bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Age on Facial Nerve Recovery After Vestibular Schwannoma Resection
Authors: Macielak Robert J. , Lohse Christine M. , Wallerius Katherine P. , Lawlor Skye K. , Neff Brian A. , Celda Maria Peris , Van Gompel Jamie J. , Driscoll Colin L.W. , Link Michael J. , Carlson Matthew L.
Published: July 2023

Objective

The objective of this study is to assess the influence of age on facial nerve recovery after microsurgical resection of sporadic vestibular schwannoma.

Study Design

A historical cohort study was performed.

Setting

The study was performed at a tertiary referral center.

Patients

The studied cohort included patients with a House-Brackmann (HB) Grade III or worse in the immediate postoperative period.

Interventions

The studied intervention was microsurgical resection.

Main Outcome Measures

The main outcome measure was complete recovery of facial nerve function to HB Grade I at least 12 months postoperatively.

Results

There were six patients with intracanalicular tumors and 100 with cerebellopontine angle (CPA) tumors eligible for study. Given the few patients with intracanalicular tumors, no further analysis was pursued in this subset. For patients with CPA tumors, a multivariable analysis of several patient and tumor characteristics demonstrated age at surgery (odds ratio for 10-year increase of 0.68; 95% confidence interval [CI], 0.47–0.98; p = 0.04) and immediate postoperative HB grade (odds ratio for one-grade increase of 0.27; 95% CI, 0.15–0.50; p < 0.001) to be jointly significantly associated with complete recovery to HB Grade I, indicating that the likelihood of complete facial nerve recovery was higher for younger patients and for those with better immediate postoperative HB grades. For example, the predicted probability of complete facial nerve recovery for a 30-year-old with immediate postoperative HB Grade III was 0.76 (or 76% when expressed as a percentage), whereas the predicted probability for a 50-year-old with immediate postoperative HB Grade V was only 0.10.

Conclusions

After considering immediate postoperative HB grade, younger age at surgery was independently significantly associated with complete facial nerve recovery, which can assist in intraoperative decision-making regarding extent of resection and postoperative counseling.
Health Economic Cost Analysis for Percutaneous Bone Conduction Devices: The Minimally Invasive Ponto Surgery Versus Linear Incision Technique with Tissue Preservation
Authors: Strijbos Ruben M. , Straatman Louise V. , Stegeman Inge , Holmberg Marcus , Johansson Martin L. , Stokroos Robert J.
Published: July 2023

Objectives

To identify differences in mean cost per patient between the Minimally Invasive Ponto Surgery (MIPS) and the linear incision technique with tissue preservation (LITT-P).

Study design

Health economic cost analysis.

Setting

The analysis was performed in a randomized multicenter controlled trial cohort.

Patients

Adult patients eligible for unilateral bone conduction device surgery.

Interventions

MIPS versus LITT-P surgery for bone conduction device implantation.

Main outcome measures

Perioperative and postoperative costs were identified and compared.

Results

The difference in mean cost per patient between both techniques was €77.83 in favor of the MIPS after 22 months follow-up. The mean costs per patient were lower in the MIPS cohort for surgery (€145.68), outpatient visits (€24.27), systemic antibiotic therapy with amoxicillin/clavulanic acid (€0.30) or clindamycin (€0.40), abutment change (€0.36), and abutment removal (€0.18). The mean costs per patient were higher for implant and abutment set (€18.00), topical treatment with hydrocortison/oxytetracycline/polymyxine B (€0.43), systemic therapy with azithromycin (€0.09) or erythromycin (€1.15), local revision surgery (€1.45), elective explantation (€1.82), and implant extrusion (€70.42). Additional analysis of scenarios in which all patients were operated under general or local anesthesia or with recalculation when using current implant survival rates showed that differences in mean cost per patient were also in favor of the MIPS.

Conclusion

The difference between the MIPS and the LITT-P in mean cost per patient was €77.83 in favor of the MIPS after 22 months of follow-up. The MIPS is an economically responsible technique and could be promising for the future.
Postoperative Outcomes After Tympanoplasty for Active Versus Inactive Otitis Media Patients With Tympanic Membrane Perforation: A Systematic Review and Meta-Analysis
Authors: Wong Zhi Yong , Park Yoon Soo , Mann Gagandeep Singh
Published: July 2023

Objectives

To compare postoperative tympanoplasty outcomes between active versus inactive otitis media (OM) patients with tympanic membrane perforation.

Databases Reviewed

Medline via PubMed, Embase, Web of Science, Cochrane Central Register of Controlled Trials, and Google Scholar for studies published from inception to March 1, 2023.

Methods

Studies of 15- to 60-year-old patients undergoing microscopic/endoscopic myringoplasty using underlay/overlay technique with reported postoperative mean hearing gain and graft uptake were included. Studies requiring simultaneous surgical procedures, reporting patients with comorbidities and with non-English full text articles were excluded. Articles were independently screened by two researchers with data extracted according to a predetermined proforma in Microsoft Excel. Cochrane risk-of-bias assessment was used for risk of bias evaluation of randomized studies and Risk of Bias in Nonrandomized Studies of Interventions for nonrandomized studies. Similar studies were pooled for meta-analysis using the inverse variance random effects model to calculate the mean difference and corresponding 95% confidence interval (CI) for mean hearing gain and DerSimonian and Laird random effects model for graft uptake.

Results

Thirty-three studies comprising 2,373 patients met the inclusion/exclusion criteria, seven were pooled for meta-analysis. Included articles showed inactive OM patients have higher average postoperative mean hearing gain of 10.84 dB and graft uptake of 88.7% compared to active OM patients (9.15 dB and 84.2%). Meta-analysis of mean hearing gain (MD, –0.76 dB; 95% CI, −2.11 to 0.60; p = 0.27, moderate certainty) and graft uptake (OD, 0.61; 95% CI, 0.34–1.09; p = 0.10, moderate certainty) have an overall p value >0.05.

Conclusion

There were no statistically significant differences in postoperative mean hearing gain and graft uptake between active and inactive OM patients undergoing tympanoplasty. Hence, tympanoplasty procedures should not be postponed solely because of patients' preoperative ear discharge status.
Diagnostic Role of Combined Electrocochleography and Pure-Tone Audiometry Monitoring During Dehydrating Test in Ménière's Disease: A Case Series
Authors: Immordino Angelo , Sireci Federico , Lorusso Francesco , La Gumina Rosario , Montalbano Calogero , Alfarghal Mohamad , Immordino Palmira , Dispenza Francesco
Published: July 2023

Objectives

To evaluate the diagnostic role of combined electrocochleography and pure-tone audiometry monitoring during dehydrating test in Ménière's disease and consider its suitability as a diagnostic tool to differentiate those patients with unclear differential diagnosis and therefore identify those with clear endolymphatic hydrops responsive to dehydrating test. To study the efficacy of dehydrating therapy on vertiginous symptoms and hearing loss in patients with Ménière's disease.

Study Design

Prospective case series.

Settings

University hospital, secondary referral center.

Patients

Thirty patients, 20 women and 10 men, age range of 25 to 75 years, matching the criteria for definite Ménière's disease according to the Barany Society classification.

Intervention

Diagnostic. During an active phase of the disease, electrocochleography and pure-tone audiometry were performed, and repeated at 30th, 45th, and 60th minutes after intramuscular injection of 40 mg furosemide and 40 mg methylprednisolone.

Main Outcome Measure

Data related to symptoms, electrocochleography, and pure-tone audiometry during the dehydrating test were collected at different times and statistically analyzed.

Results

After the administration of dehydrating therapy, we observed that both summating potential and action potential ratio and summating potential and action potential area ratio were normalized in 21 of 30 subjects. Furthermore, pure-tone audiometry thresholds improved significantly. An improvement of ear fullness was also observed, whereas tinnitus unchangeably persisted.

Conclusions

The monitoring of the electrocochleography and pure-tone audiometry thresholds during dehydrating tests with furosemide and methylprednisolone could allow to detect an improvement of instrumental features and clinical symptoms related to endolymphatic hydrops, and therefore, it could be used as a diagnostic tool in the identification of those patients affected by Ménière's disease with unclear differential diagnosis.
Effects of Nanofat in Plastic and Reconstructive Surgery: A Systematic Review
Authors: Tran Vinh Vuong The , Jin Xian , Hong Ki Yong , Chang Hak
Published: July 2023

Background:

Since nanofat was first introduced by Tonnard in 2013, numerous studies have reported positive findings with its use; however, concerns exist regarding its effects and mechanisms, and the various methods used to generate nanofat also remain unclear. The authors conducted a systematic review to evaluate the efficacy of nanofat grafting alone in plastic and reconstructive surgery.

Methods:

The MEDLINE, Embase, Cochrane Central, Web of Science, and Scopus databases were searched for studies related to the use of nanofat grafting alone in plastic and reconstructive surgery. Outcomes of interest were all clinical results in humans or animals.

Results:

Twelve studies were included. No meta-analysis was conducted due to the clinical heterogeneity of the studies. In general, included studies had a low level of evidence. Six studies (n = 253 patients) showed significant improvements in scar characteristics based on Patient and Observer Scar Assessment Scale, FACE-Q scale, physician assessment, patient satisfaction, and Vancouver Scar Scale scores. Four studies described the benefits of nanofat in skin rejuvenation (wrinkles, fine rhytides, pigmentation, and discoloration) through photographs, questionnaires, and indentation indices. Histologic evaluation illustrated overall increases in skin thickness, collagen, and elastic fibers. Three experimental studies showed the beneficial effects of nanofat on fat grafting, diabetic wound healing, and hair growth, with compelling histological evidence. No severe complication was reported.

Conclusions:

Nanofat grafting shows potential benefits in scar and antiaging treatments, with conclusive histological evidence. Clinical studies of fat grafting, wound healing, and hair growth should be conducted, based on the results of this systematic review. Nanofat grafting could be a practical and safe procedure.
Clinical Predictors of C5 Spinal Nerve Viability in Pan−Brachial Plexus Injuries
Authors: Wu Kitty Y. , Asserson Derek B. , Loosbrock Michelle F. , Bishop Allen T. , Spinner Robert J. , Shin Alexander Y.
Published: July 2023

Background:

In pan–brachial plexus injury, distinguishing between preganglionic and postganglionic injuries is crucial to reconstructive planning. This study aimed to identify preoperative factors that would accurately predict a reconstructible C5 spinal nerve.

Methods:

Patients with pan–brachial plexus injury from a single institution between 2001 and 2018 were reviewed. Patient demographics, clinical examination, diagnostic imaging, and electrodiagnostic results were recorded. C5 viability was determined based on supraclavicular exploration and intraoperative electrophysiologic testing. Univariate analysis identified significant factors for regression analysis. A multivariable parsimonious model was created using stepwise high-performance logistic regression.

Results:

A total of 311 patients (mean age, 29.9 years; 46 women and 265 men; mean Injury Severity Score, 17.2) were included. A total of 134 patients (43%) had a viable C5 nerve, and 50 patients (12%) had a viable C6 nerve. Intact C5 spinal nerve on computed tomographic (CT) myelogram (OR, 5.4), positive Tinel test (OR, 2.6), muscle strength greater than or equal to 4 (according to the modified British Medical Research Council scale) for the rhomboid (OR, 1.3) or greater than or equal to 4 for the serratus anterior (OR, 1.4), and rhomboid needle electromyography (OR, 1.8) were predictive of having a viable C5 spinal nerve. The multivariable parsimonious stepwise model (area under the curve, 0.77) included four factors: positive Tinel test, intact C5 spinal nerve on CT myelogram, hemidiaphragmatic elevation, and midcervical paraspinal fibrillations.

Conclusions:

In this cohort of pan–brachial plexus patients with major polytrauma, there was a 43% incidence of viable C5 spinal nerve. A positive Tinel test (OR, 2.1) and intact C5 spinal nerve on CT myelogram (OR, 4.9) predicted a viable C5 nerve. In contrast, hemidiaphragmatic elevation (OR, 3.1) and midcervical paraspinal fibrillations (OR, 2.92) predicted root avulsion.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, III.
Medial Plantar Artery Perforator Kiss Flap for Salvage of Extensive Palmar Skin Defect
Authors: Zheng Youmao , Zhang Shunuo , Hong Joon Pio , Hallock Geoffrey G. , Levin L. Scott , Zhang Yixin , Min Peiru
Published: July 2023

Background:

Flaps based on the medial plantar artery (MPA) accomplish favorable surgical outcomes in palmar resurfacing because of their outstanding texture, pliability, and contour, but primary closure cannot be achieved at the donor site when the flap is designed to be relatively large. In this study, the kiss technique was used for the reconstruction of extensive palmar defects, which minimized donor-site morbidity.

Methods:

A modified flap surgical strategy was systemically developed based on the perforator distribution of the MPA through a cadaver study. Two or three narrow, small skin paddles based on the MPA were raised and resembled at the recipient site as a larger flap. Static two-point discrimination, hypersensitivity and range of motion, QuickDASH, gait, and patient satisfaction were evaluated 6 months to 12 months after the operation.

Results:

From June of 2015 to July of 2021, 20 cases of reconstruction using the MPA perforator kiss flap were performed for the resurfacing of palmar skin defects. All flaps survived uneventfully, with coverage matching the texture and color of the recipients, except one flap that exhibited venous congestion and recovered after revision. Twelve flaps (60%) were double-paddled, and eight flaps (40%) were triple-paddled, with a resurfacing area of 27.19 cm2 and 41.1 cm2, respectively. All donor sites achieved primary closure without major complications.

Conclusions:

Versatile kiss flap combinations were developed based on further understanding of the MPA system. Durable and pliable characteristics of the MPA perforator flap provide excellent reconstruction for extensive palmar defects while minimizing donor-site complications.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Comparison of 2 Regenerative Peripheral Nerve Interface Techniques for the Treatment of Rat Neuroma Pain
Authors: Senger Jenna-Lynn , Thorkelsson Aline , Wang Bonnie Y. , Chan K. Ming , Kemp Stephen W. P. , Webber Christine A.
Published: July 2023

Treatment of painful neuromas has long posed a significant challenge for peripheral nerve patients. The regenerative peripheral nerve interface (RPNI) provides the transected nerve with a muscle graft target to prevent neuroma formation. Discrepancies in RPNI surgical techniques between animal models (“inlay” RPNI) and clinical studies (“burrito” RPNI) preclude direct translation of results from bench to bedside and may account for variabilities in patient outcomes. The authors compared outcomes of these 2 surgical techniques in a rodent model. Animals treated with burrito RPNI after tibial nerve neuroma formation demonstrated no improvement in pain assessment, and tissue analysis revealed complete atrophy of the muscle graft with neuroma recurrence. By contrast, animals treated with inlay RPNI had significant improvement in pain with viable muscle grafts. The results suggest superiority of the inlay RPNI surgical technique for the management of painful neuroma in rodents.

Clinical Relevance Statement:

RPNIs are currently being used to prevent and treat neuroma and phantom limb pain. This preclinical study suggests the superiority of one surgical technique over the other.
Genotyping of Acinetobacter baumannii isolates from a tertiary care hospital in Cochin, South India
Authors: RAJAN VINEETH , Vijayan Ardhra , Puthiyottu Methal Ambili , Lancy Justus , Sivaraman Gopalan Krishnan
Published: July 2023

Acinetobacter baumannii poses a significant challenge in healthcare settings across the globe, with isolates exhibiting carbapenem resistance at unprecedented rates. Here, we characterized a collection of A. baumannii isolates (n=64) recovered during the period September 2020 – November 2021 at a teaching hospital in Cochin, South India. The identity of the isolates was confirmed with blaOXA-51-like PCR. The major carbapenemase determinants identified were blaOXA-23-like (45, 70.3%) and blaNDM-1 (31, 48.4%); co-occurrence of these genes was also observed in 27 (42.2%) isolates. Other resistance genes identified included blaPER (34, 53.1%), aac(6')-Ib-cr (42, 65.6%), qnrS (25, 39.1%), sul1 (32, 50%), sul2 (33, 51.6%), strA/strB (36, 56.3%), aphA1-Iab (35, 54.7%) and tetB (32, 50%). Mapping PCR revealed the insertion element, ISAbaI upstream of blaOXA-23-like in all isolates possessing this gene. Concerning disinfectant resistance, all isolates carried the quaternary ammonium compound (QAC) resistance gene, qacEΔ1. Minimal inhibitory concentration (MIC) of benzalkonium chloride was high among the isolates and ranged from 8 to 128 µg/ml. However, low MICs were observed for chlorhexidine and triclosan, with the majority (54, 80.6%) of isolates showing an MIC of 2 µg/ml for chlorhexidine and all isolates exhibiting MICs of ≤0.125 µg/ml for triclosan. Further, all isolates were strong biofilm-producers, as assessed by the crystal violet-based microtitre plate assay. The ApaI-pulsed-field gel electrophoresis (PFGE) revealed the multi-clonal nature of the isolates, with 16 clusters and 16 unique pulsotypes identified at a cut-off of 80%. In short, this study provides useful data on the molecular features of A. baumannii from this region, which could be helpful in assessing the local epidemiology of this pathogen and also to devise infection control strategies.
Exploratory Correlation of The Human Structural Connectome with Non-MRI Variables in Alzheimer’s Disease
Authors: Aganj Iman , Mora Jocelyn , Frau-Pascual Aina , Fischl Bruce ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: July 2023

INTRODUCTION

Discovery of the associations between brain structural connectivity and clinical and demographic variables can help to better understand the vulnerability and resilience of the brain architecture to neurodegenerative diseases and to discover biomarkers.

METHODS

We used four diffusion-MRI databases, three related to Alzheimer’s disease, to exploratorily correlate structural connections between 85 brain regions with non-MRI variables, while stringently correcting the significance values for multiple testing and ruling out spurious correlations via careful visual inspection. We repeated the analysis with brain connectivity augmented with multi-synaptic neural pathways.

RESULTS

We found 85 and 101 significant relationships with direct and augmented connectivity, respectively, which were generally stronger for the latter. Age was consistently linked to decreased connectivity, and healthier clinical scores were generally linked to increased connectivity.

DISCUSSION

Our findings help to elucidate which structural brain networks are affected in Alzheimer’s disease and aging and highlight the importance of including indirect connections.
T4SEpp: a pipeline integrated with protein language models effectively predicting bacterial type IV secreted effectors
Authors: Hu Yueming , Wang Yejun , Hu Xiaotian , Chao Haoyu , Li Sida , Ni Qinyang , Zhu Yanyan , Hu Yixue , Zhao Ziyi , Chen Ming
Published: July 2023

Many pathogenic bacteria use type IV secretion systems(T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causeing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs, and compared their performance. An integrated model T4SEpp was assembled by a module searching full-length, signal sequence and effector domain homologs of known T4SEs, a machine learning module based on the hand-crafted features extracted from the signal sequences, and the third module containing three best-performing protein language pre-trained models. T4SEpp outperformed the other state-of-the-art (SOTA) software tools, achieving ∼0.95 sensitivity at a high specificity of ∼0.99, based on the assessment of an independent testing dataset. Additionally, we performed a comprehensive search among 8,761 bacterial species, leading to the discovery of 227 species belonging to 3 phyla and 117 genera that possess T4SSs. Furthermore, leveraging the power of T4SEpp, we successfully identified a grand total of 12,622 plausible T4SEs. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs, and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible athttps://bis.zju.edu.cn/T4SEpp.
Decapitated body intelligence (DBI) in cricketGryllodes sigillatus
Authors: Xue Tongyao , Yang Hewei , Wu Wen , Wang Qinghao
Published: July 2023

Background

intelligence is a highly complex problem. The decapitated insect exhibits various behaviors, indicating that they may have intelligence. Recent studies have reported organoid intelligence (OI) that lab-grown organoids also possess intelligence. This study investigated the response of decapitated crickets to different chemical stimuli to determine whether decapitated crickets have intelligence.

Methods

We used deionized water, NaCl, sucrose, and sodium hypochlorite to stimulate the front legs of the decapitated crickets and lesion the T1-T2 nerve connection of the thoracic ganglia. The behavioral response types of their forelegs were recorded. Reaction time, incidence rate, and total number of responses were calculated and analyzed.

Results

The decapitated crickets exhibit four types of responses: leg extension, leg withdrawal, leg lift, and jump. The reaction time and incidence rate varied depending on the type and concentration of the stimulant solution. The total number of responses gradually increased with deionized water, NaCl, sucrose, and sodium hypochlorite. The lesion experiments further revealed that the only T1 thoracic ganglion can control stimulating behavior.

Conclusion

The decapitated crickets possess the intelligence of perceiving stimuli and taking corresponding action. We called it decapitated body intelligence (DBI) or extrabrain intelligence (EI), which suggests that intelligence is not localized exclusively in the brain but also resides in insect ganglia. This finding opens up new ideas and avenues for the study of intelligence and the brain.
Juvenile niches select between two distinct development trajectories and symbiosis modes in vent shrimps
Authors: Methou Pierre , Guéganton Marion , Copley Jonathan T. , Watanabe Hiromi Kayama , Pradillon Florence , Cambon-Bonavita Marie-Anne , Chen Chong
Published: July 2023

Most animal species have a singular developmental pathway and adult ecology, but developmental plasticity is well-known in some like honeybees where castes display profoundly different morphology and ecology. An intriguing case is the Atlantic deep-sea hydrothermal vent shrimpRimicaris hybisae/chaceithat share dominant COI haplotypes but develops into either the symbiont-relianthybisaewith a hypertrophied head chamber (in the Mid-Cayman Spreading Centre) or the mixotrophicchaceiwith a narrow head chamber (on the Mid-Atlantic Ridge). Here, we use X-ray micro-computed tomography and fluorescentin situhybridization to show that key anatomical shifts in both occur between the juvenile-subadult transition, when those developing intohybisaehave fully established symbiosis but notchacei. On the Mid-Atlantic Ridge the diet ofR. chaceihas been hypothetically linked to competition with the obligatorily symbiotic congenerR. exoculata, and we find anatomical evidences thatR. exoculatais indeed better adapted for symbiosis – suggesting thechaceimorph could be an adaptation to prevent competitive exclusion. Our results suggest that the two distinct development trajectories are likely selected according to the diet available to the juveniles, determined by whether energetically sufficient symbiont colonisation has occurred before reaching subadult stage.
A continuous centennial Lateglacial-Early Holocene (15-10 cal kyr BP) palynological record from the Iberian Pyrenees and regional comparisons
Authors: Rull Valentí , Blasco Arnau , Calero Miguel Ángel , Blaauw Maarten , Teresa Vegas-Vilarrúbia
Published: July 2023

This paper presents the first continuous (gap-free) Lateglacial-Early Holocene (LGEH) pollen record for the Iberian Pyrenees resolved at centennial resolution. The main aims are (i) to provide a standard chronostratigraphic correlation framework, (ii) to unravel the relationships between vegetation shifts, climatic changes and fire, and (iii) to obtain a regional picture of LGEH vegetation for the Pyrenees and the surrounding lowlands. Seven pollen assemblage zones were obtained and correlated with the stadial/interstadial phases of the Greenland ice cores that serve as a global reference. Several well-dated datums were also derived for keystone individual taxa that are useful for correlation purposes. Four vegetation types were identified, two of them corresponding to conifer and deciduous forests (Cf, Df) and two representing open vegetation types (O1, O2) with no modern analogs, dominated byArtemisia-Poaceae andSaxifraga-Cichiroideae, respectively. Forests dominated during interstadial phases (Bølling/Allerød and Early Holocene), whereas O1 dominated during stadials (Oldest Dryas and Younger Dryas), with O2 being important only in the first half of the Younger Dryas stadial. The use of pollen-independent proxies for temperature and moisture allowed the reconstruction of paleoclimatic trends and the responses of the four vegetation types defined. The most relevant observation in this sense was the finding of wet climates during the Younger Dryas, which challenges the traditional view of arid conditions for this phase on the basis of former pollen records. Fire incidence was low until the early Holocene, when regional fires were exacerbated, probably due to the combination of higher temperatures and forest biomass accumulation. These results are compared with the pollen records available for the whole Pyrenean range and the surrounding lowlands within the framework of elevational, climatic and biogeographical gradients. Some potential future developments are suggested on the basis of the obtained results, with an emphasis on the reconsideration of the LGEH spatiotemporal moisture patterns and the comparison of the Pyrenees with other European ranges from different climatic and biogeographical regions.
Transcriptome brings variations of gene expression, alternative splicing, and structural variations into gene-scale trait dissection in soybean
Authors: Li Delin , Wang Qi , Tian Yu , Lyv Xiangguang , Zhang Hao , Sun Yinglu , Hong Huilong , Gao Huawei , Li Yan-Fei , Zhao Chaosen , Wang Jiajun , Wang Ruizhen , Yang Jinliang , Liu Bin , Schnable Patrick S. , Schnable James C. , Li Ying-Hui , Qiu Li-Juan
Published: July 2023

Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be a bottleneck. Transcriptome-wide association study (TWAS) addresses this by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci (eQTLs) with GWAS results. Here, we used self-pollinated soybean as a model to evaluate the application of TWAS in the genetic dissection of traits in plant species that exhibit slow LD decay. The first RNA-Seq analysis of a soybean diversity panel was conducted, which identified the genetic regulation of 29,286 genes. Different TWAS solutions were less affected by LD and robust with source of expression that identified known genes related to traits from different development stages and tissues. A novel gene named pod colorL2was identified via TWAS and functionally validated by genome editing. Our introduction of the new exon proportion feature significantly improves the capture of expression variations resulting from structural variations and alternative splicing. As a result, the genes identified by our TWAS approach exhibited a diverse range of causal variations, including SNP, insertion/deletion, gene fusion, copy number variation, and alternative splicing. Using our TWAS approach, we identified genes associated with flowering time, including both previously known candidates and novel genes that had not been linked to this trait before, providing complementary insights with GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
Intradisciplinary Growth of Sustainability-Minded Engineers through Conservation Technology
Authors: Schulz Andrew , Shriver Cassie , Patka Anika , Greiner Caroline , Seleb Benjamin , Hull Rebecca Watts , Subiño Sullivan Carol , Sonnenberg-Klein Julia M. , Moore Roxanne
Published: July 2023

Background

The need for sustainability-minded engineers prepared to address complex societal challenges has grown exponentially in recent years. Frameworks like the United Nations (UN) Sustainable Development Goals (SDGs) have begun to drive structural changes in engineering education, including new ABET accreditation focused on sustainability. The new field of conservation technology allows engineers to develop sustainability competencies and identities as conservationists and environmentalists.

Purpose

This manuscript describes an assessment of student identity development in conservation and environmentalism in the GaTech4Wildlife Vertically Integrated Project (VIP) course at Georgia Tech. The course uses the principles of Human-Centered Design along with the UN Sustainable Development Goals and project-based learning to solve conservation-oriented, real-world problems and develop sustainability-minded engineers.

Design/Method

Undergraduate students participated in the course and utilizing both in-person interviews and post-course assessment, students were assessed for course themes and identities. The sample consisted of students from the College of Engineering and the College of Computing.

Results

Since 2019, over 50 students have participated in this Tech4Wildlife course. Based on surveys and interviews of nearly 20 of the most recent students, students transitioned from identifying as engineers and coders with no sustainability knowledge to nearly doubling their identity measures as conservationists and environmentalists after only one semester.

Conclusions

To teach the next generation of sustainability-minded engineers, interdisciplinary, project-based courses grounded in Sustainable Development Goals may offer a meaningful pathway for students to develop both technical skills and conservationist identities.
Nanobead-based single-molecule pulldown for single cells
Authors: Zhao Qirui , Shen Yusheng , Li Xiaofen , Li Yulin , Tian Fang , Yu Xiaojie , Liu Zhengzhao , Tong Rongbiao , Park Hyokeun , Yobas Levent , Huang Pingbo
Published: July 2023

Investigation of cell-to-cell variability holds critical physiological and clinical implications. Thus, numerous new techniques have been developed for studying cell-to-cell variability, and these single-cell techniques can also be used to investigate rare cells. Moreover, for studying protein-protein interactions (PPIs) in single cells, several techniques have been developed based on the principle of the single-molecule pulldown (SiMPull) assay. However, the applicability of these single-cell SiMPull (sc-SiMPull) techniques is limited because of their high technical barrier and special requirements for target cells and molecules. Here, we report a highly innovative nanobead-based approach for sc-SiMPull that is based on our recently developed microbead-based, improved version of SiMPull for cell populations. In our sc-SiMPull method, single cells are captured in microwells and lysed in situ, after which commercially available, pre-surface-functionalized magnetic nanobeads are placed in the microwells to specifically capture proteins of interest together with their binding partners from cell extracts; subsequently, the PPIs are examined under a microscope at the single-molecule level. Relative to previously published methods, nanobead-based sc-SiMPull is considerably faster, easier to use, more reproducible, and more versatile for distinct cell types and protein molecules, and yet provides similar sensitivity and signal-to-background ratio. These crucial features should enable universal application of our method to the study of PPIs in single cells.

Statement of Significance

Heterogeneity between single cells holds critical physiological and clinical implications. Characterization of protein-protein interactions (PPIs) and identification of the interacting partners of a specific protein are critical for elucidating the function and regulation of the protein. However, the applicability of the currently available techniques for studying PPIs in single cells is limited by their high technical barrier and special requirements for cell/proteins types. Our single-cell single-molecule pulldown (sc-SiMPull) assay in this study is not only substantially simpler and faster than existing sc-SiMPull methods, but also considerably more widely applicable—to all cell types and to both soluble and transmembrane proteins. These two crucial features should enable universal application of our method to the study of PPIs in single cells.
Aberrant regulation of the Rap1 small GTPase in response to escalating, intermittent stress produces hippocampal synaptic and cognitive dysfunction
Authors: Bjornson Kathryn J. , Vanderplow Amanda M. , Yang Yezi , Kermath Bailey A. , Cahill Michael E.
Published: July 2023

The effects of repeated stress on cognitive impairment are thought to be mediated, at least in part, by reductions in the stability of dendritic spines in brain regions critical for proper learning and memory, including the hippocampus. Small GTPases are particularly potent regulators of dendritic spine formation, stability, and morphology in hippocampal neurons. Through the use of small GTPase protein profiling in mice, we identify increased levels of synaptic Rap1 in the hippocampal CA3 region in response to escalating, intermittent stress. We then demonstrate that increased Rap1 in the CA3 is sufficient in and of itself to produce stress-relevant dendritic spine and cognitive phenotypes. Further, using super-resolution imaging, we investigate how the pattern of Rap1 trafficking to synapses likely underlies its effects on the stability of select dendritic spine subtypes. These findings illuminate the involvement of aberrant Rap1 regulation in the hippocampus in contributing to the psychobiological effects of stress.
A CRISPR-based genetic screen inBacteroides thetaiotaomicronreveals a small RNA modulator of bile susceptibility
Authors: Prezza Gianluca , Liao Chunyu , Reichardt Sarah , Beisel Chase L. , Westermann Alexander J.
Published: July 2023

Microbiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbiota species, yet tend to be missed by traditional functional genomics approaches. Here, we establish CRISPR interference (CRISPRi) in the abundant microbiota memberBacteroides thetaiotaomicronfor genome-wide sRNA screens. By assessing the abundance of different protospacer-adjacent motifs, we identify thePrevotella bryantiiB14 Cas12a as a suitable nuclease for CRISPR screens in these bacteria and generate an inducible Cas12a expression system. Using a luciferase reporter strain, we infer guide design rules and use this knowledge to assemble a computational pipeline for automated gRNA design. By subjecting the resulting guide library to a phenotypic screen, we uncover the previously uncharacterized sRNA BatR to increase susceptibility to bile salts, likely through the regulation of genes involved inBacteroidescell surface structure. Our study lays the groundwork for unlocking the genetic potential of these major human gut mutualists and, more generally, for discovering hidden functions of bacterial sRNAs.
Unifying design principles of endocrine gland mass and its regulatory circuits
Authors: Raz Moriya , Milo Tomer , Kohanim Yael Korem , Karin Omer , Tendler Avichai , Bar Alon , Glass David S. , Mayo Avi , Alon Uri
Published: July 2023

Hormones are regulatory molecules that impact physiological functions. Much is known about individual hormones, but general rules that connect the regulatory logic of different hormone systems are limited. In this study, we analyzed a range of human hormone systems using a mathematical approach to integrate knowledge on endocrine cells, target tissues and regulation, to uncover unifying principles and regulatory circuits. We find that the number of cells in an endocrine gland is proportional to the number of cells in its target tissues, as one single endocrine cell serves approximately 2000 target cells. We identified five classes of regulatory circuits, each has specific regulatory functions such as homeostasis or allostasis. The most complex class includes an intermediate gland, the pituitary, which can otherwise be considered redundant and exposes to fragilities. We suggest a tradeoff: with the price of fragilities comes advantages -amplification, buffering of hypersecreting tumors, and faster response times. By elucidating these unifying principles and circuits, this study deepens our understanding of the control of endocrine processes and builds the foundation for systems endocrinology.
NOTCH3 signalling controls human trophoblast stem cell expansion and differentiation
Authors: Dietrich Bianca , Victoria Kunihs , Lackner Andreas I. , Meinhardt Gudrun , Koo Bon-Kyoung , Pollheimer Jürgen , Haider Sandra , Knöfler Martin
Published: July 2023

Failures in growth and differentiation of the early human placenta are associated with severe pregnancy disorders such as preeclampsia and fetal growth restriction. However, regulatory mechanisms controlling development of its epithelial cells, the trophoblasts, remain poorly elucidated. Using trophoblast stem cells (TSCs), trophoblast organoids (TB-ORGs) and primary cytotrophoblasts (CTBs) of early pregnancy, we herein show that autocrine NOTCH3 signalling controls human placental expansion and differentiation. NOTCH3 receptor was specifically expressed in proliferative CTB progenitors and its active form, the nuclear NOTCH3 intracellular domain (NOTCH3-ICD), interacted with the transcriptional co-activator Mastermind-like 1 (MAML1). Doxycyclin-inducible expression of dominant-negative MAML1 in TSC lines provoked cell fusion and upregulation of genes specific for multinucleated syncytiotrophoblasts, the differentiated hormone-producing cell type of the placenta. However, progenitor expansion and markers of trophoblast stemness and proliferation were suppressed. Accordingly, inhibition of NOTCH3 signalling diminished growth of TB-ORGs whereas overexpression of NOTCH3-ICD in primary CTBs and TSCs showed opposite effects. In conclusion, the data suggest that canonical NOTCH3 signalling plays a key role in human placental development promoting self-renewal of CTB progenitors.
Circulating MicroRNAs indicative of sex and stress in the European seabass (Dicentrarchus labrax): toward the identification of new biomarkers
Authors: Houdelet Camille , Blondeau-Bidet Eva , Estevez-Villar Mathilde , Mialhe Xavier , Hermet Sophie , Ruelle François , Dutto Gilbert , Bajek Aline , Bobe Julien , Geffroy Benjamin
Published: July 2023

MicroRNAs (miRNAs) constitute a new category of biomarkers. Studies on miRNAs in non-mammalian species have drastically increased in the last few years. Here, we explored the use of miRNAs as potential, poorly-invasive markers, to identify sex and characterize acute stress in fish. The European seabass (Dicentrarchus labrax) was chosen as model because of its rapid response to stress and its specific sex determination system, devoid of sexual chromosomes. We performed a small RNA-sequencing analysis in the blood plasma of males and females’ European seabass (mature and immature) as well as in the blood plasma of juveniles submitted to an acute stress and sampled throughout the recovery period (at 0h, 0.5h, 1.5h and 6h). In immature individuals, both miR-1388-3p and miR-7132a-5p were up-regulated in females, while miR-499a-5p was more abundant in males. However, no miRNAs were found to be differentially expressed between sexes in the blood plasma of mature individuals. For the acute stress analysis, five miRNAs (miR-155-5p, miR-200a-3p, miR-205-1-5p, miR-143-3p and miR-223-3p) followed cortisol production over time. All miRNAs identified were tested and validated by RT-qPCR on sequenced samples. A complementary analysis on the 3’UTR sequences of the European seabass allowed to predict potential mRNA targets, some of them being particularly relevant regarding stress regulation, e.g. the glucocorticoid and the mineralocorticoid receptor. The present study provides new avenues and recommendations on the use of miRNAs as biomarkers of sex or stress of the European seabass, with potential application on other fish species.
Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis
Authors: Inamo Jun , Keegan Joshua , Griffith Alec , Ghosh Tusharkanti , Horisberger Alice , Howard Kaitlyn , Pulford John , Murzin Ekaterina , Hancock Brandon , Jonsson Anna Helena , Seifert Jennifer , Feser Marie L. , Norris Jill M. , Cao Ye , Apruzzese William , Louis Bridges S. , Bykerk Vivian , Goodman Susan , Donlin Laura , Firestein Gary S. , Perlman Harris , Bathon Joan M. , Hughes Laura B. , Tabechian Darren , Filer Andrew , Pitzalis Costantino , Anolik Jennifer H. , Moreland Larry , Guthridge Joel M. , James Judith A. , Brenner Michael B. , Raychaudhuri Soumya , Sparks Jeffrey A. ,   The Accelerating Medicines Partnership RA/SLE Network, Michael Holers V. , Deane Kevin D. , Lederer James A. , Rao Deepak A. , Zhang Fan
Published: July 2023

Rheumatoid arthritis (RA) is a systemic autoimmune disease with currently no universally highly effective prevention strategies. Identifying pathogenic immune phenotypes in ‘At-Risk’ populations prior to clinical disease onset is crucial to establishing effective prevention strategies. Here, we applied mass cytometry to deeply characterize the immunophenotypes in blood from At-Risk individuals identified through the presence of serum antibodies to citrullinated protein antigens (ACPA) and/or first-degree relative (FDR) status (n=52), as compared to established RA (n=67), and healthy controls (n=48). We identified significant cell expansions in At-Risk individuals compared with controls, including CCR2+CD4+ T cells, T peripheral helper (Tph) cells, type 1 T helper cells, and CXCR5+CD8+ T cells. We also found that CD15+ classical monocytes were specifically expanded in ACPA-negative FDRs, and an activated PAX5lownaïve B cell population was expanded in ACPA-positive FDRs. Further, we developed an “RA immunophenotype score” classification method based on the degree of enrichment of cell states relevant to established RA patients. This score significantly distinguished At-Risk individuals from controls. In all, we systematically identified activated lymphocyte phenotypes in At-Risk individuals, along with immunophenotypic differences among both ACPA+ and ACPA-FDR At-Risk subpopulations. Our classification model provides a promising approach for understanding RA pathogenesis with the goal to further improve prevention strategies and identify novel therapeutic targets.
Traditional Norwegian Kveik Yeast: An Ancient Sister Group to DomesticatedSaccharomyces cerevisiae
Authors: Dondrup Michael , Eiken Hans Geir , Martinussen Atle Ove , Haugland Lisa Karine , Holdhus Rita , Dolan David , Grellscheid Sushma , Hagen Snorre , Elameen Abdelhameed , Myking Tor
Published: July 2023

Kveik is the common name of yeast that has been used in traditional farmhouse brewing of western Norway for generations. Its fast fermentation, increased flocculation, temperature tolerance, and rich flavor profile have led to growing interest in recent years. Previous genetic analyses have shown that kveik forms a distinct group within theSaccharomyces cerevisiaetree and placed its origins within the Beer I clade of industrial brewing yeasts, although with signs of mixed ancestry.

In this study, we revisited the phylogenetic position of kveik within theS. cerevisiaetree. We searched for traditional farm breweries in western Norway and collected ten samples of potential kveik yeast.

Using Illumina whole genome shotgun sequencing, we reconstructed the phylogenetic tree of kveik based onde novogenome assemblies and variant calls of our new kveik samples, along with published wild and domesticatedS. cerevisiaestrains. We calibrated and used sequential computational experiments at different thresholds to determine the most probable phylogenetic position of kveik yeast.

Previously sequenced kveik genotypes form a clade with our new samples clustering partially by place of origin. Our results indicate that kveik is indeed a compact clade withinS. cerevisiaewith significantly reduced polymorphism compared to common brewing yeasts and wild strains. Contrary to what was previously thought, our analyses support a more ancient divergence of kveik and place it closer to the root of theS. cerevisiaetree.

In conclusion, our genetic analyses suggest that kveik is a unique and ancient yeast group, distinct from other domesticatedS. cerevisiaestrains. Considering a possible far east origin of kveik yeast, the apparent endemism to western Norway remains as a big paradox These findings have important implications for the understanding of yeast domestication and the use of kveik in modern brewing practices.
Modeling Stress-Induced Responses: Plasticity in Continuous State Space and Gradual Clonal Evolution
Authors: Bukkuri Anuraag
Published: July 2023

Mathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g. epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally-driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous, gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution.