bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Optimized CRISPR/Cas12a Assay to Facilitate the BRAF V600E Mutation Detection
Authors: Etemadzadeh Azadeh , Salehipour Pouya , Motlagh Fatemeh Movahedi , Khalifeh Masoomeh , Asadbeigi Adnan , Tabrizi Mina , Shirkouhi Reza , Modarressi Mohammad Hossein 
Published: October 2024

ABSTRACTBackgroundAccurate detection of the BRAF V600E (1799T > A) mutation status can significantly contribute to selecting an optimal therapeutic strategy for diverse cancer types. CRISPR‐based diagnostic platforms exhibit simple programming, cost‐effectiveness, high sensitivity, and high specificity in detecting target sequences. The goal of this study is to develop a simple BRAF V600E mutation detection method.MethodsWe combined the CRISPR/Cas12a system with recombinase polymerase amplification (RPA). Subsequently, several parameters related to CRISPR/Cas12a reaction efficiency were evaluated. Then, we conducted a comparative analysis of three distinct approaches toward identifying BRAF V600E mutations in the clinical samples.ResultsOur data suggest that CRISPR/Cas detection is considerably responsive to variations in buffer conditions. Magnesium acetate (MgOAc) demonstrated superior performance compared to all other examined additive salts. It was observed using 150 nM guide RNA (gRNA) in an optimized reaction buffer containing 14 mM MgOAc, coupled with a reduction in the volumes of PCR and RPA products to 1 μL and 3 μL, respectively, resulted in an enhanced sensitivity. Detection time was decreased to 75 min with a 2% limit of detection (LOD), as evidenced by the results obtained from the blue light illuminator. The CRISPR/Cas12a assay confirmed the real‐time PCR results in 31 of 32 clinical samples to identify the BRAF V600E mutation status, while Sanger sequencing detected BRAF V600E mutations with lower sensitivity.ConclusionWe propose a potential diagnostic approach that is facile, fast, and affordable with high fidelity. This method can detect BRAF V600E mutation with a 2% LOD without the need for a thermocycler.
MR Elastography for Classification of Focal Liver Lesions Using Viscoelastic Parameters: A Pilot Study Based on Intrinsic and Extrinsic Activations
Authors: Baradaran Najar Amirhosein , Gilbert Guillaume , Karam Elige , Volniansky Anton , Fohlen Audrey , Barat Maxime , Montagnon Emmanuel , Castel Hélène , Giard Jeanne‐Marie , Nguyen Bich N. , Cloutier Guy , Tang An , Van Houten Elijah 
Published: October 2024

BackgroundIntrinsic activation MR elastography (iMRE) uses cardiovascular pulsations to assess tissue viscoelastic properties. Applying it to focal liver lesions extends its capabilities.PurposeTo assess the viscoelastic parameters of focal liver lesions measured by iMRE and compare its diagnostic performance with extrinsic MRE (eMRE) for differentiating malignant and benign lesions.Study typeProspective.PopulationA total of 55 participants underwent MRI with research MRE sequences; 32 participants with 17 malignant and 15 benign lesions underwent both iMRE and eMRE.Field Strength/SequenceiMRE at ~1 Hz heart rate used a 3 T scanner with a modified four‐dimensional (4D)‐quantitative flow gradient‐echo phase contrast and low‐velocity encoding cardiac‐triggered technique. eMRE employed a gradient‐echo sequence at 30, 40, and 60 Hz.AssessmentLiver displacements were measured using 4D‐phase contrast and reconstructed via a nonlinear inversion algorithm to determine shear stiffness (SS) and damping ratio (DR). iMRE parameters were normalized to the corresponding values from the spleen. Lesions were manually segmented, and image quality was reviewed.Statistical TestsKruskal–Wallis, Mann–Whitney, Dunn's test, and areas under receiver operating characteristic curves (AUC) were assessed.ResultsSS was significantly higher in malignant than benign lesions with iMRE at 1 Hz (3.69 ± 1.31 vs. 1.63 ± 0.45) and eMRE at 30 Hz (3.76 ± 1.12 vs. 2.60 ± 1.26 kPa), 40 Hz (3.76 ± 1.12 vs. 2.60 ± 1.26 kPa), and 60 Hz (7.32 ± 2.87 vs. 2.48 ± 1.12 kPa). DR was also significantly higher in malignant than benign lesions at 40 Hz (0.36 ± 0.11 vs. 0.21 ± 0.01) and 60 Hz (0.89 ± 0.86 vs. 0.22 ± 0.09). The AUC were 0.86 for iMRE SS, 0.87–0.98 for eMRE SS, 0.47 for iMRE DR, and 0.62–0.86 for eMRE DR.Data ConclusionCardiac‐activated iMRE can characterize liver lesions and differentiate malignant from benign lesions through normalized SS maps.Level of Evidence2Technical EfficacyStage 2
An ultrastructure analysis of the developing human anterior cruciate ligament tibial enthesis
Authors: Hidalgo Perea Sofia , Uppstrom Tyler J. , Lin Kenneth M. , Klinger Craig E. , Bromage Timothy G. , Shea Kevin G. , Green Daniel W. , Rodeo Scott A. 
Published: October 2024

AbstractThis study aimed to investigate the ultrastructural anatomy of the developing ACL tibial enthesis. We hypothesized that enthesis architecture would progressively mature and remodel, eventually resembling that of the adult by the early postnatal stage. Five fresh‐frozen human pediatric cadaveric knees aged 1–36 months underwent anatomical dissection to harvest the ACL insertion and underlying tibial chondroepiphysis. The samples were prepared for scanning electron microscopy (SEM) to examine the ultrastructural anatomy of the enthesis and underwent histological staining for circular polarized light (CPL) and light microscopy imaging. SEM analysis of the 1‐ and 8‐month‐old samples revealed a shallow interdigitation between the dense fibrous (ligamentous) tissue and unmineralized chondrogenic tissues, with a minimal transition zone. By 11‐month, a more complex transition zone was present. By age 19‐ and 36‐month‐old, a progressively more complex and defined fibrocartilage zone was observed. CPL analysis revealed distinct collagen fiber continuity, alignment, and organization changes over time. By 19 and 36 months, the samples exhibited complex fiber arrangements and a progression toward uniform fiber orientation. Similarly, histological analysis demonstrated progressive remodeling of the enthesis with increasing age. Our results suggest that the ACL enthesis of the developing knee begins to mimic that of an adult as early as 19 months of age, as a more complex transition between ligamentous and chondro‐epiphyseal tissue can be appreciated. We hypothesize that the observed changes are likely due to mechanical loading of the enthesis with the onset of weightbearing. Future investigations of ACL reconstruction and repair will benefit from improved understanding of the chondro‐epiphyseal/ACL regions.
Morbidity and Mortality Following Surgery for Pancreatic Cancer in Low‐ and Middle‐Income Countries: A Systematic Review and Meta‐Analysis
Authors: Khan Mustafa Ali , Sherwani Maryam , Ahmed Kaleem S. , Ali Mubeen , Kumar Priya Ashok , Tariq Javeria , Christensen Leslie , Bogale Netsanet , Schwartz Patrick B. , Zafar Syed Nabeel 
Published: October 2024

ABSTRACTBackground and ObjectivesMeasuring postoperative outcomes after complex cancer operations such as pancreatectomy is vital to improve cancer surgery in low‐ and middle‐income countries (LMICs); however, such data is often limited. This study aimed to review existing research and obtain baseline estimates for postoperative mortality and morbidity after pancreatic cancer surgery in LMICs.MethodsPubMed, Embase, Web of Science Core Collection, and Global Index Medicus were systematically searched for original articles published between January 2005 and May 2022. LMICs based studies reporting postoperative mortality, morbidity, and/or length of stay of patients with primary pancreatic tumors undergoing pancreaticoduodenectomy and/or distal pancreatectomy were included.ResultsOf 18 344 unique titles and abstracts retrieved, 114 studies met the inclusion criteria. Of these, 51 “good” quality studies comprising 7528 patients were included in the meta‐analyses. Pooled estimates for pancreatic fistula were 16.6% (95% CI 14.0–19.7, p < 0.001); 16.0% (95% CI 11.1–22.5, p < 0.001) for Clavien‐Dindo grade 3 and 4 complications; 13.4% (95% CI 9.8–17.9, p < 0.001) for wound infection; and 4.4% (95% CI 3.3–5.7, p < 0.001) for postoperative mortality.ConclusionThis is the first systematic review and meta‐analysis examining surgical complications after pancreatic surgery in LMICs. We highlight a lack of data and the need to further evaluate surgical outcomes in LMICs.
Evaluation of a novel robotic testing method for stability and kinematics of total knee arthroplasty
Authors: Holthof Sander R. , Rock Mick , van Arkel Richard , Brivio Angela , Barrett David , Amis Andrew A. 
Published: October 2024

AbstractPurposeThis work developed a novel preclinical test of total knee replacements (TKRs) in order to explain TKR instability linked to patient dissatisfaction. It was hypothesized that stability tests on the isolated moving prostheses would provide novel comparative data on the stability and kinematics among TKR designs.MethodsThree TKR designs, DePuy Synthes Attune MS, Stryker Triathlon and Zimmer Biomet Persona MC, were assessed using a robotic arm while flexing–extending 0–140°. Tests imposed 710 N body weight combined with three tibial loads: no anterior–posterior (AP) force, 90 N anterior or 90 N posterior force. Other load effects were minimized and the kinematics was recorded. Each implant was tested six times to investigate the repeatability of the method. Data were analysed using statistical parametric mapping with one‐way analysis of variance (ANOVA). If significance was found (p < 0.05), post hoc t tests with Bonferroni correction were used to contrast groups.ResultsSignificant differences were found throughout flexion–extension. Femoral rollback, AP stability, coupled internal–external rotation and AP position (roll‐back) were all influenced by implant design. AP stability of the TKRs reduced with flexion reaching Attune 15 mm, Persona 13 mm and Triathlon 21 mm at 140° flexion. Tractive rolling significantly affected kinematics in the less congruent Triathlon design, with 6 mm different paths between flexion and extension motion (p < 0.05 across 5–100°). Paradoxical anterior femoral sliding in early flexion (0–40°) occurred in Persona and Triathlon designs.ConclusionsThe novel testing technique provides, for the first time, comparative data on the inherent stability and kinematics of the TKR implants themselves across the arc of flexion–extension, independent of variables including soft tissue behaviour and surgical technique. The data show how much each prosthesis can contribute to the stability and motion of the implanted knee. Similar data from a wider range of designs will enable more informed decisions regarding implant design choice, aiming to reduce the prevalence of TKR instability in patients.Level of EvidenceControlled laboratory study.
An Injectable IPN Nanocomposite Hydrogel Embedding Nano Silica for Tissue Engineering Application
Authors: Kakapour Ali , Nouri Khorasani Saied , Khalili Shahla , Hafezi Mahshid , Sattari‐Najafabadi Mehdi , Najarzadegan Mahsa , Saleki Samin , Bagheri‐Khoulenjani Shadab 
Published: October 2024

AbstractGelatin methacrylate (GM) and sodium alginate (SA) are two biomaterials that have been widely employed in tissue engineering, particularly in 3D bioprinting. However, they have some drawbacks including undesirable physico‐mechanical properties and printability, hindering their application. This work developed an interpenetrating polymeric network (IPN) of GM and SA reinforced with silica nanoparticles (SNPs) to deal with hydrogels’ drawbacks. Besides, for cross‐linking, visible light is used as an alternative to UV light to prevent disruptions in cellular metabolism and immune system reactions. Four GM/SA/SNP hydrogels different in SNPs concentration (0, 0.5, 1, and 2 w/w%) are studied. The performance of the hydrogels is evaluated in terms of physico‐mechanical properties (viscoelasticity, compressive modulus, degradation, and swelling), rheological properties, and biological properties (fibroblast cell growth and adhesion, and MTT assay). The results demonstrated that the GM/SA/SNP hydrogel with 1% SNPs provided desirable physical (645% swelling and 59.3% degradation), mechanical strength (270 kPa), rheological (tan δ of almost 0.14), and biological performances (≈98% viability after 3 days) while maintaining appropriate printability. The findings suggest that the GM/SA/SNP hydrogel holds great potential for applications in soft tissue regeneration.
Flat top coverage pattern maintaining via boundary subarray elements thinning
Authors: Abdulqader Ahmed Jameel , Mohammed Jafar Ramadhan , Ali Y. E. Mohammed 
Published: October 2024

AbstractThis paper aims to study the effect of eliminating some elements from the original planar array (OPA) to generate a useful flat‐top coverage pattern (FTCP) using a genetic algorithm. The study involves dividing the fully planar array (i.e., OPA) into two regions with an unequal number of elements. The first region includes the elements located in the core (center) of the array, and the remaining elements are the second region, and their location is within the boundary (side) of the array. Only the elements of the first region are included in the optimization process, while the elements of the second region are eliminated in the form of a specific geometric composition without affecting the FTCP generation. Comparing the OPA that N×M elements with the first region (active subarray) elements, it is noted that the number of elements has been reduced from N×M to (N − 2x) × (M − 2y) to reduce the complexity of the system as much as possible without affecting the performance in general. Different boundary subarray shapes are presented in this paper with different numbers of elements. The obtained results showed the effectiveness of the proposed method in generating FTCP close to its counterpart in the OPA.
David Garbers' Contributions to Chemotaxis Signaling in Sperm
Authors: Kaupp U. B. , Kendall Olivia 
Published: October 2024

ABSTRACTThis review focuses on the contribution of the late David Garbers to chemotaxis of sperm, in particular from sea urchin. We will describe his discovery of chemotactic peptides and their cognate receptors, his discovery of a sperm‐specific, unique Na+/H+ exchanger that represents a chimera between a solute carrier (SLC) and an ion channel. Finally, we will discuss his contributions to the understanding of cAMP signaling in sperm via soluble adenylyl cyclase (sAC) and its control by Ca2+ ions.
Metabolite T2 relaxation times decrease across the adult lifespan in a large multi‐site cohort
Authors: Hupfeld Kathleen E. , Murali‐Manohar Saipavitra , Zöllner Helge J. , Song Yulu , Davies‐Jenkins Christopher W. , Gudmundson Aaron T. , Simicic Dunja , Lamesgin Simegn Gizeaddis , Carter Emily E. , Hui Steve C. N. , Yedavalli Vivek , Oeltzschner Georg , Porges Eric C. , Edden Richard A. E. 
Published: October 2024

AbstractPurposeRelaxation correction is crucial for accurately estimating metabolite concentrations measured using in vivo MRS. However, the majority of MRS quantification routines assume that relaxation values remain constant across the lifespan, despite prior evidence of T2 changes with aging for multiple of the major metabolites. Here, we comprehensively investigate correlations between T2 and age in a large, multi‐site cohort.MethodsWe recruited approximately 10 male and 10 female participants from each decade of life: 18–29, 30–39, 40–49, 50–59, and 60+ y old (n = 101 total). We collected PRESS data at eight TEs (30, 50, 74, 101, 135, 179, 241, and 350 ms) from voxels placed in white‐matter‐rich centrum semiovale (CSO) and gray‐matter‐rich posterior cingulate cortex (PCC). We quantified metabolite amplitudes using Osprey and fit exponential decay curves to estimate T2.ResultsOlder age was correlated with shorter T2 for tNAA2.0, tCr3.0, tCr3.9, tCho, and tissue water (CSO and PCC), as well as mI and Glx (PCC only); rs = −0.22 to −0.63, all p < 0.05, false discovery rate (FDR)‐corrected. These associations largely remained statistically significant when controlling for cortical atrophy. By region, T2 values were longer in the CSO for tNAA2.0, tCr3.9, Glx, and tissue water and longer in the PCC for tCho and mI. T2 did not differ by region for tCr3.0.ConclusionThese findings underscore the importance of considering metabolite T2 differences with aging in MRS quantification. We suggest that future 3T work utilize the equations presented here to estimate age‐specific T2 values instead of relying on uniform default values.
Patient, facility, and environmental factors associated with obesity treatment in US Veterans
Authors: Kamalumpundi Vijayvardhan , Smith Jessica K. , Robinson Kathleen M. , Saad Eddin Assim , Alatoum Aiah , Kasasbeh Ghena , Correia Marcelo L. G. , Vaughan Sarrazin Mary 
Published: October 2024

AbstractBackgroundIdentifying patient‐, facility‐, and environment‐level factors that influence the initiation and retention of comprehensive lifestyle management interventions (CLMI) for urban and rural Veterans could improve obesity treatment and reach at Veterans Affairs (VA) facilities.AimsThis study identified factors at these various levels that predicted treatment engagement, retention, and weight management among urban and rural Veterans.MethodsA retrospective cohort study of 631,325 Veterans was designed using VA databases to identify Veterans with class II and III obesity during 2015–2017. Primary outcomes were initiation of CLMI, bariatric surgery, or obesity pharmacotherapy within 1 year of index date. Secondary outcomes included treatment retention and successful weight loss. Generalized linear mixed models were used to evaluate the relationships between factors and obesity‐related outcomes, with rurality differences assessed through interaction terms.ResultsPatient characteristics associated with increased odds of initiating CLMI included female sex (p < 0.001), black race (p < 0.001), sleep apnea (p < 0.001), mood disorder (p < 0.001), and use of medications associated with weight loss (p < 0.001) or weight gain (p < 0.001). Facility use of telehealth was associated with greater odds of CLMI initiation in urban Veterans (p < 0.001) but lower retention in both populations (p = 0.003). Routine consideration of pharmacotherapy was associated with higher CLMI initiation. Environmental characteristics associated with increased odds of CLMI initiation included percent of population foreign born (OR = 1.03 per 10% increase; p < 0.001), percent black (p < 0.001), and high walkability index (p < 0.001). The relationship between total population and CLMI initiation differed by rurality, as greater population was associated with lower odds of CLMI initiation in urban areas (OR: 0.99 per 1000 population; p < 0.001), but higher odds in rural areas (OR:1.01, p = 0.01). Veterans in the south were less likely to initiate CLMI and had lower retention (p < 0.001).ConclusionTreatment and retention of CLMI among Veterans remain low, highlighting areas for improvement to expand its reach both urban and rural Veterans.
Optimizing muscle preservation during weight loss in patients with cirrhosis: A pilot study comparing continuous energy restriction to alternate‐day modified fasting for weight loss in patients with obesity and non‐alcoholic cirrhosis of the liver
Authors: Dunn Winston , Herrmann Stephen D. , Montgomery Robert N. , Hastert Mary , Honas Jeffery J. , Rachman Jessica , Donnelly Joseph E. , Steger Felicia L. 
Published: October 2024

AbstractIntroductionObesity is associated with increased morbidity in patients with advanced liver disease, but it is particularly challenging for these patients to preserve skeletal muscle mass during weight loss and accelerating sarcopenia is a concern. Alternate‐day modified fasting (ADMF) may be particularly effective for weight loss in patients with concomitant cirrhosis and obesity due to preservation of fat‐free mass (FFM).MethodsA weight loss program featuring either ADMF or a continuous low‐calorie diet (LCD) was evaluated in a 24‐week randomized clinical trial in 20 adult patients with Child‐Pugh Class A cirrhosis and obesity. Participants were randomized to either ADMF (n = 11) or LCD (n = 9). Both groups received a remotely delivered exercise program. Body composition, sarcopenia measures, and functional outcomes were assessed pre‐post.ResultsThirteen participants completed the intervention (Age = 57 ± 10; BMI = 37.7 ± 5.8 kg/m2). The median body weight lost in ADMF was 13.7 ± 4.8 kg (13.9% of initial body weight), while LCD lost 9.9 ± 6.9 kg (10.7% of initial body weight). Total body fat percentage decreased in both groups (ADMF: −4.1 ± 4.0%; LCD = −2.8 ± 1.4%). Fat‐free mass accounted for 34 ± 20% of total weight loss in ADMF and 38 ± 10% in LCD. Functional measures, such as timed chair stands, improved in both groups.ConclusionThis pilot study demonstrates the feasibility of the ADMF and LCD interventions to produce significant weight loss while improving body composition in patients with cirrhosis and obesity. Further research is needed to validate these findings in larger cohorts and to assess changes in muscle quality and visceral fat.Trial RegistrationClinicalTrials.gov Identifier: NCT05367596.
Shifting perceptions of green and blue spaces during the COVID‐19 pandemic in gentrifying neighbourhoods: Experiences of inclusion and exclusion by women and non‐binary residents
Authors: Calderón‐Argelich Amalia , Anguelovski Isabelle , Cuenca Valeria‐Carolin , Cole Helen V. S. , Triguero‐Mas Margarita , Valdivia Blanca , Baró Francesc 
Published: October 2024

Abstract

The COVID‐19 outbreak triggered a combined health, social and economic crisis, imposing multiple restrictions that altered the use and perception of public green and blue spaces (PGBS). In this article, we explored how the different stages of the COVID‐19 pandemic restrictions affected the use and perceptions of public greenspaces and seafront in gentrifying neighbourhoods, focusing specifically on women and non‐binary residents.

We conducted a comparative analysis of two densely populated neighbourhoods in Barcelona, Spain, employing a participatory mixed‐methods approach including surveys, focus groups, participatory walks and semi‐structured interviews. We collected the perceptions from women and non‐binary residents for the pre‐pandemic period, the lockdown period and the period during the post‐lockdown gradual ease of restrictions.

Our findings reveal that during the COVID‐19 lockdown, the use of neighbourhood PGBS was maintained or intensified, highlighting the existing deficit in the denser areas of the city. However, post‐lockdown, use patterns changed, with differences based on neighbourhood characteristics and gentrification pressures. This suggests that while COVID‐19 seemed to temporarily impact how people used PGBS, these changes were rapidly reversed once mobility restrictions were lifted. During and after the pandemic, PGBS facilitated informal care networks and community cohesion that helped residents endure the impacts of the pandemic, but the return of gentrification and touristification pressures disrupted these networks, heightening feelings of displacement and exclusion among women and non‐binary residents. The research underscores the dual role of PGBS as both essential community spaces and sites of exclusion, emphasizing the need for inclusive and just green planning strategies.

Policy implications. Urban planning must prioritize the quality and accessibility of PGBS with a gender‐sensitive approach and address broader issues of gentrification and touristification to protect vulnerable populations. An environmentally just greening approach should consider proximity, safety, accessibility and design to facilitate the use of PGBS by socially vulnerable groups.

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