshpande A S , Nanjunda K N , Kavyashree B
Published: September 2022

In India, masonry structures are still practiced on major scale. Causalities majorly happens in masonry structures during earthquakes in earthquake prone zones due to less bond strength and non-structured designs. The main aim of afore mentioned paper is to find solution to increase this compressive strength, so that practice of masonry structures in rural area can made safe and economic with respect to strength. This study of bond strength can be carried out by analytic approach as well as experimental approach. In analytic approach, finite element method is used for the study, which requires large numbers of properties to model materials, which are not available in literature for the Indian scenario because literature focuses about results not properties. Hence this compressive strength study is carried out by experimental approach to give it more practical and meaningful direction. In mortar, arbitrarily dispersed fibers and alccofine 1203 are generally used for fortification to resist proliferation of crack and also helps to improve strength and ductility behavior which will help the structure to get less damage and to enhance the performance during earthquakes in earthquake prone zones. This will reduce the causalities. The use of recron 3s fibers is economic and alccofine 1203, easy to practice and effective approach as well. These experimental studies are started by making mortar cubes and ended up with making masonry prism and columns by using recron 3s fibers and alccofine 1203 with different mortar bed thicknesses. The studies on brick masonry prism suggests that use of recron 3s fiber and alccofine 1203 in mortar can increase the compressive strength to enhance the performance of the masonry structure. Use of 8 mm thick mortar bed gives more convincing when compressive strengths of masonry wallets are compared.
Catalytic mechanism and activity of N2 reduction on boron-decorated crystalline carbon nitride
Authors: Zheng Mei , Cai Xu , Li Yi , Ding Kaining , Zhang Yongfan , Chen Wenkai , Sun Chenghua , Lin Wei
Published: September 2022

The development of efficient, low-cost, and eco-friendly catalysts for nitrogen fixation is essential and provides an alternative method to the traditional Haber–Bosch process. However, studies on thermal catalyst of nitrogen fixation mainly focus on metal-containing, and the microscopic mechanism of thermal reduction process is still limited. Herein, we explored an economic metal-free boron atom decorated poly(triazine imide) (B/PTI), a crystalline carbon nitride, as an excellent thermal catalyst of nitrogen fixation and proposed a substrate-hydrogen mechanism for the N2 thermal reduction reaction (NTRR). Our results reveal that the substrate hydrogen as the hydrogen source can promote the hydrogenation process with activation barrier of 0.56 eV, significantly lower than that of reported NTRR catalysts. Importantly, the B/PTI exhibits high turnover frequency, which is comparable to Fe, Ru, and Ti catalysts. Our work offers new insights into NTRR mechanism and provides an alternative solution for the sustainable ammonia synthesis.
New chromium steel grade for creep applications
Authors: Callejo Lorena M , Barbero José Ignacio , Serna-Ruiz Mónica , Eguizabal David , Martinez Roberto Fernandez , Jimbert Pello , Calleja-Saenz Beatriz , López Alejandra
Published: September 2022

In this study, a novel Chromium steel grade (COIN2) is produced as a result of a new steel composition and an innovative heat treatment. This new steel grade COIN2 evolves from the P92 steel grade and other novel steel grade recently created by the authors (COIN), and represents an enhancement of hardness, tensile properties, and creep behaviour with respect to them, which validates the metallurgical strategy used for further research in order to increase the efficiency of power plants and thus reduce the CO2 emissions. The characterization reveals a significant property improvement with the innovative thermal treatment, contributing to the production of a novel and more competitive steel grade for creep applications.
The emergence of AntibodyPlus: the future trend of antibody-based therapeutics
Authors: Zhu Yong , Wang Shawn Shouye , Zhou Zhaohui Sunny , Ho Mitchell
Published: September 2022

To date, close to 100 canonical monoclonal antibody drugs have been approved by the FDA; furthermore, a number of antibody-derived therapeutics in nontraditional formats have reached late development stages and the market, and many more are being evaluated in early-stage development. To better reflect this trend and to set up a framework for forward thinking, we herein introduce the concept of AntibodyPlus, embracing any therapeutics with an antibody component. AntibodyPlus therapeutics contain effector modules, in the form of small molecules, nucleic acids, proteins or even cells, to enhance their therapeutic activities against cancer, virus infection and other diseases. In this short review, we discuss historic perspective and current status of therapeutic antibody development, and the scope and categories of AntibodyPlus therapeutics along with their advantages, applications and challenges. We also present several examples that highlight their design principles, potentials and future trends.
Homologue series detection and management in LC-MS data with homologueDiscoverer
Authors: Mildau Kevin , van der Hooft Justin J J , Flasch Mira , Warth Benedikt , El Abiead Yasin , Koellensperger Gunda , Zanghellini Jürgen , Büschl Christoph
Published: September 2022

Untargeted metabolomics data analysis is highly labour intensive and can be severely frustrated by both experimental noise and redundant features. Homologous polymer series is a particular case of features that can either represent large numbers of noise features or alternatively represent features of interest with large peak redundancy. Here, we present homologueDiscoverer, an R package that allows for the targeted and untargeted detection of homologue series as well as their evaluation and management using interactive plots and simple local database functionalities.

Availability and implementation

homologueDiscoverer is freely available at GitHub https://github.com/kevinmildau/homologueDiscoverer.

Supplementary information

Supplementary data are available at Bioinformatics online.
CarcinoHPVPred: An ensemble of machine learning models for HPV carcinogenicity prediction using genomic data
Authors: Karamveer Karamveer , Tiwary Basant K
Published: September 2022

Human papillomavirus (HPV) infections often show no symptoms but sometimes lead to either warts or carcinoma based on the HPV genotype. The relationship between HPV infections and cervical cancer have been well studied in the past two decades. However, distinguishing carcinogenic HPV variants from non-carcinogenic ones remains a major challenge in clinical genetic testing of HPV-induced cancer samples. All of the published HPV carcinogenicity prediction methods are neither publically available nor tested with two-thirds of available HPV variants. The nucleotide composition-based studies are the simplest and most precise methods of characterizing new genomes. Hence, there is a need for machine learning models which can predict the carcinogenic nature of newly discovered HPV based on their genomic composition. We developed a standalone and web tool, CarcinoHPVPred (h t t p :// test5.bicpu.edu.in/CarcinoHPVPred.php), for predicting the phenotype of HPV with a range of a high accuracy between 94% - 100%. This tool consists of machine learning models build upon genomic features of two genes namely E2 and E6. Overall, the accurate and early prediction of carcinogenic nature of HPV can be performed with this only available tool of its kind till date.
A totally endoscopic approach for aortic valve surgery
Authors: Yilmaz Alaaddin , Van Genechten Silke , Claessens Jade , Packlé Loren , Maessen Jos , Kaya Abdullah
Published: September 2022

OBJECTIVES

Our goal was to describe a new approach for totally endoscopic aortic valve replacement.

METHODS

From October 2017 through December 2020, a total of 266 consecutive patients underwent totally endoscopic aortic valve replacement. Reoperations and combinations were excluded.

RESULTS

A total of 266 patients with a median age of 72 (64, 79) years underwent totally endoscopic aortic valve replacement; of these, 250 (93.98%) patients were designated to undergo surgery because of aortic valve stenosis. The median follow-up index was 0.69 (0.30, 0.90). Major adverse cardiac and cerebrovascular events occurred in 4 (1.50%) patients within 30 days. Overall hospital mortality was 1.50%. Twenty additional deaths (7.52%) occurred during the 3-year follow-up period. An early thoracoscopic revision was needed in 7 patients due to signs of bleeding or cardiac tamponade. Fourteen patients required a permanent pacemaker implant.

CONCLUSIONS

Retrospective analysis of our early experience with totally endoscopic aortic valve replacement in 266 consecutive patients demonstrated satisfactory results, with low mortality and acceptable morbidity rates.
Discordance of apolipoprotein B with low-density lipoprotein cholesterol or non-high-density lipoprotein cholesterol and coronary atherosclerosis
Authors: Su Xin , Cai Xueli , Pan Yuesong , Sun Jingping , Jing Jing , Wang Mengxing , Meng Xia , Wang Yongjun , Wei Tiemin , He Yan
Published: September 2022

Aims

High level of apolipoprotein B (Apo B) is associated with incident subclinical atherosclerosis. The present study evaluated the associations between discordant Apo B with low-density lipoprotein cholesterol (LDL-C), non-high-density lipoprotein cholesterol (non-HDL-C), and coronary atherosclerotic burden.

Methods and results

This study enrolled 3043 participants aged 50–75 years from the PolyvasculaR Evaluation for Cognitive Impairment and vaScular Events (PRECISE) study that was conducted in the community in Lishui City, China. Discordant Apo B with LDL-C and non-HDL-C were defined by residuals and medians. Coronary atherosclerotic burden was evaluated by segment involvement score (SIS) and segment stenosis score (SSS) which were determined by computed tomography angiography. We performed discordance analyses examining associations of discordant Apo B with LDL-C or non-HDL-C with the coronary atherosclerotic burden. The mean age of participants was 61.2 ± 6.7 years, 53.6% were females. Participants with discordant high Apo B relative to non-HDL-C were at higher odds of plaques [odds ratio (OR), 1.30; 95% confidence interval (CI), 1.08–1.57], SIS [common odds ratio (cOR), 1.35; 95% CI, 1.14–1.60], and SSS (cOR, 1.40; 95% CI, 1.18–1.67) compared with concordant group. However, discordantly low Apo B with non-HDL-C was associated with decreased odds of the coronary atherosclerotic plaques and its burden. Similar results were shown for discordant analyses for Apo B with LDL-C.

Conclusion

Discordantly high Apo B with LDL-C and non-HDL-C were associated with an increased odds of the coronary atherosclerotic plaques and its burden. These findings highlighted the importance of Apo B for primary prevention of coronary atherosclerosis.
Volatiles released byBeauveria bassianainduce oviposition behavior in the fall armywormSpodoptera frugiperda(Lepidoptera: Noctuidae)
Authors: Ramírez-Ordorica Arturo , Contreras-Cornejo Hexon Angel , Orduño-Cruz Nuvia , Luna-Cruz Alfonso , Winkler Robert , Macías-Rodríguez Lourdes
Published: September 2022

Microbial volatile organic compounds may act as semiochemicals, inciting different behavioral responses in insects. Beauveria bassiana is an entomopathogenic fungus, and physiological and environmental factors are positively related to fungal virulence. In this study, we examined the volatile profiles produced by eight B. bassiana strains, isolated from soil plots and mycosed insect cadavers, with different speeds of kill and determined if these compounds induce oviposition behavior in Spodoptera frugiperda. Fungal volatilome analysis revealed differences between the isolates. Isolates from mycosed insects showed higher virulence, larger egg mass area and length, and a higher number of eggs by mass, than those obtained from soil. Furthermore, a dilution of the fungal odoriferous compounds increased the insect response, suggesting that S. frugiperda is highly susceptible to the fungal compound’s fingerprint. Otherwise, the insect response to the natural blend of volatiles released by the fungus was different from that obtained with 3-methylbutanol, which was the most abundant compound in all isolates. The ability of an entomopathogen to produce volatiles that can induce olfactory stimulation of egg-laying behavior could represent an ecological adaptive advantage in which the entomopathogen stimulates the insect population growth.
Outsourcing Issues of Wood Supply Chain Management in the Forest Industry
Authors: Palander Teijo
Published: September 2022

Supply-chain management of the forest industry focuses on improving client services which requires efficient collaboration between organizations in practice. Therefore, collaboration of third party logistics (3PL) and fourth party logistics (4PL) companies were analyzed using a survey and the inductive organizational gap-analysis. The supply-chain companies of the 3PLs asked for better quality information from client factories for improving logistics. They also needed online information for improving the quality control of logistics provided by their subcompanies. In addition to the quality, all companies (3PL, 4PL, clients) will need new information technology for synchronizing supply-chain operations efficiently. In this respect, the findings show how 3PLs want to adopt 4PL’s coordination mechanism for creating advanced collaboration on triadic relationships of the companies. This knowledge can be used by industry in engineering the 3PL and 4PL towards franchise-provided multiclient supply chains; cloud-service applications of collaboration groups for synchronizing wood-harvesting and transportation operations are especially important in the future. Implications of this background theory for practice are discussed mainly from perspective of decentralized wood procurement.
A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis
Authors: Sun Yongxin , Liu Xiangfeng , Xie Xi , Bai Yongan , Wang Shuo , Teng Weiming , Li Dacheng , Li Hualin , Yu Zuoan , Zhang Ming , Zhou Zunchun , Liu Xu , Nie Hongtao , Du Shaojun , Li Xiaodong , Li Qi , Wang Qingzhi
Published: September 2022

Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.
Development and Validation of a Japanese Version of the Inflammatory Bowel Disease Self-efficacy Scale and Cross-culture Study in Japan and the United States
Authors: Tanaka Makoto , Kawakami Aki , Sakagami Kayoko , Terai Tomoko , Fernandez Jovelle , Keefer Laurie , Ito Hiroaki
Published: September 2022

Background

Self-efficacy is an important health outcome for patients with inflammatory bowel disease (IBD). We aimed to develop a Japanese version of the IBD-Self-Efficacy Scale (IBD-SES.J) and compare characteristics of self-efficacy of IBD patients with previously reported results from patients in the United States.

Methods

We conducted a questionnaire survey of patients with IBD from a specialized IBD clinic and respondents recruited online. Self-efficacy of patients in Japan and the United States were compared by Student t test and Cohen d coefficient to gauge effect size.

Results

A total of 919 valid responses were obtained: 482 patients from the specialized IBD clinic and 437 patients from the online survey. Significant differences (P < .01) were observed in the following 3 subscales: “managing stress and emotions,” “managing symptoms and disease,” and “maintaining remission” when comparing remission and active periods; and known-group validity was mostly confirmed. Cronbach’s alpha coefficients of each subscale ranged between 0.85 and 0.94. Intraclass correlation coefficients (95% confidence intervals [CIs]) to assess test-retest reliability of each item were between 0.56 (95% CI, 0.47-0.64) and 0.78 (95% CI, 0.73-0.82). Self-efficacy scores for most items in Japanese patients with IBD were lower compared with patients in the United States, with moderate effect size (Cohen d > 0.5), especially in the subscale “managing stress and emotions.”

Conclusions

The study demonstrates the reliability and validity of the IBD-SESJ. Self-efficacy scores for most items in Japanese patients were lower than those of patients in the United States. Further investigation is required to understand cross-cultural score differences.
Recovery of a space-time-dependent diffusion coefficient in subdiffusion: stability, approximation and error analysis
Authors: Jin Bangti , Zhou Zhi
Published: September 2022

In this work we study an inverse problem of recovering a space-time-dependent diffusion coefficient in the subdiffusion model from the distributed observation, where the mathematical model involves a Djrbashian–Caputo fractional derivative of order $\alpha \in (0,1)$ in time. The main technical challenges of both theoretical and numerical analyses lie in the limited smoothing properties due to the fractional differential operator and high degree of nonlinearity of the forward map from the unknown diffusion coefficient to the distributed observation. We establish two conditional stability results using a novel test function, which leads to a stability bound in $L^2(0,T;L^2(\varOmega ))$ under a suitable positivity condition. The positivity condition is verified for a large class of problem data. Numerically, we develop a rigorous procedure for recovering the diffusion coefficient based on a regularized least-squares formulation, which is then discretized by the standard Galerkin method with continuous piecewise linear elements in space and backward Euler convolution quadrature in time. We provide a complete error analysis of the fully discrete formulation, by combining several new error estimates for the direct problem (optimal in terms of data regularity), a discrete version of fractional maximal $L^p$ regularity and a nonstandard energy argument. Under the positivity condition, we obtain a standard $\ell ^2(L^2(\varOmega ))$ error estimate consistent with the conditional stability. Further, we illustrate the analysis with some numerical examples.
The value of community-integrated health information exchanges: three recent examples from El Paso, Texas
Authors: Sloan-Aagard Chantel , Helgesen Wanda , Nañez Juan , Law Jon , Currey J C , Meils Jacob , Bishop Joel , Hartmann Emily
Published: September 2022

The foundational role of health information exchanges (HIEs) is to facilitate communication between clinical partners in real time. Once this infrastructure for the secure and immediate flow of patient information is built, however, HIEs can benefit community public health and clinical care in myriad other ways that are in line with their mission, goals, patient privacy, and funding structures. We encourage the development of community-integrated HIEs and list specific steps that can be taken toward community integration. We give three examples of those steps in action from a community HIE in El Paso, TX. Each local partnership, in combination with technology innovation, resulted in the development of informatics tools to address community health needs and generated long-term benefits, especially for the most vulnerable patients. Two examples relate to different aspects of the COVID-19 pandemic and a third to the Afghan refugee evacuation.
Regulation of the SNARE protein Ykt6 function by diprenylation and phosphorylation
Authors: Rikitake Yoshiyuki
Published: September 2022

For proper intracellular vesicle transport, it is essential for transport vesicle membranes to fuse with the appropriate target membranes. Ykt6 is a SNARE protein with functions in diverse vesicle transport pathways, including secretory, endocytotic and autophagic pathways. To exert these functions, the association of Ykt6 with vesicle membranes and the change of its conformation from closed to open play key roles. Recent studies have revealed regulatory mechanisms involved in Ykt6 membrane association and conformation change. When in the cytosol, the vicinal cysteine residues within the C-terminal CCAIM sequence of Ykt6 undergo diprenylation (farnesylation of the distal cysteine residues by farnesyltransferase; this is followed by geranylgeranylation of the proximal cysteine residue by geranylgeranyltransferase-III). Phosphorylation of a serine residue within the SNARE domain triggers the conversion of the Ykt6 conformation from closed to open, allowing Ykt6 membrane association. In this commentary, I briefly summarize and discuss the recently revealed regulatory mechanisms of Ykt6 function by diprenylation and phosphorylation.
Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile
Authors: Hishiki Asami , Okazaki Sumire , Hara Kodai , Hashimoto Hiroshi
Published: September 2022

The sliding DNA clamp is a ring-shaped protein that encircles DNA within its central channel. It binds to multiple proteins, such as DNA polymerases and DNA repair enzymes, and stimulates their enzymatic activities, thereby playing a crucial role in cell survival and proliferation. Accordingly, the bacterial clamp DnaN is considered to be a promising target for bacterial infection therapy. In this regard, 3D structures of DnaN from pathogenic bacteria are essential for the development of chemical compounds with antimicrobial activity. Here, the crystal structure of DnaN from a Gram-positive bacterium Clostridioides difficile, a human pathogen causing infectious diarrhoea, has been determined at 2.13 Å resolution. A comparison of the structures of DnaN from other bacteria indicates that the structural features of DnaN in terms of overall organization are essentially conserved within Gram-positive and Gram-negative bacteria. However, DnaN from C. difficile has structural differences in the potential binding pocket for partner proteins, implying a non-conventional interaction with its binding partners. Our findings will provide insight into the development of new therapies for C. difficile infection.
The Contribution of Urgenda to the Mitigation of Climate Change
Authors: Mayer Benoit
Published: September 2022

Dutch courts in Urgenda ordered the government of the Netherlands to reduce national greenhouse gas emissions by 25% by 2020, compared with 1990. The case has been presented as a remarkable judicial victory of climate action advocates. With hindsight, this article questions the case’s contribution to the mitigation of climate change. If the Urgenda target has been met, this had little to do with the few measures that the government took too late and too hurriedly to achieve genuine mitigation outcomes. Rather, these measures likely caused a slight increase in global long-term emissions. And while the case has raised awareness, there is no reason to assume that it has translated into momentum for climate action more than it has hindered new policy developments. This case study sheds light on practical limitations of court-imposed climate targets that may justify the greater restraint that other courts have exercised in comparable cases.
Some results on relation algebra reducts: Residuated and semilattice-ordered semigroups
Authors: Rogozin Daniel
Published: September 2022

In this paper, we show that the class of representable residuated semigroups has the finite representation property. That is, every finite representable residuated semigroup is representable over a finite base. This result gives a positive solution to Hirsch and Hodkinson (2002, Relation Algebras by Games). The finite representation property for residuated semigroups also implies that the Lambek calculus has the finite model property with respect to relational models, the so-called $R$-models. We also show that the class of representable join semilattice-ordered semigroups is pseudo-universal and it has a recursively enumerable axiomatization. For this purpose, we introduce representability games for join semilattice-ordered semigroups.
A CLAVATA3-like Gene Acts as a Gynoecium Suppression Function in White Campion
Authors: Kazama Yusuke , Kitoh Moe , Kobayashi Taiki , Ishii Kotaro , Krasovec Marc , Yasui Yasuo , Abe Tomoko , Kawano Shigeyuki , Filatov Dmitry A
Published: September 2022

How do separate sexes originate and evolve? Plants provide many opportunities to address this question as they have diverse mating systems and separate sexes (dioecy) that evolved many times independently. The classic “two-factor” model for evolution of separate sexes proposes that males and females can evolve from hermaphrodites via the spread of male and female sterility mutations that turn hermaphrodites into females and males, respectively. This widely accepted model was inspired by early genetic work in dioecious white campion (Silene latifolia) that revealed the presence of two sex-determining factors on the Y-chromosome, though the actual genes remained unknown. Here, we report identification and functional analysis of the putative sex-determining gene in S. latifolia, corresponding to the gynoecium suppression factor (GSF). We demonstrate that GSF likely corresponds to a Y-linked CLV3-like gene that is specifically expressed in early male flower buds and encodes the protein that suppresses gynoecium development in S. latifolia. Interestingly, GSFY has a dysfunctional X-linked homolog (GSFX) and their synonymous divergence (dS = 17.9%) is consistent with the age of sex chromosomes in this species. We propose that female development in S. latifolia is controlled via the WUSCHEL-CLAVATA feedback loop, with the X-linked WUSCHEL-like and Y-linked CLV3-like genes, respectively. Evolution of dioecy in the S. latifolia ancestor likely involved inclusion of ancestral GSFY into the nonrecombining region on the nascent Y-chromosome and GSFX loss of function, which resulted in disbalance of the WUSCHEL-CLAVATA feedback loop between the sexes and ensured gynoecium suppression in males.
CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells
Authors: Wang Jiankang , Nakato Ryuichiro
Published: September 2022

Cohesin is a multifunctional protein responsible for transcriptional regulation and chromatin organization. Cohesin binds to chromatin at tens of thousands of distinct sites in a conserved or tissue-specific manner, whereas the function of cohesin varies greatly depending on the epigenetic properties of specific chromatin loci. Cohesin also extensively mediates cis-regulatory modules (CRMs) and chromatin loops. Even though next-generation sequencing technologies have provided a wealth of information on different aspects of cohesin, the integration and exploration of the resultant massive cohesin datasets are not straightforward. Here, we present CohesinDB (https://cohesindb.iqb.u-tokyo.ac.jp), a comprehensive multiomics cohesin database in human cells. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. By integrating these large-scale data, CohesinDB summarizes three types of ‘cohesin objects’: 751 590 cohesin binding sites, 957 868 cohesin-related chromatin loops and 2 229 500 cohesin-related CRMs. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information. CohesinDB features a user-friendly interface for browsing, searching, analyzing, visualizing and downloading the desired information. CohesinDB contributes a valuable resource for all researchers studying cohesin, epigenomics, transcriptional regulation and chromatin organization.
Serum testosterone concentrations and outcomes in hemodialysis patients enrolled in the EVOLVE trial
Authors: Nilsson Erik , Stenvinkel Peter , Liu Sai , Stedman Margaret R , Chertow Glenn M , Floege Jürgen
Published: September 2022

Background

Hypogonadism is common in end-stage kidney disease and may contribute to morbidity and mortality.

Methods

Using data from the randomized controlled Evaluation of Cinacalcet Therapy to Lower Cardiovascular Events (EVOLVE) trial of cinacalcet, we analyzed the associations of total testosterone, free testosterone and sex hormone–binding globulin (SHBG) serum concentrations with mortality and major cardiovascular events in 1692 men and 1059 women receiving hemodialysis. We also describe the effect of cinacalcet treatment on serum concentrations of testosterone.

Results

Among men, lower serum free testosterone [odds ratio (OR) 0.18, 95% confidence interval (CI) 0.04–0.82, P = .026] and higher SHBG (OR 1.05 per 10 nmol/L, 95% CI 1.01–1.10, P = .012), but not total testosterone, were associated with higher risk of death or cardiovascular event. Only SHBG was associated with all-cause mortality (OR 1.07 per 10 nmol/L, 95% CI 1.02–1.12, P = .0073). Among women, neither total nor free testosterone, nor SHBG were associated with outcomes. We found no statistically significant effect of cinacalcet treatment on SHBG, free or total testosterone.

Conclusions

Lower free testosterone and higher SHBG in serum are associated with higher risk of death or cardiovascular event in men undergoing chronic hemodialysis.
TP53 Alterations Are Associated With Poor Survival in Patients With Primary Mediastinal Nonseminoma Germ Cell Tumors
Authors: Bacon Jack V W , Giannatempo Patrizia , Cataldo Giovanna , Fazli Ladan , Saxena Neetu , Ozgun Guliz , Soleimani Maryam , Chi Kim , Nichols Craig , Necchi Andrea , Wyatt Alexander W , Kollmannsberger Christian K , Nappi Lucia
Published: September 2022

Background

Primary mediastinal nonseminoma germ cell tumors (PMNSGCT) are a subgroup of nonseminoma germ cell tumors (GCT) with poor prognosis. In this study, PMNSGCT-specific genomic landscape was analyzed and correlated with clinical outcomes.

Methods

DNA was extracted and sequenced from 28 archival tumor tissue of patients with mediastinal GCT (3 seminoma and 25 nonseminoma). Overall survival (OS) and association with gene alterations were estimated using the Kaplan-Meier and univariate Cox regression methods.

Results

Three patients (11%) had a karyotype XXY, 17/28 (61%) tumor samples presented chromosome 12p amplification. Somatic mutations were detected in 19/28 (68%) samples. The most frequently mutated genes were: TP53 (13/28; 46%), KIT (5/28; 18%), and KRAS (5/28; 18%). Deleterious TP53 alterations were associated with significantly reduced overall survival (HR: 7.16; P = .012).

Conclusions

TP53 alterations are common in PMNSGCT and are associated with reduced overall survival, potentially underlying the poor sensitivity to chemotherapy observed in these patients.
Functional metabolite reserves and lipid homeostasis revealed by the MA-10 Leydig cell metabolome
Authors: Koganti Prasanthi P , Tu Lan N , Selvaraj Vimal
Published: September 2022

In Leydig cells, intrinsic factors that determine cellular steroidogenic efficiency is of functional interest to decipher and monitor pathophysiology in many contexts. Nevertheless, beyond basic regulation of cholesterol storage and mobilization, systems biology interpretation of the metabolite networks in steroidogenic function is deficient. To reconstruct and describe the different molecular systems regulating steroidogenesis, we profiled the metabolites in resting MA-10 Leydig cells. Our results identified 283-annotated components (82 neutral lipids, 154 membrane lipids, and 47 other metabolites). Neutral lipids were represented by an abundance of triacyglycerols (97.1%), and low levels of cholesterol esters (2.0%). Membrane lipids were represented by an abundance of glycerophospholipids (77.8%), followed by sphingolipids (22.2%). Acylcarnitines, nucleosides, amino acids and their derivatives were the other metabolite classes identified. Among nonlipid metabolites, we recognized substantial reserves of aspartic acid, choline, creatine, betaine, glutamine, homoserine, isoleucine, and pantothenic acid none of which have been previously considered as a requirement in steroidogenic function. Individually limiting use of betaine, choline, or pantothenic acid, during luteinizing hormone-induced steroidogenesis in MA-10 cells resulted in substantial decreases to acute steroidogenic capacity, explained by intermediary metabolite imbalances affecting homeostasis. As such, our dataset represents the current level of baseline characterization and unravels the functional resting state of steroidogenic MA-10 Leydig cells. In identifying metabolite stockpiles and causal mechanisms, these results serve to further comprehend the cellular setup and regulation of steroid biosynthesis.
Fiction And Content in Hume’s Labyrinth
Authors: Ehli Bridger
Published: September 2022

In the ‘Appendix’ to the Treatise, Hume claims that he has discovered a ‘very considerable’ mistake in his earlier discussion of the self. Hume's expression of the problem is notoriously opaque, leading to a vast scholarly debate as to exactly what problem he identified in his earlier account of the self. I propose a new solution to this interpretive puzzle. I argue that a tension generated by Hume's conceptual scepticism about real ‘principles of union’ and his account of fictions of the imagination is the defect identified in the ‘Appendix’.
Association of sleep with cognitive function during retirement transition: the Whitehall II study
Authors: Teräs Tea , Rovio Suvi , Pentti Jaana , Head Jenny , Kivimäki Mika , Stenholm Sari
Published: September 2022

Study Objectives

Sleep duration and difficulties have been shown to associate with cognitive function. This study examined how changes in sleep and in cognitive function are associated during retirement transition.

Methods

The study population consisted of 2980 Whitehall II study participants, who retired during the follow-up, whose sleep was queried, and cognitive function measured (inductive reasoning and verbal memory) before and after retirement (follow-up 16 years). Using the last information on sleep before and the first after retirement, participants were categorized into constantly without (59%), increasing (13%), decreasing (11%), and constantly with (18%) sleep difficulties; and constantly short (26%), increasing (19%), decreasing (8.5%), and constantly mid-range (47%) sleep duration. Change in cognitive function during retirement transition was examined by sleep change groups using linear regression analyses with generalized estimating equations.

Results

More pronounced decline in inductive reasoning during retirement transition was observed among participants with increasing sleep difficulties (−1.96, 95% CI −2.52 to −1.41) compared to those constantly without sleep difficulties (−1.25, 95% CI −1.52 to −0.98) and constantly with sleep difficulties (−1.26, 95% CI −1.75 to −0.92). Decreasing sleep difficulties (−0.64, 95% CI −0.86 to −0.43) were associated with a more pronounced decline in verbal memory when compared to constantly without sleep difficulties (−0.42, 95% CI −0.52 to −0.32) in post-retirement period. No statistically significant differences across sleep duration groups in cognitive function were observed.

Conclusions

Increasing and decreasing sleep difficulties may be associated with accelerated decline in cognitive function during retirement transition and post-retirement.
Incrementing and clarifying the diversity and early evolution of termites (Blattodea: Isoptera)
Authors: Jouault Corentin , Engel Michael S , Legendre Frédéric , Huang Diying , Grandcolas Philippe , Nel André
Published: September 2022

The past diversity of Isoptera is relatively poorly documented. Many early-diverging families are only represented today by relicts of their Mesozoic and Cenozoic richness. Therefore, the onset of their evolutionary history and the transitions between families, or even between subsocial and eusocial ways of life, remain difficult to decipher and require additional fossil occurrences. Here, we report the oldest worker/pseudergate trapped in amber and a new Mastotermitidae, both from Hkamti amber. We document a diverse assemblage of species representing early-diverging families from the ‘Mid’-Cretaceous of Myanmar, including two new genera and four new species in as many different genera: Anisotermes bourguignoni sp. nov., Longitermes pulcher gen. et sp. nov., Magnifitermes krishnai gen. et sp. nov. and Mastotermes myanmarensis sp. nov. These descriptions provide significant morphological evidence to discuss the placement of the genus Anisotermes, confidently place the new genera and confirm the monophyly of Mastotermitidae. The diversity of Cretaceous isopterans, in light of the biology of their extant representatives, is used to discuss palaeoecological implications and highlights the radiation of early diverged Isoptera in the complex Cretaceous ecosystem. The validity of the species Meiatermes cretacicus is discussed.
Improving hepatitis C screening and access to treatment
Authors: Alberts Ryan , Zimmermann AnnMarie , Martinez Anthony
Published: September 2022

The rising prevalence of opioid use disorder and injection drug use has resulted in an increasing incidence of chronic hepatitis C virus (HCV) infection. Although older adults historically have represented the bulk of HCV infections in the United States, demographics have shifted and most new infections are presenting in younger patients. As a result, screening guidelines for HCV have evolved, moving toward a near-universal screening paradigm. Rates of screening and linkage to care remain low, attributed to the fact that underserved populations are disproportionately affected and often have limited access to specialty care. Collaborative models to treat HCV using primary care providers have been proposed to facilitate linkage to care and reduce transmission.
Albuterol
Authors: Pitonzo David G.
Published: September 2022

Albuterol has been a cornerstone of asthma treatment for several decades, but evidence suggests that it may be overused at the expense of more efficacious treatment. Albuterol may not even be appropriate for sole first-line rescue medication in some patients. Inflammatory mechanisms have been shown to play a role early in the course of developing bronchospasm, suggesting that inhaled corticosteroids should be included as part of initial rescue treatment. Newer biologics target inflammatory cytokine pathways, which may be needed in patients with moderate to severe disease. Evidence-based recommendations for the management of asthma and bronchospasm are continuing to evolve.
Early diagnosis in polycystic ovary syndrome
Authors: Blanco Christy E.
Published: September 2022

NPs are in an ideal position to educate patients on the lifelong implications of polycystic ovary syndrome (PCOS). A timely diagnosis and comprehensive plan are needed to appropriately manage patients with PCOS. This article highlights diagnostic criteria, common comorbid conditions, psychological impacts of the clinical manifestations, management approaches, and implications for NPs.
Functional neurologic disorder (FND) in pediatrics
Authors: Baidoo Lauren
Published: September 2022

Functional neurologic disorder is a complex disorder of truly experienced neurologic symptoms without evidence of underlying neurologic disease. This clinical review focuses on the pediatric population and includes the impacts of the COVID-19 pandemic. Clinician knowledge and early identification can substantially improve patient outcomes.