bluuebunny/crossref_metadata_2025 huggingface dataset:
PNPLA3 risk allele is associated with risk of hepatocellular carcinoma but not decompensation in compensated cirrhosis
Authors: Urias Esteban , Tedesco Nicholas R. , Burkholder Daniel A. , Moran Isabel J. , Miller Matthew J. , Jasty Venkata Sai J. , Patil Snehal , Zoellner Sebastian , Wijarnpreecha Karn , Chen Vincent L.
Published: May 2024

Background:

The PNPLA3-rs738409-G, TM6SF2-rs58542926-T, and HSD17B13-rs6834314-A polymorphisms have been associated with cirrhosis, hepatic decompensation, and HCC. However, whether they remain associated with HCC and decompensation in people who already have cirrhosis remains unclear, which limits the clinical utility of genetics in risk stratification as HCC is uncommon in the absence of cirrhosis. We aimed to characterize the effects of PNPLA3, TM6SF2, and HSD17B13 genotype on hepatic decompensation, HCC, and liver-related mortality or liver transplant in patients with baseline compensated cirrhosis.

Methods:

We conducted a single-center retrospective study of patients in the Michigan Genomics Initiative who underwent genotyping. The primary predictors were PNPLA3, TM6SF2, and HSD17B13 genotypes. Primary outcomes were either hepatic decompensation, HCC, or liver-related mortality/transplant. We conducted competing risk Fine-Gray analyses on our cohort.

Results:

We identified 732 patients with baseline compensated cirrhosis. During follow-up, 50% of patients developed decompensation, 13% developed HCC, 24% underwent liver transplant, and 27% died. PNPLA3-rs738409-G genotype was associated with risk of incident HCC: adjusted subhazard hazard ratio 2.42 (1.40–4.17), p=0.0015 for PNPLA3-rs738409-GG vs. PNPLA3-rs738409-CC genotype. The 5-year cumulative incidence of HCC was higher in PNPLA3-rs738409-GG carriers than PNPLA3-rs738409-CC/-CG carriers: 15.6% (9.0%–24.0%) vs. 7.4% (5.2%–10.0%), p<0.001. PNPLA3 genotype was not associated with decompensation or the combined outcome of liver-related mortality or liver transplant. TM6SF2 and HSD17B13 genotypes were not associated with decompensation or HCC.

Conclusions:

The PNPLA3-rs738409-G allele is associated with an increased risk of HCC among patients with baseline compensated cirrhosis. People with cirrhosis and PNPLA3-rs738409-GG genotype may warrant more intensive HCC surveillance.
Quality-of-life and beliefs about medication in relation to a therapy adherence intervention in resistant hypertension: the Resistant HYpertension: MEasure to ReaCh Targets trial
Authors: Zeijen Victor J.M. , Peeters Laura E.J. , Asman Azra , Boersma Eric , Massey Emma K. , van Dijk Liset , Daemen Joost , Versmissen Jorie
Published: May 2024

Objective:

To assess the impact of personalized feedback on therapy adherence testing results on quality of life and beliefs about medication in patients with resistant hypertension, as well as to identify patient-oriented predictors of therapy adherence.

Methods:

This study was a prespecified post hoc analysis of the multicenter randomized controlled trial Resistant HYpertension: MEasure to ReaCh Targets (RHYME-RCT). Patients were randomized to a personalized feedback conversation on measured antihypertensive drug levels additional to standard-of-care, or standard-of-care only. The primary outcomes consisted of EuroQol EQ-5D-5L and Beliefs about Medicine Questionnaire (BMQ) scores at 12 months.

Results:

A total of 56 patients with median age 61.5 [25th–75th percentile: 55.8–69.3] years (21.4% women) were included. Mean blood pressure ±SD was 149.8/84.1 ± 14.9/13.8 mmHg while being on a median of 5.6 [4.8–7.3] defined daily dosages (DDD) of antihypertensive drugs. At 12 months, no differences were observed in EQ-5D-5L index (0.81 [0.69–0.89] vs. 0.89 [0.73–1.00]; P = 0.18) and visual analogue scale score on general patient-perceived health (70 [60–80] vs. 70 [60–82]; P = 0.53) between the intervention-arm and the standard-of-care only-arm. Likewise, individual EQ-5D-5L domain scores and BMQ scores did not differ between both arms. Irrespective of the intervention, independent positive predictors of the percentage adherence were patient age, EQ-5D-5L index score, BMQ-specific necessity score and concern score, whereas the total number of drugs prescribed was a negative predictor.

Conclusion:

Within this prespecified subanalysis of the randomized RHYME-RCT trial, implementation of a personalized feedback conversation targeting therapy adherence did not improve health-related quality-of-life and beliefs about medication in patients with resistant hypertension.
Laser of the Haptic-Optic Junction to Fix a Tilted Yamane Intrascleral-Fixated Lens
Authors: Piccini Angelica , Meshkin Ryan S. , Hoyek Sandra , Doobin David J , Chaaya Celine , Patel Nimesh A.
Published: May 2024

Purpose:

To report a case of tilted sutureless intrascleral fixated IOL, emphasizing its management with 23-gauge laser to strengthen the haptic-optic junction.

Methods:

Case report.

Results:

A 27-year-old man was referred for treatment of traumatic cataracts in his left eye. He underwent pars plana vitrectomy, lensectomy, membrane peel, and capsulectomy without complications. Five days after the surgery, he developed ocular hypertension that ultimately required insertion of an Ahmed glaucoma valve in the left eye. 16 months after the initial procedure, the patient underwent secondary lens implantation with a CT Lucia 602 IOL in the left eye using the Yamane technique. The day following surgery, the patient presented with a significantly tilted lens. Three weeks later, the patient underwent surgery for IOL repositioning. The manipulation of the haptics was ineffective in repositioning the IOL. The temporal sclerotomy was removed and a 23-gauge probe was used to laser both optic-haptic junctions while a light pipe held the lens in place. The tilt was corrected, and visual acuity improved to 20/40 at one year follow-up.

Conclusions:

Successful repositioning of tilted sutureless intrascleral fixated IOLs can be achieved using 23-gauge laser reinforcement at the haptic-optic junction. Consideration could be made to perform this laser at the time of implantation as a prophylactic approach to mitigate tilt and reduce the risk of reoperation.
Prospective Assessment of Adjuvant Netarsudil Use in Patients Undergoing Descemet Stripping Only
Authors: Bal Sila , Pineda Roberto , Davies Emma
Published: May 2024

Purpose:

We sought to determine whether adjuvant use of netarsudil improves corneal clearance rate and regeneration of corneal endothelial cells in patients undergoing Descemet stripping only (DSO).

Methods:

We conducted a prospective assessment on the use of adjuvant netarsudil in 50 eyes from 25 patients undergoing DSO at Massachusetts Eye and Ear between May 2021 and May 2023. Our comparison group was a retrospective cohort of patients (23 eyes from 15 patients) who previously underwent DSO without the use of a postoperative rho-kinase inhibitor between September 2014 and March 2020.

Results:

Use of netarsudil after DSO statistically significantly reduced time to corneal clearance, improved best corrected visual acuity, reduced pachymetric thickness, and increased central endothelial cell count (ECC) at 6 months postoperatively. Importantly, central ECC continued to increase beyond 12 months after DSO with central ECC still statistically significantly greater in eyes that received netarsudil than in eyes that received no netarsudil.

Conclusions:

A rho-kinase inhibitor, such as netarsudil, after DSO should be used if available to achieve the best corneal clearance, best corrected visual acuity, and ECC after surgery.
Efficacy and Safety of Surgical Peripheral Iridectomy, Goniosynechialysis, and Goniotomy for Advanced Primary Angle Closure Glaucoma Without Cataract: 1-Year Results of a Multicenter Study
Authors: Gao Xinbo , Lin Fengbin , Lu Ping , Xie Lin , Tang Li , Zhu Xiaomin , Zhang Yao , Lv Aiguo , Tang Guangxian , Zhang Hengli , Yan Xiaowei , Song Yunhe , Xu Jiangang , Huang Jingjing , Zhang Yingzhe , Hu Kun , Peng Yuying , Wang Zhenyu , Li Xiaoyan , Chen Weirong , Wang Ningli , Barton Keith , Park Ki Ho , Aung Tin , Weinreb Robert N. , Lam Dennis S.C. , Fan Sujie , Tham Clement C. , Zhang Xiulan ,   for the TVG study group
Published: May 2024

Précis:

The combination of surgical peripheral iridectomy, goniosynechialysis, and goniotomy is a safe and effective surgical approach for advanced primary angle closure glaucoma without cataract.

Purpose:

To evaluate the efficacy and safety of surgical peripheral iridectomy (SPI), goniosynechialysis (GSL), and goniotomy (GT) in advanced primary angle closure glaucoma (PACG) eyes without cataract.

Patients and Methods:

A prospective multicenter observational study was performed for patients who underwent combined SPI, GSL, and GT for advanced PACG without cataract. Patients were assessed before and after the operation. Complete success was defined as achieving intraocular pressure (IOP) between 6 and 18 mm Hg with at least a 20% reduction compared with baseline, without the use of ocular hypotensive medications or reoperation. Qualified success adopted the same criteria but allowed medication use. Factors associated with surgical success were analyzed using logistic regression.

Results:

A total of 61 eyes of 50 advanced PACGs were included. All participants completed 12 months of follow-up. Thirty-six eyes (59.0%) achieved complete success, and 56 eyes (91.8%) achieved qualified success. Preoperative and postsurgical at 12 months mean IOPs were 29.7±7.7 and 16.1±4.8 mm Hg, respectively. The average number of ocular hypotensive medications decreased from 1.9 to 0.9 over 12 months. The primary complications included IOP spike (n=9), hyphema (n=7), and shallow anterior chamber (n=3). Regression analysis indicated that older age (odds ratio [OR]=1.09; P=0.043) was positively associated with complete success, while a mixed angle closure mechanism (OR=0.17; P=0.036) reduced success rate.

Conclusions:

The combination of SPI, GSL, and GT is a safe and effective surgical approach for advanced PACG without cataract. It has great potential as a first-line treatment option for these patients.
Effect of Social Distancing Caused by Heavy Snowfall on Seasonal Influenza Epidemic in a Local Region in Japan
Authors: Yamada Kenta , Shinozaki Tomohiro , Ohshima Yusei
Published: May 2024

Background:

The effectiveness of social distancing in controlling influenza epidemics is debatable. We analyzed the local impact of large-scale social distancing caused by heavy snowfall on influenza epidemic.

Methods:

Surveillance data from the National Institute of Infectious Diseases on influenza diagnosed at registered Fukui Prefecture institutions were plotted in epidemic curves. We also compared the number of elementary and junior high school students suspended attendance due to influenza during the 2017/2018 season between the northern and southern Fukui Prefecture territories. Weekly incidence influenza rates and average rates before, during and after school closure caused by heavy snowfall in the northern territory were compared with those of the southern territory using Poisson generalized estimating equations to account for school variability.

Results:

The northern territory epidemic curve, like the nationwide trend, rapidly declined during the heavy snowfall and formed a second peak 4 weeks later. The southern territory’s curve was like the nationwide trend throughout. Weekly incidence rate ratios in schools for the northern versus southern territories varied from 0.23 during heavy snowfall to 2.32, 4 weeks after the snowfall. Cumulative incidence ratio (95% confidence interval) of the northern-to-southern territories was 0.92 (0.74–1.13; P = 0.42). School closure significantly reduced the incidence rate to 0.41 (95% confidence interval, 0.19–0.89; P = 0.02).

Conclusions:

Although relatively large-scale, simultaneous school closures and social distancing could temporarily suppress seasonal influenza epidemic, they could not impede the cumulative incidence. Large-scale social distancing may contribute to slowing infection spread during seasonal influenza epidemics.
The Effect of Proprioceptive Insoles on Gait Kinematics in Healthy Participants
Authors: Tramonti Caterina , Griguoli Francesca , Di Martino Siria , Lamola Giuseppe , Falossi Francesca , Palattella Giovanni , Raffaetà Gloria , Chisari Carmelo , Parchi Paolo
Published: May 2024

Introduction

Proprioceptive neuromuscular stimulating insoles (PNIs) enhance somatosensory information from the plantar region, thus modifying standing posture, balance, and ambulatory function. The present study investigated the short-term effects of customized PNIs on lower-limb kinematics during human locomotion.

Materials and Methods

Fifteen able-bodied volunteers were recruited and first examined with clinical evaluation of postural and feet behavior. Subjects performed 3-dimensional gait analysis (GA) while walking at self-selected speed in three different conditions: baseline, subjects barefoot; placebo, subjects wearing neutral insoles; and proprioceptive, subjects wearing PNIs. Spatiotemporal and kinematics data of the main lower-limb joints were acquired through a system of six photogrammetric infrared cameras acquiring at a sampling frequency of 100 Hz. Then, acquired parameters were compared in the three different conditions.

Results

We found a significant difference in the percentage of double-support phase (P = 0.022) and in ankle plantarflexion values during the toe-off phase of gait cycle (P = 0.022) between the three conditions. Post hoc analysis revealed that subjects wearing PNIs presented a significant reduction in percentage of double-support phase (P = 0.009) and reduced values of ankle plantarflexion during the toe-off phase of gait cycle (P = 0.02), compared with subjects in placebo condition.

Conclusions

Results suggest that proprioceptive insoles may induce modifications of gait biomechanics in able-bodied subjects, thus modulating movement strategies during human locomotion.

Clinical Relevance

These findings provide a basis for future investigation of the efficacy of these foot devices in a long-term period in able-bodied individuals and potentially in subjects with neurological impairment.
A New Normal: A Pilot Examination of the Modern Cephalic Index
Authors: Chaikind Sarah R. , Utay Joshua B. , Wang Jijia , Graham Tiffany D.F.
Published: May 2024

Introduction

The cephalic index (CI) is the width-to-length ratio of the head. Brachycephalic head shapes are wider than the norm and have a higher CI. In 1994, the American Academy of Pediatrics recommended babies sleep on their backs to combat rates of sudden infant death syndrome, which correlated to a sudden increase in the incidence of brachycephaly in the American population. The commonly accepted “normal” CI comes from a table that was published in the 1970s and should be updated for the modern population. The purpose of this study is to examine the modern average CI, compare measurements from today’s population to the highly referenced 1970s table, and examine what genealogical factors may impact a person’s CI measurement.

Methods

Fifty-nine subjects were measured for cephalic width and length. CI was calculated for all subjects, and statistical analysis was performed.

Results

There was a clinically significant increase in CI in every age group since the 1970s. The only statistically significant differences were between ethnicity and ethnicity-sex subgroups (not between age or sex groups).

Conclusions

The CI has changed in recent years, and based on these pilot data, the modern CI may be impacted more by ethnicity than age and sex.

Clinical Relevance

The typical CI in the modern generation is higher from the previously used 1970s standard tables. Updated measurements would aid clinicians when determining the need for cranial remolding orthoses and provide insight into the outcomes of treatment for deformational head shapes (whether via orthoses or other methods).
Advanced Hospital Healthcare at Home—How Is It Going?
Authors: Powell Suzanne K.
Published: May 2024

The Centers for Medicare & Medicaid Services’ (CMS) Acute Hospital Care at Home (AHCAH) waiver, which launched in November 2020, has prompted hundreds of hospitals across the country to initiate programs that allow certain patients to complete their acute care stays in the familiar comfort of their homes. But this waiver is about to expire in December 2024. It is a success; but can we continue it?
Rethinking the Abnormal Uterine Bleeding Consult: Creating a Patient-Centered, See-and-Treat Model of Care
Authors: Robinson Erica F. , Desai Vrunda B. , Chudnoff Scott
Published: May 2024

Historically, the evaluation of abnormal uterine bleeding (AUB) has involved a multi-visit process that uses a multitude of care settings (eg, in-office, imaging, laboratory), with the potential for lengthy delays in care due to the now-commonplace scheduling difficulties many clinics face. Although there is strong evidence for the use of in-office uterine assessment as a best practice, uptake has been limited by the learning curve, technology acquisition costs, and other factors. However, due to the coronavirus disease 2019 (COVID-19) pandemic, clinical practice has faced rapid adaptations that have resulted in the redesigned clinical care model of evaluating this common gynecologic condition in a more patient-centered and streamlined way while maximizing the patient experience, health care efficiency, and physician engagement. This procedure would specifically involve one telehealth or initial visit to assess patient history, perform necessary laboratory testing, review results, and plan outpatient procedures to be conducted in the office or the operating room. Due to the COVID-19 pandemic, clinics have, by necessity, implemented this proposed reimagined pathway in a variety of outpatient settings nationally. We propose that, moving forward, this new procedure be permanently adopted in clinics nationwide as the patient-focused evaluation strategy for AUB.
Bone Scan With SPECT/CT Demonstrated Phthisis Bulbi
Authors: Lin Shih-Tsung , Wang Yuh-Feng , Chuang Tzyy-Ling
Published: May 2024

A 46-year-old man has a history of right eye vision loss from childhood due to an injury, right hypopharyngeal cancer with metastasis to right neck lymph nodes treated with concurrent chemoradiotherapy, and left tonsillar cancer after resection and adjuvant chemotherapy. Whole-body bone scan showed abnormal uptake to the right eye region, whereas SPECT/CT imaging localized this uptake to sharply defined, round to oval bone density foci of calcium scattered in the sclera and surrounding tissues, indicative of phthisis bulbi with posttraumatic calcification. Phthisis bulbi represents a shrunken ocular globe with calcification or ossification, typically as a sequela of trauma.
Pediatric Gastrointestinal Outcomes During the Post-Acute Phase of COVID-19: Findings from RECOVER Initiative from 29 Hospitals in the US
Authors: Zhang Dazheng , Stein Ronen , Lu Yiwen , Zhou Ting , Lei Yuqing , Li Lu , Chen Jiajie , Arnold Jonathan , Becich Michael J. , Chrischilles Elizabeth A. , Chuang Cynthia H. , Christakis Dimitri A , Fort Daniel , Geary Carol R. , Hornig Mady , Kaushal Rainu , Liebovitz David M. , Mosa Abu Saleh Mohammad , Morizono Hiroki , Mirhaji Parsa , Dotson Jennifer L. , Pulgarin Claudia , Sills Marion R. , Suresh Srinivasan , Williams David A. , Baldassano Robert N. , Forrest Christopher B. , Chen Yong
Published: May 2024

Importance

The profile of gastrointestinal (GI) outcomes that may affect children in post-acute and chronic phases of COVID-19 remains unclear.

Objective

To investigate the risks of GI symptoms and disorders during the post-acute phase (28 days to 179 days after SARS-CoV-2 infection) and the chronic phase (180 days to 729 days after SARS-CoV-2 infection) in the pediatric population.

Design

We used a retrospective cohort design from March 2020 to Sept 2023.

Setting

twenty-nine healthcare institutions.

Participants

A total of 413,455 patients aged not above 18 with SARS-CoV-2 infection and 1,163,478 patients without SARS-CoV-2 infection.

Exposures

Documented SARS-CoV-2 infection, including positive polymerase chain reaction (PCR), serology, or antigen tests for SARS-CoV-2, or diagnoses of COVID-19 and COVID-related conditions.

Main Outcome(s) and Measure(s)

Prespecified GI symptoms and disorders during two intervals: post-acute phase and chronic phase following the documented SARS-CoV-2 infection. The adjusted risk ratio (aRR) was determined using a stratified Poisson regression model, with strata computed based on the propensity score.

Results

Our cohort comprised 1,576,933 patients, with females representing 48.0% of the sample. The analysis revealed that children with SARS-CoV-2 infection had an increased risk of developing at least one GI symptom or disorder in both the post-acute (8.64% vs. 6.85%; aRR 1.25, 95% CI 1.24-1.27) and chronic phases (12.60% vs. 9.47%; aRR 1.28, 95% CI 1.26-1.30) compared to uninfected peers. Specifically, the risk of abdominal pain was higher in COVID-19 positive patients during the post-acute phase (2.54% vs. 2.06%; aRR 1.14, 95% CI 1.11-1.17) and chronic phase (4.57% vs. 3.40%; aRR 1.24, 95% CI 1.22-1.27).

Conclusions and Relevance

In the post-acute phase or chronic phase of COVID-19, the risk of GI symptoms and disorders was increased for COVID-positive patients in the pediatric population.

Key Points

Question

Does COVID-19 increase the risk of gastrointestinal (GI) symptoms and diseases during the post-acute phase in children and adolescents?

Findings

Newly diagnosed GI symptoms and disorders such as diarrhea, constipation, and vomiting are seen more commonly in children and adolescents with SARS-CoV-2 infection.

Meaning

Clinicians need to be mindful that after SARS-CoV-2 infection in children, lingering GI symptoms without a unifying diagnosis may be more common than among uninfected children.
Open-source machine learning pipeline automatically flags instances of acute respiratory distress syndrome from electronic health records
Authors: Morales Félix L. , Xu Feihong , Lee Hyojun Ada , Navarro Helio Tejedor , Bechel Meagan A. , Cameron Eryn L. , Kelso Jesse , Weiss Curtis H. , Nunes Amaral Luís A.
Published: May 2024

Physicians could greatly benefit from automated diagnosis and prognosis tools to help address information overload and decision fatigue. Intensive care physicians stand to benefit greatly from such tools as they are at particularly high risk for those factors. Acute Respiratory Distress Syndrome (ARDS) is a life-threatening condition affecting >10% of critical care patients and has a mortality rate over 40%. However, recognition rates for ARDS have been shown to be low (30-70%) in clinical settings. In this work, we present a reproducible computational pipeline that automatically adjudicates ARDS on retrospective datasets of mechanically ventilated adult patients. This pipeline automates the steps outlined by the Berlin Definition through implementation of natural language processing tools and classification algorithms. First, we used labeled chest imaging reports from two different hospitals over three different time periods to train an XGBoost model to detect bilateral infiltrates, and a subset of attending physician notes from one hospital labeled for the most common ARDS risk factor (pneumonia) to train another XGBoost model to detect a pneumonia diagnosis. Both models achieve high performance when tested on out-of-bag samples—an area under the receiver operating characteristic curve (AUROC) of 0.88 for adjudicating chest imaging reports, and an AUROC of 0.86 for detecting pneumonia on attending physician notes. Next, we integrate the models and validate the entire pipeline on a fourth cohort from a third hospital (MIMIC-III) and find a sensitivity of 93.5% — an extraordinary improvement over the 22.6% ARDS recognition rate reported for these encounters — along with a false positive rate of 18.8%. We conclude that our reproducible, automated diagnostic pipeline exhibits promising ARDS retrospective adjudication performance, thus providing a valuable resource for physicians aiming to enhance ARDS diagnosis and treatment strategies. We surmise that real-time integration of the pipeline with EHR systems has the potential to aid clinical practice by facilitating the recognition of ARDS cases at scale.
Measuring Institutional Research Culture: An Analysis of Accepted Abstracts at the Academic Surgical Congress
Authors: Sathe Tejas S. , Sathe Ojas S.
Published: May 2024

Introduction

Understanding which institutions have a strong research culture is important for trainees, but existing metrics such as NIH funding do not always reflect a trainee’s lived experience. Here, we present a descriptive analysis of accepted abstracts at the Academic Surgical Congress (ASC).

Methods

We analyzed accepted abstracts at the Academic Surgical Congress between 2016 and 2024. We identified institutions with the most accepted abstracts, overall and by year. We also identified institutions with the greatest year-over-year improvement between 2022 and 2024. Finally, we calculated associations between accepted abstracts and NIH funding and also between accepted abstracts and leadership in the ASC’s hosting societies.

Results

A total of 12,142 abstracts were accepted by the ASC between 2016 and 2024. The University of Alabama and the University of Michigan led overall abstract acceptances and also led in most years. Baylor and Massachusetts General Hospital had the greatest absolute and percent year-over-year increase in abstract acceptances in the post-COVID era. There was a positive association between NIH funding and abstract acceptances. Among the top 40 institutions by accepted abstracts in 2024, institutions in the top 10 were over 10 times as likely to have leadership representation in the societies that host the ASC.

Conclusions

Conference abstracts may serve as a useful measure of trainee-relevant research culture. Trainees can utilize this information when selecting residency programs, and programs can use this information to optimize trainee research experiences.
Intrinsic Dynamics and Neural Implementation of a Hypothalamic Line Attractor Encoding an Internal Behavioral State
Authors: Vinograd Amit , Nair Aditya , Linderman Scott W. , Anderson David J.
Published: May 2024

Line attractors are emergent population dynamics hypothesized to encode continuous variables such as head direction and internal states. In mammals, direct evidence of neural implementation of a line attractor has been hindered by the challenge of targeting perturbations to specific neurons within contributing ensembles. Estrogen receptor type 1 (Esr1)-expressing neurons in the ventrolateral subdivision of the ventromedial hypothalamus (VMHvl) show line attractor dynamics in male mice during fighting. We hypothesized that these dynamics may encode continuous variation in the intensity of an internal aggressive state. Here, we report that these neurons also show line attractor dynamics in head-fixed mice observing aggression. We exploit this finding to identify and perturb line attractor-contributing neurons using 2-photon calcium imaging and holographic optogenetic perturbations. On-manifold perturbations demonstrate that integration and persistent activity are intrinsic properties of these neurons which drive the system along the line attractor, while transient off-manifold perturbations reveal rapid relaxation back into the attractor. Furthermore, stimulation and imaging reveal selective functional connectivity among attractor-contributing neurons. Intriguingly, individual differences among mice in line attractor stability were correlated with the degree of functional connectivity among contributing neurons. Mechanistic modelling indicates that dense subnetwork connectivity and slow neurotransmission are required to explain our empirical findings. Our work bridges circuit and manifold paradigms, shedding light on the intrinsic and operational dynamics of a behaviorally relevant mammalian line attractor.
A deep dive into theFALSIFLORAcontribution to tomato reproductive development through a comprehensive allelic series analysis
Authors: Quevedo-Colmena Abraham S. , Vriezen Wim H. , Wesselink Pieter G.A. , Pérez José M. , Pineda Benito , García-Sogo Begoña , Angosto Trinidad , Moreno Vicente , Yuste-Lisbona Fernando J. , Lozano Rafael
Published: May 2024

Plants undergo continuous growth and development thanks to meristems, specialized groups of pluripotent stem cells that remain in their undifferentiated state throughout the plant’s life cycle. Meristem transition from the vegetative to the reproductive phase heavily influences plant reproductive success and agricultural productivity. In tomato (Solanum lycopersicumL.),FALSIFLORA(FA), the orthologue of the ArabidopsisLEAFYgene, promotes floral transition by specifying floral meristem identity and regulating the expression of genes responsible for floral organ identity and development. In this study, the allelic series ofFAhas been expanded by combining the screening of a tomato EMS mutant collection with overexpression, gene silencing and CRISPR/Cas9 genome editing approaches, aimed to deepen the understanding of the functional role ofFAduring tomato reproductive development. The phenotypic and molecular characterization of theFAallelic series revealed the multifaceted role ofFAacting in both early and late stages of floral ontogeny. Thus, in addition to promoting floral transition and specifying floral meristem identity,FAalso plays a role in inflorescence meristem maturation and termination, thereby regulating the inflorescence architecture. Furthermore,FAexerts regulatory control over the expression of the tomato homologs ofAGAMOUS(TOMATO AGAMOUS1,TAG1) andWUSCHEL(SlWUS), underscoring its function in promoting carpel development and suppressing floral stem cell activity, thereby establishing floral determinacy. In conclusion, our findings demonstrate the potential of employing mutant allelic series as powerful tools for elucidating gene functions and deciphering the intricate molecular basis underlying biological processes.

Plain Language Summary

Our research aims to gain a deeper understanding of the role ofFALSIFLORAin tomato reproductive development. TheFALSIFLORAallelic spectrum was expanded through mutant screening, along with overexpression, silencing, and CRISPR/Cas9 editing approaches. Our findings reveal thatFALSIFLORAhas a dual function in early and late floral development stages. In addition to promoting floral transition and specifying floral meristem identity,FAregulates the expression of tomato genes homologous toWUSCHELandAGAMOUS, which play an essential role in stem cell regulation and carpel development. This study highlights the value of allelic series in elucidating gene functions and intricate biological mechanisms.
Activity of prefrontal cortex serotonin 2A receptor expressing neurons is necessary for the head-twitch response of mice to psychedelic drug DOI in a sex-dependent manner
Authors: Ozols Annika B. , Wei Jing , Campbell Janet M. , Hu Chengcheng , Qiu Shenfeng , Gallitano Amelia L.
Published: May 2024

Serotonin 2A receptors (5-HT2ARs) mediate the effects of psychedelic drugs. 5-HT2AR agonists, such as (-)-2,5-dimethoxy-4-iodoamphetamine hydrochloride (DOI), that produce a psychedelic experience in humans induce a head-twitch response (HTR) behavior in rodents. However, it is unknown whether the activity of 5-HT2AR expressing neurons is sufficient to produce the HTR in the absence of an agonist, or in which brain region 5-HT2ARs control the HTR. Here, we use an optogenetic approach to examine whether activation of 5-HT2AR expressing neurons in the mouse prefrontal cortex (PFC) is sufficient to induce HTRs alone, or may augment the HTR produced by DOI, and if inhibition of these neurons prevents DOI-induced HTRs in mice. We crossedHtr2a-Cre mice to Cre-dependent optogenetic lines Ai32 (channelrhodopsin) and Ai39 (halorhodopsin) to selectively activate and inhibit (respectively) 5-HT2AR-expressing neurons in the PFC of adult mice. We found that optogenetic stimulation of PFC 5-HT2AR expressing neurons in the absence of an agonist does not increase HTRs in mice. In both male and female Ai32 mice that received vehicle, there was no difference in HTRs in mice that expressedHtr2a-Cre compared with control mice, indicating that optogenetic activation of 5-HT2AR+ cells in the PFC was not sufficient to produce HTRs in the absence of an agonist. In female mice, activation of PFC 5-HT2AR expressing neurons augmented the HTR produced by DOI. However, this result was not seen inmalemice. In contrast, inhibition of 5-HT2AR expressing neurons in the PFC prevented the increase in HTR produced by DOI in male, but not in female, mice. Together, these findings suggest that activation of 5-HT2ARs in the PFC is not sufficient to induce HTRs in the absence of a 5-HT2AR agonist but is necessary for induction of HTRs by a 5-HT2AR agonist in a sex-dependent manner.
User-friendly genome assembly and gene annotation pipelines for vertebrates
Authors: Wu Siwen , Yuan Sisi , Su Zhengchang
Published: May 2024

High-quality genome assembly and accurate gene annotation are critical to understand the biology and evolutionary history of a species. With the advance in sequencing technologies, assembling large vertebrate genomes using a combination of low-costing short reads and noisy long reads is in the reach of an individual lab. Although many tools have been developed, no single one is able to produce a chromosome-level assembly. Instead, a pipeline involving multiple steps using different tools is needed to achieve the goal. Nonetheless, it is difficult for a newcomer to choose an appropriate tool for each stage of pipeline and their combination for optimal performance. Moreover, most existing gene annotation tools cannot sufficiently and accurately identify both protein-coding genes and pseudogenes. Although gene annotation pipelines have been described such as those by NCBI and ENSEMBL, they are not available for individual labs due to the complexity of their use and required computational resources. To overcome these obstacles, here, we introduce user-friendly optimized genome assembly and gene annotation pipelines for vertebrates. Our genome assembly pipeline is able to produce chromosome-level assemblies with high quality using a combination of PacBio/Nanopore long reads, Illumina short reads and Hi-C short reads, and our gene annotation pipeline can accurately and sufficiently annotate both protein-coding genes and pseudogenes in an assembled genome using a combination of homology-based and RNA-seq data-based methods. Both pipelines show superior performances to existing ones in applications.
MicroRNA-374b regulates SARS-CoV-2 viral protein mediated endothelial to mesenchymal transition by targeting c-FLIP
Authors: Raji Grace R. , Poyyakkara Aswini , Ramachandran Vishnu , Anjali K , Sameer Kumar VB
Published: May 2024

The pathophysiological consequences of COVID-19 disease are still unclear, however, endothelial cell (EC) dysfunction has been observed to play a key role in disease progression and severity. Many reports suggests that SARS-CoV-2 mediated endothelial dysfunction is the result of intracellular signaling initiated by the binding of the spike protein to ACE2, which can modify endothelial cell phenotype. Recent reports suggests endothelial to mesenchymal transition (Endo MT) as a process heavily involved in lung fibrosis of COVID 19 patients. EndoMT is involved in many chronic and fibrotic diseases and appears to be regulated by complex molecular mechanisms and different signaling pathways, in particular microRNAs (miRNAs), which constitute a crucial mediator of EndoMT. MicroRNAs (miRNAs), small endogenous RNA molecules that regulate several physiological processes including endothelial homeostasis, and vascular diseases, can be perturbed by infecting viruses. Based on these facts, this study was designed to decipher the role of miR-374b, which was found to be significantly downregulated upon profiling of SARS-CoV-2 viral protein stimulated endothelial cells. Gene profiling of endothelial cells revealed c-FLIP (CFLAR) to be among the most significantly upregulated gene. In silico target prediction analysis using targetscan revealed c-FLIP as the major target of miR-374b. Further it was identified that miR-374b can reverse c-FLIP mRNA and protein levels in SARS-CoV-2 viral protein stimulated endothelial cells under conditions of miR-374b overexpression. Since vascular dysfunction involve, under many circumstances, loss of vascular tone due to mesenchymal transition of endothelial cells, we next checked if fibrotic events are initiated downstream of c-FLIP pathway. Further mechanistic studies involving identification of the expression pattern of mesenchymal markers in SARS-CoV-2 viral protein stimulated endothelial cells in presence or absence of miR-374b provide evidence for the important role of miR-374b in regulating SARS CoV-2 mediated EndoMT and fibrotic events downstream of c-FLIP pathway and may highlight possible new therapeutic approaches targeted at the damaged endothelium.
Fast and robust objective EEG audiometry
Authors: Guyonnet-Hencke T. , Portoles O. , de Vries M. , Koderman E. , Winkler A. , Goodall J. , Desain P. , Thielen J. , Schulte M. , Beynon A. J. , van Kesteren M.
Published: May 2024

The current ‘gold standard’ of audiometry relies on subjective behavioral responses, which is impractical and unreliable for certain groups such as children, individuals with severe disabilities, or the disabled elderly. This study presents a novel electroencephalography (EEG) system that is easy to setup and estimates audiometric thresholds quickly. Air-conduction audiometric thresholds at 250, 500, 1000, 2000, 4000, and 8000 Hz and 5 dB resolution were estimated from ten elderly patients with asymmetric sensorineural hearing loss and five normal hearing young adults using three different systems: the novel EEG system, conventional pure-tone audiometry (PTA), and an automated behavioral test with the same stimulus properties as in the EEG test. EEG data was collected for 15 minutes from 32 semi-dry EEG electrodes. Later, the EEG system was trimmed to 8 electrodes and 7.5 minutes of data with satisfactory results. Correlation and regression analysis validated the hearing thresholds derived from both EEG configurations relative to the behavioral hearing thresholds–Pearson’s correlation of 0.82 between PTA and 8-electrode 7.5-minute EEG data. The results of this study open the door to fast and objective hearing threshold estimation with EEG.
Mechanisms of axoneme and centriole elimination inNaegleria gruberi
Authors: Woglar Alexander , Busso Coralie , Garcia-Rodriguez Gabriela , Douma Friso , Croisier-Coeytaux Mary-Claude , Knott Graham , Gönczy Piere
Published: May 2024

The excavateNaegleria gruberi,a basal eukaryote related to the “brain eating”Naegleria fowleri, can transform transiently from an amoeboid life form lacking flagella and centrioles to a flagellate life form where these elements are present, followed by reversion to an amoeboid state. The mechanisms imparting elimination of axonemes and centrioles during this reversion process are not known. Here, we uncover that flagella primarily fold onto the cell surface and fuse within milliseconds with the plasma membrane. Once internalized, axonemes are severed by Spastin into equally-sized fragments, which are then enclosed by membranes, after which their contents are eliminated through the lysosomal pathway. Moreover, we discovered that centrioles undergo progressive K63 autophagy-linked poly-ubiquitination and K48 proteasome-promoting poly-ubiquitination, and that ubiquitination occurs next to centriolar microtubules. Most centrioles are eliminated in lysosomes or the cytoplasm in a lysosomal- and proteasome-dependent manner. Strikingly, we uncover in addition that centrioles can be shed in the extracellular milieu and taken up by other cells. Collectively, these findings reveal fundamental mechanisms governing the elimination of essential cellular constituents inNaegleriathat may operate broadly in eukaryotic systems.

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From birds to mammals: spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle led to efficient intra- and interspecies transmission
Authors: Caserta Leonardo C , Frye Elisha A. , Butt Salman L. , Laverack Melissa A , Nooruzzaman Mohammed , Covalenda Lina M. , Thompson Alexis , Prarat Koscielny Melanie , Cronk Brittany , Johnson Ashley , Kleinhenz Katie , Edwards Erin E , Gomez Gabriel , Hitchener Gavin R. , Martins Mathias , Kapczynski Darrell R. , Suarez David L. , Alexander Morris Ellen Ruth , Hensley Terry , Beeby John S. , Lejeune Manigandan , Swinford Amy , Elvinger Francois , Dimitrov Kiril M , Diel Diego G.
Published: May 2024

Infections with the highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b virus have resulted in the death of millions of domestic birds and thousands of wild birds in the U.S. since January, 2022. Throughout this outbreak, spillovers of the virus to mammals have been frequently documented. Here, we report the detection of HPAI H5N1 virus in dairy cattle herds across several states in the U.S. The affected cows displayed clinical signs encompassing decreased feed intake, altered fecal consistency, respiratory distress, and decreased milk production with abnormal milk. Infectious virus and RNA were consistently detected in milk collected from affected cows. Viral staining in tissues revealed a distinct tropism of the virus for the epithelial cells lining the alveoli of the mammary gland in cows. Analysis of whole genome sequences obtained from dairy cows, birds, domestic cats, and a racoon from affected farms indicated multidirectional interspecies transmissions. Epidemiologic and genomic data revealed efficient cow-to-cow transmission after healthy cows from an affected farm were transported to a premise in a different state. These results demonstrate the transmission of HPAI H5N1 clade 2.3.4.4b virus at a non-traditional interface and to a new and highly relevant livestock species, underscoring the ability of the virus to cross species barriers.
Biological activity of a stable 6-aryl-2-benzoyl-pyridine colchicine-binding site inhibitor, 60c, in metastatic, triple-negative breast cancer
Authors: Oluwalana Damilola , Adeleye Kelli L , Krutilina Raisa I , Chen Hao , Playa Hilaire , Deng Shanshan , Parke Deanna N , Abernathy John , Middleton Leona , Cullom Alexandra , Thalluri Bhargavi , Ma Dejian , Meibohm Bernd , Miller Duane D , Seagroves Tiffany N , Li Wei
Published: May 2024

Background

Improving survival for patients diagnosed with metastatic disease and overcoming chemoresistance remain significant clinical challenges in treating breast cancer. Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by a lack of therapeutically targetable receptors (ER/PR/HER2). TNBC therapy includes a combination of cytotoxic chemotherapies, including microtubule-targeting agents (MTAs) like paclitaxel (taxane class) or eribulin (vinca class); however, there are currently no FDA-approved MTAs that bind to the colchicine-binding site. Approximately 70% of patients who initially respond to paclitaxel will develop taxane resistance (TxR). We previously reported that an orally bioavailable colchicine-binding site inhibitor (CBSI), VERU-111, inhibits TNBC tumor growth and treats pre-established metastatic disease. To further improve the potency and metabolic stability of VERU-111, we created next-generation derivatives of its scaffold, including 60c.

Results

60c shows improved in vitro potency compared to VERU-111 for taxane-sensitive and TxR TNBC models, and suppress TxR primary tumor growth without gross toxicity. 60c also suppressed the expansion of axillary lymph node metastases existing prior to treatment. Comparative analysis of excised organs for metastasis between 60c and VERU-111 suggested that 60c has unique anti-metastatic tropism. 60c completely suppressed metastases to the spleen and was more potent to reduce metastatic burden in the leg bones and kidney. In contrast, VERU-111 preferentially inhibited liver metastases and lung metastasis repression was similar. Together, these results position 60c as an additional promising CBSI for TNBC therapy, particularly for patients with TxR disease.
Structural Determinants ofVibrio choleraeFeoB Nucleotide Promiscuity
Authors: Lee Mark , Magante Kate , Gómez-Garzón Camilo , Payne Shelley M. , Smith Aaron T.
Published: May 2024

Ferrous iron (Fe2+) is required for the growth and virulence of many pathogenic bacteria, includingVibrio cholerae(Vc), the causative agent of the disease cholera. For this bacterium, Feo is the primary system that transports Fe2+into the cytosol. FeoB, the main component of this system, is regulated by a soluble cytosolic domain termed NFeoB. Recent reanalysis has shown that NFeoBs can be classified as either GTP-specific or NTP-promiscuous, but the structural and mechanistic bases for these differences were not known. To explore this intriguing property of FeoB, we solved the X-ray crystal structures ofVcNFeoB in both the apo and GDP-bound forms. Surprisingly, this promiscuous NTPase displayed a canonical NFeoB G-protein fold like GTP-specific NFeoBs. Using structural bioinformatics, we hypothesized that residues surrounding the nucleobase could be important for both nucleotide affinity and specificity. We then solved the X-ray crystal structures of N150TVcNFeoB in the apo and GDP-bound forms to reveal H-bonding differences surround the guanine nucleobase. Interestingly, isothermal titration calorimetry revealed similar binding thermodynamics of the WT and N150T proteins to guanine nucleotides, while the behavior in the presence of adenine nucleotides was dramatically different. AlphaFold models ofVcNFeoB in the presence of ADP and ATP showed important conformational changes that contribute to nucleotide specificity among FeoBs. Combined, these results provide a structural framework for understanding FeoB nucleotide promiscuity, which could be an adaptive measure utilized by pathogens to ensure adequate levels of intracellular iron across multiple metabolic landscapes.
Anchorage of H3K9-methylated heterochromatin to the nuclear periphery helps mediate P-cell nuclear migration though constricted spaces inCaenorhabditis elegans
Authors: Gregory Ellen F. , Luxton G.W. Gant , Starr Daniel A.
Published: May 2024

Nuclei adjust their deformability while migrating through constrictions to enable structural changes and maintain nuclear integrity. The effect of heterochromatin anchored at the nucleoplasmic face of the inner nuclear membrane on nuclear morphology and deformability duringin vivonuclear migration through constricted spaces remains unclear. Here, we show that abolishing peripheral heterochromatin anchorage by eliminating CEC-4, a chromodomain protein that tethers H3K9-methylated chromatin to the nuclear periphery, disrupts constrained P-cell nuclear migration inCaenorhabditis eleganslarvae in the absence of the established LINC complex-dependent pathway. CEC-4 acts in parallel to an actin and CDC-42-based pathway. We also demonstrate the necessity for the chromatin methyltransferases MET-2 and JMJD-1.2 during P-cell nuclear migration in the absence of functional LINC complexes. We conclude that H3K9-nethylated chromatin needs to be anchored to the nucleoplasmic face of the inner nuclear membrane to help facilitate nuclear migration through constricted spacesin vivo.