bluuebunny/crossref_metadata_2025 huggingface dataset:
An Inexpensive 3D Printed Mouse Model of Successful, Complication-free Long Bone Distraction Osteogenesis
Authors: Tevlin Ruth , Shah Harsh N. , Salhotra Ankit , Di Iorio Sarah E. , Griffin Michelle , Januszyk Michael , Wan Derrick C. , Longaker Michael T.
Published: February 2023

Background:

Distraction osteogenesis (DO) is used for skeletal defects; however, up to 50% of cases exhibit complications. Previous mouse models of long bone DO have been anecdotally hampered by postoperative complications, expense, and availability. To improve clinical techniques, cost-effective, reliable animal models are needed. Our focus was to develop a new mouse tibial distractor, hypothesized to result in successful, complication-free DO.

Methods:

A lightweight tibial distractor was developed using CAD and 3D printing. The device was fixed to the tibia of C57Bl/6J mice prior to osteotomy. Postoperatively, mice underwent 5 days latency, 10 days distraction (0.15 mm every 12 hours), and 28 days consolidation. Bone regeneration was examined on postoperative day 43 using micro-computed tomography (μCT) and Movat’s modified pentachrome staining on histology (mineralized volume fraction and pixels, respectively). Costs were recorded. We compared cohorts of 11 mice undergoing sham, DO, or acute lengthening (distractor acutely lengthened 3.0 mm).

Results:

The histological bone regenerate was significantly increased in DO (1,879,257 ± 155,415 pixels) compared to acute lengthening (32847 ± 1589 pixels) (P < 0.0001). The mineralized volume fraction (bone/total tissue volume) of the regenerate was significantly increased in DO (0.9 ± 0.1) compared to acute lengthening (0.7 ± 0.1) (P < 0.001). There was no significant difference in bone regenerate between DO and sham. The distractor was relatively low cost ($11), with no complications.

Conclusions:

Histology and µCT analysis confirmed that the proposed tibial DO model resulted in successful bone formation. Our model is cost-effective and reproducible, enabling implementation in genetically dissectible transgenic mice.
Customized corneal crosslinking with excimer laser–assisted epithelium removal for progressive keratoconus: 1-year results
Authors: Gil João Q. , Rosa Andreia M. , Costa Esmeralda , Quadrado Maria J. , Murta Joaquim N.
Published: February 2023

Purpose:

To evaluate the 1-year visual and tomographic results of customized crosslinking using excimer laser–assisted epithelium removal and topography-guided irradiation in the treatment of progressive keratoconus.

Setting:

Coimbra Ophthalmology Unit, Private Practice, Coimbra, Portugal.

Design:

Prospective nonrandomized clinical trial.

Methods:

Eyes with documented progressive keratoconus were enrolled. After de-epithelialization with phototherapeutic keratectomy, customized UV irradiation was performed, designed as 3 concentric circular areas centered on the thinnest point (Mosaic System). Energy exposure was 5.4 J/cm2 in the outer circle and then increased centripetally to 7.2 J/cm2 and 10 J/cm2. Corrected distance visual acuity (CDVA), refractive outcomes, and Scheimpflug tomographies (Allegro Oculyzer) were assessed at baseline, and 6 months, and 12 months postoperatively.

Results:

37 eyes of 32 patients were enrolled in this prospective study. The mean diameter for treated areas was 6.17 ± 0.80 mm, 4.45 ± 0.47 mm, and 2.58 ± 0.14 mm for the outer, medium, and inner circle, respectively. At the 1-year follow-up, the mean CDVA improved significantly from 0.38 ± 0.19 to 0.20 ± 0.16 logMAR (P < .01), with 34 (91.89%) of the 37 eyes retaining or improving CDVA. The mean preoperative minimum pachymetry decreased from 449.26 ± 41.62 to 443.26 ± 41.06 μm (P = .02). The maximum keratometry decreased significantly from 58.50 ± 7.84 to 57.05 ± 7.27 diopters (P < .01). After 1 year, 34 eyes (91.89%) showed no signs of progression.

Conclusions:

1 year postoperatively, patients showed a significant improvement in visual acuity while achieving stabilization of disease progression.
Comparison of cataract surgery outcomes in patients with type 1 vs type 2 diabetes mellitus and patients without diabetes mellitus
Authors: Xia Julia L. , Patnaik Jennifer L. , Lynch Anne M. , Christopher Karen L.
Published: February 2023

Purpose:

To report outcomes of cataract surgery in type 1 diabetes mellitus (T1DM) compared with type 2 diabetes mellitus (T2DM) and patients without diabetes mellitus (DM).

Setting:

Academic tertiary referral university hospital eye center, Aurora, Colorado.

Design:

Retrospective chart review using the University of Colorado Cataract Outcomes Database for all cataract surgeries between 2014 and 2020.

Methods:

Demographics, ocular history, and postoperative outcomes were compared across groups using general linear and logistic regression modeling with estimating equations to account for some patients having 2 eyes included.

Results:

8117 patients and 13 383 eyes were included. Compared with T2DM eyes undergoing cataract surgery (n = 3115), T1DM eyes (n = 233) were more likely to have a history of diabetic retinopathy (DR) (60.5% vs 23.6%, P < .0001), of which proliferative DR was the most common (63.1% vs 42.4%, P < .0001). T1DM eyes were also more likely to have a history of retinal detachment (RD) (9.0% vs 2.9%, P < .0001) and prior vitrectomy surgery (12.9% vs 4.0%, P < .0001). Despite having similar preoperative corrected distance visual acuity (CDVA) as T2DM eyes (logMAR 0.52 vs 0.44, P = .092), T1DM eyes had worse CDVA after cataract surgery (logMAR 0.27 vs 0.15, P = .0003). In a multivariate analysis, a history of proliferative DR and prior RD were significant predictors of worse postoperative CDVA (P < .0001) but type of DM was not (P = .894).

Conclusions:

T1DM eyes have worse visual outcomes after cataract surgery compared with T2DM eyes. Worse postoperative visual acuity was associated with worse preoperative DR and history of RD rather than type of DM.
Endoscopic-Assisted Decompression of the Greater Occipital Nerve for Treatment of Migraines, Occipital Neuralgia, and New Daily Persistent Headaches
Authors: Amirlak Bardia , Lu Karen B. , Chung Michael , Sanniec Kyle
Published: February 2023

In the occipital trigger site for migraine, the greater occipital nerve (GON) is thought to be irritated by surrounding structures, including the semispinalis capitus muscle and occipital artery (OA), producing headaches in the back of the neck. Thus, standard decompression involves removal of surrounding tissue and dissection away from the vessel. We noticed a consistent pattern between the GON and OA more distally: the OA approaching laterally and diving under GON, the OA looping back over GON, intertwining of OA and the medial branch of the GON, and lastly traveling parallel to the GON. The technique described uses a modified endoscopic approach using a counter incision, endoscopic assistance, and radical artery lysis to address distal sites in addition to the standard release. At the counter incision, distal intertwining between vessel and nerve were released. An HD endoscope was used to address dynamic compression points more proximally, including hidden areas where the vessel dives under the GON, as well as facilitate cautery and removal of the vessel. Without the use of an endoscope and counter incision, it is difficult to achieve complete decompression of the nerve distally without injury to the proximal body of the nerve.
Outcomes of Abdominal Wall Reconstruction with a Bovine Versus a Porcine Acellular Dermal Matrix: A Propensity Score-Matched Analysis of 725 Patients
Authors: Hassan Abbas M. , Asaad Malke , Brook Derek S. , Shah Nikhil R. , Kumar Saloni C. , Liu Jun , Adelman David M. , Clemens Mark W. , Selber Jesse C. , Butler Charles E.
Published: February 2023

Background:

Abdominal wall reconstruction (AWR) is one of the most commonly performed procedures, yet large comparative studies comparing outcomes of AWR using bovine acellular dermal matrix (BADM) and porcine acellular dermal matrix (PADM) are lacking.

Methods:

In this retrospective cohort study of patients who underwent AWR from March 2005 to June 2019, the primary comparative outcome measure was hernia recurrence with BADM versus PADM. The secondary outcome was the incidence of surgical site occurrence (SSO) and surgical site infection (SSI). Propensity score matching approach was applied to compare the clinical outcomes between the two study groups.

Results:

We identified 725 patients who underwent AWR using BADM (50.5%) or PADM (49.5%). Their mean (± SD) age was 59.8 ± 11.5 years, mean body mass index was 31.4 ± 6.7 kg/m 2, and mean follow-up time was 42 ± 29 months. With propensity score matching, 219 matched pairs were identified. Hernia recurrence rates in BADM (11.4%) and PADM (13.7%) groups did not differ significantly (P = .793). SSOs (26.5% versus 29.2%; P = .518) and SSIs (13.2% versus 11%; P = .456) rates did not differ significantly in the PADM and BADM groups, respectively. Conditional logistic regression model and marginal Cox proportional hazards regression model determined that type of ADM was not significantly associated with SSOs (adjusted OR=1.11, 95%CI=0.74-1.70, p=0.589) or hernia recurrence (adjusted HR=0.85, 95% CI=0.50-1.42, p=0.52).

Conclusion:

Both BADMs and PADMs provide durable, long-term outcomes. The hernia recurrence and postoperative surgical complication rates were not significantly different between BADM and PADM.
Patient-Reported Data Augment Health Record Data for Prediction Models of Persistent Opioid Use after Elective Upper Extremity Surgery
Authors: Giladi Aviram M. , Shipp Michael M. , Sanghavi Kavya K. , Zhang Gongliang , Gupta Samir , Miller Kristen E. , Belouali Anas , Madhavan Subha
Published: February 2023

Background:

Opioids play a role in pain management after surgery, but prolonged use contributes to developing opioid use disorder. Identifying patients at risk of prolonged use is critical for deploying interventions that reduce or avoid opioids; however, available predictive models do not incorporate patient-reported data (PRD) and it remains unclear if PRD can predict post-operative use behavior. We used a machine learning (ML) approach leveraging preoperative PRD and electronic health record (EHR) data to predict persistent opioid use after upper extremity (UE) surgery.

Methods:

Included patients underwent UE surgery, completed preoperative PRD questionnaires, and were prescribed opioids after surgery. We trained models using a 2018 cohort and tested in a 2019 cohort. Opioid use was determined by patient report and filled prescriptions up to 6 months after surgery. We assessed model performance using AUROC, sensitivity, specificity, and Brier score.

Results:

Among 1656 patients, 19% still used opioids at 6 weeks, 11% at 3 months, and 9% at 6 months. The XGBoost model trained on PRD plus EHR data achieved AUROC 0.73 at 6 months. Factors predictive of prolonged opioid use included income, education, tobacco, drug or alcohol abuse, cancer, depression, and race. Protective factors included preoperative PROMIS Global Physical Health and preoperative PROMIS Upper Extremity scores.

Conclusion:

This opioid use prediction model using pre-intervention data had good discriminative performance. PRD variables augmented EHR-based ML algorithms in predicting post-surgical use behaviors and were some of the strongest predictors. PRD should be used in future efforts to guide proper opioid stewardship.
Carbon fiber ankle-foot orthoses in impaired populations: A systematic review
Authors: Grunst Megan M. , Wiederien Robert C. , Wilken Jason M.
Published: February 2023

Background:

Carbon fiber is increasingly being used in ankle-foot orthoses (AFOs). Orthotic devices and carbon fiber-containing devices have been shown to reduce pain and improve function in multiple patient populations. Although the number of publications and interest in carbon fiber AFOs is growing, a systematic evaluation of their effects is lacking.

Objectives:

To characterize the effects of carbon fiber AFOs in impaired individuals.

Study design:

Qualitative systematic review.

Methods:

Systematic searches in PubMed, Embase, CINAHL, and Cochrane Library were completed in July 2020. The results were deduplicated, screened, and assessed for quality by independent reviewers. Articles were excluded if they had nonhuman subjects, only healthy subjects, or included active control systems, motors, or other power sources.

Results:

Seventy-eight articles were included in the qualitative synthesis. Most articles were of low to moderate methodological quality. Five commonly used devices were identified: the Intrepid Dynamic Exoskeletal Orthosis, ToeOff, WalkOn, Neuro Swing, and Chignon. The devices have unique designs and are associated with specific populations. The Intrepid Dynamic Exoskeletal Orthosis was used in individuals with lower-limb trauma, the Neuro Swing and ToeOff in individuals with neurological disorders, the Chignon in individuals with hemiplegia and stroke, and the WalkOn in people with hemiplegia and cerebral palsy. Each device produced favorable outcomes in their respective populations of interest, such as increased walking speed, reduced pain, or improved balance.

Conclusions:

The mechanical characteristics and designs of carbon fiber AFOs improve outcomes in the populations in which they are most studied. Future literature should diligently report patient population, device used, and fitting procedures.
Acute retroviral syndrome is associated with lower CD4+ T cell nadir and delayed viral suppression, which are blunted by immediate antiretroviral therapy initiation
Authors: Gabert Rose , Lama Javier R. , Valdez Rogelio , Dasgupta Sayan , Cabello Robinson , Sanchez Hugo , Leon Mey , Huamani Javier Valencia , MacRae John , Montalban Esmelda , Pasalar Siavash , Ignacio Rachel Bender , Duerr Ann
Published: February 2023

Objectives:

To describe the prevalence of acute retroviral syndrome (ARS) and associated findings during primary HIV, and explore the relationship of ARS to clinical, virological, and immunological outcomes within a longitudinal screen, retest and treat study that minimized ascertainment bias.

Design:

We evaluated ARS symptoms and signs among 216 persons with acute and early incident HIV within the Sabes study of timing of antiretroviral therapy (ART) initiation during primary HIV in Peru.

Methods:

We evaluated patient reported symptoms and signs during primary HIV and used logistic regression and generalized linear models to evaluate associations with CD4+ and CD8+ T cell counts, HIV viral load, and a panel of 23 soluble markers of immune activation.

Results:

Sixty-one percent of participants had at least one ARS finding and 35% had at least 3. More ARS findings were reported in those enrolled within a month of estimated date of detectable infection (EDDI). Having more ARS signs/symptoms was associated with increased risk of CD4+ cell decrease below 350 cells/ml within the first 24 weeks, failure to suppress HIV viral load, and was most strongly associated with elevated IP-10. Immediate ART blunted effects on symptoms, CD4+ cell count and viral load, as associations were strongest in the arm that started ART after 24 weeks. Detrimental associations of ARS with CD4+ counts, and CD4+/CD8+ ratio were not maintained at 2 or 4 years.

Conclusions:

ARS has marked associations with short-term immunologic function and virologic suppression, which were mitigated in participants randomized to initiate ART immediately during primary infection.
3D-printing and cylinder buckling: challenges and opportunities
Authors: Cooley S. A. , Yang H. , Virgin L. N.
Published: February 2023

Cylinder buckling is notoriously sensitive to small geometric imperfections. This is an underlying motivation for the use of knock-down factors in the design process, especially in circumstances in which minimum weight is a key design goal, an approach well-established at NASA, for example. Not only does this provide challenges in the practical design of this commonly occurring structural load-bearing configuration, but also in the carefully controlled laboratory setting. The recent development of 3D-printing (additive manufacturing) provides an appealing experimental platform for conducting relatively high-fidelity experiments on the buckling of cylinders. However, in addition to geometric precision, there are a number of shortcomings with this approach, and this article seeks to describe the challenges and opportunities associated with the use of 3D-printing in cylinder buckling in general, and probing the robustness of equilibrium configurations in particular.

This article is part of the theme issue ‘Probing and dynamics of shock sensitive shells’.
Gametic Selection and Mating Systems show Mutually Dependent Evolution
Authors: Scott Michael F , Immler Simone
Published: February 2023

Competition among pollen or sperm (gametic selection) can cause evolution. Mating systems shape the intensity of gametic selection by determining the competitors involved, which can in turn cause mating system evolution. We model the bidirectional relationship between gametic selection and mating systems, focussing on variation in female mating frequency (monandry-polyandry) and self-fertilisation (selfing-outcrossing). First, we find that mating systems affect evolutionary responses to gametic selection, with more effective gametic selection when fertilisation success depends on haploid genotypes, rather than the diploid genotype of the father. Monandry and selfing both reduce the efficacy of gametic selection despite creating intense selection among pollen/sperm from heterozygous males with haploid expression. This effect means selfing can increase mutation load, in contrast to classic predictions where selfing purges deleterious mutations. Second, we show that mating systems can evolve via their effect on gametic selection, with polyandry evolving because it removes deleterious alleles more efficiently and increases offspring fitness. Our population genetic models reveal that this ‘good sperm’ effect could plausibly give a selective advantage for polyandry over monandry of only around 1%. Selection for polyandry is lessened further if some loci experience balancing selection and is likely to be overwhelmed by any direct fitness effects of mating systems. Similarly, the indirect benefits from manipulating gametic selection have a weak influence on the evolution of selfing, which is dominated by ‘automatic selection’ and inbreeding depression in our model. Nevertheless, gametic selection can be potentially decisive for selfing evolution because it significantly reduces inbreeding depression, which favours selfing. One test of the predicted interactions between gametic selection and mating system evolution would be to compare evolutionary rates in genes with different expression patterns across different mating systems.
Overestimation of anticoagulant benefit in patients with atrial fibrillation and low life expectancy: evidence from 12 randomized trials
Authors: Shah Sachin J. , van Walraven Carl , Jeon Sun Young , Boscardin W. John , Hobbs FD Richard , Connolly Stuart , Ezekowitz Michael , Covinsky Kenneth E. , Fang Margaret C. , Singer Daniel E.
Published: February 2023

Background

Patients with atrial fibrillation (AF) have a high rate of all-cause mortality that is only partially attributable to vascular outcomes. While the competing risk of death may affect expected anticoagulant benefit, guidelines do not account for it. We sought to determine if using a competing risks framework materially affects the guideline-endorsed estimate of absolute risk reduction attributable to anticoagulants.

Methods

We conducted a secondary analysis of 12 RCTs that randomized patients with AF to oral anticoagulants or either placebo or antiplatelets. For each participant, we estimated the absolute risk reduction (ARR) of anticoagulants to prevent stroke or systemic embolism using two methods. First, we estimated the ARR using a guideline-endorsed model (CHA2DS2-VASc) and then again using a Competing Risk Model that uses the same inputs as CHA2DS2-VASc but accounts for the competing risk of death and allows for non-linear growth in benefit over time. We compared the absolute and relative differences in estimated benefit and whether the differences in estimated benefit varied by life expectancy.

Results

7933 participants had a median life expectancy of 8 years (IQR 6, 12), determined by comorbidity-adjusted life tables. 43% were randomized to oral anticoagulation (median age 73 years, 36% women). The guideline-endorsed CHA2DS2-VASc model estimated a larger ARR than the Competing Risk Model (median ARR at 3 years, 6.9% vs. 5.2%). ARR differences varied by life expectancies: for those with life expectancies in the highest decile, 3-year ARR difference (CHA2DS2-VASc model – Competing Risk Model 3-year risk) was −1.2% (42% relative underestimation); for those with life expectancies in the lowest decile, 3-year ARR difference was 5.9% (91% relative overestimation).

Conclusion

Anticoagulants were exceptionally effective at reduced stroke risk. However, anticoagulant benefits were misestimated with CHA2DS2-VASc, which does not account for the competing risk of death nor decelerating treatment benefit over time. Overestimation was most pronounced in patients with the lowest life expectancy and when benefit was estimated over a multi-year horizon.
Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease
Authors: Zhang Kejia , Eldin Patrick , Ciesla Jessica H. , Briant Laurence , Lentini Jenna M. , Ramos Jillian , Cobb Justin , Munger Joshua , Fu Dragony
Published: February 2023

Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wildtype human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
Human subcortical pathways automatically detect collision trajectory without attention and awareness
Authors: Guo Fanhua , Zou Jinyou , Wang Ye , Fang Boyan , Zhou Huafen , Wang Dajiang , He Sheng , Zhang Peng
Published: February 2023

Detecting imminent collisions is essential for our survival and is likely supported by evolutionarily conserved mechanisms in the brain. Using high-resolution 7T fMRI, we investigated subcortical pathways for detecting collision trajectories in healthy human subjects and hemianopic patients. When healthy participants focused their attention on a central fixation task, their superior colliculus (SC), ventromedial pulvinar (vmPul) and ventral tegmental area (VTA) elicited stronger responses to a peripheral object approaching on head-collision courses compared to near-miss trajectories. Correlation and path analyses of collision-sensitive responses revealed collision sensitivity in the SC-vmPul and SC-VTA pathways without attention and cortical influence. Both behavioral performance and SC responses showed higher sensitivity to looming stimuli from the upper visual field. For hemianopic patients with unilateral lesions of the geniculostriate pathway, the ipsilesional SC, vmPul and VTA showed collision sensitivity to looming stimuli in their blind visual field, in the absence of their awareness. Stronger responses in the SC were also associated with better detection performance of the collision events. These findings clearly demonstrate that human tectofugal pathways, without attention and awareness, automatically detects approaching objects on a collision course, supporting blindsight to impending visual threats.

Highlights

SC-vmPul and SC-VTA pathways show collision sensitivity without attention and cortical influence in healthy participants.

Both behavioral performance and SC responses show higher sensitivity to looming stimuli from the upper visual field.

The ipsilesional SC, vmPul and VTA of hemianopic patients automatically detects collision trajectories in their blind visual field without awareness.

SC response is associated with “blindsight” detection of impending collisions.
Eggplant’s foliar chlorogenic acid provides resistance against the tropical armyworm
Authors: Kumar Manish , Umesh K.P. , Pandey Prashasti P. , Firake D. M. , Pandit Sagar S
Published: February 2023

Lepidopteran pests are the major crop devastators. Farmers have to resort to heavy synthetic pesticide application for their control. It increases the pesticide residue contamination on produce and causes health hazards. Synthetic pesticides also endanger beneficial insects and pollute the environment. Therefore, the use of safe and eco-friendly botanicals as biopesticides is rapidly increasing. Despite their high demand, only a few botanicals are commercially available. Consequently, biopesticide discovery research boomed in the last decade.

Spodoptera lituraFabricius (armyworm) is a polyphagous multi-insecticide-resistant lepidopteran pest. It is a serious concern for several commercially important crops. In this study, we employed a chemical ecology approach to discover a biopesticide against it. As a biopesticide source, we explored secondary metabolite-richSolanum melongenaL. (eggplant), one of the armyworm’s hosts. We found that the armyworm larvae show differential occurrence on seven eggplant varieties; the Himalayan eggplant variety RC-RL-22 (RL22) showed no armyworm infestation. When reared in a no-choice condition on RL22, larval mortality was two-fold higher, and mass was three-fold lower than the varieties showing high infestation. We tested whether RL22’s secondary metabolite(s) were associated with this hampered larval performance. Using LC-ESI-QTOF-based non-targeted metabolomics of eggplant varieties, we identified candidate metabolites. 5-O-caffeoylquinic acid (chlorogenic acid; CGA) showed a strong negative correlation (r= -0.88;p= 0.008) with the larval performance. CGA-spiked (average physiological concentration) artificial diet (CGA-AD)-fed larvae showed a three-fold mass reduction and two-fold mortality increase than the control artificial diet (AD)-fed larvae; pupation and eclosion also significantly reduced (1.3-fold and 1.4-fold, respectively) in the CGA-ingested larvae. We used a reverse genetics approach to assess thein plantainsecticidal potential of CGA. When RL22’s CGA biosynthesis gene hydroxycinnamoyl-CoA quinate transferase (SmHQT) was silenced using virus-induced gene silencing (VIGS), CGA levels decreased by three-fold. This CGA depletion rendered RL22 two-fold armyworm-susceptible than controls. Foliar CGA application restored RL22’s armyworm resistance.

Overall, this study showed that CGA exhibits larvicidal properties against the armyworm. It is also safe for beneficial organisms. CGA is a well-known dietary supplement and an antioxidant for humans. Thus, it is safe for human consumption. Together, high CGA-containing varieties can be used to reduce the armyworm infestation risk. CGA is a promising biopesticide candidate for the field trial phase against the lepidopteran pests, especially armyworm. If successful, it can be integrated into the pest control measures.
Temporal Dynamics of Normalization Reweighting
Authors: Baker Daniel H. , Marinova Daniela , Aveyard Richard , Hargreaves Lydia J. , Renton Alice , Castellani Ruby , Hall Phoebe , Harmens Miriam , Holroyd Georgia , Nicholson Beth , Williams Emily L. , Hobson Hannah M. , Wade Alex R.
Published: February 2023

1

For decades, neural suppression in early visual cortex has been thought to be fixed. But recent work has challenged this assumption by showing that suppression can bereweightedbased on recent history; when pairs of stimuli are repeatedly presented together, suppression between them strengthens. Here we investigate the temporal dynamics of this process using a steady-state visual evoked potential (SSVEP) paradigm that provides a time-resolved, direct index of suppression between pairs of stimuli flickering at different frequencies (5 and 7Hz). Our initial analysis of an existing EEG dataset (N=100) indicated that suppression increases substantially during the first 2-5 seconds of stimulus presentation (with some variation across stimulation frequency). We then collected new EEG data (N=100) replicating this finding for both monocular and dichoptic mask arrangements in a preregistered study designed to measure reweighting. A third experiment (N=20) used source localized MEG, and found that these effects are apparent in primary visual cortex (V1), consistent with results from neurophysiological work. Because long-standing theories propose inhibition/excitation differences in autism, we also compared reweighting between individuals with high vs low autistic traits, and with and without an autism diagnosis, across our 3 data sets (total N=220). We find no compelling differences in reweighting that are associated with autism. Our results support the normalization reweighting model, and indicate that for prolonged stimulation, increases in suppression occur on the order of 2-5 seconds after stimulus onset.
A Horizontal View of Primary Metabolomes in Vegetative Desiccation Tolerance
Authors: Dace Halford J.W. , Reus Robbin , Ricco Celeste Righi , Hall Robert , Farrant Jill M. , Hilhorst Henk W.M.
Published: February 2023

Vegetative desiccation tolerance (VDT), the ability of such tissues to survive the near complete loss of cellular water, is a rare but polyphyletic phenotype. It is a complex multifactorial trait, typified by some near universal (core) factors but with many and varied adaptations due to plant architecture, biochemistry and biotic/abiotic dynamics of particular ecological niches. The ability to enter into a quiescent biophysically stable state is what ultimately determines desiccation tolerance. Thus, understanding of the metabolomic complement of plants with VDT gives insight into the nature of survival as well as evolutionary aspects of VDT. In this study we measured the soluble carbohydrate profiles and the polar, TMS-derivatisable metabolomes of 7 phylogenetically diverse species with VDT, in contrast with 3 desiccation sensitive (DS) species, under conditions of full hydration, severe water deficit stress, and desiccated.

Our study confirmed the existence of core mechanisms of VDT systems relying on either constitutively abundant trehalose, or the accumulation of raffinose family oligosaccharides and sucrose, with threshold ratios conditioned by other features of the metabolome. DS systems did not meet these ratios. Considerable chemical variations among VDT species suggest that similar stresses, e.g. photosynthetic stress, are dealt with using different chemical regimes. Furthermore, differences in timing of metabolic shifts suggest there is not a single “desiccation programme”, but that subprocesses are coordinated differently at different phases of drying. There is likely to be constraints on the composition of a viable dry state and how different adaptive strategies interact with the biophysical constraints of VDT.
The Genome of the Soybean Gall Midge (Resseliella maxima)
Authors: Melotto Gloria , Jones Megan W. , Bosley Kathryn , Flack Nicole , Frank Lexi E. , Jacobson Emily , Kipp Evan J. , Nelson Sally , Ramirez Mauricio , Walls Carrie , Koch Robert L. , Lindsey Amelia R. I. , Faulk Christopher
Published: February 2023

The cecidomyiid fly, soybean gall midge,Resseliella maximaGagné, is a recently discovered insect that feeds on soybean plants in the Midwest US.Resseliella maximalarvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble aR. maximareference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. TheR. maximagenome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated thatR. maximaassembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge,Orseolia oryzae(Wood-Mason). TheR. maximagenome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.
SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens
Authors: Balaji Advait , Liu Yunxi , Nute Michael G. , Hu Bingbing , Kappell Anthony , LeSassier Danielle S. , Godbold Gene D. , Ternus Krista L. , Treangen Todd J.
Published: February 2023

The COVID-19 pandemic forever underscored the need for biosurveillance platforms capable of rapid detection of previously unseen pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening the door to real-time, in-field biosurveillance. Though a promising technology, streaming assignment of accurate functional and taxonomic labels with nanopore reads remains challenging given: (i) individual reads can span multiple genes, (ii) individual reads may contain truncated genes, and pseudogenes, (iii) the error rate of the ONT platform that may introduce frameshifts and missense errors, and (iv) the computational costs of read-by-read analysis may exceed that of in-field computational equipment. Altogether, these challenges highlight a need for novel computational approaches. To this end, we describe SeqSeqscreen-Nano, a novel and portable computational platform for the characterization of novel pathogens. Based on results from simulated and synthetic microbial communities, SeqScreen-Nano can identify Open Reading Frames (ORFs) across the length of raw ONT reads and then use the predicted ORFs for accurate functional characterization and taxonomic classification. SeqScreen-Nano can run efficiently in a memory-constrained environment (less than 32GB of RAM), allowing it to be utilized in resource-limited settings. SeqScreen-Nano can also process reads directly from the ONT MinlON sequencing device, enabling rapid, in-field characterization of previously unseen pathogens. SeqScreen-Nano (v4.0) is available on GitLab at:https://gitlab.com/treangenlab/seqscreen
Benchmarking robust spatial transcriptomics approaches to capture the molecular landscape and pathological architecture of archived cancer tissues
Authors: Vo Tuan , Jones Kahli , Yoon Sohye , Lam Pui Yeng , Kao Yung-Ching , Zhou Chenhao , Prakrithi P. , Crawford Joanna , Walters Shaun , Gupta Ishaan , Soyer H. Peter , Khosrotehrani Kiarash , Stark Mitchell S. , Nguyen Quan
Published: February 2023

Abtracts

Applying spatial transcriptomics (ST) to explore a vast amount of formalin-fixed paraffin-embedded (FFPE) archival cancer tissues has been highly challenging due to several critical technical issues. In this work, we optimised ST protocols to generate unprecedented spatial gene expression data for FFPE skin cancer. Skin is among the most challenging tissue types for ST due to its fibrous structure and a high risk of RNAse contamination. We evaluated tissues collected from ten years to two years ago, spanning a range of tissue qualities and complexity. Technical replicates and multiple patient samples were assessed. Further, we integrated gene expression profiles with pathological information, revealing a new layer of molecular information. Such integration is powerful in cancer research and clinical applications. The data allowed us to detect the spatial expression of non-coding RNAs. Together, this work provides important technical perspectives to enable the applications of ST on archived cancer tissues.
Deep sequencing of the T cell Receptor reveals common and reproducible CD8+signatures of response to checkpoint immunotherapy
Authors: Watson Robert A. , Taylor Chelsea A. , Tong Orion , Cooper Rosalin , Jungkurth Elsita , Kumar Sharma Piyush , Storey Bethan , Ye Weiyu , Sun Bo , de los Aires Alba Verge , Matos Santo Flavia , Nassiri Isar , Gilchrist James J. , Ieremia Eleni , Middleton Mark R. , Fairfax Benjamin P.
Published: February 2023

Immune checkpoint blockade (ICB) has markedly improved outcomes across a range of tumours, including metastatic melanoma (MM). However, peripheral biomarkers of response remain lacking and underlying mechanisms of action incompletely described. A number of studies have demonstrated the value of T cell receptor (TCR) repertoire analysis in determining associations with response, however identifying key groups of T cells based on their TCR usage has remained elusive. Here we performed deep sequencing of the TCR of CD8+T cells isolated from peripheral blood of patients receiving ICB for MM (n=91) at multiple time points, along with healthy control samples (n=42) and resected tumour specimens (from n=7 patients). Using the GLIPH2 algorithm to cluster TCR based on putative shared antigen specificity, we describe groups of TCR which expand post-ICB in responding patients which we term ‘Emergent Responder’ (ER) clones. We find that these ER clones are typically large and of a memory phenotype, with increased expression of genes encoding cytotoxic proteins. Analysis of tumours resected in advance of ICB demonstrates ER clones are enriched and expanded within the tumour compared to the periphery at pre-treatment. Significantly, we note the proportion of the peripheral repertoire occupied by ER clones strongly correlates with long-term clinical response. Clinical outcome further associated with HLA type and, crucially, can be validated across replication and independent datasets. This work provides the first-in-kind description of TCR-defined CD8+T cells that mediate the response to ICB in MM, demonstrating the prognostic utility of the peripheral immune repertoire with potential widespread therapeutic and prognostic applications.
The Crown Pearl V2: an improved genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)
Authors: Gomes-dos-Santos André , Lopes-Lima Manuel , Machado André M. , Forest Thomas , Achaz Guillaume , Teixeira Amílcar , Prié Vincent , Castro L. Filipe C. , Froufe Elsa
Published: February 2023

Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly ofMargaritifera margaritifera(Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. Theab initiogene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species’ unique biological and evolutionary features that ultimately will help to promote its conservation.
Hierarchical and fine-scale mechanisms of binocular rivalry for conscious perception
Authors: Qian Chencan , Chen Zhiqiang , de Hollander Gilles , Knapen Tomas , Zhang Zihao , He Sheng , Zhang Peng
Published: February 2023

Conscious perception alternates between the two eyes’ images during binocular rivalry. How hierarchical processes in our brain interact to resolve visual competition to generate conscious perception remains unclear. Here we investigated the mesoscale neural circuitry for binocular rivalry in human cortical and subcortical areas using high-resolution functional MRI at 7 Tesla. Eye-specific response modulation in binocular rivalry was strongest in the superficial layers of V1 ocular dominance columns (ODCs), and more synchronized in the superficial and deep layers. The intraparietal sulcus (IPS) generated stronger eye-specific response modulation and increased effective connectivity to the early visual cortex during binocular rivalry compared to monocular “replay” simulations. Although there was no evidence of eye-specific rivalry modulation in the lateral geniculate nucleus (LGN) of the thalamus, strong perceptual rivalry modulation can be found in its parvocellular (P) subdivision. Finally, IPS and ventral pulvinar showed robust perceptual rivalry modulation and increased connectivity to the early visual cortex. These findings demonstrate that local interocular competition arises from lateral mutual inhibition between V1 ODCs, and feedback signals from IPS to visual cortex and visual thalamus further synchronize and resolve visual competition to generate conscious perception.

Graphical abstract

Highlights

Eye-specific rivalry modulation is strongest in the superficial layers of V1 ODCs and more synchronized in superficial and deep layers

IPS generates stronger eye-specific response modulation and increases connectivity to V1 during rivalry compared to replay

LGN activity shows no evidence of eye-specific rivalry modulation but strong perceptual rivalry modulation in its P subdivision

IPS and ventral pulvinar show robust perceptual rivalry modulation and increased connectivity to the early visual cortex
Impact of aging on the immunological and microbial landscape of the lung during non-tuberculous mycobacterial infection
Authors: Cinco Isaac R. , Rhoades Nicholas S. , Napier Ethan G. , Davies Michael , Allison Derek B. , Kohama Steven G. , Bermudez Luiz , Winthrop Kevin , Fuss Cristina , Spindel Eliot R. , Messaoudi Ilhem
Published: February 2023

Nontuberculous mycobacteria (NTM) are environmentally ubiquitous and predominately cause pulmonary disease (NTMPD). The incidence of NTMPD has steadily increased and is now more prevalent than that ofMycobacterium tuberculosis(M. tb) in the US. Moreover, the prevalence of NTMPD increases with age; therefore, it is likely that the burden of NTMPD will continue to increase in the coming decades as the number of those over the age of 65 increased in the U.S population. However, the mechanisms leading to higher susceptibility and severity of NTMPD with aging are poorly defined. Here, we used a rhesus macaque model of intrabronchial infection withM. aviumcomplex in young and aged animals to address this knowledge gap. Unilateral infection resulted in a robust inflammatory response predominantly in the inoculated lung, however, immune cell infiltration and antigen-specific T cell responses were detected in both lungs. Nasal, oral, and fecal swabs, and BAL samples were profiled using 16S amplicon sequencing. These data suggested that decompartmentalization of the lower respiratory microbiome was occurring, evidenced by detection of bacterial DNA typically found in the gut and oral-pharyngeal cavity in bronchoalveolar samples following infection. Radiographic studies, gross pathology, and histopathology examination revealed increased disease severity in aged compared to young animals with pulmonary consolidation, edema, and lesions. Finally, single cell RNA sequencing indicated that aged animals generated a dysregulated macrophage and CD8 T cell response to MAC infection.
Evolutionary conserved and divergent responses to copper zinc superoxide dismutase inhibition in plants
Authors: Frohn Stephanie , Haas Fabian B. , Dreyer Bernd H. , Reiss Erik V. , Ziplys Anne , Weichert Heiko , Chavez Benjamin G. , D’Auria John C. , Rensing Stefan A. , Schippers Jos H.M.
Published: February 2023

Life evolved in the presence of reactive oxygen species (ROS) and was further challenged by two consecutive great oxidation events. Therefore, ROS are deeply intertwined into the physological, morphological and transcriptional responses of organisms. Copper zinc superoxide dismutases (CuZnSODs) evolved around the first great oxidation event and have next to their classical role in ROS detoxification also important roles in signaling and transcriptional regulation. Here we addressed the role of CuZnSODs in early land plant evolution. We show, that pharmaceutical inhibition of CuZnSODs with Lung Cancer Screen 1 (LCS-1) in different plant species, includingMarchantia polymorphaandPhyscomitrium patens, representing the evolutionary early stages of land plants, andArabidopsis thalianaas a modern vascular plant, lead to impairment of development and growth. Interestingly, Marchantia only possesses the cytosolic CuZnSOD isoform, whereasPhyscomitriumadditionally contains a plastidial isoform and Arabidopsis contains next to that a third peroxisomal isoform. An RNA-seq analysis revealed that the inhibition of CuZnSODs provoked a similar core response in all plant species analyzed, while those that contain more isoforms showed an extended response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Through the above approach the oxidative stress provoked by LCS-1 in plants can be specified and we argue that CuZnSOD functions are evolutionary conserved and might be important for plant terrestrialization.
Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
Authors: Wang Michael X. , Lou Esther G. , Sapoval Nicolae , Kim Eddie , Kalvapalle Prashant , Kille Bryce , Leo Elworth R. A. , Liu Yunxi , Fu Yilei , Stadler Lauren B. , Treangen Todd J.
Published: February 2023

Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 2 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer SNPs overlapping with primers and predicted PCR byproducts. We also compared Olivar head-to-head with ARTIC v4.1, the most widely used primer set for SARS-CoV-2 sequencing, and show Olivar yields similar read mapping rates (∼90%) and better coverage to the manually designed ARTIC v4.1 amplicons. We also evaluated Olivar on real wastewater samples and found that Olivar had up to 3-fold higher mapping rates while retaining similar coverage. In summary, Olivar automates and accelerates the generation of tiled amplicons, even in situations of high mutation frequency and/or density. Olivar is available as a web application athttps://olivar.rice.edu. Olivar can also be installed locally as a command line tool with Bioconda. Source code, installation guide and usage are available athttps://github.com/treangenlab/Olivar.