bluuebunny/crossref_metadata_2025 huggingface dataset:
Root components for tensor product of affine Kac-Moody Lie algebra modules
Authors: Jeralds Samuel , Kumar Shrawan
Published: July 2022

Let

g

\mathfrak {g}

be an affine Kac-Moody Lie algebra and let

λ
,
μ

\lambda , \mu

be two dominant integral weights for

g

\mathfrak {g}

. We prove that under some mild restriction, for any positive root

β
\beta

,

V
(
λ
)
⊗
V
(
μ
)

V(\lambda )\otimes V(\mu )

contains

V
(
λ
+
μ
−
β
)

V(\lambda +\mu -\beta )

as a component, where

V
(
λ
)

V(\lambda )

denotes the integrable highest weight (irreducible)

g

\mathfrak {g}

-module with highest weight

λ
\lambda

. This extends the corresponding result by Kumar from the case of finite dimensional semisimple Lie algebras to the affine Kac-Moody Lie algebras. One crucial ingredient in the proof is the action of Virasoro algebra via the Goddard-Kent-Olive construction on the tensor product

V
(
λ
)
⊗
V
(
μ
)

V(\lambda )\otimes V(\mu )

. Then, we prove the corresponding geometric results including the higher cohomology vanishing on the

G

\mathcal {G}

-Schubert varieties in the product partial flag variety

G

/

P

×

G

/

P

\mathcal {G}/\mathcal {P}\times \mathcal {G}/\mathcal {P}

with coefficients in certain sheaves coming from the ideal sheaves of

G

\mathcal {G}

-sub-Schubert varieties. This allows us to prove the surjectivity of the Gaussian map.
Implementation of targeted deprescribing of potentially inappropriate medications in patients on hemodialysis
Authors: Gerardi Savannah , Sperlea David , Levy Shirel Ora-Lee , Bondurant-David Kaitlin , Dang Sébastien , David Pierre-Marie , Lizotte Annie , Senécal Lysane , Paquette François , Vanier Marie-Claude
Published: July 2022

Purpose

Patients on hemodialysis have a high risk of medication-related problems. Studies using deprescribing algorithms to reduce the number of inappropriate medications in this population have been published, but none have used a patient-partnership approach. Our study evaluated the impact of a similar intervention with a patient-partnership approach.

Methods

The objective was to describe the implementation of a pharmacist-led intervention with a patient-partnership approach using deprescribing algorithms and its impact on the reduction of inappropriate medications in patients on hemodialysis. Eight algorithms were developed by pharmacists and nephrologists to assess the appropriateness of medications. Pharmacists identified patients taking targeted medications. Following patient enrollment, pharmacists assessed medications with patients and applied the algorithms. With patient consent, deprescription was suggested to nephrologists if applicable. Specific data on each targeted medication were collected at 4 and 16 weeks. Descriptive statistics were used to examine the effects of the deprescribing intervention.

Results

Of 270 patients, 256 were taking at least one targeted medication. Of the 122 patients taking at least one targeted medication who were approached to participate, 66 were included in the study. At enrollment, these patients were taking 252 targeted medications, of which 59 (23.4%) were determined to be inappropriate. Deprescription was initiated for 35 of these 59 medications (59.3%). At 4 weeks, 33 of the 59 medications (55.9%) were still deprescribed, while, at 16 weeks, 27 of the 59 medications (45.8%) were still deprescribed. Proton pump inhibitors and benzodiazepines or Z-drugs were the most common inappropriate medications, and allopurinol was the most deprescribed medication.

Conclusion

A pharmacist-led intervention with a patient-partnership approach and using deprescribing algorithms reduced the number of inappropriate medications in patients on hemodialysis.
RhgKL and CcpA directly regulate the rhiLFGN-rhgR-yesTUV operon involved in the metabolism of rhamnogalacturonan type I in Bacillus subtilis
Authors: Hirooka Kazutake
Published: July 2022

The Bacillus subtilis rhiLFGN-rhgR-yesTUVWXYZ (formerly yesOPQRSTUVWXYZ) gene cluster includes genes for metabolizing rhamnogalacturonan type I (RG-I), a major pectin constituent, and the rhgR gene encoding an AraC/XylS transcriptional activator. The yesL-rhgKL (formerly yesLMN) operon, adjacent to the rhiL gene, includes the rhgKL genes encoding a two-component regulatory system. The reporter analyses showed that 3 promoters immediately upstream of the rhiL, yesW, and yesL genes were induced by RG-I and repressed by glucose in the medium. The reporter analyses also showed that RhgL and RhgR contribute to the RG-I-dependent induction of the rhiL promoter and that CcpA mediates the catabolite repression of the rhiL and yesL promoters. The in vitro experiments demonstrated that the RhgL response regulator and the CcpA complex bind to each site in the rhiL promoter region. The RT-PCR analysis and the different properties of the rhiL and yesW promoters suggested the rhiLFGN-rhgR-yesTUV genes as an operon.
Environment and mate attractiveness in a wild insect
Authors: Tregenza Tom , Niemelä Petri T , Rodríguez-Muñoz Rolando , Hopwood Paul E
Published: July 2022

The role of female choice in sexual selection is well established, including the recognition that females choose their mates based on multiple cues. These cues may include intrinsic aspects of a male’s phenotype as well as aspects of the environment associated with the male. The role of the spatial location of a potential mate has been well studied in territorial vertebrates. However, despite their role as laboratory models for studies of sexual selection, the potential for insects to choose their mates on the basis of location has scarcely been studied. We studied a natural population of individually tagged crickets (Gryllus campestris) in a meadow in Northern Spain. Adults typically move between burrows every few days, allowing us to examine how pairing success of males can be predicted by the burrow they occupy, independent of their own characteristics. We observed the entirety of ten independent breeding seasons to provide replication and to determine whether the relative importance of these factors is stable across years. We find that both male ID and the ID his burrow affect the likelihood that he is paired with a female, but the burrow has a consistently greater influence. Furthermore, the two factors interact: the relative attractiveness of an individual male depends on which burrow he occupies. Our finding demonstrates a close interaction between naturally and sexually selected traits. It also demonstrates that mate choice studies may benefit from considering not only obvious secondary sexual traits, but also more cryptic traits such as microhabitat choice.
Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling
Authors: Pei Jimin , Zhang Jing , Cong Qian
Published: July 2022

Motivation

Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein–protein interactions (PPIs) and modeling protein complexes at the proteome level.

Results

We applied RoseTTAFold and AlphaFold, two of the latest deep-learning methods for structure predictions, to analyze coevolution of human proteins residing in mitochondria, an organelle of vital importance in many cellular processes including energy production, metabolism, cell death and antiviral response. Variations in mitochondrial proteins have been linked to a plethora of human diseases and genetic conditions. RoseTTAFold, with high computational speed, was used to predict the coevolution of about 95% of mitochondrial protein pairs. Top-ranked pairs were further subject to modeling of the complex structures by AlphaFold, which also produced contact probability with high precision and in many cases consistent with RoseTTAFold. Most top-ranked pairs with high contact probability were supported by known PPIs and/or similarities to experimental structural complexes. For high-scoring pairs without experimental complex structures, our coevolution analyses and structural models shed light on the details of their interfaces, including CHCHD4–AIFM1, MTERF3–TRUB2, FMC1–ATPAF2 and ECSIT–NDUFAF1. We also identified novel PPIs (PYURF–NDUFAF5, LYRM1–MTRF1L and COA8–COX10) for several proteins without experimentally characterized interaction partners, leading to predictions of their molecular functions and the biological processes they are involved in.

Availability and implementation

Data of mitochondrial proteins and their interactions are available at: http://conglab.swmed.edu/mitochondria.

Supplementary information

Supplementary data are available at Bioinformatics online.
Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
Authors: Li Longjie , Kolinjivadi Arun Mouli , Ong Kok Haur , Young David M , Marini Gabriel Pik Liang , Chan Sock Hoai , Chong Siao Ting , Chew Ee Ling , Lu Haoda , Gole Laurent , Yu Weimiao , Ngeow Joanne
Published: July 2022

Motivation

DNA fibre assay has a potential application in genomic medicine, cancer and stem cell research at the single-molecule level. A major challenge for the clinical and research implementation of DNA fibre assays is the slow speed in which manual analysis takes place as it limits the clinical actionability. While automatic detection of DNA fibres speeds up this process considerably, current publicly available software have limited features in terms of their user interface for manual correction of results, which in turn limit their accuracy and ability to account for atypical structures that may be important in diagnosis or investigative studies. We recognize that core improvements can be made to the GUI to allow for direct interaction with automatic results to preserve accuracy as well as enhance the versatility of automatic DNA fibre detection for use in variety of situations.

Results

To address the unmet needs of diverse DNA fibre analysis investigations, we propose DNA Stranding, an open-source software that is able to perform accurate fibre length quantification (13.22% mean relative error) and fibre pattern recognition (R > 0.93) with up to six fibre patterns supported. With the graphical interface, we developed, user can conduct semi-automatic analyses which benefits from the advantages of both automatic and manual processes to improve workflow efficiency without compromising accuracy.

Availability and implementation

The software package is available at https://github.com/lgole/DNAStranding.

Supplementary information

Supplementary data are available at Bioinformatics online.
US Immigration Politics, Sanctions Threats and Private Prison Corporations’ Stock Market Values
Authors: Park Jihye
Published: July 2022

Although politics play pivotal roles in the emergence and operation of private prison corporations (PPCs), less is known about the effects of politics on PPCs’ financial performance. This paper examines the economic consequences of US immigration politics on PPCs using stock market data. Results show that PPCs benefit from restrictive immigration politics through increased stock values and certainty of future profitability. In contrast, their stock values are more likely to fall when the federal government announces sanctions threats on PPCs. These immigration politics only shape PPCs because of their unique business partnership with governments, but do not have meaningful impacts on private security companies that hold weak commercial interests in immigration politics. Finally, this study offers policy implications by revealing consequential effects of national-level politics on PPCs’ financial performance, suggesting future directions for federal roles in regulating PPCs.
Immigrant Threat, Political Articulation by Extreme Right Parties and Support for Capital Punishment: A Multilevel Analysis of European Countries
Authors: Piatkowska Sylwia J , Abreu Rivera Laisa F , Messner Steven F
Published: July 2022

This study examines connections between the political articulation of immigration by extreme right parties, perceived immigrant threat, and support for capital punishment across European countries. We merged data from the 2017 European Values Study with the Manifesto Project Dataset, a comparative dataset on statements by political parties. The results reveal positive effects of the perceived immigrant threat and positive effects of political articulation of immigration by extreme right parties on support for capital punishment. We also find that the political articulation of immigration by extreme right parties amplifies the effect of immigrant threat on support for capital punishment. The results of our analyses underscore the important role that political rhetoric can play in shaping a social context conducive to punitiveness.
Surface Lin28A expression consistent with cellular stress parallels indicators of senescence
Authors: Broughton Kathleen , Esquer Carolina , Echeagaray Oscar , Firouzi Fareheh , Shain Grant , Ebeid David , Monsanto Megan , Yaareb Dena , Golgolab Leila , Gude Natalie , Sussman Mark A
Published: July 2022

Aims

Declining cellular functional capacity resulting from stress or ageing is a primary contributor to impairment of myocardial performance. Molecular pathway regulation of biological processes in cardiac interstitial cells (CICs) is pivotal in stress and ageing responses. Altered localization of the RNA-binding protein Lin28A has been reported in response to environmental stress, but the role of Lin28A in response to stress in CICs has not been explored. Surface Lin28A redistribution is indicative of stress response in CIC associated with ageing and senescence.

Methods and results

Localization of Lin28A was assessed by multiple experimental analyses and treatment conditions and correlated to oxidative stress, senescence, and ploidy in adult murine CICs. Surface Lin28A expression is present on 5% of fresh CICs and maintained through Passage 2, increasing to 21% in hyperoxic conditions but lowered to 14% in physiologic normoxia. Surface Lin28A is coincident with elevated senescence marker p16 and beta-galactosidase (β-gal) expression in CICs expanded in hyperoxia, and also increases with polyploidization and binucleation of CICs regardless of oxygen culture. Transcriptional profiling of CICs using single-cell RNA-Seq reveals up-regulation of pathways associated with oxidative stress in CICs exhibiting surface Lin28A. Induction of surface Lin28A by oxidative stress is blunted by treatment of cells with the antioxidant Trolox in a dose-dependent manner, with 300 μM Trolox exposure maintaining characteristics of freshly isolated CICs possessing low expression of surface Lin28A and β-gal with predominantly diploid content.

Conclusion

Surface Lin28A is a marker of environmental oxidative stress in CICs and antioxidant treatment antagonizes this phenotype. The biological significance of Lin28 surface expression and consequences for myocardial responses may provide important insights regarding mitigation of cardiac stress and ageing.
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues
Authors: Zatorski Nicole , Stein David , Rahman Rayees , Iyengar Ravi , Schlessinger Avner
Published: July 2022

Structural features of proteins provide powerful insights into biological function and similarity. Specifically, previous work has demonstrated that structural features of tissue and drug-treated cell line samples can be used to predict tissue type and characterize drug relationships, respectively. We have developed structural signatures, a web server for annotating and analyzing protein features from gene sets that are often found in transcriptomic and proteomic data. This platform provides access to a structural feature database derived from normal and disease human tissue samples. We show how analysis using this database can shed light on the relationship between states of single-cell RNA-sequencing lung cancer samples. These various structural feature signatures can be visualized on the server itself or downloaded for additional analysis. The structural signatures server tool is freely available at https://structural-server.kinametrix.com/.
Expression of antimicrobial host defence peptides in the central nervous system during health and disease
Authors: Smith Katie J , Gwyer Findlay Emily
Published: July 2022

Antimicrobial host defence peptides (HDP) are critical for the first line of defence against bacterial, viral, and fungal pathogens. Over the past decade we have become more aware that, in addition to their antimicrobial roles, they also possess the potent immunomodulatory capacity. This includes chemoattracting immune cells, activating dendritic cells and macrophages, and altering T-cell differentiation. Most examinations of their immunomodulatory roles have focused on tissues in which they are very abundant, such as the intestine and the inflamed skin. However, HDP have now been detected in the brain and the spinal cord during a number of conditions. We propose that their presence in the central nervous system (CNS) during homeostasis, infection, and neurodegenerative disease has the potential to contribute to immunosurveillance, alter host responses and skew developing immunity. Here, we review the evidence for HDP expression and function in the CNS in health and disease. We describe how a wide range of HDP are expressed in the CNS of humans, rodents, birds, and fish, suggesting a conserved role in protecting the brain from pathogens, with evidence of production by resident CNS cells. We highlight differences in methodology used and how this may have resulted in the immunomodulatory roles of HDP being overlooked. Finally, we discuss what HDP expression may mean for CNS immune responses.
Health economic evaluation of nation-wide screening programmes for atrial fibrillation in the Netherlands
Authors: van Hulst Marinus , Tieleman Robert G , Zwart Lennaert A R , Pomp Marc , Jacobs Maartje S , Meeder Joan G , van Ofwegen-Hanekamp Clara E E , Hollander Monika , Smits Paul , Hemels Martin E W
Published: July 2022

Aims

Screening for atrial fibrillation (AF) is recommended by the European Society of Cardiology guidelines to prevent strokes. Cost-effectiveness analyses of different screening programmes for AF are difficult to compare because of varying settings and models used. We compared the impact and cost-effectiveness of various AF screening programmes in the Netherlands.

Methods and results

The base case economic analysis was conducted from the societal perspective. Health effects and costs were analysed using a Markov model. The main model inputs were derived from the ARISTOTLE, RE-LY, and ROCKET AF trials combined with Dutch observational data. Univariate, probabilistic sensitivity, and various scenario analyses were performed. The maximum number of newly detected AF patients in the Netherlands ranged from 4554 to 39 270, depending on the screening strategy used. Adequate treatment with anticoagulation would result in a maximum of >3000 strokes prevented using single-time point AF screening. Compared with no screening, screening 100 000 people provided a gain in QALYs ranging from 984 to 8727 and a mean cost difference ranging from –6650 000€ to 898 000€, depending on the screening strategy used. The probabilistic sensitivity analysis (PSA) demonstrated a 100% likelihood that screening all patients ≥75 years visiting the geriatric outpatient clinic was cost-saving. Four out of six strategies were cost-saving in ≥74% of the PSA simulations. Out of these, opportunistic screening of all patients ≥65 years visiting the GPs office had the highest impact on strokes prevented.

Conclusion

Most single-time point AF screening strategies are cost-saving and have an important impact on stroke prevention.
The relationship of family functioning and family health with hospital readmission in patients with heart failure: insights from an international cross-sectional study
Authors: Shamali Mahdi , Østergaard Birte , Svavarsdóttir Erla Kolbrún , Shahriari Mohsen , Konradsen Hanne
Published: July 2022

Aims

The growing hospital readmission rate among patients with heart failure (HF) has imposed a substantial economic burden on healthcare systems. Therefore, it is essential to identify readmission associating factors to reduce hospital readmission. This study aimed to investigate the relationship of family functioning and family health with hospital readmission rates over 6 months in patients with HF and identify the sociodemographic and/or clinical variables associated with hospital readmission.

Methods and results

This international multicentre cross-sectional study involved a sample of 692 patients with HF from three countries (Denmark 312, Iran 288, and Iceland 92) recruited from January 2015 to May 2020. The Family Functioning, Health, and Social Support questionnaire was used to collect the data. The number of patients’ hospital readmissions during the 6-month period was retrieved from patients’ hospital records. Of the total sample, 184 (26.6%) patients were readmitted during the 6-month period. Of these, 111 (16%) had one readmission, 68 (9.9%) had two readmissions, and 5 (0.7%) had three readmissions. Family functioning, family health, being unemployed, and country of residence were significant factors associated with hospital readmission for the patients.

Conclusions

This study highlights the critical roles of family functioning and family health in 6-month hospital readmission among patients with HF. Moreover, the strategy of healthcare systems in the management of HF is a key determinant that influences hospital readmission. Our findings may assist the investigation of potential strategies to reduce hospital readmission in patients with HF.
Psychometric evaluation of the Thai version of the Self-Care of Coronary Heart Disease Inventory Version 3
Authors: Koson Naruebeth , Srisuk Nittaya , Rattanaprom Arunsri , Thompson David R , Ski Chantal F
Published: July 2022

Aims

Engaging in self-care is an important aspect of the prevention and management of coronary heart disease (CHD), the leading cause of premature death in Thailand. As no validated tool exists to measure self-care in Thai people with CHD, we translated and examined the psychometric properties of the Self-Care of Coronary Heart Disease Inventory Version 3 (SC-CHDI-V3) in a Thai population.

Methods and results

The SC-CHDI-V3 was translated into Thai using the standard forward and backward translation procedure for self-care instruments. A cross-sectional design was used to examine the psychometric properties of the Thai version of the SC-CHDI-V3 in 250 patients with confirmed CHD in a tertiary hospital in southern Thailand. Cronbach’s alpha and McDonald’s omega coefficients were used to assess internal consistency, and confirmatory factor analysis was performed to assess construct validity. The Thai version of the SC-CHDI-V3 demonstrated acceptable internal consistency (Cronbach’s alpha and McDonald’s omega coefficients of each scale ranged from 0.821 to 0.910). Reliability estimates were adequate for each scale (range 0.863–0.906). Confirmatory factor analysis supported the original factor structure of the instrument, with good fit indices for all three scales (comparative fit index = 0.996–1.000; root mean square error of approximation = <0.001–0.040).

Conclusions

The Thai version of the SC-CHDI-V3 appears to be a valid and reliable instrument for measuring engagement in self-care maintenance, self-care monitoring, and self-care management among Thai people with CHD.
Evolved Transcriptional Responses and Their Trade-Offs after Long-Term Adaptation of Bemisia tabaci to a Marginally Suitable Host
Authors: Tadmor Ella , Juravel Ksenia , Morin Shai , Santos-Garcia Diego
Published: July 2022

Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally suitable hosts. What happens, both in performance and gene expression regulation, if these marginally suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly Bemisia tabaci, a generalist phloem-feeding species, adapted to a marginally suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30°C) and mild-stressful (24°C) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the nonadapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as “evolved” with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation–reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.
Trends of in-hospital and ICU mortality in COVID-19 patients over the fourth and fifth COVID-19 surges in Iran: a retrospective cohort study from Iran
Authors: Abdi Sepideh , Nemati Saeed , Nederi darbaghshahi Nader , Mohammadi Mehdi , Saeedi Elnaz , Naji Parnian , Taheri Negar , Qandian Ali , Joshang Narges , Fattahi Pedram , Namdar Peyman , Vand rajabpour Mojtaba
Published: July 2022

Objective

The current study aimed to investigate the temporal trend of in-hospital and intensive care unit (ICU) mortality of coronavirus disease 2019 (COVID-19) patients over 6 months in the spring and summer of 2021 in Iran.

Design

We performed an observational retrospective cohort study.

Setting

Qazvin Province- Iran during 6 month from April to September 2021.

Participants

All 14355 patients who were hospitalized with confirmed COVID-19 in hospitals of Qazvin Province.

Intervention

No intervention.

Main outcome measures

The trends of overall in-hospital mortality and ICU mortality were the main outcome of interest. We obtained crude and adjusted in-hospital and ICU mortality rates for each month of admission and over surge and lull periods of the disease.

Results

The overall in-hospital mortality, early mortality and ICU mortality were 8.8%, 3.2% and 67.6%, respectively. The trend for overall mortality was almost plateau ranging from 6.5% in July to 10.7% in April. The lowest ICU mortality was 60.0% observed in April, whereas it reached a peak in August (ICU mortality = 75.7%). Admission on surge days of COVID-19 was associated with an increased risk of overall mortality (Odds ratio = 1.3, 95% confidence interval = 1.1, 1.5). The comparison of surge and lull status showed that the odds of ICU mortality in the surge of COVID-19 was 1.7 higher than in the lull period (P-value < 0.001).

Conclusions

We found that the risk of both overall in-hospital and ICU mortality increased over the surge period and fourth and fifth waves of severe acute respiratory syndrome coronavirus 2 infection in Iran. The lack of hospital resources and particularly ICU capacities to respond to the crisis during the surge period is assumed to be the main culprit.
Fitness effects of blaCTX-M-15-harbouring F2:A1:B− plasmids on their native Escherichia coli ST131 H30Rx hosts
Authors: Palkovicova Jana , Sukkar Iva , Delafuente Javier , Valcek Adam , Medvecky Matej , Jamborova Ivana , Bitar Ibrahim , Phan Minh-Duy , San Millan Alvaro , Dolejska Monika
Published: July 2022

Objectives

To investigate the fitness effects of large blaCTX-M-15-harbouring F2:A1:B− plasmids on their native Escherichia coli ST131 H30Rx hosts.

Methods

We selected five E. coli ST131 H30Rx isolates of diverse origin, each carrying an F2:A1:B− plasmid with the blaCTX-M-15 gene. The plasmid was eliminated from each isolate by displacement using an incompatible curing plasmid, pMDP5_cureEC958. WGS was performed to obtain complete chromosome and plasmid sequences of original isolates and to detect chromosomal mutations in ‘cured’ clones. High-throughput competition assays were conducted to determine the relative fitness of cured clones compared with the corresponding original isolates.

Results

We were able to successfully eliminate the F2:A1:B− plasmids from all five original isolates using pMDP5_cureEC958. The F2:A1:B− plasmids produced non-significant fitness effects in three isolates and moderate reductions in relative fitness (3%–4%) in the two remaining isolates.

Conclusions

We conclude that F2:A1:B− plasmids pose low fitness costs in their E. coli ST131 H30Rx hosts. This plasmid-host fitness compatibility is likely to promote the maintenance of antibiotic resistance in this clinically important E. coli lineage.
ArchShapesNet: a novel dataset for benchmarking architectural building information modeling element classification algorithms
Authors: Yu Youngsu , Ha Daemok , Lee Koeun , Choi Jiwon , Koo Bonsang
Published: July 2022

Recent studies in the domain of semantic enrichment have employed artificial intelligence (AI) approaches to distinguish and classify building information modeling (BIM) elements to check their conformance with open standard data formats. Training AI algorithms requires the development of well-balanced and robust datasets of BIM elements. However, collection is difficult as sources are limited to existing models and sample libraries. This study developed a parametric augmentation approach to create synthetic copies of BIM elements, and thus rapidly supplement manually collected samples. The approach was used to create ArchShapesNet, a dataset consisting of 11 common architectural elements with an equal size of 4,000 samples per class. Two multi-view convolutional neural networks (CNN), a geometric deep learning algorithm, were trained and tested separately on ArchShapesNet and an initial dataset with sample imbalances. Results showed significant improvement in the accuracy and F1 scores, providing evidence of the utility of ArchShapesNet. The size and scope of the dataset are considered to be the first of their kind and provide a benchmark for testing the semantic integrity of BIM models. The augmentation approach also provides a general framework to create custom datasets for different specialties in the Architectural Engineering and Construction industry.
Eugène Bouchut’s (1818–1891) Early Anticipation of the Concept of Brain Death
Authors: Saad Toni
Published: July 2022

The conventional historical account of the concept of brain death credits developments and discoveries of the twentieth century with its inception, emphasizing the role of technological developments and professional conferences, notably the 1968 Ad Hoc Committee of the Harvard Medical School to Examine the Definition of Brain Death. This essay argues that the French physician Eugène Bouchut anticipated the concept of brain death as early as 1846. Correspondence with Bouchut’s understanding of brain death and one important contemporary concept of brain death is established then contrasted with current trends of defining death as the death of the brain. The philosophical factors that influenced Bouchut and the later developments of concepts of brain death are considered, with special reference to mechanistic philosophy and vitalism.
Differential diagnoses of right lower quadrant pain in late pregnancy
Authors: Daume Diana L , Becker Pauline M , Linke Katja , Ries Jean-Jacques , Fourie Lana , Klasen Jennifer M
Published: July 2022

We present two patients with right lower quadrant pain during the 36th week of pregnancy. In both cases, the challenges in diagnosing acute appendicitis in late pregnancy is underlined by misleading imaging results, revealing fluid in the lower abdomen, suggesting an appendicitis. Surgery was performed. Pre- and intraoperative gynecological examinations showed no signs of fetal distress. In patient 1, surgery revealed a torsion and necrosis of the right ovary and a 7-cm cyst of the fallopian tube. Open ovariectomy and appendectomy were performed. In patient 2, we saw a perforated appendicitis and cloudy ascites. Histology after appendectomy showed spots of endometriosis and serositis infiltrating into the appendix with signs of perforation at the tip. Patient 1 recovered after a short period of bowel paralysis. Patient 2 needed Caesarean section due to severe deceleration in the cardiotocograph and irregular uterine contractions. The newborn was kept in the neonatal ICU for 10 days.
Rapid intraoperative diagnosis of pediatric brain tumors using Raman spectroscopy: A machine learning approach
Authors: Jabarkheel Rashad , Ho Chi-Sing , Rodrigues Adrian J , Jin Michael C , Parker Jonathon J , Mensah-Brown Kobina , Yecies Derek , Grant Gerald A
Published: July 2022

Background

Surgical resection is a mainstay in the treatment of pediatric brain tumors to achieve tissue diagnosis and tumor debulking. While maximal safe resection of tumors is desired, it can be challenging to differentiate normal brain from neoplastic tissue using only microscopic visualization, intraoperative navigation, and tactile feedback. Here, we investigate the potential for Raman spectroscopy (RS) to accurately diagnose pediatric brain tumors intraoperatively.

Methods

Using a rapid acquisition RS device, we intraoperatively imaged fresh ex vivo brain tissue samples from 29 pediatric patients at the Lucile Packard Children’s Hospital between October 2018 and March 2020 in a prospective fashion. Small tissue samples measuring 2-4 mm per dimension were obtained with each individual tissue sample undergoing multiple unique Raman spectra acquisitions. All tissue samples from which Raman spectra were acquired underwent individual histopathology review. A labeled dataset of 678 unique Raman spectra gathered from 160 samples was then used to develop a machine learning model capable of (1) differentiating normal brain from tumor tissue and (2) normal brain from low-grade glioma (LGG) tissue.

Results

Trained logistic regression model classifiers were developed using our labeled dataset. Model performance was evaluated using leave-one-patient-out cross-validation. The area under the curve (AUC) of the receiver-operating characteristic (ROC) curve for our tumor vs normal brain model was 0.94. The AUC of the ROC curve for LGG vs normal brain was 0.91.

Conclusions

Our work suggests that RS can be used to develop a machine learning-based classifier to differentiate tumor vs non-tumor tissue during resection of pediatric brain tumors.
Candidatus Liberibacter asiaticus accumulation in the phloem inhibits callose and reactive oxygen species
Authors: Bernardini Chiara , Turner Donielle , Wang Chunxia , Welker Stacy , Achor Diann , Artiga Yosvanis Acanda , Turgeon Robert , Levy Amit
Published: July 2022

CLas inhibits callose deposition in the sieve pores and the accumulation of reactive oxygen species to favor its cell-to-cell movement.
Cortical Abnormalities in Patients with Fibromyalgia: A Pilot Study of Surface-Based Morphometry Analysis
Authors: Tu Ye , Wang Jihong , Xiong Fei , Gao Feng
Published: July 2022

Background

Although neuroanatomical studies correlated to fibromyalgia (FM) are gaining increasing interest, the cortical morphology of patients are largely unknown, and data on cortical gyrification are scarce. The objective of the present study is to assess the cortical morphology in female patients with FM compared with healthy controls (HC) using surface-based morphometry (SBM) analysis of magnetic resonance imaging (MRI).

Methods

T1-MRIs and clinical data of 20 FM patients and 20 HC subjects were obtained from a public data set via OpenNeuro. For each subject, surface parameters including cortical thickness, local gyrification index (LGI), sulcal depth, and fractal dimensionality were estimated using SBM analysis. These data were compared between two groups controlled by age. The correlations between regional SBM parameters showing group differences and clinical profiles were analyzed.

Results

Compared with HC subjects, FM patients showed reduced cortical thickness in right primary motor cortex, lower LGI in right rostral anterior cingulate and higher sulcal depth in right precuneus (P < 0.05 cluster level family- wise error corrected). In FM patients, correlation analysis showed that the cortical thickness in right primary motor cortex were inversely correlated with scores of pain catastrophizing scale (r = -0.498, P = 0.030) and pain self-perception scale (r = -0.527, P = 0.020), and disease duration (r = -0.488, P = 0.034), respectively.

Conclusions

Our findings provide evidence of neuroanatomical aberrations in FM patients, which may provide insight into the neuropathology of FM.
Myth and Truth in Opioid Consumption with Intrathecal Morphine Pump Implantation in Chronic Pain: A Retrospective Cohort Study with Claims Database in South Korea
Authors: Yoo Yongjae , Oh Joo Hyeon , Lee Haine , Choi Hyunsook , Joo Somin , Han Andrew Hogyu , Moon Jee Youn
Published: July 2022

Objective

To investigate the opioid consumption and the healthcare resource utilization in patients with the intrathecal drug delivery system (IDDS) therapy and the comprehensive medical management (CMM) alone.

Design

A retrospective cohort study with a customized claims database.

Setting

In a university-based hospital.

Subjects

Patients with complex regional pain syndrome, post-laminectomy syndrome, and fibromyalgia.

Methods

Using propensity score matching (1:3), we selected patients with morphine infusion through IDDS (IDDS group) and CMM alone (CMM group). The primary endpoints were comparisons of average morphine equivalents daily dosages (MEDD, mg/day) for 6 and 12 months from an index date. The number of emergency room (ER) visits and hospitalizations and the total medical expenditures were compared as secondary outcomes.

Results

In total, 82 patients (N = 23 in the IDDS group and N = 59 in the CMM group) were analyzed. Although a 6-month average MEDD did not reach statistical significance, a 12-month average MEDD was significantly decreased in the IDDS group compared to the CMM group (53.2 ± 46.3 vs 123.9 ± 176.4, respectively; P = 0.008). ER visits were more frequent in the IDDS group than the CMM group at baseline (5.4 vs 0.5, respectively; P = .002), which was maintained for 12 months (P < 0.001). Otherwise, the number of hospitalization and the medical expenditures for pain management were not different between the groups for 12 months.

Conclusions

The combined IDDS therapy had some benefits in reducing opioid consumption for 1-year follow-up compared to the CMM alone in chronic noncancer pain patients.
Modeling biological age and its link with the aging process
Authors: Beltrán-Sánchez Hiram , Palloni Alberto , Huangfu Yiyue , McEniry Mary C
Published: July 2022

Differences in health status at older ages are a result of genetic predispositions and physiological responses to exposure accumulation over the lifespan. These vary across individuals and lead to health status heterogeneity as people age. Chronological age (CA) is a standard indicator that reflects overall risks of morbidity and mortality. However, CA is only a crude proxy for individuals’ latent physiological deterioration. An alternative to CA is biological age (BA), an indicator of accumulated age-related biological change reflected in markers of major physiological systems. We propose and validate two BA estimators that improve upon existing ones. These estimators (i) are based on a structural equation model (SEM) that represents the relation between BA and CA, (ii) circumvent the need to impose arbitrary assumptions about the relation between CA and BA, and (iii) provide tools to empirically test the validity of assumptions the researcher may wish to invoke. We use the US National Health and Nutrition Examination Survey 1988–1994 and compare results with three commonly used methods to compute BA (principal components—PCA, multiple regression—MLR, and Klemera–Doubal’s method—KD). We show that SEM-based estimates of BA differ significantly from those generated by PCA and MLR and are comparable to, but have better predictive power than KD’s. The proposed estimators are flexible, allow testing of assumptions about functional forms relating BA and CA, and admit a rich interpretation as indicators of accelerated aging.
Multicolor plate reader fluorescence calibration
Authors: Beal Jacob , Telmer Cheryl A , Vignoni Alejandro , Boada Yadira , Baldwin Geoff S , Hallett Liam , Lee Taeyang , Selvarajah Vinoo , Billerbeck Sonja , Brown Bradley , Cai Guo-nan , Cai Liang , Eisenstein Edward , Kiga Daisuke , Ross David , Alperovich Nina , Sprent Noah , Thompson Jaclyn , Young Eric M , Endy Drew , Haddock-Angelli Traci
Published: July 2022

Plate readers are commonly used to measure cell growth and fluorescence, yet the utility and reproducibility of plate reader data is limited by the fact that it is typically reported in arbitrary or relative units. We have previously established a robust serial dilution protocol for calibration of plate reader measurements of absorbance to estimated bacterial cell count and for green fluorescence from proteins expressed in bacterial cells to molecules of equivalent fluorescein. We now extend these protocols to calibration of red fluorescence to the sulforhodamine-101 fluorescent dye and blue fluorescence to Cascade Blue. Evaluating calibration efficacy via an interlaboratory study, we find that these calibrants do indeed provide comparable precision to the prior calibrants and that they enable effective cross-laboratory comparison of measurements of red and blue fluorescence from proteins expressed in bacterial cells.
One session of fMRI-Neurofeedback training on motor imagery modulates whole-brain effective connectivity and dynamical complexity
Authors: De Filippi Eleonora , Marins Theo , Escrichs Anira , Gilson Matthieu , Moll Jorge , Tovar-Moll Fernanda , Deco Gustavo
Published: July 2022

In the past decade, several studies have shown that Neurofeedback (NFB) by functional magnetic resonance imaging can alter the functional coupling of targeted and non-targeted areas. However, the causal mechanisms underlying these changes remain uncertain. Here, we applied a whole-brain dynamical model to estimate Effective Connectivity (EC) profiles of resting-state data acquired before and immediately after a single-session NFB training for 17 participants who underwent motor imagery NFB training and 16 healthy controls who received sham feedback. Within-group and between-group classification analyses revealed that only for the NFB group it was possible to accurately discriminate between the 2 resting-state sessions. NFB training-related signatures were reflected in a support network of direct connections between areas involved in reward processing and implicit learning, together with regions belonging to the somatomotor, control, attention, and default mode networks, identified through a recursive-feature elimination procedure. By applying a data-driven approach to explore NFB-induced changes in spatiotemporal dynamics, we demonstrated that these regions also showed decreased switching between different brain states (i.e. metastability) only following real NFB training. Overall, our findings contribute to the understanding of NFB impact on the whole brain’s structure and function by shedding light on the direct connections between brain areas affected by NFB training.
Age‐Related Perturbations in the Sarcolemmal Environment are Attenuated by Lifelong Caloric Restriction and Voluntary Wheel Running
Authors: Hord Jeffrey M , Garcia Marcela , Lawler John M
Published: July 2022

Sarcopenia is the age‐related reduction in skeletal muscle mass and strength. Previously we observed that lifelong mild caloric restriction (CR) and wheel running (WR) attenuated sarcopenia, in part by reducing the age‐induced disruptions of the sarcolemmal dystrophin‐glycoprotein complex (DGC) proteins. The purpose of this study was to determine if mild (8%) CR and lifelong CR + voluntary WR could maintain a phenotypically young sarcolemmal environment in plantaris muscle fibers. Fischer 344 rats were assigned into four groups: 6‐month‐old sedentary ad libitum (YAL), 24‐month‐old sedentary ad libitum group (OAL), 8% caloric restriction from 11 months – 24 months (OCR), and 8% CR plus voluntary wheel running from 11 months – 24 months (OCRWR). We observed significant age‐related increases in key membrane repair proteins (MG53, p < 0.0001; dysferlin, p < 0.0001; annexin A6, p < 0.0001; and annexin A2, p = 0.004) in the OAL plantaris. Lifelong mild CR and CRWR interventions were effective at maintaining membrane repair proteins near YAL levels. Consistent with a perturbed sarcolemmal environment, we also found reduced protein content of NADPH oxidase isoform 2 (Nox2) subunits (p67phox, p = 0.03; p47phox, p = 0.01; and gp91phox, p = 0.096). Lifelong CR and CRWR protected against the age‐related reduction in gp91phox, p47phox, and p67phox proteins. Nox2 subunit abundance in OCR and OCRWR were not significantly different than YAL, while p67phox was significantly higher in OCR than YAL (p = 0.03). Novel data presented here are consistent with the hypothesis that lifelong CR and WR mitigate sarcopenia, in part, by ameliorating age‐induced alterations in the myofiber membrane environment.

Support or Funding Information

NIH (AR054084), NASA (NNX12AR62G), the Sydney and J.L. Huffines Institute, and the College of Health and Education at Texas A&M University
Anthocyanin‐rich blueberry diets enhance protection of critical brain regions exposed to acute levels of 56Fe cosmic radiation
Authors: Poulose Shibu M , Kelly Megan E , Bielinski Donna F , Miller Marshall G , Rabin Bernard , Shukitt‐Hale Barbara
Published: July 2022

The protective effects of anthocyanin‐rich blueberries on brain health are well documented and are particularly important under conditions of high oxidative stress which can lead to “accelerated aging”. One such scenario is exposure to space radiation, which consists of high‐energy and ‐charge particles (HZE), which are known to cause cognitive dysfunction, carcinogenic effects, and deleterious neurochemical alterations. In the current study we assessed the effects of 8 weeks of blueberry supplementation in young animals exposed to 56Fe‐HZE particles, particularly those effects related to behavior and neurochemical alteration. Acute effects were measured within 4 to 48 h after radiation exposure. Animals were randomized into a “learning” group, which were irradiated prior to conditioning and a “memory” group, which were irradiated between conditioning and testing. Results indicated that the radiation primarily affected the memory group but not the learning group. These effects were dependent on the resilience of the brain to readjust its endogenous anti‐oxidant and anti‐inflammatory systems within specific brain regions, particularly the hippocampus and frontal cortex. Dietary blueberry significantly attenuated hippocampal and fronto‐cortical 56Fe irradiation‐induced declines in protein carbonyl content, a marker for oxidative protein degradation, relative to controls. Furthermore, dietary blueberry significantly attenuated 56Fe irradiation‐induced increases in pro‐oxidant NOX2 and pro‐inflammatory COX2 and up‐regulated Nrf2, a key regulatory protein which is critical for antioxidant response elements (AREs), in both hippocampus and frontal cortex. These findings support the role of diet in combatting the negative effects of exposure to space radiation through the consumption of anthocyanin‐rich foods such as blueberry.

Support or Funding Information

Supported by NASA Grant No. NNX13AB73G.