bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiological study of genitourinary syndrome of menopause in Japan (GENJA study)
Authors: Tomoe Hikaru , Ozaki Yumi , Yamamoto Mayuko , Kuwajima Mami , Ninomiya Noriko , Sekiguchi Yuki , Sato Yoshikazu , Takahashi Satoru , Nagao Koichi
Published: January 2023

Objective

This study aimed to investigate the prevalence of genitourinary syndrome of menopause (GSM) in Japan using the Japanese translation of the Vulvovaginal Symptoms Questionnaire (VSQ) with online survey. In addition, we examined the relationship between sexual activity and GSM symptoms.

Methods

An online survey on GSM was conducted with 4,134 women aged 40 to 79 years, who were registered in an online survey company. Several questionnaires with Japanese translations of linguistic validity were used in this study. GSM was defined as a condition in women older than 40 years with vulvovaginal symptoms on the VSQ.

Results

The percentage of postmenopausal women 40 years and older was 69.6%. The percentage of women with sexual activity was 22%. The prevalence of GSM with vulvovaginal symptoms was 11.6%, and 31.7% in sexually active women. The prevalence of GSM was associated with age and was significantly lower in the 70s age group than in other age groups. Vulvar hurting and dryness were both age-related only in the sexual activity group, with a statistically significantly higher prevalence in the 70s group than in the 40s group. The prevalence of vulvar dryness during sexual activity was significantly lower in the 40s age group.

Conclusions

An online epidemiological survey of GSM was conducted for the first time in Japan using the linguistically validated Japanese translation of the VSQ. The prevalence of GSM with genital or sexual symptoms was 11.6% in Japanese women 40 years and older, and 31.7% in sexually active women.
Cost and value in liver disease guidelines: 2011–2022
Authors: Aby Elizabeth S. , Kaplan Alyson , Ufere Nneka N.
Published: January 2023

Background:

Chronic liver disease (CLD) is associated with rising health care utilization and cost. We aimed to describe the frequency of cost/value (C/V) statements in CLD-related clinical guidance documents (CGDs).

Methods:

CGD with a focus on CLD published between January 2011 and February 2022 from 3 US societies [Association for the Study of Liver Diseases (AASLD), American College of Gastroenterology (ACG), and American Gastroenterological Association (AGA)] were analyzed.

Findings:

Forty-five CGDs were identified. Eighty of 1334 guidance statements were C/V statements (6%). Only 1.1% reported patient-level costs and none reported out-of-pocket costs. Despite the increased importance of incorporating cost and value into care, the proportion of C/V statements in CGDs related to liver disease is low.
Serum FGF19 predicts outcomes of Kasai portoenterostomy in biliary atresia
Authors: Nyholm Iiris , Hukkinen Maria , Pihlajoki Marjut , Davidson Joseph R. , Tyraskis Athanasios , Lohi Jouko , Heikkilä Päivi , Hänninen Satu , Andersson Noora , Eloranta Katja , Carpén Olli , Heikinheimo Markku , Davenport Mark , Pakarinen Mikko P.
Published: January 2023

Background and Aims:

Outcomes after Kasai portoenterostomy (KPE) for biliary atresia remain highly variable for unclear reasons. As reliable early biomarkers predicting KPE outcomes are lacking, we studied the prognostic value of FGF19.

Approach and Results:

Serum and liver specimens, obtained from biliary atresia patients (N=87) at KPE or age-matched cholestatic controls (N=26) were included. Serum concentration of FGF19 and bile acids, liver mRNA expression of FGF19, and key regulators of bile acid synthesis were related to KPE outcomes and liver histopathology. Immunohistochemistry and in situ hybridization were used for the localization of liver FGF19 expression. Serum levels (223 vs. 61 pg/mL, p<0.001) and liver mRNA expression of FGF19 were significantly increased in biliary atresia. Patients with unsuccessful KPE (419 vs. 145 pg/mL, p=0.047), and those subsequently underwent liver transplantation (410 vs. 99 pg/mL, p=0.007) had significantly increased serum, but not liver, FGF19, which localized mainly in hepatocytes. In Cox hazard modeling serum FGF19 <109 pg/mL predicted native liver survival (HR: 4.31, p<0.001) also among patients operated <60 days of age (HR: 8.77, p=0.004) or after successful KPE (HR: 6.76, p=0.01). Serum FGF19 correlated positively with increased serum primary bile acids (R=0.41, p=0.004) and ductular reaction (R=0.39, p=0.004).

Conclusions:

Increased serum FGF19 at KPE predicted inferior long-term native liver survival in biliary atresia and was associated with unsuccessful KPE, elevated serum primary bile acids, and ductular reaction.
Longitudinal Anthropometry and Body Composition in Children With SARS-CoV-2-Associated Multisystem Inflammatory Syndrome
Authors: Di Profio Elisabetta , Leone Alessandro , Vizzuso Sara , Fiore Giulia , Pascuzzi Martina Chiara , Agostinelli Marta , Dilillo Dario , Mannarino Savina , Fiori Laura , D’Auria Enza , Fabiano Valentina , Carlucci Patrizia , Bova Stefania Maria , Zoia Elena , Bosetti Alessandra , Calcaterra Valeria , Bertoli Simona , Verduci Elvira , Zuccotti Gianvincenzo
Published: January 2023

Objectives:

Acute coronavirus disease 2019 infection has been shown to negatively affect body composition among adult and malnourished or obesity children. Our aim is to longitudinally evaluate body composition in children affected by the Multisystem Inflammatory Syndrome (MIS-C).

Methods:

In this cohort study, we recruited 40 patients affected by MIS-C, aged 2–18 years old, who were admitted in our clinic between December 2020 and February 2021. Physical examination for each participant included weight, height, body mass index (BMI) z score, circumferences, and skinfolds assessment. The same measurements were repeated during outpatient follow-up at 10 (T2), 30 (T3), 90 (T4), and 180 (T5) days after hospital discharge. Fat mass and fat free mass were calculated according to skinfolds predictive equations for children and adolescents. A control group was randomly selected among patients attending a pediatric nutritional outpatient clinic.

Results:

BMI z score significantly decrease between preadmission and hospital discharge. Similarly, arm circumference z score, arm muscular area z score, and arm fat area z score significantly decreased, during hospital stay. Fat mass index (FMI) significantly increased over time, peaking at T3. Fat free mass index decreased during hospitalization.

Conclusions:

To the best of our knowledge, this is the first study to assess body composition in a numerically large pediatric MIS-C population from acute infection to 6 months after triggering event. FMI and anthropometric parameters linked to fat deposits were significantly higher 6 months after acute event. Thus, limiting physical activity and having sedentary lifestyle may lead to an accumulation of adipose tissue even in healthy children who experienced MIS-C and long hospitalization.
The Yield of Routine Tissue Sampling in Pediatric Gastrointestinal Endoscopy
Authors: Anafy Adi , Amir Achiya Z. , Brazowski Eli , Weintraub Yael , Yerushalmy Feler Anat , Moran-Lev Hadar , Dali Levy Margalit , Ziv-Baran Tomer , Cohen Shlomi , Ben-Tov Amir
Published: January 2023

Objectives:

Societies’ guidelines suggest routine tissue sampling in all children undergoing esophagogastroduodenoscopy and ileocolonoscopy, even in the absence of visible endoscopy abnormalities. We aimed to determine the agreement between endoscopic and histopathological findings in pediatric endoscopy and to assess the yield of routine biopsies from all sites.

Methods:

Since January 2019, our endoscopy institute protocol has included routine biopsies sampling from the esophagus, stomach, duodenum, ileum, and colon in all diagnostic procedures. Agreement between tests was done using the kappa coefficient (κ). The study included all endoscopies performed during 2019.

Results:

In total, 541 diagnostic endoscopies were done during the study period with 434 (80%) esophagogastroduodenoscopy and 107 (20%) were ileocolonoscopy. Compared to histology, endoscopic findings performance were: esophagus—sensitivity 33%, specificity 98%; stomach—sensitivity 60%, specificity 89%; duodenum—sensitivity 50%, specificity 97%; duodenal bulb—sensitivity 47%, specificity 89%; terminal ileum—sensitivity 82%, specificity 100%; colon—sensitivity 84%, specificity 96%. Assessment of concordance between endoscopic and histopathologic findings reveals an overall low level of agreement in esophagogastroduodenoscopy (κ of 0.39, 0.51, 0.53, and 0.24 for the esophagus, stomach, duodenal second part, and bulb, respectively), and good agreement in ileocolonoscopy (κ of 0.88 and 0.81 for the ileum and colon, respectively).

Conclusions:

Endoscopy findings are highly specific for histologic pathology, whereas the absence of findings correlates poorly with histologic findings. Ileocolonoscopy shows better agreement than esophagogastroduodenoscopy. Our data support routine tissue sampling in pediatric endoscopy.
Treatment Completion With Three-Dose Series of Benzathine Penicillin Among People Diagnosed With Late Latent and Unknown Duration Syphilis, Maricopa County, Arizona
Authors: Mangone Elizabeth , Bell Jonathan , Khurana Renuka , Taylor Melanie M.
Published: January 2023

Background

Syphilis is a public health concern as cases are rising each year. If untreated, syphilis is associated with significant morbidity and risk of vertical transmission during pregnancy. For people with late latent and unknown duration stages, 3 injections of benzathine penicillin G (BPG) at 1-week intervals are recommended. Our study quantified treatment for people diagnosed with late latent and unknown duration syphilis in Maricopa County, Arizona with a secondary analysis of pregnant women to assess completion of 3 injections of BPG in multiple time intervals.

Methods

Maricopa County syphilis case data were extracted from the state-run database (PRISM). Records were reviewed for people with late latent and unknown duration syphilis during January 1, 2016, to December 31, 2021. Treatment types and time intervals between treatments were analyzed.

Results

Of a total of 14,924 people with syphilis reported in Maricopa County, 5372 (36.0%) were staged as late latent or unknown duration syphilis. Completion of 3 BPG injections in the time frame of 7 to 9 days was 42.9% (n = 2302). Completion among pregnant women (n = 406) with 3 injections was 68.7% (n = 279).

Conclusions

The completion rate of 3 BPG injections for people with late latent or unknown duration syphilis is low. An unmet need exists to identify barriers to treatment including access to BPG and public health follow-up after the first injection. Prioritized effort is needed to identify and classify patients as having earlier stages of syphilis that require only 1 BPG injection.
Silver In Situ Hybridization for the Rapid Assessment of MDM2 Amplification in Soft Tissue and Bone Tumors. Validation Based on an Audit of 192 Consecutive Cases Evaluated by Silver In Situ Hybridization and Fluorescence In Situ Hybridization
Authors: Farshid Gelareh , Otto Sophia , Collis Maria , Napper Setha , Nicola Mario
Published: January 2023

The discovery of almost invariable mouse double minute 2 (MDM2) amplification among atypical lipomatous tumors (ALT)/well-differentiated liposarcoma and dedifferentiated liposarcoma is incorporated into the contemporary diagnostic workup of fatty lesions. MDM2 amplifications are also found frequently in intimal sarcomas and in low-grade osteogenic sarcoma. At present, fluorescence in situ hybridization (FISH) is the reference test for MDM2 assessment. We are interested in evaluating silver in situ hybridization (SISH) for this purpose. Between October 2016 and May 2020, in 192 consecutive cases requiring MDM2 FISH, SISH was also performed concurrently, including 77 (40.1%) core biopsies and 115 (58.9%) surgical specimens. The mean patient age was 61.0 years. SISH results were available overnight or within 48 hours if repeat testing was required. FISH results were available within 2 to 5 weeks. The cost of SISH was one third of FISH. FISH demonstrated MDM2 amplification in 44 cases (23.6%), was negative in 144 cases (74.4%) and nondiagnostic in 4 decalcified cases (2.0%). SISH showed MDM2 amplification in 33 cases (17.2%), no amplification in 119 cases (62.0%), and indeterminate results because of poor signal in 40 (20.8%) cases. All 33 (100%) SISH-amplified tumors and 113 of 119 (95.0%) nonamplified results were confirmed by FISH. There were no clear differences in the performance of SISH on NCB versus surgical specimens. The overall performance indices of SISH are sensitivity 75%, specificity 78.5%, positive predictive value 100%, and negative predictive value 95.8%. FISH is not required when SISH is clearly amplified. This is clinically useful and improves efficiency. Nonamplified SISH results provide early indications of the likely FISH findings, but there is a 4.2% chance of FISH being positive. At present, the main drawback of SISH is the high rate of nondiagnostic tests. Optimization of SISH signal detection to reduce the proportion of indeterminate results is our current focus.
Impact of cross-ancestry genetic architecture on GWAS in admixed populations
Authors: Mester Rachel , Hou Kangcheng , Ding Yi , Meeks Gillian , Burch Kathryn S. , Bhattacharya Arjun , Henn Brenna M. , Pasaniuc Bogdan
Published: January 2023

Genome-wide association studies (GWAS) have identified thousands of variants for disease risk. These studies have predominantly been conducted in individuals of European ancestries, which raises questions about their transferability to individuals of other ancestries. Of particular interest are admixed populations, usually defined as populations with recent ancestry from two or more continental sources. Admixed genomes contain segments of distinct ancestries that vary in composition across individuals in the population, allowing for the same allele to induce risk for disease on different ancestral backgrounds. This mosaicism raises unique challenges for GWAS in admixed populations, such as the need to correctly adjust for population stratification to balance type I error with statistical power. In this work we quantify the impact of differences in estimated allelic effect sizes for risk variants between ancestry backgrounds on association statistics. Specifically, while the possibility of estimated allelic effect-size heterogeneity by ancestry (HetLanc) can be modeled when performing GWAS in admixed populations, the extent of HetLanc needed to overcome the penalty from an additional degree of freedom in the association statistic has not been thoroughly quantified. Using extensive simulations of admixed genotypes and phenotypes we find that modeling HetLanc in its absence reduces statistical power by up to 72%. This finding is especially pronounced in the presence of allele frequency differentiation. We replicate simulation results using 4,327 African-European admixed genomes from the UK Biobank for 12 traits to find that for most significant SNPs HetLanc is not large enough for GWAS to benefit from modeling heterogeneity.
Using Micro-Cognition Biomarkers of Neurosystem Dysfunction to Define ADHD Subtypes: A Scalable Digital Path to Diagnosis Based on Brain Function
Authors: Wexler Bruce E. , Kish Ryan
Published: January 2023

Background

Diagnostic categories in psychiatry are based on symptoms and include individuals with different underlying pathology. This within-diagnosis heterogeneity confounds new treatment development and treatment selection for individual patients. A research priority is to discover biomarkers that define groups of patients with similar neuropathology. Digital neurocognitive therapy (DNT) and assessment can provide micro-cognition biomarkers of unprecedented precision. The brain is hierarchically organized from single cells to neurosystems that integrate action of millions of neurons across the brain necessary for cognition and emotion. Micro-cognition biomarkers identify dysfunction at the level of neurosystems that produce clinical illness. We used micro-cognition biomarkers to identify subgroups of children diagnosed with ADHD but with different neuropathology.

Methods

K-means clustering was applied to 69 children 6-9 years old with ADHD using performance variables from a Go/NoGo test and the results analyzed against 58 typically developing (TD) children. Neurosystem dysfunction in each group was further characterized by micro-cognition biomarkers extracted from thousands of responses by each child during DNT.

Findings

Four highly reproducible clusters were identified that differed on emblematic features of ADHD. Cluster 4 showed two core ADHD features, poor response inhibition and inconsistent attention. Cluster 3 showed only poor response inhibition and the other two showed neither. Cluster 2 showed faster and more consistent responses, higher detection of simple targets and better working memory than TD children but showed the most marked performance decrements when required to track multiple targets or ignore distractors. Cluster 1 showed much greater ability recognizing members of abstract categories rather than natural categories that children learn through physical interaction with the environment while Cluster 4 was the opposite.

Interpretation

DNT provides data-rich fine-grained, low-cost, noninvasive, and scalable micro-cognition biomarkers that characterize subgroups of patients with the same symptom-based psychiatric diagnosis but differing neuropathology.
High-sensitive detection and quantitation of thyroid-stimulating hormone (TSH) from capillary/fingerstick and venepuncture whole-blood using fluorescence-based rapid lateral flow Immunoassay (LFIA)
Authors: Shurbaji Samar , Al Tamimi Faleh , Al Ghwairi Mahmoud M. , El Chaar Dayana , Younes Salma , Majdalawieh Amin F. , Pintus GianFranco , Dweik Nader , Nasrallah Gheyath K.
Published: January 2023

Background

In the last decade, point of care testing (POCT) such as lateral flow immunoassays (LFIA) were developed for rapid TSH measurement. Most of these TSH-LFIAs are designed for qualitative measurements (i.e., if TSH values >5, or >15 IU/L) and as screening tests for primary hypothyroidism in children and adults. Serum or plasma, but not venepuncture whole-blood, or fingerstick/capillary, are usually used for accurate quantitation of TSH. Studies on performance evaluation of TSH-LFIAs POCT using venepuncture or fingerstick whole-blood are limited.

Aim

We aim to evaluate the performance of a new fluorescence-based LFIA and its Finecare™ fluorescent reader for quantitative measurement of TSH from a fingerstick, venepuncture whole-blood, and serum.

Methods

102 fingerstick, venepuncture whole-blood, and serum samples (with normal and abnormal TSH values) were analyzed by Finecare™ Rapid Quantitative LFIA test and Roche CobasPro-c503 as a reference test.

Results

Using serum, when compared to CobasPro-c503 reference method, Finecare™ showed high sensitivity (90.5%) and specificity (96.3%) for diagnosis of thyroid abnormalities (<0.35 or > 4.5 mIU/L). The actual test values (mIU/L) of Finecare™ showed excellent agreement (Cohen’s Kappa=0.85) and strong correlation (r=0.93, p<0.0001) with CobasPro-c503. Using venepuncture whole-blood samples, Finecare™ showed similar results to serum with high sensitivity (95.2%), specificity (97.5%), excellent agreement (Cohen’s Kappa=0.91), and very strong correlation (r=0.95, p<0.0001) with CobasPro-c503. These results suggest that Finecare™ can be used for quantitative measurement of TSH using serum or venepuncture whole-blood. These key performance indicators were slightly decreased when fingerstick whole-blood samples were used: Sensitivity (85.7%), specificity (90.0%), good agreement (Cohen’s Kappa=0.7) and very strong correlation (r=0.9, p<0.0001) with CobasPro-c503.

Conclusion

Our results indicate that the Finecare™ is appropriate for TSH screening and quantitative measurement of TSH using serum samples and fingersticks, particularly in none or small laboratory settings.

Highlights

Finecare presented high sensitivity & specificity for diagnosing thyroid diseases

Strong correlations were observed between Finecare and the reference method

Sample types (serum, venepuncture, fingerstick) do not affect TSH Finecare results

Fingerstick/capillary sample is appropriate for TSH quantitation by Finecare
Delirium in a Young Predominantly Hispanic Population with COVID-19
Authors: Talkington Kelsey C. , Alvarado Luis A. , Castaneda Christopher A. , Tonarelli Silvina B.
Published: January 2023

Purpose

To study a primarily Hispanic population of adults younger than 65 to determine if COVID-19 patients with a concurrent delirium diagnosis had worse clinical outcomes in terms of hospital stay, ventilation and mortality, than those without a delirium diagnosis.

Methods

After approval by the appropriate Institutional Review Board, a retrospective cohort study was performed looking at demographics, vital statistics, and clinical outcomes of patients aged 18-65 admitted to a hospital in the United States – Mexico border region with COVID-19 between March 1 and June 30, 2020. Data were analyzed using Fisher’s exact test, or an unpairedt-test where appropriate, and a univariate analysis was performed to establish relative risk. Confidence intervals were set at 95% andpvalues ≤0.05 were considered significant.

Results

133 patients with confirmed COVID-19 diagnoses (58% men, 92% Hispanic) were included. Mean age was 50.5 with a standard deviation of 11.7 years (range 20-65 years). The prevalence of delirium was 6%. Fifty percent of delirium patients died during hospitalization compared to 15% of patients without delirium. Patients with delirium were found to spend more days hospitalized, in the intensive care unit, and intubated than their counterparts without delirium. Delirium was associated with increased risk of being placed on mechanical ventilation (RR 3.91, 95% CI 1.46—10.41,pvalue 0.006).

Conclusions

Delirium was associated with worse COVID-19 outcomes independent of age. COVID-19 patients need to be actively assessed for signs of delirium and appropriate precautionary measures should be implemented. Proper documentation of delirium is key to continue learning about the incidence of delirium in COVID-19 patients.
In-silicoAnalysis of SARS-Cov2 Spike Proteins of Different Field Variants
Authors: Haseeb Muhammad , Amir Afreenish , Ikram Aamer
Published: January 2023

Background

Coronaviruses belong to the group of RNA family of viruses which trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world, and the situation in the world is getting worse with the emergence of novel variants. Our study aims to explore the genome of SARS-,CoV2 followed byin silicoanalysis of its proteins.

Methods

Different nucleotide and protein variants of SARS-Cov2 were retrieved from NCBI. Contigs & consensus sequences were developed to identify variations in these variants by using SnapGene. Data of variants that significantly differ from each other was run through Predict Protein software to understand changes produced in protein structure The SOPMA web server was used to predict the secondary structure of proteins. Tertiary structure details of selected proteins were analyzed using the online web server SWISS-MODEL.

Findings

Sequencing results shows numerous single nucleotide polymorphisms in surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein. While envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes have no or few SNPs. Contigs were mto identifyn of variations in Alpha & Delta Variant of SARs-CoV-2 with reference strain (Wuhan). The secondary structures of SARs-CoV-2 proteins were predicted by using sopma software & were further compared with reference strain of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plot. By Swiss-model, a comparison of the tertiary structure model of SARS-COV-2 spike protein of Alpha & Delta Variant was made with reference strain (Wuhan). Alpha & Delta Variant of SARs-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with reference strain & 3D structure mapping of spike glycoprotein and mutations in amino acid were seen.

Conclusion

The surprising increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employedin silicocomputational tools to analyze SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in functional, immunological, physicochemical, & structural variations in SARS-CoV-2 isolates. However real impact of these SNPs can only be determined further by experiments. Our results can aidin vivoandin vitroexperiments in the future.
Personalized Inhaled Bacteriophage Therapy Decreases Multidrug-ResistantPseudomonas aeruginosa
Authors: Chan BK , Stanley GL , Kortright KE , Modak M , Ott IM , Sun Y , Würstle S , Grun C , Kazmierczak B , Rajagopalan G , Harris Z , Britto CJ , Stewart J , Talwalkar JS , Appell C , Chaudary N , Jagpal SK , Jain R , Kanu A , Quon BS , Reynolds JM , Mai QA , Shabanova V , Turner PE , Koff JL
Published: January 2023

Bacteriophage therapy, which uses lytic viruses as antimicrobials, has received renewed interest to address the emerging antimicrobial resistance (AMR) crisis. Cystic fibrosis (CF), a disease complicated by recurrentP. aeruginosapulmonary infections that cause lung function decline, is an example where AMR is already a clinical problem. While bacteria evolve bacteriophage resistance, we developed a strategy to select bacteriophages that target bacterial cell surface receptors that contribute to antibiotic resistance or virulence. Thus, in addition to killing bacteria, these phages steer surviving, evolved bacteria to antibiotic re-sensitivity or attenuated virulence. Here, we present outcomes from nine CF adults treated with nebulized bacteriophage therapy for AMRP. aeruginosausing this personalized approach. Results showed that phage therapy: 1) reduced sputumP. aeruginosa, 2) showed evidence for predicted trade-offs in most subjects, and 3) improved lung function, which may reflect the combined effects of decreased bacterial sputum density and phage-driven evolved trade-offs.
Short-term CaMKII inhibition with tatCN19o does not erase pre-formed memory and is neuroprotective in non-rodents
Authors: Rumian Nicole L. , Brown Carolyn Nicole , Hendry-Hofer Tara B. , Rossetti Thomas , Orfila James E. , Tullis Jonathan E. , Dwoskin Linda P. , Buonarati Olivia R. , Lisman John E. , Quillinan Nidia , Herson Paco S. , Bebarta Vikhyat S. , Bayer K. Ulrich
Published: January 2023

The Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a central regulator of learning and memory, which poses a problem for targeting it therapeutically. Indeed, our study supports prior conclusions that long-term interference with CaMKII signaling can erase pre-formed memories. By contrast, short-term pharmacological CaMKII inhibition with tatCN19o interfered with learning in mice only mildly and transiently (for less than 1 h) and did not at all reverse pre-formed memories. This was at ≥500fold of the dose that protected hippocampal neurons from cell death after a highly clinically relevant pig model of transient global cerebral ischemia: ventricular fibrillation followed by advanced life support and electrical defibrillation to induce return of spontaneous circulation. Of additional importance for therapeutic development, cardiovascular safety studies in mice and pig did not indicate any concerns with acute tatCN19o injection. Taken together, even though prolonged interference with CaMKII signaling can erase memory, acute short-term CaMKII inhibition with tatCN19o did not cause such retrograde amnesia that would pose a contraindication for therapy.
Notch1 cortical signaling regulates epithelial architecture and cell-cell adhesion
Authors: White Matthew J. , Jacobs Kyle A. , Singh Tania , Kutys Matthew L.
Published: January 2023

Notch receptors control tissue morphogenic processes that involve coordinated changes in cell architecture and gene expression, but how a single receptor can produce these diverse biological outputs is unclear. Here we employ a 3D organotypic model of a ductal epithelium to reveal tissue morphogenic defects result from loss of Notch1, but not Notch1 transcriptional signaling. Instead, defects in duct morphogenesis are driven by dysregulated epithelial cell architecture and mitogenic signaling which result from loss of a transcription-independent Notch1 cortical signaling mechanism that ultimately functions to stabilize adherens junctions and cortical actin. We identify that Notch1 localization and cortical signaling are tied to apical-basal cell restructuring and discover a Notch1-FAM83H interaction underlies stabilization of adherens junctions and cortical actin. Together, these results offer new insights into Notch1 signaling and regulation, and advance a paradigm in which transcriptional and cell adhesive programs might be coordinated by a single receptor.
Foraging on host synthesized metabolites enables the bacterial symbiontSnodgrassella alvito colonize the honey bee gut
Authors: Quinn Andrew , El Chazli Yassine , Escrig Stéphane , Daraspe Jean , Neuschwander Nicolas , McNally Aoife , Genoud Christel , Meibom Anders , Engel Philipp
Published: January 2023

Dietary nutrients and microbial cross-feeding allow diverse bacteria to colonize the animal gut. Less is known about the role of host-derived nutrients in enabling gut bacterial colonization. We examined metabolic interactions within the evolutionary ancient symbiosis between the honey bee (Apis mellifera) and the core gut microbiota memberSnodgrassella alvi. This Betaproteobacteria is incapable of metabolizing saccharides, yet colonizes the honey bee gut in the presence of only a sugar diet. Using comparative metabolomics,13C tracers, and Nanoscale secondary ion mass spectrometry (NanoSIMS), we showin vivothatS. alvigrows on host-derived organic acids, including citrate, glycerate and 3-hydroxy-3-methylglutarate which are actively secreted by the host into the gut lumen.S. alviadditionally modulates tryptophan metabolism in the gut by converting kynurenine to anthranilate. These results suggest thatS. alviis adapted to a specific metabolic niche in the gut that depends on host-derived nutritional resources.
Effects of structural complexity and water depth on the juvenile blue crabCallinectes Sapidusin a simulated salt marsh mesocosm
Authors: Hyman A. Challen , Miller Cole R. , Shi Daniel , Lipcius Romuald N.
Published: January 2023

The blue crab (Callinectes sapidus) is ecologically and economically important in Chesapeake Bay. Nursery habitats, which disproportionately contribute individuals to the adult segment of populations, are essential to blue crab population dynamics.Spartina alterniflorasalt marshes are productive but fragmented intertidal nursery habitats which may serve as a refuge from predation for juvenile blue crabs. However, the effects of various characteristics of salt marshes on nursery metrics, such as survival, have not been quantified. Using mesocosm experiments, we examined the effects of shoot density and water depth on juvenile blue crab survival using adult blue crabs as predators. Survival increased significantly with shoot density, whereas water depth did not affect survival. Thus, in contrast to several previous studies, water depth did not influence survival of juvenile blue crabs, possibly due to different environmental conditions from prior studies. These findings indicate that salt marsh structural complexity enhances juvenile survival, and that the beneficial effect of shallow water on juvenile survival differs by environmental conditions.
Stretchable, nano-crumpled MXene multilayers impart long-term antibacterial surface properties
Authors: Nagpal Neha , Tokmedash Mohammad Asadi , Chen Po-Yen , VanEpps J. Scott , Min Jouha
Published: January 2023

Infections are a significant risk to patients who receive medical implants, and can often lead to implant failure, tissue necrosis, and even amputation. So far, although various surface modification approaches have been proposed for prevention and treatment of microbial biofilms on indwelling medical devices, most are too expensive/complicated to fabricate, unscalable, or limited in durability for clinical use. Here we present a new bottom-up design for fabricating scalable and durable nano-pattered coatings with dynamic topography for long-term antibacterial effects. We show that MXene layer-by-layer (LbL) self-assembled coatings -- with finely tunable crumple structures with nanometer resolution and excellent mechanical durability -- can be successfully fabricated on stretchable poly(dimethylsiloxane) (PDMS). The crumpled MXene coating with sharp-edged peaks shows potent antibacterial effects againstStaphylococcus aureusandEscherichia coli. In addition, we find that on-demand dynamic deformation of the crumpled coating can remove ≥99% of adhered bacterial cells for both species, resulting in a clean surface with restored functionality. This approach offers improved practicality, scalability, and antibacterial durability over previous methods, and its flexibility may lend itself to many types of biomaterials and implantable devices.
A reliable and efficient adaptive Bayesian method to assess static lower limb position sense
Authors: Wood Jonathan M , Morton Susanne M , Kim Hyosub E
Published: January 2023

Background

Lower limb proprioception is critical for maintaining stability during gait and may impact how individuals modify their movements in response to changes in the environment and body state, a process termed “sensorimotor adaptation”. However, the connection between lower limb proprioception and sensorimotor adaptation during human gait has not been established. We suspect this gap is due in part to the lack of reliable, efficient methods to assess global lower limb proprioception in an ecologically valid context.

New Method

We assessed static lower limb proprioception using an alternative forced choice task, administered twice to determine test-retest reliability. Participants stood on a dual-belt treadmill which passively moved one limb to stimulus locations selected by a Bayesian adaptive algorithm. At the stimulus locations, participants judged relative foot positions and the algorithm estimated the point of subjective equality (PSE) and the uncertainty of lower limb proprioception.

Results

Using the Bland-Altman method, combined with Bayesian statistics, we found that both the PSE and uncertainty estimates had good reliability.

Comparison with Existing Method(s)

Current methods assessing static lower limb proprioception do so within a single joint, in non-weight bearing positions, and rely heavily on memory. One exception assessed static lower limb proprioception in standing but did not measure reliability and contained confounds impacting participants’ judgments, which we experimentally controlled here.

Conclusions

This efficient and reliable method assessing lower limb proprioception will aid future mechanistic understanding of locomotor adaptation and serve as a useful tool for basic and clinical researchers studying balance and falls.
Prediction of SARS-CoV-2 spike protein mutations using Sequence-to-Sequence and Transformer models
Authors: Ahmadi Hamed , Nikoofard Vahid , Nikoofard Hossein , Abdolvahab Rouhollah , Nikoofard Narges , Esmaeilzadeh Mahdi
Published: January 2023

In the study of viral epidemics, having information about the structural evolution of the virus can be very helpful in controlling the disease and making vaccines. Various deep learning and natural language processing techniques (NLP) can be used to analyze genetic structure of viruses, namely to predict their mutations. In this paper, by using Sequence-to-Sequence (Seq2Seq) model with Long Short-Term Memory (LSTM) cell and Transformer model with the attention mechanism, we investigate the spike protein mutations of SARS-CoV-2 virus. We make time-series datasets of the spike protein sequences of this virus and generate upcoming spike protein sequences. We also determine the mutations of the generated spike protein sequences, by comparing these sequences with the Wuhan spike protein sequence. We train the models to make predictions in December 2021, February 2022, and October 2022. Furthermore, we find that some of our generated spike protein sequences have been reported in December 2021 and February 2022, which belong to Delta and Omicron variants. The results obtained in the present study could be useful for prediction of future mutations of SARS-CoV-2 and other viruses.
Distant sequence regions of JBP1 contribute to J-DNA binding
Authors: de Vries Ida , Ammerlaan Danique , Heidebrecht Tatjana , Celie Patrick H. N. , Geerke Daan P. , Joosten Robbie P. , Perrakis Anastassis
Published: January 2023

Base-J (β-D-Glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J Binding Protein 1 (JBP1), that has a thymidine hydroxylase domain (THD) and a J-DNA binding domain (JDBD). How the THD synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for Molecular Dynamics (MD) simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.
PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion
Authors: Williams Natecia L. , Hong Lauren , Jaffe Maya , Shields Cara E. , Haynes Karmella A.
Published: January 2023

Scientists have used small molecule inhibitors and genetic knockdown of gene-silencing polycomb repressive complexes (PRC1/2) to determine if restoring the expression of tumor suppressor genes can block proliferation and invasion of cancer cells. A major limitation of this approach is that inhibitors can not restore key transcriptional activators that are mutated in many cancers, such as p53 and members of the BRAF SWI/SNF complex. Furthermore, small molecule inhibitors can alter the activity of, rather than inhibit, the polycomb enzyme EZH2. While chromatin has been shown to play a major role in gene regulation in cancer, poor clinical results for polycomb chromatin-targeting therapies for diseases like triple-negative breast cancer (TNBC) could discourage further development of this emerging avenue for treatment. To overcome the limitations of inhibiting polycomb to study epigenetic regulation, we developed an engineered chromatin protein to manipulate transcription. The synthetic reader-actuator (SRA) is a fusion protein that directly binds a target chromatin modification and regulates gene expression. Here, we report the activity of an SRA built from polycomb chromodomain and VP64 modules that bind H3K27me3 and subunits of the Mediator complex, respectively. In SRA-expressing BT-549 cells, we identified 122 upregulated differentially expressed genes (UpDEGs, ≥ 2-fold activation, adjustedp< 0.05). On-target epigenetic regulation was determined by identifying UpDEGs at H3K27me3-enriched, closed chromatin. SRA activity induced activation of genes involved in cell death, cell cycle arrest, and the inhibition of migration and invasion. SRA-expressing BT-549 cells showed reduced spheroid size in Matrigel over time, loss of invasion, and activation of apoptosis. These results show that Mediator-recruiting regulators broadly targeted to silenced chromatin activate silenced tumor suppressor genes and stimulate anti-cancer phenotypes. Therefore further development of gene-activating epigenetic therapies might benefit TNBC patients.
Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq
Authors: Geiger-Schuller Kathryn , Eraslan Basak , Kuksenko Olena , Dey Kushal K. , Jagadeesh Karthik A. , Thakore Pratiksha I. , Karayel Ozge , Yung Andrea R. , Rajagopalan Anugraha , Meireles Ana M , Yang Karren Dai , Amir-Zilberstein Liat , Delorey Toni , Phillips Devan , Raychowdhury Raktima , Moussion Christine , Price Alkes L. , Hacohen Nir , Doench John G. , Uhler Caroline , Rozenblatt-Rosen Orit , Regev Aviv
Published: January 2023

E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comβVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.
A fluid biomarker reveals loss of TDP-43 splicing repression in pre-symptomatic ALS
Authors: Irwin Katherine E. , Jasin Pei , Braunstein Kerstin E. , Sinha Irika , Bowden Kyra D. , Moghekar Abhay , Oh Esther S. , Raitcheva Denitza , Bartlett Dan , Berry James D. , Traynor Bryan , Ling Jonathan P. , Wong Philip C.
Published: January 2023

Loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well-documented in postmortem tissues of amyotrophic lateral sclerosis (ALS), yet whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects functional loss of TDP-43, and thus detection of cryptic exon-encoded peptides in cerebrospinal fluid (CSF) could reveal the earliest stages of TDP-43 dysregulation in patients. Here, we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found inHDGFL2) to show that loss of TDP-43 splicing repression occurs inC9ORF72-associated ALS, including pre-symptomatic mutation carriers. In contrast to neurofilament light and heavy chain proteins, cryptic HDGFL2 accumulates in CSF at higher levels during early stages of disease. Our findings indicate that loss of TDP-43 splicing repression occurs early in disease progression, even pre-symptomatically, and that detection of HDGFL2’s cryptic neoepitope may serve as a prognostic test for ALS which should facilitate patient recruitment and measurement of target engagement in clinical trials.
Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase
Authors: Tota Ember M. , Devaraj Neal K.
Published: January 2023

Bacterial tRNA guanine transglycosylases (TGTs) catalyze the exchange of guanine for the 7-deazaguanine queuine precursor, prequeuosine1 (preQ1). While the native nucleic acid substrate for bacterial TGTs is the anticodon loop of queuine-cognate tRNAs, the minimum recognition sequence for the enzyme is a structured hairpin containing the target G nucleobase in a “UGU” loop motif. Previous work has established an RNA modification system, RNA-TAG, in which E. coli TGT exchanges the target G on an RNA of interest for chemically modified preQ1 substrates linked to a small molecule reporter such as biotin or a fluorophore. While extending the substrate scope of RNA transglycosylases to include DNA would enable numerous applications, it has been previously reported that TGT is incapable of modifying native DNA. Here we demonstrate that TGT can in fact recognize and label specific DNA substrates. Through iterative testing of rationally mutated DNA hairpin sequences, we determined the minimal sequence requirements for transglycosylation of unmodified DNA by E. coli TGT. Controlling steric constraint in the DNA hairpin dramatically affects labeling efficiency, and, when optimized, can lead to near quantitative site-specific modification. We demonstrate the utility of our newly developed DNA-TAG system by rapidly synthesizing probes for fluorescent Northern blotting of spliceosomal U6 RNA and RNA FISH visualization of the long noncoding RNA, MALAT1. The ease and convenience of the DNA-TAG system will provide researchers with a tool for accessing a wide variety of affordable modified DNA substrates.
“Development and Implementation of Novel Chatbot-based Genomic Research Consent”
Authors: Smith Erica D. , Savage Sarah K. , Andrew E. Hallie , Martin Gloria Mas , Kahn-Kirby Amanda H. , LoTempio Jonathan , Délot Emmanuèle , Cohen Andrea J. , Pitsava Georgia , Berger Seth , Fusaro Vincent A. , Vilain Eric
Published: January 2023

Objective

To conduct a retrospective analysis comparing traditional human-based consenting to an automated chat-based consenting process.

Materials and Methods

We developed a new chat-based consent using our IRB-approved consent forms. We leveraged a previously developed platform (Gia®, or “Genetic Information Assistant”) to deliver the chat content to candidate participants. The content included information about the study, educational information, and a quiz to assess understanding. We analyzed 144 families referred to our study during a 6-month time period. A total of 37 families completed consent using the traditional process, while 35 families completed consent using Gia.

Results

Engagement rates were similar between both consenting methods. The median length of the consent conversation was shorter for Gia users compared to traditional (44 vs. 76 minutes). Additionally, the total time from referral to consent completion was faster with Gia (5 vs. 16 days). Within Gia, understanding was assessed with a 10-question quiz that most participants (96%) passed. Feedback about the chat consent indicated that 86% of participants had a positive experience.

Discussion

Using Gia resulted in time savings for both the participant and study staff. The chatbot enables studies to reach more potential candidates. We identified five key features related to human-centered design for developing a consent chat.

Conclusion

This analysis suggests that it is feasible to use an automated chatbot to scale obtaining informed consent for a genomics research study. We further identify a number of advantages when using a chatbot.