bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome and metabolome analysis reveal the mechanisms of iron absorption differences in apple rootstocks under alkaline condition
Authors: Li Yanmei , Chen Peng , Zeng Fanwei , Wang Han , Ma Weifeng , Wu Aiyuan , Ma Zonghuan , Mao Juan , Chen Baihong 
Published: February 2025

AbstractIron (Fe) is an essential micronutrient for plant growth and development. Fe deficiency leads to growth restriction, developmental disorders, chlorosis, and yield loss of fruit trees. This study investigated the molecular and biochemical mechanisms underlying the differences in Fe absorption among various apple rootstocks under alkaline conditions. Results showed that ‘Oregon Spur II’ grafted onto Qingzhen No.2 (OS/Q2) exhibited foliage etiolation, while ‘Oregon Spur II’ grafted onto Qingzhen No.1 (OS/Q1) did not display such etiolation under alkaline conditions. Physiological experiments revealed that total Fe, ferrous Fe, and chlorophyll content in OS/Q2 were significantly lower than those in OS/Q1, whereas the Fe reductase activity in OS/Q2 was higher than that in OS/Q1. Additionally, a total of 7,025 and 9,102 differentially expressed genes (DEGs), including 488 transcription factors (TFs), were identified in OS/Q1L vs. OS/Q2L and OS/Q1R vs. OS/Q2R, respectively. Subsequently, the pathways associated with “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “hydrogen ion export across plasma membrane”, “heme binding”, and “iron binding” were identified as critical for responding to Fe deficiency under alkaline conditions. Furthermore, a total of 244 differentially accumulated metabolites (DAMs) were identified in OS/Q1R vs. OS/Q2R. A combined analysis of the transcriptome and metabolome revealed that “ABC transporters”, “biosynthesis of amino acids”, and “carbon fixation in photosynthetic organisms” were significantly overrepresented in the KEGG pathways of both DEGs and DAMs. These newly acquired genes and metabolites involved in Fe metabolism will enhance our capacity to employ genetic engineering technologies to maintain Fe homeostasis in plants in the future.
Haplotype‐resolved genome assembly of Ficus carica L. reveals allele‐specific expression in the fruit
Authors: Usai Gabriele , Giordani Tommaso , Vangelisti Alberto , Castellacci Marco , Simoni Samuel , Bosi Emanuele , Natali Lucia , Mascagni Flavia , Cavallini Andrea 
Published: February 2025

SUMMARYIn this study, we produced a haplotype‐phased genome sequence of the fig tree (Ficus carica L.), a non‐Rosaceae fruit tree model species, providing a systematic overview of the organization of a heterozygous diploid genome and, for the first time in a fruit tree, evidence of allelic expression direction‐shifting among haplotypes. The genome was used for whole genome analysis of heterozygosis, allelic cytosine methylation, and expression profiles in peel and pulp fruit tissues. The two pseudo‐haplotypes spanned approximately 355 and 346 Mbp, respectively, and 97% of the sequences were associated with 13 chromosome pairs of the fig tree. Overall, the methylation profile in peel and pulp tissues showed no variations between the homologous chromosomes. However, we detected differential DNA methylation within defined heterozygous allelic gene regions, particularly in upstream regions. Among 6768 heterozygous coding sequences identified, 4024 exhibited allele‐specific expression, with approximately 18% specific to the peel and 14% to the pulp. Specifically, 2715 genes were consistent, with one allele always more expressed than the other in both peel and pulp. On the contrary, 22 allele‐specific expressed genes switched allele expression among the fig fruit peel and pulp tissues, indicating evidence of overdominance and suggesting that the genome can express one of the two alleles higher or lower depending on developmental or environmental triggers. Notably, these genes were associated with key biological processes, including fruit maturation regulation, seed maturation, and stress response, highlighting their potential role in the plant's developmental and adaptive functions in view of gene editing‐based breeding.
Xenotransplantation Literature Update July–December 2024
Authors: Shirini Kasra , Ladowski Joseph M. , Meier Raphael P. H. 
Published: February 2025

ABSTRACTThis review highlights groundbreaking progress from July to December 2024, including developments in gene‐edited pigs, cellular therapies, organ preservation, and transplantation techniques. Recent advancements, particularly in gene‐editing technologies and immunosuppressive protocols, have brought the field closer to clinical application. While significant ethical, immunological, and societal challenges remain, this progress underscores the immense potential of xenotransplantation to revolutionize transplantation medicine.
Lorentzian polynomials and the independence sequences of graphs
Authors: Bendjeddou Amire , Hardiman Leonard 
Published: February 2025

AbstractWe study the multivariate independence polynomials of graphs and the log‐concavity of the coefficients of their univariate restrictions. Let be the operator defined on simple and undirected graphs which replaces each edge with a caterpillar of size 4. We prove that all graphs in the image of are what we call pre‐Lorentzian, that is, their multivariate independence polynomial becomes Lorentzian after appropriate manipulations. In particular, as pre‐Lorentzian graphs have log‐concave (and therefore unimodal) independence sequences, our result makes progress on a conjecture of Alavi, Malde, Schwenk and Erdős which asks if the independence sequence of trees or forests is unimodal.
Peeling pressure-sensitive adhesive elastica from circular cylinder
Authors: Plaut Raymond H. 
Published: February 2025

Abstract
Quasi-static peeling of a pressure-sensitive tape from the outside of a rigid circular cylinder is analyzed. The finite-length tape is perpendicular to the axis of the cylinder and up to half the circumference. The tape is modeled as an inextensible elastica, so that bending resistance predominates and stretching of the tape is neglected. A transversality (debonding) condition is derived for peeling, based on the common fracture mechanics approach. The tape is unstrained when straight, and will not stick to the curved substrate if the adhesion is sufficiently weak. Displacement control is considered, and the deflections and rotations may be large. The pulled end of the tape may have an initial unbonded straight segment at the pulled end. Equilibrium curves of force versus vertical deflection of the pulled end are determined, along with curves of the maximum force, which occurs at the initiation of peeling. Detachment of the tape from the substrate is examined. The effects of the initial bonded and unbonded lengths of the tape, the angle of pulling, the work of adhesion, and the radius of curvature of the cylinder are investigated.
Effects of Combined Versus Single Supplementation of Creatine, Beta-Alanine, and L-Citrulline During Short Sprint Interval Training on Basketball Players’ Performance: A Double-Blind Randomized Placebo-Controlled Trial
Authors: Li Menghao , Sheykhlouvand Mohsen 
Published: February 2025

Purpose: Athletes often use sport supplements to improve their physical and physiological performance. This randomized, double-blind, placebo (PL) -controlled study aimed to investigate the effects of combined versus single supplementation of creatine (Cr), beta-alanine (BA), and L-citrulline (L-Cit) during short sprint interval training (SSIT) on basketball players’ physical and physiological performance over a period of 28 days. Methods: Forty-eight basketball players were equally assigned to 6 groups of Cr (0.1 g/kg of Cr monohydrate daily), BA (4.8 g daily), L-Cit (6 g daily), combined supplementation, PL, and an active control group, and each group consisted of 8 participants. The training groups participated in SSIT (3 sets of 10 repetitions of 5-s all-out runs) sessions 3 times a week for 4 weeks. Physical (vertical jump, 20-m sprint, Illinois change of direction) and physiological (Wingate anaerobic power and cardiorespiratory fitness test) performance were evaluated before and after the training period. Results: All training groups (Cr, BA, L-Cit, combined, and PL) showed significant improvements in physical and physiological performance over the 4-week intervention (P < .05). Interestingly, the supplement groups displayed significantly (P = .001) greater changes than the PL group, indicating better outcomes in performance adaptations. However, significant differences in performance variables were observed among the supplement groups. Conclusion: Our findings indicate that short-term supplementation with Cr, BA, and L-Cit, as well as a combination of them during SSIT, can significantly improve the physical and physiological performance of basketball players compared to a PL.
The Value of Practicing the “Wrong” Way: Skill Development and Affordance Perception Through Broad Exploration of the Solution Space
Authors: Gray Rob 
Published: February 2025

Traditionally, in sports, we spend the majority of practice time trying to do the “right” things; that is, producing the desired performance outcomes (e.g., hitting a golf shot down the middle of the fairway, shooting a basketball into the net, hitting a baseball into fair play). An alternative is to practice doing the “wrong” thing (i.e., an undesired outcome) sometimes. This could give the performer more information about the solution space and available affordances. In two experiments, a baseball batting virtual environment was used to compare these two types of training. In Experiment 1, the constant goal group always attempted to “hit the ball hard into fair play” (i.e., the desired outcome) and were given technical instructions about the swing and corrective feedback from an experienced coach. The variable goal group received no technical instruction and had different outcome goals for each session, including undesired ones: Hit the ball as far to the right (or left) as you can, pop the ball up into air, and drive the ball into the ground. In Experiment 2, the constant goal group did not receive explicit instructions or corrective feedback. All groups trained for 6 weeks. In pre- and posttests, batters completed simulated games in which the pitch speed, type, and location were varied, an umpire called balls and strikes, and the fielders shifted locations (e.g., they all moved to the left or right side of the field). In both experiments, the variable goal group had a significantly larger increase in hits, adapted more effectively to variations in pitch trajectory, and demonstrated superior affordance perception (e.g., not swinging at pitches out of the strike zone and ones that would have likely led to hitting into the defense).
The Effects of Different Core Stability Training on Trunk Stability and Athletic Performance in Adolescent Female Basketball Players
Authors: Liang Ian-Ju , Lin Linda L. , Huang Chen-Chia 
Published: February 2025

Purpose: Trunk function is not only related to physical fitness performance, but also important for the balance, and stability of the whole body. This study aimed to investigate the effects of 2 training methods on trunk stability and athletic performance in adolescent female basketball players. Methods: Fifty-one healthy elite female basketball players (age: 14.76 [1.84] y, body mass index: 21.41 [1.96] kg/m2) were assigned to TRX training (n = 17), Swiss ball training (n = 17), or control groups (n = 17). Participants performed a progressive program of unstable core muscle training consisting of 8 different exercises, with each exercise performed in 3 sets, twice a week for 8 weeks. The outcome measures were a plank test, the modified double leg lowering task, and athletic performance including jumping, speed, agility, cardiopulmonary endurance, and the ankle proprioception. Results: Significant group and time interaction were identified in the modified double leg lowering task (P = .032, η2 = .134), with post hoc comparisons revealing improvements in the TRX group (P = .014). The TRX group (8.6%) improved significantly more than the Swiss ball group (2.9%) when it comes to the modified double leg lowering average change percentage. The plank test also exhibited a significant group and time interaction (P = .033, partial η2 = .133), with notable improvements in both the Swiss ball (P = .001) and the TRX groups (P = .001). Athletic performance measures showed no significant differences among groups. Conclusions: The results indicate that both TRX and Swiss ball training can increase core muscle strength and stability without compromising athletic performance after 8 weeks of training. Furthermore, incorporating core muscle training enhances power transmission capabilities. Nevertheless, considering the goal was to improve speed and ankle proprioception during preseason training, careful consideration must be given to the timing and intensity of any intervention involving unstable core muscle training.
Sleep quantity and quality during the first week postinjury and time to symptom resolution in youth with concussion
Authors: VonDeylen Olivia , Alshaikh Enas , Wheeler Krista , Recker Robyn , Malerba Paola , Valasek Amy , Yeates Keith Owen , Yang Jingzhen 
Published: February 2025

ObjectiveTo examine bidirectional associations between objective measures of sleep quantity and quality with postconcussion symptoms (PCS) scores in concussed youth during the first week postinjury and to explore the associations between sleep measures and time to symptom resolution.Study designWe conducted a secondary analysis of a prospectively enrolled cohort of youth (11–17 years) with a physician diagnosed concussion within 72 hours of injury. During the first week postconcussion, sleep quantity (time in bed, total sleep time and daytime sleep) and sleep quality (sleep efficiency, WASO and number of awakenings) were measured using an ActiGraph. We evaluated bidirectional temporal associations between the sleep measures and PCS during the first week postinjury using cross-lagged panel models. We assessed the associations between sleep measures and time to symptom resolution using Cox proportional hazard models.ResultsParticipants included 78 concussed youth, 34.6% females, mean age of 14.2 years (SD=2.1). Significant bidirectional associations were observed between PCS and both total sleep time and daytime total sleep in the first week postinjury. Increased daytime sleep was also associated with a decreased likelihood of symptom resolution, adjusted HR (aHR)=0.88, 95% CI=0.78, 0.999. An optimal total sleep time of 418 min per day was associated with a 2.1-fold increased likelihood of symptom resolution (aHR=2.1, 95% CI=1.3, 3.2).ConclusionsClinicians should provide guidance on sleep hygiene, including limiting daytime sleep/naps and getting the appropriate amount of nighttime sleep acutely postconcussion to aid recovery in youth.
Effector T cells under hypoxia have an altered transcriptome similar to tumor-stressed T cells found in non-responsive melanoma patients
Authors: Nagy Mate Z , Plaza-Rojas Lourdes B , Boucher Justin C , Kostenko Elena , Austin Anna L , Tarhini Ahmad A , Chen Zhihua , Du Dongliang , Ojwang' Awino Maureiq E , Davis Joshua , Obermayer Alyssa , Rejniak Katarzyna A , Shaw Timothy I , Guevara-Patino Jose A 
Published: February 2025

BackgroundIn the tumor microenvironment (TME), hypoxia stands as a significant factor that modulates immune responses, especially those driven by T cells. As T cell-based therapies often fail to work in solid tumors, this study aims to investigate the effects of hypoxia on T cell topo-distribution in the TME, gene expression association with T cell states, and clinical responses in melanoma.MethodsTo generate detailed information on tumor oxygenation and T cell accessibility, we used mathematical modeling of human melanoma tissue microarrays that incorporate oxygen supply from vessels, intratumoral diffusion, and cellular uptake. We created tumor maps and derived plots showing the fraction of CD4 and CD8 T cells against the distance to the nearest vessel and oxygen pressure. To assess their function and transcriptional changes caused by hypoxia, effector T cells were generated and cultured under hypoxia (0.5% oxygen) or normoxia (21% oxygen). The T cell hypoxia-transcriptional signature was compared against datasets from msigDB, iATLAS (clinical trials of melanoma patients treated with immune checkpoint inhibitors (ICIs)), ORIEN AVATAR (real-world melanoma patients treated with ICIs), and a single-cell atlas of tumor-infiltrating lymphocytes.ResultsWe made three specific observations: (1) in melanoma T cells preferentially accumulated in oxygenated areas close to blood vessels (50–100 µm from the vasculature in the regions of high oxygen availability) but not in hypoxic areas far from blood vessels. (2) Our analysis confirmed that under hypoxia, T cell functions were significantly reduced compared with normoxic conditions and accompanied by a unique gene signature. Furthermore, this hypoxic gene signature was prevalent in resting and non-activated T cells. Notably and clinically relevant, the hypoxic T cell gene set was found to correlate with reduced overall survival and reduced progression-free survival in melanoma patients, which was more pronounced in non-responder patients undergoing ICI therapy. (3) Finally, compared with a single-cell atlas of tumor-infiltrating T cells, our hypoxia signature aligned with a population of cells at a state termed stress response state (TSTR).ConclusionsOur study highlights the critical role of hypoxia in shaping T cell distribution and its correlation with clinical outcomes in melanoma. We revealed a preferential accumulation of T cells in oxygenated areas. Moreover, hypoxic T cells develop a distinct hypoxic gene signature prevalent in resting, non-activated T cells and TSTRthat was also associated with poorer outcomes, particularly pronounced among non-responders to ICIs.
Fc-competent TIGITx4-1BB bispecific antibody exerts potent long-lasting antitumor activity by potentiating CD8+T cell activity and Fcγ receptor-mediated modulation of the tumor microenvironment
Authors: Son Wonjun , Lee Yangsoon , Park Yelim , Park Kyeong-Su , Kim Sora , Youn Hyunseong , Seo Arim , Sung Byungje , Lee Sang Hoon , Won Jonghwa 
Published: February 2025

BackgroundTIGIT was identified as a target immune checkpoint for overcoming resistance to PD-(L)1-blocking antibodies. However, the clinical efficacies of TIGIT antibodies were moderate in monotherapy and mixed in combination with PD-(L)1 antibodies. 4-1BB, a strong inducible costimulatory receptor, is another attractive target in antitumor therapeutics. This study investigated whether ABL112, an Fc-competent bispecific antibody targeting TIGIT and 4-1BB (TIGITx4-1BB), would enhance antitumor activity via Fcγ receptor (FcγR)-mediated macrophage activation and antibody-dependent cell-mediated functions.MethodsTIGIT-dependent 4-1BB activation and TIGIT-blocking activity were assessed using reporter Jurkat T cell lines expressing 4-1BB and TIGIT, respectively. In vivo antitumor activity was confirmed in h4-1BB knock-in mice. The main immune cell subsets associated with the antitumor activity of ABL112 were identified using antibodies for depleting specific immune cell subtypes or FcγR-blocking antibodies. The effects of a combined pembrolizumab or atezolizumab treatment with ABL112 were assessed in two mouse models with different genetic backgrounds. Statistical analysis was performed using one-way or two-way analysis of variance (ANOVA) with Dunnett’s multiple-comparison test or one-way ANOVA with Fisher’s multiple-comparison test.ResultsABL112 restored T cell activity by blocking TIGIT–CD155 interactions, based on a TIGIT blockade reporter assay. ABL112, an Fc-competent TIGITx4-1BB bispecific antibody, showed strong FcγRI-dependent 4-1BB activation along with TIGIT-dependent 4-1BB activation. In H22 tumor models expressing high levels of endogenous CD155, both ABL112 and parent TIGIT single-domain Ab showed potent tumor-suppressive activity; however, only ABL112 exerted long-lasting antitumor activity. ABL112 induced a marked decrease in Treg numbers, while augmenting the absolute number of CD8+T cells and proportion of CD226+CD8+T cells. The expressions of CXCL10, CXCL11, IFN-γ, and TNF-α increased, indicating myeloid cell activation and potential modification of the tumor microenvironment to an inflammatory phenotype. ABL112 not only showed outstanding antitumor activity as a monotherapy, but also showed synergistic effects with PD-(L)1 mAb compared with the combined TIGIT–PD-(L)1 mAb treatments.ConclusionsThrough multiple mechanisms of action, ABL112 exerted potent tumor-killing activity and immune memory response alone or in combination with anti-PD-(L)1 therapies, representing a promising new cancer treatment strategy.
Chromosomal and molecular perspectives on Potamotrygon motoro (Müller & Henle, 1841) from central Amazon
Authors: Ferreira Alex M.V. , Viana Patrik F. , Marajó Leandro , Feldberg Eliana 
Published: February 2025

Cytogenetic studies on Potamotrygon motoro (Müller & Henle, 1841) are limited to classical cytogenetic techniques, but they do reveal great karyotypic variation. The main differences are related to the karyotypic formula and the absence/presence of sex chromosome systems. Thus, this study aimed to expand knowledge of the karyotypic composition of Potamotrygon motoro from different locations of the Central Amazon using Fluorescence in situ Hybridization to investigate the distribution of ribosomal DNAs (rDNA) and microsatellites sequences (SSRs). In addition, we used the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) to perform neighbor-joining analysis to investigate the relationships among the individuals sampled. In our study, Potamotrygon motoro presented 2n = 66 chromosomes, with 18m + 12sm + 10st + 26a and heterochromatic blocks on centromeric region of all chromosomes. The 18S rDNA is present in three chromosomal pairs and 5S rDNA is located in the pair 16, which is a feature shared among freshwater stingray species. Regarding the mapping of SSRs, dinucleotide sequences showed a greater number of sites, usually on terminal regions of chromosomal pairs, with an accumulation throughout the long arms of the pair 17. Our molecular analyses did not reveal differences between the sequences used. In general, the karyotypic differences previously reported for Potamotrygon motoro indicate the presence of different cytotypes within the species.