bluuebunny/crossref_metadata_2025 huggingface dataset:
“Gender Affirmative Surgery: A collaborative approach between the surgeon and mental health professional”
Authors: Roblee Cole , Hamidian Jahromi Alireza , Ferragamo Brooke , Radix Asa , De Cuypere Griet , Green Jamison , Dorafshar Amir H. , Ettner Randi , Monstrey Stan , Schechter Loren
Published: February 2023

Gender incongruence describes a condition in which an individual’s gender identity does not align with their sex assigned at birth, based on anatomic characteristics. Individuals with gender incongruence may request surgical interventions, and gender-affirmation surgery plays an important role for these individuals. The basis of care derives from principles elucidated in The Standards of Care; international guidelines that help inform clinical decision-making. Historically, mental healthcare professionals (MHPs) and surgeons have worked collaboratively to select “appropriate” surgical candidates. However, as our understanding of gender identity evolves, so does the relationship between the MHP and the surgeon. The role of the MHP has shifted from a requirement to verify an individual’s identity to that of supporting and participating in a shared decision-making process between the individual and their healthcare team. This article discusses the evolution of the relationship between the MHP and surgeon as well as providing insight into the history of this relationship.
Individual Heterogeneity in the Relations Between Sleep, Inflammation, and Somatic Symptoms
Authors: Jonker Iris , Visschedijk Sjoerd , Rosmalen Judith G.M. , Schenk Hendrika Maria , Van Ockenburg Sonja L.
Published: February 2023

Objective

Poor sleep is associated with the experience of more somatic symptoms and a proinflammatory state, whereas a proinflammatory state may also result in the experience of more somatic symptoms. However, existing studies ignore individual differences in these associations. We aimed to study relations between sleep, inflammatory markers, and somatic symptoms at a within-individual level.

Methods

Time series of daily data on sleep, somatic symptoms, and inflammation markers in 10 healthy individuals (age, 19–58 years; three men) for 63 days were analyzed. Bidirectional lagged (t − 1) and contemporaneous (t) relations between sleep duration, inflammatory markers (C-reactive protein, interferon-α, interleukin 1RA), and somatic symptoms were analyzed using 24-hour urine and diary data. Unified structural equation modeling was used to analyze the association between sleep duration, the three inflammatory markers, and the amount of somatic symptoms at the individual level.

Results

Associations were found between sleep and at least one of three inflammatory markers in four individuals, both positive (three associations) and negative (five associations) and contemporaneous (four associations) and lagged (four associations). Sleep was related to somatic symptoms in four individuals, both positive (n = 2) and negative (n = 2) and contemporaneous (n = 3) and lagged (n = 1). Inflammatory markers were associated with somatic symptoms in three individuals, both positive (three associations) and negative (one association) and contemporaneous (three associations) and lagged (one associations). Two individuals showed no associations between sleep, inflammatory markers, and somatic symptoms.

Conclusions

We observed a large variability in presence, strength, and direction of associations between sleep, inflammatory markers, and somatic symptoms.
Traumatic Events, Posttraumatic Stress Disorder, and Central Sensitization in Chronic Pain Patients of a German University Outpatient Pain Clinic
Authors: Manuel Jorge , Rudolph Linda , Beissner Florian , Neubert Till-Ansgar , Dusch Martin , Karst Matthias
Published: February 2023

Objective

Posttraumatic stress disorder (PTSD) and traumatic life events are often coupled to chronic pain, possibly linked by central sensitization. We wanted to assess the prevalence of traumatic events and PTSD in chronic pain patients of a German university hospital outpatient pain clinic. Moreover, we evaluated the extent of indicators and co-occurring traits of central sensitization in comorbid patients.

Methods

We retrospectively divided 914 chronic pain patients into four groups depending on their trauma severity: no trauma, accidental trauma, interpersonal trauma, and PTSD. We collected electronic pain drawings focusing on pain area and widespreadness, as well as information about pain intensity, sleep impairment, disability, stress, anxiety, depression, and somatization. Differences between groups were calculated using Kruskal-Wallis with post-hoc Mann-Whitney tests.

Results

Of 914 patients, 231 (25%) had no trauma, 210 (23%) had accidental traumas, 283 (31%) had interpersonal traumas, 99 (11%) had PTSD, and 91 (10%) could not be classified. We observed statistically significant differences between groups in pain area and widespreadness, as well as maximal pain, sleep impairment, disability, stress, anxiety, depression, and somatization. The severity of symptoms increased with trauma severity.

Conclusions

Traumatic life events and PTSD are frequent in chronic pain patients. The increased pain area and widespreadness, as well as the increased negative impact on co-occurring traits of sensory sensitivity (anxiety, depression, somatization), are compatible with central sensitization in comorbid patients. Therefore, a heightened awareness of the comorbidity between traumatic experiences and chronic pain is recommended.
Multiparametric MRI
Authors: Hagiwara Akifumi , Fujita Shohei , Kurokawa Ryo , Andica Christina , Kamagata Koji , Aoki Shigeki
Published: February 2023

With the recent advancements in rapid imaging methods, higher numbers of contrasts and quantitative parameters can be acquired in less and less time. Some acquisition models simultaneously obtain multiparametric images and quantitative maps to reduce scan times and avoid potential issues associated with the registration of different images. Multiparametric magnetic resonance imaging (MRI) has the potential to provide complementary information on a target lesion and thus overcome the limitations of individual techniques. In this review, we introduce methods to acquire multiparametric MRI data in a clinically feasible scan time with a particular focus on simultaneous acquisition techniques, and we discuss how multiparametric MRI data can be analyzed as a whole rather than each parameter separately. Such data analysis approaches include clinical scoring systems, machine learning, radiomics, and deep learning. Other techniques combine multiple images to create new quantitative maps associated with meaningful aspects of human biology. They include the magnetic resonance g-ratio, the inner to the outer diameter of a nerve fiber, and the aerobic glycolytic index, which captures the metabolic status of tumor tissues.
Reliability and Validity of the Japanese Version of the Basel Assessment of Adherence to Immunosuppressive Medications Scale in Kidney Transplant Recipients
Authors: Kosoku Akihiro , Iwai Tomoaki , Masuda Hiroo , Kabei Kazuya , Nishide Shunji , Maeda Keiko , Yoshikawa Yuki , Nakamura Yasutaka , De Geest Sabina , Uchida Junji
Published: February 2023

Background.

A valid and reliable instrument that can measure adherence is needed to identify nonadherent patients and to improve adherence. However, there is no validated Japanese self-report instrument to evaluate adherence to immunosuppressive medications for transplant patients. The purpose of this study was to determine the reliability and validity of the Japanese version of the Basel Assessment of Adherence to Immunosuppressive Medications Scale (BAASIS).

Methods.

We translated the BAASIS into Japanese and developed the Japanese version of the BAASIS (J-BAASIS) according to the International Society of Pharmacoeconomics and Outcomes Research task force guidelines. We analyzed the reliability (test–retest reliability and measurement error) and validity of the J-BAASIS (concurrent validity with the medication event monitoring system and the 12-item Medication Adherence Scale) referring to the COSMIN Risk of Bias checklist.

Results.

A total of 106 kidney transplant recipients were included in this study. In the analysis of test–retest reliability, Cohen’s kappa coefficient was found to be 0.62. In the analysis of measurement error, the positive and negative agreement were 0.78 and 0.84, respectively. In the analysis of concurrent validity with the medication event monitoring system, sensitivity and specificity were 0.84 and 0.90, respectively. In the analysis of concurrent validity with the 12-item Medication Adherence Scale, the point-biserial correlation coefficient for the “medication compliance” subscale was 0.38 (P < 0.001).

Conclusions.

The J-BAASIS was determined to have good reliability and validity. Using the J-BAASIS to evaluate adherence can help clinicians to identify medication nonadherence and institute appropriate corrective measures to improve transplant outcomes.
Emerging trends in gene and bipolar disorder research: a bibliometric analysis and network visualisation
Authors: Zakaria Wan Nur Amalina , Wijaya Adi , Al-Rahbi Badriya , Ahmad Asma Hayati , Zakaria Rahimah , Othman Zahiruddin
Published: February 2023

This study aims to use a bibliometric technique to evaluate the scientific output of gene and bipolar disorder research. The search query related to gene and bipolar disorder from the Scopus database identified 1848 documents from 1951 to 2020. The growth in the publications increased since early 1990, peaked in 2011, and started to decline thereafter. High occurrence in author keywords suggests that some research topics, such as “polymorphism”, “linkage” and “association study” have waned over time, whereas others, such as “DNA methylation,” “circadian rhythm,” “” and “meta-analysis,” are now the emerging trends in gene and bipolar disorder research. The USA was the country with the highest production followed by the UK, Canada, Italy and Germany. The leading institutions were Cardiff University in the UK, the National Institute of Mental Health (NIMH) in the USA, King’s College London in the UK and the University of California, San Diego in the USA. The leading journals publishing gene and bipolar literature were the American Journal of Medical Genetics Neuropsychiatric Genetics, Molecular Psychiatry and Psychiatric Genetics. The top authors in the number of publications were Craddock N, Serretti A and Rietschel M. According to the co-authorship network analysis of authors, the majority of the authors in the same clusters were closely linked together and originated from the same or neighbouring country. The findings of this study may be useful in identifying emerging topics for future research and promoting research collaboration in the field of genetic studies related to bipolar disorder.
PRODUCTION OF XYLANASE BY Aspergillus niger GIO AND Bacillus megaterium THROUGH SOLID-STATE FERMENTATION
Authors: Fasiku Samuel Adedayo , Bello Mobolaji Akeem , Odeniyi Olubusola Ayoola
Published: February 2023

Xylanase breaks xylan down to xylose which is used in industries such as pulp and paper, food, and feed, among others. The utilization of wastes for xylanase production is economical, hence, this work aimed at producing xylanase through solid-state fermentation and characterizing the enzyme. Xylanase-producing strains of Bacillus megaterium and Aspergillus niger GIO were inoculated separately in a 5 and 10 days solid fermentation study on maize straw, rice straw, sawdust, corn cob, sugarcane bagasse, conifer liters, alkaline-pretreated maize straw (APM), and combined-alkaline and biological-pretreated maize straw, respectively. The best substrate was selected for xylanase production. The crude enzyme was extracted from the fermentation medium and xylanase activity was characterized using parameters such as temperature, cations, pH, and surfactants. Among different substrates, the highest xylanase activity of 3.18 U/mL was recorded when Aspergillus niger GIO was grown on APM. The xylanase produced by Aspergillus niger GIO and Bacillus megaterium had their highest activities (3.67 U/mL, 3.36 U/mL) at 40 °C after 30 and 45 minutes of incubation, respectively. Optimum xylanase activities (4.58 and 3.58 U/mL) of Aspergillus niger GIO and Bacillus megaterium, respectively were observed at pH 5.0 and 6.2. All cations used enhanced xylanase activities except magnesium ion. Sodium dodecyl sulfate supported the highest xylanase activity of 6.13 and 6.90 U/mL for Aspergillus niger GIO and Bacillus megaterium, respectively. High yields of xylanase were obtained from Aspergillus niger GIO and Bacillus megaterium cultivated on alkaline pretreated maize straw.  The xylanase activities were affected by pH, temperature, surfactants, and cations.
Igniting children’s enthusiasm for microbes with an origami paper microscope
Authors: Gardner Joshua , Perry Cynthia , Cervantes Jorge
Published: February 2023

The COVID-19 pandemic has highlighted the urgent need for microbiology literacy in society. Microbiology knowledge, and its dissemination, can help inform and increase the objectivity of important decisions, such as treatment or vaccination.
A microbiology learning experience, titled “What you can’t see can hurt you” was delivered as part of a larger outreach event (Medventure) where children were exposed to various aspects of medicine and health care fields. The activity involved an introduction to and a discussion of bacteria of clinical importance, and the use of a smartphone-attachable paper-based foldable microscope.
To explore the impact of this activity on participants’ interest in science and microbiology, a pre- and post-activity survey of 5 questions in an emoji-based Likert scale was completed by the participants.
A statistically significant increase in their interest in microbes and where to find them was observed after the event.
Making microbes visible to children and allowing them to capture images of microbes exposes them directly and personally to microscopy and microbiology. An affordable low-cost paper-based microscope can become an alternative approach to teaching and learning to deliver clinical microbiology information to a wide audience range.
Thermomonas paludicola sp. nov., isolated from a lotus wetland
Authors: Kim Mirae , Park Miri S. , Kang Ilnam , Cho Jang-Cheon
Published: February 2023

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated IMCC34681T, was isolated from a lotus wetland in the Republic of Korea. Cellular growth occurred at 10–37 °C (optimum, 30 °C), pH 6–9 (optimum, pH 7) and with 0–2 % (w/v) NaCl (optimum, 0.5 % NaCl). The results of 16S rRNA gene sequence analysis indicated that IMCC34681T represented a member of the genus

Thermomonas

, sharing 95.3–96.9 % similarities with type strains of species of the genus. The whole-genome sequence of IMCC34681T was 2.72 Mbp in size with 66.2 % DNA G+C content. The IMCC34681T genome shared the highest average nucleotide identity (ANI) value, 82.8 %, with that of

Thermomonas brevis

KACC 16975T among species of the genus

Thermomonas

, indicating that the strain represents a novel genomic species. The major respiratory quinone of the strain was ubiquinone-8 (Q-8) and the predominant cellular fatty acids were iso-C15 : 0 (25.7 %) and iso-C14 : 0 (20.8 %). The strain harboured diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as major fatty polar lipids. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, IMCC34681T was assigned to the genus

Thermomonas

as the type strain of a novel species, for which the name Thermomonas paludicola sp. nov. is proposed. The type strain is IMCC34681T (=KACC 21793T=NBRC 114635T).
Cohort Profile: Zhejiang Environmental and Birth Health Research Alliance (ZEBRA) Maternity Cohort
Authors: Sun Haitong Zhe , Tang Haiyang , Xiang Qingyi , Xu Siyuan , Fang Jing , Dai Haizhen , Shi Rui , Pan Yuxia , Luo Ting , Jin Hangbiao , Ji Chenyang , Chen Yuanchen , Liu Hengyi , Zhao Meirong , Tang Kung , Guo Yuming , Xu Wei , Bai Xiaoxia ,   the Zhejiang Environmental and Birth Health Research Alliance (ZEBRA) collaborative group
Published: February 2023

The Zhejiang Environmental and Birth Health Research Alliance (ZEBRA) established a maternity cohort to investigate the relationship between perinatal abnormalities and various risk factors among the Chinese maternal population. The primary aim of ZEBRA is to explore the feasibility of early-stage risk prediction and the forecast of adverse perinatal symptoms and gestational outcomes. The cohort is ambidirectional, with a retrospective arm tracking 6,275 pregnant females enrolled between 2013 and 2016, and a prospective arm recruiting 112,414 participants since the baseline year of 2017. The current ZEBRA maternity cohort database comprises a diverse range of sociodemographic features, physiological characteristics, medical history, therapeutic interventions, and measurements of environmental exposures. Going forward, the cohort will continue to enrol a wider range of participants and collect an even more extensive array of features. ZEBRA is seeking collaborations with both national and international multi-cohort studies to contribute to the field of epidemiology, and provide valuable evidence-based insights for global maternal and child healthcare.
Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model
Authors: Massey Alexander , Boennec Corentin , Restrepo-Ortiz Claudia Ximena , Blanchet Christophe , Alizon Samuel , Sofonea Mircea T.
Published: February 2023

Background

Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes.

Methods

We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three standard statistical forecasting methods (auto-regression, exponential smoothing, and ARIMA).

Results

For anticipating risk of critical care unit overload, our model performed worse than pure statistical methods at the one- and two-week horizons, but had better point forecasts at the four-week horizon for 8 of the 13 regions considered. Our model also suffered from over-confidence with respect to its prediction intervals.

Conclusions

Online visualisation tools and consideration of how metrics can be affected by distortion from non-pharmaceutical government interventions are essential in the assessment of forecasting models for hospital strain.

What is already known on this topic

The US and European Covid-19 Forecast Hubs do not provide more direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which was essential for the provisioning of healthcare resources during the COVID-19 pandemic.

In France, statistical modelling approaches have been proposed to anticipate hospital stain at the sub-national level but are limited by a two-week forecast horizon.

What this study adds

We present a sub-national French modelling framework and online application for anticipating hospital strain at the four-week horizon that can account for abrupt changes in key epidemiological parameters.

It was the only publicly available real-time non-Markovian mechanistic model for the French epidemic when implemented in January 2021 and, to our knowledge, it still was at the time it stopped in early 2022.

How this study might affect research, practice or policy

Further adaptations of this surveillance system can serve as an anticipation tool for hospital strain across sub-national localities to aid in the prevention of short-noticed ward closures and patient transfers.
Increased Hippocampal Blood Flow in People at Clinical High Risk for Psychosis and Effects of Cannabidiol
Authors: Davies Cathy , Bossong Matthijs G , Martins Daniel , Wilson Robin , Appiah-Kusi Elizabeth , Blest-Hopley Grace , Zelaya Fernando , Allen Paul , Brammer Michael , Perez Jesus , McGuire Philip , Bhattacharyya Sagnik
Published: February 2023

Background

Hippocampal hyperperfusion has been observed in people at Clinical High Risk for Psychosis (CHR), is associated with adverse longitudinal outcomes and represents a potential treatment target for novel pharmacotherapies. Whether cannabidiol (CBD) has ameliorative effects on hippocampal blood flow (rCBF) in CHR patients remains unknown.

Methods

Using a double-blind, parallel-group design, 33 CHR patients were randomised to a single oral 600mg dose of CBD or placebo. Nineteen healthy controls were studied under identical conditions but did not receive any drug. Hippocampal rCBF was measured using Arterial Spin Labelling. We examined differences relating to CHR status (controls vs placebo), effects of CBD in CHR (placebo vs CBD) and linear between-group relationships, such that placebo>CBD>controls or controls>CBD>placebo, using a combination of hypothesis-driven and exploratory wholebrain analyses.

Results

Placebo-treated patients had significantly higher hippocampal rCBF bilaterally (all pFWE<.01) compared to controls. There were no suprathreshold effects in the CBD vs placebo contrast. However, we found a significant linear relationship in the right hippocampus (pFWE=.035) such that rCBF was highest in the placebo group, lowest in controls and intermediate in the CBD group. Exploratory wholebrain results replicated previous findings of hyperperfusion in the hippocampus, striatum and midbrain in CHR patients, and provided novel evidence of increased rCBF in inferior-temporal and lateral-occipital regions in patients under CBD compared to placebo.

Conclusions

These findings suggest that hippocampal blood flow is elevated in the CHR state and may be partially normalised by a single dose of CBD. CBD therefore merits further investigation as a potential novel treatment for this population.
Antimicrobial Resistance pattern in Gram-Negative Uropathogens in Duhok City, Northern Iraq
Authors: Yasen Razvan Luqman
Published: February 2023

Antimicrobial resistance (AMR) is one of the most dangerous global threats since antimicrobial discovery. The world health organization(WHO) has implemented a program called GLASS to mitigate resistance across the globe. Urinary tract infection(UTI) are the second most common infections and are the most common reason for prescription of antimicrobials, the rise in AMR has caused concerns of UTI Overuse and misuse of prescriptions and decrease of treatment options hence many researches conducted across the globe are on uropathogens resistance rate and trend. This retrospective study was conducted in duhok province of KRI to measure antimicrobial resistance percentages and identify the most common uropathogens.

309 urine samples were collected in a time span of 12 months. Urine samples were collected by clean catch midstream and inoculated on blood and MacConkey agars, Antibiotic sensitivity test (AST) was performed to identify Gram negative uropathogen and its sensitivity pattern.

We found out most common Gram negative uropathogen in females were E.coli and Klebsiella pneumonia while in males it was E.coli and Pseudomonas aeruginosa and common Klebsiella pneumonia. E.coli was most resistance to amoxicillin/amp(64.2%) and it was least resistant to carbapenems(6.1%). Klebsiella pneumonia had similar resistant pattern to E.coli. pseudomonas aeruginosa was highly resistant to all antimicrobials, third gen cephalosporins were the highest 95.7%.

AMR has risen to concerning levels in duhok and if not controlled would result in simple infections causing death in future we recommend guidelines for control of Overuse, misuse and ease of availability of antimicrobials as a measure to decrease AMR. Continues monitoring should be performed on AMR development in the future.
Risk factors for severe respiratory syncytial virus infection during the first year of life: development and validation of a clinical prediction model
Authors: Vartiainen Pekka , Jukarainen Sakari , Rhedin Samuel Arthur , Prinz Alexandra , Hartonen Tuomo , Vabalas Andrius , Viippola Essi , Rodosthenous Rodosthenis S. , Kuitunen Sara , Liu Aoxing , Lundholm Cecilia , Smew Awad I. , Osvald Emma Caffrey , Helle Emmi , Perola Markus , Almqvist Catarina , Heinonen Santtu , Ganna Andrea
Published: February 2023

Background

Novel immunisation methods against respiratory syncytial virus (RSV) are emerging, but knowledge of risk factors for severe RSV disease is insufficient for their optimal targeting. We aimed to identify predictors for RSV hospitalisation, and to develop and validate a clinical prediction model to guide RSV immunoprophylaxis for under 1-year-old infants.

Methods

In this retrospective cohort study using nationwide registries, we studied all infants born in 1997-2020 in Finland (n = 1 254 913) and in 2006-2020 in Sweden (n = 1 459 472), and their parents and siblings. We screened 1 510 candidate predictors and we created a logistic regression model with 16 predictors and compared its performance to a machine learning model (XGboost) using all 1 510 candidate predictors.

Findings

In addition to known predictors such as severe congenital heart defects (CHD, adjusted odds ratio (aOR) 2·89, 95% confidence interval 2·28-3·65), we identified novel predictors for RSVH, most notably esophageal malformations (aOR 3·11, 1·86-5·19) and lower complexity CHDs (aOR 1·43, 1·25-1·63).

In validation data from 2018-2020, the C-statistic was 0·766 (0·742-0·789) in Finland and 0·737 (0·710-0·762) in Sweden. The clinical prediction model’s performance was similar to the machine learning model (C-statistic in Finland 0·771, 0·754-0·788). Calibration varied according to epidemic intensity. Model performance was similar across different strata of parental income.

The infants in the 90th percentile of predicted RSVH probability hospitalisation had 3·3 times higher observed risk than the population’s average. Assuming 60% effectiveness, immunisation in this top 10% of infants at highest risk would have a number needed to treat of 23 in Finland and 40 in Sweden in preventing hospitalisations.

Interpretation

The identified predictors and the prediction model can be used in guiding RSV immunoprophylaxis in infants.

Funding

Sigrid Jusélius Foundation, European Research Council, Pediatric Research Foundation (for complete list of funding sources, see Acknowledgements).
Dissecting neuron-specific functions of circadian genes using modified cell-specific CRISPR approaches
Authors: Richhariya Shlesha , Shin Daniel , Le Jasmine Quynh , Rosbash Michael
Published: February 2023

Circadian behavioral rhythms inDrosophila melanogasterare regulated by about 75 pairs of brain neurons. They all express the core clock genes but have distinct functions and gene expression profiles. To understand the importance of these distinct molecular programs, neuron-specific gene manipulations are essential. Although RNAi based methods are standard to manipulate gene expression in a cell-specific manner, they are often ineffective, especially in assays involving smaller numbers of neurons or weaker Gal4 drivers. We and others recently exploited a neuron-specific CRISPR-based method to mutagenize genes within circadian neurons. Here we further explore this approach to mutagenize three well-studied clock genes: the transcription factor genevrille,the photoreceptor geneCryptochrome(cry) and the neuropeptide genePdf. The CRISPR-based strategy not only reproduced their known phenotypes but also assignedcryfunction for different light mediated phenotypes to discrete, different subsets of clock neurons. We further tested two recently published methods for temporal regulation in adult neurons, inducible Cas9 and auxin-inducible gene expression system (AGES). The results were not identical, but both approaches successfully showed that the adult-specific knockout of the neuropeptidePdfreproduces the canonical loss-of-function mutant phenotypes. In summary, a CRISPR-based strategy is a highly effective, reliable, and general method to temporally manipulate gene function in specific adult neurons.

Significance statement

Most animals have specific brain neurons that regulate sleep-wake cycles and other aspects of circadian behavior.Drosophilahas only about 150 of these clock neurons. Despite their small numbers, they have remarkably diverse anatomy and gene expression profiles. To address the different functions of these neurons, we used highly specific and efficient CRISPR-based methods to create cell type-specific disruptions of three traditional circadian genes. We were able to assign the function of the photoreceptor cryptochrome to two tiny subsets of clock neurons. In addition, two independent methods assigned the neuropeptide PDF to the adult stage. In summary, we find that the CRISPR-based methods are very efficient at studying adult specific functions of genes in small, discrete sets of neurons.
Multi-omic screening of invasive GBM cells in engineered biomaterials and patient biopsies reveals targetable transsulfuration pathway alterations
Authors: Garcia Joseph H. , Akins Erin A. , Jain Saket , Wolf Kayla J. , Zhang Jason , Choudhary Nikita , Lad Meeki , Shukla Poojan , Gill Sabraj , Carson Will , Carette Luis , Zheng Allison , Kumar Sanjay , Aghi Manish K.
Published: February 2023

While the poor prognosis of glioblastoma arises from the invasion of a subset of tumor cells, little is known of the metabolic alterations within these cells that fuel invasion. We integrated spatially addressable hydrogel biomaterial platforms, patient site-directed biopsies, and multi-omics analyses to define metabolic drivers of invasive glioblastoma cells. Metabolomics and lipidomics revealed elevations in the redox buffers cystathionine, hexosylceramides, and glucosyl ceramides in the invasive front of both hydrogel-cultured tumors and patient site-directed biopsies, with immunofluorescence indicating elevated reactive oxygen species (ROS) markers in invasive cells. Transcriptomics confirmed upregulation of ROS-producing and response genes at the invasive front in both hydrogel models and patient tumors. Amongst oncologic ROS, hydrogen peroxide specifically promoted glioblastoma invasion in 3D hydrogel spheroid cultures. A CRISPR metabolic gene screen revealed cystathionine gamma lyase (CTH), which converts cystathionine to the non-essential amino acid cysteine in the transsulfuration pathway, to be essential for glioblastoma invasion. Correspondingly, supplementing CTH knockdown cells with exogenous cysteine rescued invasion. Pharmacologic CTH inhibition suppressed glioblastoma invasion, while CTH knockdown slowed glioblastoma invasionin vivo. Our studies highlight the importance of ROS metabolism in invasive glioblastoma cells and support further exploration of the transsulfuration pathway as a mechanistic and therapeutic target.
Rapid genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) using MinION nanopore sequencing
Authors: Caserta Leonardo Cardia , Zhang Jianqiang , Piñeyro Pablo , Diel Diego G.
Published: February 2023

The global distribution and constant evolution are challenges for the control of porcine reproductive and respiratory syndrome virus (PRRSV), one of the most important viruses affecting swine worldwide. Effective control of PRRSV benefits from genotyping, which currently relies on Sanger sequencing. Here we developed and optimized procedures for real-time genotyping and whole genome sequencing of PRRSV directly from clinical samples based on targeted amplicon- and long amplicon tiling sequencing using the MinION Oxford Nanopore platform. Procedures were developed and tested on 154 clinical samples (including lung, serum, oral fluid and processing fluid) with RT-PCR Ct values ranging from 15 to 35. The targeted amplicon sequencing (TAS) approach was developed to obtain sequences of the complete ORF5 (main target gene for PRRSV genotyping) and partial ORF4 and ORF6 sequences of both PRRSV-1 and PRRSV-2 species. After only 5 min of sequencing, PRRSV consensus sequences with identities to reference sequences above 99% were obtained, enabling rapid identification and genotyping of clinical PRRSV samples into lineages 1, 5 and 8. The long amplicon tiling sequencing (LATS) approach targets type 2 PRRSV, the most prevalent viral species in the U.S. and China. Complete PRRSV genomes were obtained within the first hour of sequencing for samples with Ct values below 24.9. Ninety-two whole genome sequences were obtained using the LATS procedure. Fifty out of 60 sera (83.3%) and 18 out of 20 lung samples (90%) had at least 80% of genome covered at a minimum of 20X sequence depth per position. The procedures developed and optimized in this study here are valuable tools with potential for field application during PRRSV elimination programs.
Age-related differences in fMRI subsequent memory effects are directly linked to local grey matter volume differences
Authors: Kizilirmak Jasmin M. , Soch Joram , Richter Anni , Schott Björn H.
Published: February 2023

Episodic memory performance declines with increasing age, and older adults typically show reduced activation of inferior temporo-parietal cortices in functional magnetic resonance imaging (fMRI) studies of episodic memory formation. Given the age-related cortical volume loss, it is conceivable that age-related reduction of memory-related fMRI activity may be partially attributable to reduced grey matter volume (GMV). We performed a voxel-wise multimodal neuroimaging analysis of fMRI correlates of successful memory encoding, using regional GMV as covariate. In a large cohort of healthy adults (106 young, 111 older), older adults showed reduced GMV across the entire neocortex and reduced encoding-related activation of inferior temporal and parieto-occipital cortices compared to young adults. Importantly, these reduced fMRI activations during successful encoding in older adults could in part be attributed to lower regional GMV. Our results highlight the importance of controlling for structural MRI differences in fMRI studies in older adults but also demonstrate that age-related differences in memory-related fMRI activity cannot be attributed to structural variability alone.
Striatal ensemble activity in an innate naturalistic behavior
Authors: Minkowicz Samuel , Mathews Mychaela Alexandria , Mou Felicia Hoilam , Yoon Hyoseo , Freda Sara Nicole , Cui Ethan S , Kennedy Ann , Kozorovitskiy Yevgenia
Published: February 2023

Self-grooming is an innate, naturalistic behavior found in a wide variety of organisms. The control of rodent grooming has been shown to be mediated by the dorsolateral striatum through lesion studies and in-vivo extracellular recordings. Yet, it is unclear how populations of neurons in the striatum encode grooming. We recorded single-unit extracellular activity from populations of neurons in freely moving mice and developed a semi-automated approach to detect self-grooming events from 117 hours of simultaneous multi-camera video recordings of mouse behavior. We first characterized the grooming transition-aligned response profiles of striatal projection neuron and fast spiking interneuron single units. We identified striatal ensembles whose units were more strongly correlated during grooming than during the entire session. These ensembles display varied grooming responses, including transient changes around grooming transitions or sustained changes in activity throughout the duration of grooming. Neural trajectories computed from the identified ensembles retain the grooming related dynamics present in trajectories computed from all units in the session. These results elaborate striatal function in rodent self-grooming and demonstrate that striatal grooming-related activity is organized within functional ensembles, improving our understanding of how the striatum guides action selection in a naturalistic behavior.
A Suspension Trapping–Based Sample Preparation Workflow for Sensitive Plant Phosphoproteomics
Authors: Chen Chin-Wen , Tsai Chia-Feng , Lin Miao-Hsia , Lin Shu-Yu , Hsu Chuan-Chih
Published: February 2023

Plant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants; however, it demands high-throughput methods with sensitive detection and accurate quantification. Although protein precipitation is indispensable for removing contaminants and improving sample purity, it limits the sensitivity and throughput of plant phosphoproteomic analysis. The multiple handling steps involved in protein precipitation lead to sample loss and process variability. Herein, we developed an approach based on suspension trapping (S-Trap), termed tandem S-Trap-IMAC (immobilized metal ion affinity chromatography), by integrating an S-Trap micro column with an Fe-IMAC tip. Compared with a precipitation-based workflow, the tandem S-Trap-IMAC method deepened the coverage of the Arabidopsis (Arabidopsis thaliana) phosphoproteome by more than 30%, with improved quantification accuracy and short sample processing time. We applied the tandem S-Trap-IMAC method for studying abscisic acid (ABA) signaling in Arabidopsis seedlings. We thus identified 24,055 phosphopeptides and quantified several key phosphorylation sites on core ABA signaling components across four time points. Our results show that the optimized workflow aids high-throughput phosphoproteome profiling of low-input plant samples.
Genetic dependencies associated with transcription factor activities in human cancer cell lines
Authors: Thatikonda Venu , Supper Verena , Ravichandran Madhwesh C. , Lipp Jesse J. , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Grosche Sara , Neumüller Ralph A. , Mair Barbara , Mauri Federico , Popa Alexandra
Published: February 2023

Transcription factors (TFs) are key components of the aberrant transcriptional programs in cancer cells. In this study, we used TF activity (TFa), inferred from the downstream regulons as a potential biomarker to identify associated genetic vulnerabilities in cancer cells. Our linear model framework, integrating TFa and genome-wide CRISPR knockout datasets identified 1,770 candidate TFa-target pairs across different cancer types and assessed their survival impact in patient data. As a proof of concept, through inhibitor screens and genetic depletion assays in cell lines, we validated the dependency of cell lines on predicted targets linked to TEAD1, the most prominent TF from our analysis. Overall, these candidate pairs represent an attractive resource for early-stage targets and drug discovery programs in oncology.
Glutamine metabolism inhibition has dual immunomodulatory and antibacterial activities againstMycobacterium tuberculosis
Authors: Parveen Sadiya , Shen Jessica , Lun Shichun , Zhao Liang , Koleske Benjamin , Leone Robert D. , Rais Rana , Powell Jonathan D. , Murphy John R. , Slusher Barbara S. , Bishai William R.
Published: February 2023

As one of the most successful human pathogens,Mycobacterium tuberculosis(Mtb) has evolved a diverse array of determinants to subvert host immunity and alter host metabolic patterns. However, the mechanisms of pathogen interference with host metabolism remain poorly understood. Here we show that a novel glutamine metabolism antagonist, JHU083, inhibitsMtbproliferation in vitro and in vivo. JHU083-treated mice exhibit weight gain, improved survival, a 2.5 log lower lung bacillary burden at 35 days post-infection, and reduced lung pathology. JHU083 treatment also initiates earlier T-cell recruitment, increased proinflammatory myeloid cell infiltration, and a reduced frequency of immunosuppressive myeloid cells when compared to uninfected and rifampin-treated controls. Metabolomics analysis of lungs from JHU083-treatedMtb-infected mice revealed reduced glutamine levels, citrulline accumulation suggesting elevated NOS activity, and lowered levels of quinolinic acid which is derived from the immunosuppressive metabolite kynurenine. When tested in an immunocompromised mouse model ofMtbinfection, JHU083 lost its therapeutic efficacy suggesting the drug’s host-directed effects are likely to be predominant. Collectively, these data reveal that JHU083-mediated glutamine metabolism inhibition results in dual antibacterial and host-directed activity against tuberculosis.
Enhanced inflammatory signaling driven by metabolic switch in Aicardi-Goutières syndrome
Authors: Batignes Maxime , Luka Marine , Jagtap Surabhi , de Cevins Camille , Nemazanyy Ivan , Fali Tinhinane , García-Paredes Víctor , Carbone Francesco , Pérot Brieuc P. , Neven Bénédicte , Bader-Meunier Brigitte , Quartier dit Maire Pierre , Hully Marie , Belot Alexandre , Lepelley Alice , Frémond Marie-Louise , Crow Yanick J. , Fischer Alain , Ménager Mickaël M.
Published: February 2023

Aicardi-Goutières syndrome (AGS) is a genetic type I interferon (IFN)-mediated disease characterised by neurological involvement with onset in childhood. Chronic inflammation in response to uncontrolled type I IFN production is, among other things, associated with IP-10 secretion. We analysed, at the single-cell transcriptomic levels, peripheral blood samples from patients bearing AGS-causing mutations inSAMHD1,RNASEH2BorADAR1genes. Using machine-learning approaches and differential gene expression we identified a drastic loss of transcription factor hypoxia induced factor 1 α (HIF-1α) expression and activity associated with features of a metabolic switch and mitochondrial stress in monocytes/dendritic cells. Chemical stabilization of HIF-1α, with a synthetic drug in anin vitromodel of AGS, allowed us to reverse the energy metabolic switch, attenuate mitochondrial stress and markedly reduce IP-10 production. We therefore propose that energy metabolic switch contributes to exacerbated chronic inflammation in AGS, and that targeting this pathway might represent a promising therapeutic approach.
Predicting the Three-dimensional Structure of the c-KITOncogene Promoter and the Dynamics of Strongly Coupled Guanine-Quadruplexes
Authors: Bignon Emmanuelle , Spinello Angelo , Miclot Tom , D’ Anna Luisa , Ducani Cosimo , Grandemange Stéphanie , Barone Giampaolo , Monari Antonio , Terenzi Alessio
Published: February 2023

Guanine-quadruplexes (G4s) are non-canonical DNA structures that play important protective and regulatory roles within cells, influencing, for instance, gene expression. Although the secondary structure of many human G4s is well characterized, in several gene-promoter regions multiple G4s are located in close proximity and may form three-dimensional structures which could ultimately influence their biological roles. In this contribution, we analyze the interplay between the three neighboring G4s present in the c-KITproto-oncogene promoter, namely WK1, WSP and WK2. In particular, we highlight how these three G4s are structurally linked and how their crosstalk favors the formation of a parallel structure for WSP, differently from what observed for this isolated G4 in solution. Relying on all-atom molecular dynamic simulations exceeding the μs time-scale and using enhanced sampling methods, we provide the first computationally-resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. Our results indicate that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool to predict and interpret complex DNA structures that ultimately can be used as starting point for drug discovery purposes.
Anesthesia suppresses gastric myoelectric power in the ferret
Authors: Tomaselli Lorenzo , Sciullo Michael , Fulton Stephanie , Yates Bill J. , Fisher Lee E. , Ventura Valérie , Horn Charles C.
Published: February 2023

Background

Gastrointestinal myoelectric signals have been the focus of extensive research; although it is unclear how general anesthesia affects these signals, studies have often been conducted under general anesthesia. Here, we explore this issue directly by recording gastric myoelectric signals during awake and anesthetized states in the ferret and also explore the contribution of behavioral movement to observed changes in signal power.

Methods

Ferrets were surgically implanted with electrodes to record gastric myoelectric activity from the serosal surface of the stomach, and, following recovery, were tested in awake and isoflurane-anesthetized conditions. Video recordings were also analyzed during awake experiments to compare myoelectric activity during behavioral movement and rest.

Key Results

A significant decrease in gastric myoelectric signal power was detected under isoflurane anesthesia compared to the awake condition. Moreover, a detailed analysis of the awake recordings indicates that behavioral movement is associated with increased signal power compared to rest.

Conclusions & Inferences

These results suggest that both general anesthesia and behavioral movement can affect the amplitude of gastric myoelectric. In summary, caution should be taken in studying myoelectric data collected under anesthesia. Further, behavioral movement could have an important modulatory role on these signals, affecting their interpretation in clinical settings.
Combinatory EHMT and PARP inhibition induces an interferon response and a CD8 T cell-dependent tumor regression in PARP inhibitor-resistant models
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gbaja Veronica , Arnoult Nausica , Chuong Edward B. , Bitler Benjamin G.
Published: February 2023

Euchromatic histone lysine methyltransferases 1 and 2 (EHMT1/2), which catalyze demethylation of histone H3 lysine 9 (H3K9me2), contribute to tumorigenesis and therapy resistance through unknown mechanisms of action. In ovarian cancer, EHMT1/2 and H3K9me2 are directly linked to acquired resistance to poly-ADP-ribose polymerase (PARP) inhibitors and are correlated with poor clinical outcomes. Using a combination of experimental and bioinformatic analyses in several PARP inhibitor resistant ovarian cancer models, we demonstrate that combinatory inhibition of EHMT and PARP is effective in treating PARP inhibitor resistant ovarian cancers. Ourin vitrostudies show that combinatory therapy reactivates transposable elements, increases immunostimulatory dsRNA formation, and elicits several immune signaling pathways. Ourin vivostudies show that both single inhibition of EHMT and combinatory inhibition of EHMT and PARP reduces tumor burden, and that this reduction is dependent on CD8 T cells. Together, our results uncover a direct mechanism by which EHMT inhibition helps to overcome PARP inhibitor resistance and shows how an epigenetic therapy can be used to enhance anti-tumor immunity and address therapy resistance.