bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring traditional and novel spike traits associated with seed retention in perennial ryegrass by integrating 2D and 3D image analysis
Authors: Tubbs Travis B. , Chastain Thomas G. 
Published: September 2024

AbstractSeed shattering is a major economic problem in seed production of perennial ryegrass (Lolium perenne L.). The objective was to identify potential relationships between phenotypic traits and seed retention in a 2‐year field trial with 21 diverse global accessions of perennial ryegrass. Accessions were grouped according to level of seed retention. Phenotypic traits examined were growth habit, spike length, curvature of the spike, spikelets per spike, spikelet length, internode length between spikelets, angle of spikelet insertion into the rachis, seeds per spike, and seed weight. Traits were captured and measured by use of novel two‐dimensional (2D) and three‐dimensional (3D) imaging tools. Among accessions, median seed retention values for the high and low seed retention groups were 61% and 36%, respectively. Four traits were found to significantly impact seed shattering: spike length (p ≤ 0.01), seed weight (p ≤ 0.001), seeds per spike (p ≤ 0.05), and internode length between spikelets (p ≤ 0.01). Seed retention was highest in accessions with short spikes. Most of the accessions that had high seed retention also had lower mean seed weight than the commercial plant materials. Accession (PI 231620) had both high levels of seed retention and a mean seed weight that is acceptable in the marketplace. These qualities may be used to improve seed retention in the breeding of perennial ryegrass cultivars. The 2D and 3D imaging methods have applicability in measurement of other plant morphological traits and across a broad range of plant species.
Prospective assessment of probe‐based confocal laser endomicroscopy under direct cholangioscopic visualization for biliary strictures that could not be definitively diagnosed using endoscopic retrograde cholangiopancreatography (with video)
Authors: Tanisaka Yuki , Ryozawa Shomei , Mizuide Masafumi , Fujita Akashi , Jinushi Ryuhei , Watanabe Ryuichi , Sato Ryo , Tashima Tomoaki , Mashimo Yumi 
Published: September 2024

AbstractThe definitive diagnosis of patients with indeterminate biliary strictures remains challenging. Probe‐based confocal laser endomicroscopy (pCLE) provides real‐time histological assessment of bile duct tissues. Since no previous studies have evaluated the efficacy of pCLE under direct cholangioscopic visualization for biliary strictures that cannot be definitively diagnosed through endoscopic retrograde cholangiopancreatography using fluoroscopy, we prospectively assessed the feasibility and safety of this procedure in three cases. pCLE findings were obtained in three cases, providing accurate diagnoses. Additionally, no adverse event was reported. pCLE under direct cholangioscopic visualization for indeterminate biliary strictures might be feasible and safe, even though these strictures were not previously diagnosed using endoscopic retrograde cholangiopancreatography. Further studies with more cases are warranted to clarify the effectiveness of pCLE under direct cholangioscopic visualization.
A rigid‐flexible coupled rocking structure with nonlinear stress distribution along its base: Analytical modeling, validation and parametric investigation
Authors: Bao Yu , Liu Ying‐Qi 
Published: September 2024

AbstractStructures allowing their bases to uplift and rock during an earthquake event usually experience less damage; thus, they are more resilient to seismic hazards. Accurate simulation is critical to design and seismic performance evaluation of these flexible rocking structures. Motivated from this, this article presents a new rigid‐flexible coupled rocking model for numerical evaluation of flexible rocking structures under both cyclic and dynamic loadings. The key idea in the model formulation is that the total motion of flexible rocking structure can be decomposed into a rigid‐body motion and an associated flexible deformation. The flexible deformation of the rocking body is described using displacement field of classical Timoshenko beam. Using this approach and appropriate degrees‐of‐freedom (DOFs), the governing equations‐of‐motion for flexible rocking structures are formulated using the variational principle. Multiple springs with appropriate constitutive model are distributed along rocking base to represent the inelastic behavior of rocking body. Potential post‐tensioned tendons are also considered in this model. In addition, nonlinear stress distribution along the rocking base, which cannot be considered in existing flexible rocking model, is also incorporated in the developed model. The proposed model is subsequently validated against published experimental data through quasi‐static and shake table tests, showing good accuracy when the rocking structure is relatively stockier. Finally, a parametric investigation on the effect of flexibility, nonlinear stress distribution and yield stress of rocking body on the rocking response is performed. This preliminary investigation shows that influence of flexibility and yield stress is significant while impact of nonlinear stress distribution is minor.
Diagnostic and Therapeutic Implications of a FUS::TFCP2 Fusion and ALK Activation in a Metastatic Rhabdomyosarcoma
Authors: Csizmok Veronika , Grisdale Cameron J. , Williamson Laura M. , Lim Howard J. , Lee Lawrence , Renouf Daniel J. , Jones Steven J. M. , Marra Marco A. , Laskin Janessa , Smrke Alannah 
Published: September 2024

ABSTRACTThe identification of gene fusions in rare sarcoma subtypes can have diagnostic, prognostic, and therapeutic impacts for advanced cancer patients. Here, we present a case of a 31‐year‐old male with a lytic lesion of the left mandible initially diagnosed as an osteosarcoma but found to have a TFCP2 fusion and ALK alteration, redefining the diagnosis and providing rationale for a novel treatment strategy. Histologically, the tumor displayed hypercellular, spindled to epithelioid neoplasm and nuclear pleomorphism, while immunohistochemistry showed diffuse SATB2 and focal desmin staining. Whole genome and transcriptome analysis revealed a FUS::TFCP2 fusion, the defining alteration of a rare molecularly characterized subtype of soft tissue sarcoma termed intraosseous rhabdomyosarcoma. An internal ALK deletion and extremely high ALK RNA expression were also identified, suggesting potential benefit of an ALK inhibitor. This patient displayed a rapid and dramatic clinical and radiographic response to an ALK inhibitor, alectinib. Unfortunately, the response was short‐lived, likely due to the advanced stage and aggressiveness of the disease. This report describes genome and transcriptome characterization of an intraosseous rhabdomyosarcoma, few of which exist in the literature, as well as providing evidence that inhibition of ALK may be a rational treatment strategy for patients with this exceedingly rare soft tissue sarcoma subtype characterized by TFCP2 fusions and ALK activation.
17p13 (TP53) Deletions Are Associated With an Aggressive Phenotype but Unrelated to Patient Prognosis in Urothelial Bladder Carcinomas
Authors: Kluth Martina , Hitzschke Melanie , Furlano Kira , Plage Henning , Hofbauer Sebastian , Weinberger Sarah , Ralla Bernhard , Fendler Annika , de Martino Michela , Roßner Florian , Schallenberg Simon , Elezkurtaj Sefer , Lennartz Maximilian , Marx Andreas H. , Samtleben Henrik , Fisch Margit , Rink Michael , Slojewski Marcin , Kaczmarek Krystian , Ecke Thorsten , Koch Stefan , Adamini Nico , Weischenfeldt Joachim , Klatte Tobias , Minner Sarah , Simon Ronald , Sauter Guido , Schlomm Thorsten , Horst David , Zecha Henrik 
Published: September 2024

ABSTRACT17p13 deletions including TP53 and other genes represent a common cause for reduced/lost p53 function in tumor cells. In this study, we analyzed the impact of 17p13 (TP53) deletions and p53 expression on tumor aggressiveness and patient prognosis in urothelial carcinoma. The 17p13 copy number status was analyzed by fluorescence in situ hybridization (FISH) on more than 2700 urothelial bladder carcinomas in a tissue microarray format. 17p13 deletion data were compared to p53 expression data measured by immunohistochemistry (IHC) in a previous study. Different types of p53 alterations were compared with tumor phenotype and clinical outcome data. Deletions of 17p13 occurred in 23% of 2185 analyzable carcinomas. The fraction of tumors with 17p13 deletions increased from pTa G2 low (9%) to pTa G3 (24%, p < 0.0001). In muscle‐invasive carcinomas, 17p13 deletions were associated with advanced pT stage (p = 0.0246), but unrelated to patient prognosis (p > 0.5). 17p13 deletions were significantly related to p53 immunostaining (p = 0.0375). 17p13 deletions were most common in tumors with complete lack of p53 staining (31%), which supports the concept that many of these tumors have a complete loss of p53 function (p53 null phenotype). 17p13 deletions were also increased in tumors with high p53 staining (25%). In conclusion, 17p13 deletions were most commonly seen in p53 negative cancers, supporting their role as a cause for the p53 null phenotype in urothelial cancer. The association of 17p13 deletions with high grade and advanced pT stage may reflect increasing genomic instability going along with stage and grade progression.
Effects of virtual reality on stroke rehabilitation: An umbrella review of systematic reviews
Authors: Hao Jie , Crum Gretchen , Siu Ka‐Chun 
Published: September 2024

AbstractBackground and AimsVirtual reality is an emerging technology in rehabilitation. This umbrella review aimed to identify, critically appraise, and summarize current systematic reviews on the effects of virtual reality on stroke rehabilitation.MethodsFive biomedical databases, PubMed, Embase, CINAHL, PsycINFO, and Scopus were searched from inception to December 30th, 2023, for systematic reviews with or without meta‐analyses published in English. Two reviewers independently conducted abstract screening, full‐text selection, and quality assessments. The methodological quality of included studies was evaluated by the Assessing the Methodological Quality of Systematic Reviews 2. Results were qualitatively synthesized according to domains of function to ascertain the effects of virtual reality intervention on functional improvement within stroke rehabilitation.ResultsA total of 78 articles were included; 23 were systematic reviews, and 55 were systematic reviews with meta‐analyses. Among them, 30 studies were evaluated as critically low quality, 32 as low, 15 as moderate, and one as good. Outcomes regarding upper extremity motor function, upper extremity activity, participation, functional independence, balance, functional mobility, walking speed, and cognitive function were summarized. While positive effects in favor of virtual reality were revealed by a majority of systematic reviews on these outcomes, evidence supporting the significantly different effects of virtual reality compared to conventional rehabilitation on participation and cognitive function was lacking.ConclusionThe umbrella review demonstrated promising clinical outcomes regarding the use of virtual reality as an advanced therapeutic approach in stroke rehabilitation to optimize patient care. Future systematic reviews and meta‐analyses in this field should adhere to established guidelines to enhance the quality of evidence.
Unlocking the medicinal arsenal of Cissus assamica: GC‐MS/MS, FTIR, and molecular docking insights
Authors: Taher Mohammad Abdullah , Kundu Ripa , Laboni Aysha Akter , Shompa Suriya Akter , Moniruzzaman Md. , Hasan Mohammad Mahmudul , Hasnat Hasin , Hasan Md. Mehedi , Khan Mala 
Published: September 2024

AbstractBackground and aimsThis study investigated the biochemical components present in the leaves of Cissus assamica. The primary aim was to analyze these components using advanced techniques and assess their potential therapeutic applications.MethodologyFourier Transform Infrared (FT‐IR) spectroscopy, Gas Chromatography‐Mass Spectrometry (GC‐MS), and Mass Spectral analysis were employed to identify and characterize the compounds in Cissus assamica leaves. The mass spectra of each compound were compared with data from the Wiley and NIST libraries to determine their names, molecular masses, and chemical structures. FT‐IR analysis identified characteristic functional groups by their specific frequencies.Results and discussionFT‐IR spectroscopic analysis revealed significant molecular vibrations at frequencies of 3265.63, 2853.81, 1638.60, 1469.21, and 1384.95 cm⁻¹, indicating the presence of specific functional groups. The GC‐MS analysis identified distinct compounds, such as “aR‐Turmerone,” “Curlone,” “7,8‐Epoxylanostan‐11‐ol, 3‐acetoxy‐,” “13‐Docosenamide, (Z)‐,” “Phenol, 3,5‐bis(1,1‐dimethylethyl)‐,” “9,19‐Cyclolanostan‐3‐ol, 24,24‐epoxymethano‐, acetate,” and “Quinoline‐5,8‐dione‐6‐ol, 7‐[[(4‐cyclohexylbutyl)amino]methyl]‐.” These compounds exhibited potential therapeutic applications. Their cytotoxic, antimicrobial, antidiarrheal, anti‐hyperglycemic, and pain‐relieving properties were evaluated by comparing them with reference ligands targeting specific receptors, including dihydrofolate reductase (DHFR), epidermal growth factor receptor (EGFR), kappa opioid receptor (KOR), glucose transporter 3 (GLUT 3), and cyclooxygenase 2 (COX‐2).ConclusionThe results of this study suggest that Cissus assamica leaves contain bioactive compounds with potential therapeutic benefits for treating infections, diarrhea, hyperglycemia, and pain. However, further research is needed to conduct comprehensive phytochemical screening and establish the precise mechanisms of action for the crude extract or the plant‐derived compounds.
Development of a machine learning‐based target‐specific scoring function for structure‐based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors
Authors: Meng Jinhui , Zhang Li , He Zhe , Hu Mengfeng , Liu Jinhan , Bao Wenzhuo , Tian Qifeng , Feng Huawei , Liu Hongsheng 
Published: September 2024

AbstractHuman dihydroorotate dehydrogenase (hDHODH) is a flavin mononucleotide‐dependent enzyme that can limit de novo pyrimidine synthesis, making it a therapeutic target for diseases such as autoimmune disorders and cancer. In this study, using the docking structures of complexes generated by AutoDock Vina, we integrate interaction features and ligand features, and employ support vector regression to develop a target‐specific scoring function for hDHODH (TSSF‐hDHODH). The Pearson correlation coefficient values of TSSF‐hDHODH in the cross‐validation and external validation are 0.86 and 0.74, respectively, both of which are far superior to those of classic scoring function AutoDock Vina and random forest (RF) based generic scoring function RF‐Score. TSSF‐hDHODH is further used for the virtual screening of potential inhibitors in the FDA‐Approved & Pharmacopeia Drug Library. In conjunction with the results from molecular dynamics simulations, crizotinib is identified as a candidate for subsequent structural optimization. This study can be useful for the discovery of hDHODH inhibitors and the development of scoring functions for additional targets.
Scalable production of siRNA‐encapsulated extracellular vesicles for the inhibition of KRAS‐mutant cancer using acoustic shock waves
Authors: Kim Hyo Kyeong , Choi Yujeong , Kim Kyoung Hwa , Byun Yeongju , Kim Tae Hee , Kim Jae Hwan , An Shung Hyun , Bae DaeHo , Choi Myeong Kwan , Lee Minyoung , Kang Gwansuk , Chung Jihwa , Kim Seok‐Hyun , Kwon Kihwan 
Published: September 2024

AbstractExtracellular vesicles (EVs) have emerged as a potential delivery vehicle for nucleic‐acid‐based therapeutics, but challenges related to their large‐scale production and cargo‐loading efficiency have limited their therapeutic potential. To address these issues, we developed a novel “shock wave extracellular vesicles engineering technology” (SWEET) as a non‐genetic, scalable manufacturing strategy that uses shock waves (SWs) to encapsulate siRNAs in EVs. Here, we describe the use of the SWEET platform to load large quantities of KRASG12C‐targeting siRNA into small bovine‐milk‐derived EVs (sBMEVs), with high efficiency. The siRNA‐loaded sBMEVs effectively silenced oncogenic KRASG12C expression in cancer cells; they inhibited tumour growth when administered intravenously in a non‐small cell lung cancer xenograft mouse model. Our study demonstrates the potential for the SWEET platform to serve as a novel method that allows large‐scale production of cargo‐loaded EVs for use in a wide range of therapeutic applications.
Lateral meniscus posterior root repairs show superior healing, reduced meniscal extrusion and improved clinical outcomes compared to medial meniscus posterior root repairs: A systematic review
Authors: Dzidzishvili Lika , Pedemonte‐Parramón Gloria , Garcia‐Oltra Ester , López Vicente , Hernández‐Hermoso José A. 
Published: September 2024

AbstractPurposeTo systematically review and summarize the available literature on (1) postoperative healing rates, meniscal extrusion (ME) and clinical outcomes following lateral (LMPRR) versus medial (MMPRR) root repair and (2) potential correlations between residual ME and healing outcomes.MethodsA comprehensive literature search was conducted using the Scopus, PubMed and Embase databases. Clinical studies evaluating healing status on second‐look arthroscopy and magnetic resonance imaging (MRI) after LMPRR and MMPRR were included. Study quality was assessed using the Methodological Index for Non‐Randomized Studies criteria and the modified Coleman Methodology Score.ResultsTwenty‐three studies comprising 871 patients with LMPRR (n = 406) and MMPRR (n = 465) were included. Overall, 223 (54.9% of total) and 149 (32.04% of total) patients underwent second‐look arthroscopy in the LMPRR and MMPRR groups, respectively. Complete root healing was observed in 190 (85.2%) patients in the LMPRR group versus 78 (52.3%) in the MMPRR group (p < 0.001). There were six (2.7%) failed repairs in the LMPRR group compared to 21 (14.09%) in the MMPRR group (p < 0.001). On postoperative MRI, 109 (75.7%) root repairs were healed in the LMPRR group compared to 192 (53.3%) in the MMPRR group (p < 0.001). Failure rates were lower after all‐inside and transtibial pullout repairs in the LMPRR group but higher in the MMPRR group, with no significant mean difference between preoperative and postoperative ME in the MMPRR group (p = 0.95). Significantly better clinical outcomes were observed in the LMPRR group compared to the MMPRR group. A greater degree of postoperative ME was associated with lower healing rates (R = −0.78, p < 0.0005). Postoperative ME did not influence clinical outcomes (R = 0.28, p = 0.29).ConclusionsLateral meniscus posterior root repairs showed higher healing rates compared to MMPRR on both second‐look arthroscopy and postoperative MRI. Meniscal extrusion decreased after LMPRR but not after MMPRR. Greater residual ME correlated inversely with healing rates, as more extrusion was associated with lower healing. Postoperative clinical improvement did not affect ME or healing status.Study DesignSystematic review of level III and IV studies.Level of EvidenceLevel IV.
Effect of tibia‐first, restricted functional alignment technique on gap width changes, and component positioning in robotic arm‐assisted total knee arthroplasty
Authors: Yang Hong Y. , Cheon Jae H. , Kang Sung J. , Seon Jong K. 
Published: September 2024

AbstractPurposeThis study aims to quantitatively assess the predictability of post‐resection gap dimensions and the attainment of balanced gaps using robotic arm‐assisted total knee arthroplasty (TKA).MethodsThis retrospective cohort study included 100 consecutive patients who underwent robotic arm‐assisted TKA for knee osteoarthritis using a restricted functional alignment (FA) technique. Tibial cuts were performed based on preoperative tibial anatomy within predefined boundaries, followed by femoral component adjustments according to tensioned soft tissues to optimise gap balance. The primary outcome was the proportion of balanced gaps, defined as differential laxities of ≤2 mm, across extension, flexion, lateral, and medial gap measurements. Ligament balancing in lateral and medial compartments was assessed using a robotic system at 10° and 90° flexion to evaluate if restricted FA facilitated a balanced knee. Secondary outcomes included implant alignment, resection depth, and patient‐reported outcome measures (PROMs).ResultsSignificant increases in both lateral and medial gaps at 10° and 90° flexion were observed following tibial and femoral bone resections (p < 0.001). At extension, average gap changes were 0.9 mm (lateral) and 1.6 mm (medial) after tibial cuts, and 0.5 mm (lateral) and 1.2 mm (medial) after femoral cuts. At 90° flexion, changes were 0.3 mm (lateral) and 1.7 mm (medial) following tibial cuts, and 1.0 mm (lateral) and 1.4 mm (medial) after femoral cuts. Despite these variations, the tibia‐first, gap‐balancing technique achieved overall balance in 98% of gap measurements. The tibial component was placed at an average of 2.1° varus, while the femoral component was positioned at 0.3° varus and 1.3° external rotation relative to the surgical transepicondylar axis. Significant improvements in PROMs were noted between preoperative and one‐year postoperative evaluations (all p < 0.05).ConclusionsThe tibia‐first, restricted FA technique achieved a well‐balanced knee in 98% of cases, despite inconsistent gap increments observed between initial assessments and post‐resection.Level of EvidenceTherapeutic Level IV.
Dedicator of cytokinesis 8 (DOCK8) mutation impairs the differentiation of helper T cells by regulating the glycolytic pathway of CD4+ T cells
Authors: Jiang Panpan , Zhao Siyu , Li Xiaoyu , Hu Shiyan , Chen Shuhan , Liang Yinming , Zhang Lichen , Lu Liaoxun , Fang Guofeng , Yang Lu , Huang Yanmei , Miller Heather , Guan Fei , Lei Jiahui , Liu Chaohong 
Published: September 2024

AbstractDedicator of cytokinesis 8 (DOCK8) deficiency is a primary immunodeficiency disease caused by mutations in exon 45 of the DOCK8 gene. The clinical signs primarily consist of increased serum IgE levels, eczema, repeated skin infections, allergies, and upper respiratory tract infections. Using CRISPR/Cas9 technology, we generated a DOCK8 exon 45 mutation in mice, mirroring the mutation found in patients. The results indicated that DOCK8 mutation impairs peripheral T cell homeostasis, disrupts regulatory T cells (Tregs) development, increases ICOS expression in Tregs within peripheral lymph nodes (pLn), and promotes Th17 cell differentiation within the spleen and pLn. Upon virus infection, DOCK8 mutation CD4+ T cells have a Th2 effector fate. RNA‐bulk sequencing data revealed alternations in the mTOR pathway of DOCK8 mutant CD4+ T cells. We observed that DOCK8 mutation upregulates the glycolysis levels in CD4+ T cells, which is related to the Akt/mTOR/S6/HIF‐1α pathway. In summary, our research elucidates that DOCK8 regulates the differentiation of helper T cells by modulating the glycolytic pathway in CD4+ T cells, thereby advancing the comprehension and offering potential treatment of diseases in DOCK8‐deficient patients.