bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sexual Dimorphism of Radiomic Features in the Brain
Authors: Mayerhoefer Marius E. , Shepherd Timothy M. , Weber Michael , Leithner Doris , Woo Sungmin , Pan Jullie W. , Pardoe Heath R. 
Published: June 2024

Objectives
The aim of this study was to determine whether MRI radiomic features of key cerebral structures differ between women and men, and whether detection of such differences depends on the image resolution.

Materials and Methods
Ultrahigh resolution (UHR) 3D MP2RAGE (magnetization-prepared 2 rapid acquisition gradient echo) T1-weighted MR images (voxel size, 0.7 × 0.7 × 0.7 mm3) of the brain of 30 subjects (18 women and 12 men; mean age, 39.0 ± 14.8 years) without abnormal findings on MRI were retrospectively included. MRI was performed on a whole-body 7 T MR system. A convolutional neural network was used to segment the following structures: frontal cortex, frontal white matter, thalamus, putamen, globus pallidus, caudate nucleus, and corpus callosum. Eighty-seven radiomic features were extracted respectively: gray-level histogram (n = 18), co-occurrence matrix (n = 24), run-length matrix (n = 16), size-zone matrix (n = 16), and dependence matrix (n = 13). Feature extraction was performed at UHR and, additionally, also after resampling to 1.4 × 1.4 × 1.4 mm3 voxel size (standard clinical resolution). Principal components (PCs) of radiomic features were calculated, and independent samples t tests with Cohen d as effect size measure were used to assess differences in PCs between women and men for the different cerebral structures.

Results
At UHR, at least a single PC differed significantly between women and men in 6/7 cerebral structures: frontal cortex (d = −0.79, P = 0.042 and d = −1.01, P = 0.010), frontal white matter (d = −0.81, P = 0.039), thalamus (d = 1.43, P < 0.001), globus pallidus (d = 0.92, P = 0.020), caudate nucleus (d = −0.83, P = 0.039), and corpus callosum (d = −0.97, P = 0.039). At standard clinical resolution, only a single PC extracted from the corpus callosum differed between sexes (d = 1.05, P = 0.009).

Conclusions
Nonnegligible differences in radiomic features of several key structures of the brain exist between women and men, and need to be accounted for. Very high spatial resolution may be required to uncover and further investigate the sexual dimorphism of brain structures on MRI.
Application of Free Flaps in Reconstruction of Head and Neck Soft Tissue Defects With Bone Exposure
Authors: Zhang Mingjun , Fu Jile , Liu Xiaojun , Liu Bincheng , Mao Xiaoyan , Hu Zhiqi 
Published: June 2024

Background
Reconstruction of head and neck soft tissue defects with bone exposure is both challenging and technically demanding for plastic surgeon. Objectives in head and neck soft tissue defects with bone exposure reconstruction are consistent restoration of functionality while also improving appearance. This study retrospectively analyzed the results of head and neck reconstructions using various types of free flaps over the past 4 years.

Methods
A retrospective analysis was conducted from June 2019 to June 2023 on 12 patients treated at our hospital for head and neck soft tissue defects with bone exposure due to various causes. These included 4 cases of trauma from car accidents, 1 burn case, and 7 postoperative malignant tumor removals. The defect sizes ranged from 4 × 6 to 15 × 45 cm. Different free flaps were used for repair based on the defect, including 6 anterolateral thigh flaps, 3 forearm flaps, 2 latissimus dorsi flaps, and 1 dorsalis pedis flap. Flaps were designed and harvested to match the defect size and transplanted via anastomosed vessels.

Results
All 12 flaps survived successfully. One patient required flap thinning surgery postoperatively. All patients were followed up for over 3 months, showing good color and texture of the transplanted flaps, satisfactory healing, and significant aesthetic improvement. Donor sites showed significant scarring without functional impairment.

Conclusion
Free flap repair for head and neck soft tissue defects with bone exposure is feasible and yields good results.
Upper Blepharoplasty through Infrabrow Skin Excision to Treat Dermatochalasis with Lateral Hooding and Medial Orbital Fat Loss in Selected Patients
Authors: Wang DaoHe , Cai TianYi , Guo FanLi , James Andrew J. , Yang JunYi , Yang YanWen 
Published: June 2024

Purpose
Dermatochalasis with lateral hooding and medial orbital fat loss are common signs of aging in the upper eyelid. Removing the excess skin in this area through infrabrow skin excision can effectively lift the loose skin of the upper eyelid and minimizes visible scarring. Additionally, we have identified three compartments of orbital fat prolapse based on orbital anatomy. Transferring volume from the lateral compartment to the intermediate region can flatten the lateral upper eyelid and create medial fullness, which ultimately rejuvenates the upper eyelid. This study presents an operative method for correcting age-related changes in the upper eyelid using this technique.

Methods
A total of 34 eyelids from 17 patients underwent a surgical procedure involving infrabrow skin excision, along with repositioning and lifting of lateral orbital fat. The inclusion criteria consisted of patients with moderate to severe upper eyelid dermatochalasis, coupled with middle fat loss and lateral hooding. To correct lateral hooding and restore midfacial fullness, lateral orbital fat was repositioned to an intermediate position, and the orbicularis oculi muscle was fold-sutured to the corrugator supercilii muscle.

Results
The mean age of the patients was 55.59 ± 3.20 years, with a range of 48 to 61 years. The mean follow-up period was 9.94 ± 1.35 months, ranging from 8 to 12 months. Patients were evaluated at 1-month, 3-month, and 6-month intervals. The Strasser system was used to evaluate the surgical outcomes at 3 months. All patients achieved good surgical outcomes, expressed through satisfactory cosmetic improvements, and improved visual field. The procedure effectively corrected lateral hooding and loss of middle orbital fat through infrabrow skin excision. No complications, such as wound dehiscence, lagophthalmos, noticeable scarring, ocular dyskinesia, or sensory changes, were observed.

Conclusions
The combination of infrabrow skin excision, repositioning of lateral orbital fat, and lifting of the orbicularis oculi muscle effectively addresses moderate to severe dermatochalasis, lateral hooding, medial fat loss, and improves elasticity of the anterior wall of the upper lid in our patients. This procedure can produce satisfactory and long-lasting aesthetic results with an inconspicuous scar beneath the brow.
Surgical Intraoperative Handoff Initiative: Standardizing Operating Room Communication Using SHRIMPS
Authors: Stephens Wesley A , Anderson Madeline J , Levy Brittany E , Lantz Sherry , Harris Andrew M , Newcomb Melissa R 
Published: June 2024

BACKGROUND:
Operating room (OR) handoffs are not universally standardized, although standardized sign outs have been proven to provide effective communication in other aspects of healthcare. We hypothesize that creating a standardized handoff will improve communication between OR staff.

STUDY DESIGN:
A frontline stakeholder approached our quality improvement team with concern regarding inadequate quality surgical technician handoffs during staff changes. An audit tool was created for a pilot cohort of 23 cases to evaluate surgical technician handoffs from May 2022 to November 2022. Handoffs occurred in 82.6% of cases. Elements of handoff varied significantly, with an average of 34.4% completion of critical handoff elements. Audits were reviewed with stakeholders to develop a standardized communication checklist, including domains regarding sponges, sharps, hidden items, replaced items, instruments, implants, medications, procedure overview, and specimens. An acronym of these domains, SHRIMPS, was affixed to each OR wall.

RESULTS:
In the initial Plan-Do-Study-Act cycle, piloted in urology, general surgery, and neurosurgery, 100% of the 15 observed cases included handoff, averaging 76 seconds per handoff. Additionally, 100% of cases announced a handoff to the surgeon, and all elements were addressed 99.6% of the time. Plan-Do-Study-Act cycle 2 involved implementation to all service lines. Of the 68 cases observed, 100% included handoff, averaging 69.4 seconds per handoff, with 98.2% of elements addressed, though only 97.1% of handoffs were announced.

CONCLUSIONS:
Little communication standardization exists within the OR, especially regarding intraoperative staff changes. Implementation of a standardized handoff between surgical technicians resulted in substantial improvement in critical communication during staff changes.
Resident and Fellow Performance and Supervision in Surgical Oncology Procedures
Authors: Underwood Patrick W , Balch Jeremy A , Filiberto Amanda C , Cloyd Jordan M , Pawlik Timothy M , Sarosi George A , Upchurch Gilbert R , Loftus Tyler J 
Published: June 2024

BACKGROUND:
Previous research has highlighted concerns among trainees and attendings that general surgery training and fellowship are inadequately preparing trainees for practice. Providing trainees with supervision that matches their proficiency may help bridge this gap. We sought to benchmark operative performance and supervision levels among senior surgery residents (PGY-4 or -5) and fellows performing general surgical oncology procedures.

STUDY DESIGN:
Observational data were obtained from the Society for Improving Medical Procedural Learning OR application for core general surgical oncology procedures performed at 103 unique residency and fellowship programs. Procedures were divided into breast and soft tissue, endocrine, and hepatopancreatobiliary. Case evaluations completed by trainees and attendings were analyzed to benchmark trainee operative performance and level of supervision.

RESULTS:
There were 4,907 resident cases and 425 fellow cases. Practice-ready performance, as assessed by trainees and faculty, was achieved by relatively low proportions of residents and fellows for breast and soft tissue cases (residents: 38%, fellows: 48%), endocrine cases (residents: 22%, fellows: 41%), and hepatopancreatobiliary cases (residents: 10%, fellows: 40%). Among cases in which trainees did achieve practice-ready performance, supervision only was provided for low proportions of cases as rated by trainees (residents: 17%, fellows: 18%) and attendings (residents: 21%, fellows 25%).

CONCLUSIONS:
In a sample of 103 residency and fellowship programs, attending surgeons rarely provided senior residents and fellows with levels of supervision commensurate to performance for surgical oncology procedures, even for high-performing trainees. These findings suggest a critical need for surgical training programs to prioritize providing greater levels of independence to trainees that have demonstrated excellent performance.
Metamaterial applications of Tmatsolver, an easy-to-use software for simulating multiple wave scattering in two dimensions
Authors: Hawkins Stuart C. , Bennetts Luke G. , Nethercote Matthew A. , Peter Malte A. , Peterseim Daniel , Putley Henry J. , Verfürth Barbara 
Published: June 2024

Multiple scattering of waves is eminent in a wide range of applications and extensive research is being undertaken into multiple scattering by ever more complicated structures, with emphasis on the design of metamaterial structures that manipulate waves in a desired fashion. Ongoing research investigates the design of structures and new solution methods for the governing partial differential equations. There is a pressing need for easy-to-use software that empowers rapid prototyping of designs and for validating other solution methods. We develop a general formulation of the multiple scattering problem that facilitates efficient application of the multipole-based method. The shape and morphology of the scatterers is not restricted, provided their T-matrices are available. The multipole method is implemented in the Tmatsolversoftware package, which uses our general formulation and the T-matrix methodology to simulate accurately multiple scattering by complex configurations with a large number of identical or non-identical scatterers that can have complex shapes and/or morphologies. This article provides a mathematical description of the algorithm and demonstrates application of the software to four contemporary metamaterial problems. It concludes with a brief overview of the object-oriented structure of the Tmatsolvercode.
A Multi-Omics Approach to Defining Target Organ Injury in Youth with Primary Hypertension
Authors: Ananthamohan Kalyani , Brady Tammy M. , Arif Mohammed , Daniels Stephen , Falkner Bonita , Ferguson Michael , Flynn Joseph T. , Hanevold Coral , Hooper Stephen R. , Ingelfinger Julie , Lande Marc , Martin Lisa J. , Meyers Kevin E. , Mitsnefes Mark , Rosner Bernard , Samuels Joshua A. , Kuffel Gina , Zilliox Michael J. , Becker Richard C. , Urbina Elaine M. , Sadayappan Sakthivel 
Published: June 2024

ABSTRACTBACKGROUNDPrimary hypertension in childhood tracks into adulthood and may be associated with increased cardiovascular risk. Studies conducted in children and adolescents provide an opportunity to explore the early cardiovascular target organ injury (CV-TOI) in a population free from many of the co-morbid cardiovascular disease risk factors that confound studies in adults.METHODSYouths (n=132, mean age 15.8 years) were stratified by blood pressure (BP) as low, elevated, and high-BP and by left ventricular mass index (LVMI) as low- and high-LVMI. Systemic circulating RNA, miRNA, and methylation profiles in peripheral blood mononuclear cells and deep proteome profiles in serum were determined using high-throughput sequencing techniques.RESULTSVASH1gene expression was elevated in youths with high-BP with and without high-LVMI.VASH1expression levels positively correlated with systolic BP (r=0.3143, p=0.0034). The expression of hsa-miR-335-5p, one of theVASH1-predicted miRNAs, was downregulated in high-BP with high-LVMI youths and was inversely correlated with systolic BP (r=-0.1891, p=0.0489).GSE1hypermethylation, circulating PROZ upregulation (log2FC=0.61, p=0.0049 and log2FC=0.62, p=0.0064), and SOD3 downregulation (log2FC=-0.70, p=0.0042 and log2FC=-0.64, p=0.010) were observed in youths with elevated BP and high-BP with high-LVMI. Comparing the transcriptomic and proteomic profiles revealed elevatedHYAL1levels in youths displaying high-BP and high-LVMI.CONCLUSIONSThe findings are compatible with a novel blood pressure-associated mechanism that may occur through impaired angiogenesis and extracellular matrix degradation through dysregulation of Vasohibin-1 and Hyaluronidase1 was identified as a possible mediator of CV-TOI in youth with high-BP and suggests strategies for ameliorating TOI in adult-onset primary hypertension.
Isolation and Genomic Analysis of Escherichia Phage AUBRB02: Implications for Phage Therapy in Lebanon
Authors: Ahmad Tasnime Abdou , Houjeiry Samar El , Abou Fayad Antoine , Kanj Souha , Matar Ghassan , Saba Esber 
Published: June 2024

ABSTRACTWe obtained a new and unique Escherichia phage, AUBRB02, from sewage water in Beirut, Lebanon, as part of this research. AUBRB02 has an incubation period of around 45 minutes, a lysis period of about 10 minutes, and a burst size of around 30 plaque-forming units per cell. The phage exhibited strong biological stability over a pH range of 5.0–9.0 and temperatures ranging from 4°C to 60°C. AUBRB02 was found to have a genome size of 166,871 base pairs and a G+C content of 35.47% using whole-genome sequencing. A comparative analysis revealed that AUBRB02, a newly found phage, shares 93% intergenomic similarity to closest relative in refseq. Functional annotation revealed the presence of 10 tRNA and 262 coding sequences, out of which 123 are categorized as putative proteins. These results indicate that AUBRB02 is a highly infectious virus that belongs to theTequatrovirusgenus. This study is significant reference information that can be used in the development of phage therapy.IMPORTANCEEscherichia coli, a gram-negative bacterium, is a widely distributed pathogen in the natural environment and a frequent cause of illnesses. The extensive utilization of antibiotics has resulted in a rise of clinically resistant strains, posing a substantial obstacle to antimicrobial therapy. This urgent circumstance highlights the necessity for antibiotic substitutes to combatE. coliinfections. In this context, we introduce AUBRB02, a novel Escherichia phage isolated from an untreated sewage source in Beirut. Our findings indicate that AUBRB02 is highly lytic, stable against extreme culturing conditions, and has a biofilm elimination capability.
Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass
Authors: Wang Peipei , Meng Fanrui , Del Azodi Christina B , Abá Kenia Segura , Casler Michael D. , Shiu Shin-Han 
Published: June 2024

AbstractGenomic prediction, the use of genetic information for predicting traits, has accelerated the breeding processes and provided mechanistic insights into the genetic bases of complex traits. While substantial efforts have been devoted to optimize genomic prediction, there remain areas that need to be further explored, including the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures. Here, we assess the impact of these factors on the prediction of 20 complex traits in switchgrass (Panicum virgatumL.), a perennial biofuel feedstock. We found that short read-based genome assembly perform comparably to or even better than long read-based assembly in trait prediction; exome capture-based models have higher prediction accuracy than genotyping-by-sequencing-based models for 13 traits; bi-allelic insertion/deletions are as useful as bi-allelic single nucleotide polymorphisms in trait prediction, whereas multi-allelic variants outperform bi-allelic ones for 15 traits. Models built for tetraploids have higher prediction accuracy than those for octoploids for most traits. Traits of individuals with higher within-population genetic distances tend to have higher prediction accuracy. Finally, integrating different types of variants can improve the prediction accuracy. By exploring these factors, anthesis date prediction models built using multi-allelic insertion/deletions derived from exome capture led to the largest number of orthologs of benchmark flowering time genes compared to other models. Our study provides insights into the factors influencing genomic prediction outcomes that inform best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.
One-for-all gene inactivation via PAM-independent base editing in bacteria
Authors: Li Xin , Wei Ying , Wang Shu-Yan , Wang Shu-Guang , Xia Peng-Fei 
Published: June 2024

AbstractBase editing is preferable for bacterial gene inactivation without generating double strand breaks, requiring homology recombination or highly efficient DNA delivery capability. However, the potential of base editing is limited by the adjoined dependence on the editing window and protospacer adjacent motif (PAM). Herein, we report an unconstrained base editing system to enable the inactivation of any genes of interests (GOIs) in bacteria. We first employed a dCas9 derivative, dSpRY, as the effector to build a base editor with activation-induced cytidine deaminase, releasing the dependence on PAM. Then, we programmed the base editor to exclude the START codon of a GOI instead of introducing STOP codons to obtain a universal approach for gene inactivation, namely XSTART, with an overall efficiency approaching 100%. By using XSTART, we successfully manipulated the amino acid metabolisms inEscherichia coli, generating glutamine, arginine, and aspartate auxotrophic strains. The effectiveness of XSTART was also demonstrated in probioticE. coliNissle 1917 and photoautotrophic cyanobacteriumSynechococcus elongatus, illustrating its potential in reprogramming clinically and industrially relevant chassis. To be noticed, we observed a relatively high frequency of off-target events as a trade-off for the efficacy and universality.
A model for accurate quantification of CRISPR effects in pooled FACS screens
Authors: Pimentel Harold , Freimer Jacob W. , Arce Maya M. , Garrido Christian M. , Marson Alexander , Pritchard Jonathan K. 
Published: June 2024

AbstractCRISPR screens are powerful tools to identify key genes that underlie biological processes. One important type of screen uses fluorescence activated cell sorting (FACS) to sort perturbed cells into bins based on the expression level of marker genes, followed by guide RNA (gRNA) sequencing. Analysis of these data presents several statistical challenges due to multiple factors including the discrete nature of the bins and typically small numbers of replicate experiments. To address these challenges, we developed a robust and powerful Bayesian random effects model and software package called Waterbear. Furthermore, we used Waterbear to explore how various experimental design parameters affect statistical power to establish principled guidelines for future screens. Finally, we experimentally validated our experimental design model findings that, when using Waterbear for analysis, high power is maintained even at low cell coverage and a high multiplicity of infection. We anticipate that Waterbear will be of broad utility for analyzing FACS-based CRISPR screens.
Systems Modeling Reveals Shared Metabolic Dysregulation and Potential Treatments in ME/CFS and Long COVID
Authors: Li Gong-Hua , Han Feifei , Kalafatis Efthymios , Kong Qing-Peng , Xiao Wenzhong 
Published: June 2024

AbstractMyalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Long COVID are complex, multisystem conditions that pose significant challenges in healthcare. Accumulated research evidence suggests that ME/CFS and Long COVID exhibit overlapping metabolic symptoms, indicating potential shared metabolic dysfunctions. This study aims to systematically explore shared metabolic disturbances in the muscle tissue of patients. Utilizing genome-wide metabolic modeling, we identified key metabolic irregularities in the muscle of patients with ME/CFS, notably the downregulation of the alanine and aspartate metabolism pathway and the arginine and proline metabolism pathway. Further,in silicoknockout analyses suggested that supplementation with aspartate (ASP) or asparagine (ASN) could potentially ameliorate these metabolic deficiencies. In addition, assessments of metabolomic levels in Long COVID patients also showed the significant downregulation of ASP during post-exertional malaise (PEM) in both muscle and blood. Consequently, we propose that a combination of l-ornithine and l-aspartate (LOLA) is a potential candidate to alleviate metabolic symptoms in ME/CFS and Long COVID for future clinical trials.