bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overall Survival in Advanced Stage Mantle Cell Lymphoma after Early Autologous Stem Cell Transplantation with Cisplatin, Etoposide, Cytarabine and Melphalan (PEAM) As a Conditioning Regimen
Authors: Franco Daniel , Tellez Fernando , Solis-Armenta Ruben , Leal Alanis Araceli , Cruz Castillo Carlos , Valero Saldaña Luis Manuel , Acosta Maldonado Brenda Lizeth 
Published: December 2023

Introduction.
Autologous hematopoietic stem cell transplantation (ASCT) currently is the standard of treatment for patients in first remission diagnosed with Mantle cell Lymphoma (MCL). Overall survival (OS) was reported at five-years of 57.2% in a single center retrospective study published in 2011. OS has been improved by using conventional and high intensity induction chemo immunotherapy continuing with maintenance therapy as the GELA study reports a 5 year OS of 75%. LyMa Trial has proved an improvement in the global survival and progression free survival. In this study we aimed to describe the OS patients diagnosed with MCL with PEAM as a conditioning regimen.
Methods
A retrospective study was conducted on patients diagnosed with MCL and ASCT as consolidation therapy at the Instituto Nacional de Cancerología in Mexico City between 2011 and 2022. Our institutional conditioning regimen PEAM: Cisplatin 100 mg/m2 (-4), etoposide 750 mg/m2 (-4,-3), cytarabine 800 mg/m2 (-4,-3,-2) and melphalan 140 mg/m2( 4).OS results were obtained using the Kaplan-Meier method.
Results
We analyzed 19 patients with MCL after ASCT as consolidation therapy, a median follow-up of 10 years, the median age at transplantation was 56 years (range 39- 68 y), with male predominance (68.4%). Eleven patients with at least one comorbidity, the most predominant being diabetes mellitus type II (45.5%). Most patients with ECOG score of 1 (58%), 12 patients (63%) with high risk according to Mantle Cell lymphoma International Prognostic Index (MIPI), all patients with clinical stage III-IV, 26% of them with bone marrow infiltration.
Eighteen patients (95%) received one line of chemoimmunotherapy, most were treated with R-CHOP plus + R-DHAP( 58%), 3 receive Hiper-CVAD (16%), 4 R-CHOP (21%) and only one R-DHAP . Eighteen patients (79%) with complete response, three (16%) with partial response and one patient (5%) with stable
disease before ASCT. Sixteen patients (84%) received PEAM plus rituximab as myeloablative conditioning regimen, Three (16%) PEAM without rituximab. Neutrophil recovery median was 10 days, eleven patients (58%) developed complications being febrile neutropenia the most common (82%). Fifteen patients (79%) received maintenance with rituximab. Fourteen (74%) had complete response at last follow up after ASCT, three (20%) with relapsed disease, two stable disease (10%)
Conclusion
Conventional chemoimmunotherapy is effective followed by ASCT as consolidation therapy in mantle cell lymphoma with advanced stage disease. We describe higher OS 5-years (81%) as compared with other series (57% and 75%) with similar chemo immunotherapy and conventional conditioning regimen. Three patients relapsed, all died. The OS at 5-years was 81%.
Outcomes of Multiple Myeloma Hospitalization Undergoing Autologous Stem Cell Transplantation with and without CKD: A NIS 2016 to 2020 Database Study
Authors: Neupane Niraj , Srivastava Arnav , Agrawal Shubham , Shah Anish , Budhathoki Pravash , Mahmoud Amir , Sanjeevi Aditya , Kharel Himal , Joshi Utsav , Dhakal Binod 
Published: December 2023

Outcomes of Multiple Myeloma Hospitalization undergoing autologous stem cell transplantation with and without CKD: A NIS 2016 to 2020 database study.
Objective:
This study aimed to compare hospital outcomes between multiple myeloma patients undergoing autologous stem cell transplantation (ASCT) with and without chronic kidney disease (CKD) using data from the National Inpatient Sample (NIS) from 2016 to 2020.
Methods:
A retrospective analysis of the NIS database was conducted using International Classification of Diseases (ICD-10) codes to identify hospitalization who underwent ASCT for multiple myeloma. STATA version MP14.2 was used mainly for analysis. We used Fischer's exact test to compare proportions, the student's t-test to compare continuous variables, and multivariate regression analysis to calculate the adjusted odds ratio. Following are included in transplant complications (transplant rejection, failure, transplant infection).
Results:
Among 31,390 hospitalized, 4,930 had co-existing CKD. The mean age was 61.65 years. The majority were male (64.2%), with an increased Charlson comorbidity index with a majority &gt;6. On multivariant analysis compared to hospitalization without CKD, those with CKD showed a significantly higher risk of transplant complications (adjusted odds ratio [AOR]: 1.90, 95% confidence interval [CI]: 1.21-2.99, P = 0.006), AKI (AOR: 5.43, 95% CI: 4.47-6.59, P &lt; 0.001), AKI requiring dialysis (AOR: 2.16, 95% CI: 2.14-11.94, P &lt; 0.001), blood transfusion (AOR: 1.32, 95% CI: 1.00-1.75, P = 0.048), and in-hospital mortality (AOR: 2.16, 95% CI: 1.13-4.12, P = 0.02). Additionally, there was a non-significant increase in the rate of platelet transfusion and ICU admission. Hence, patients with CKD had a significantly longer average length of hospital stay (18.27 vs. 16.26. p&lt; 0.001) and higher total cost of hospital stay ($217,202 vs. $199,062, P=0.02) compared to those without CKD.
Conclusion:
Multiple myeloma patients undergoing ASCT with co-existing CKD experienced poorer hospital outcomes, including a higher risk of transplant-related complications, AKI, blood transfusion, and in-hospital mortality resulting in prolonged hospital stays and higher healthcare costs. Since multiple myeloma has a higher incidence of CKD, further studies are warranted to explore interventions based on the stage of CKD to improve the outcomes of ASCT in multiple myeloma patients with CKD.
Clinical and immunological features in ACKR1/DARC-associated neutropenia
Authors: Palmblad Jan , Sohlberg Ebba , Nilsson Christer C. , Lindqvist Henric , Deneberg Stefan , Ratcliffe Paul , Meinke Stephan , Mörtberg Anette , Klimkowska Monika , Höglund Petter 
Published: December 2023

Abstract
ACKR1/DARC-associated neutropenia (NP; ADAN; Online Mendelian Inheritance in Man 611862), caused by a variation in the ACKR1/DARC gene (rs2814778), is common in persons of African or Middle Eastern descent. In a cohort of 66 genetically confirmed subjects with ADAN, we show that absolute neutrophil counts (ANCs) may occasionally be lower than previously recognized (0.1 × 109-0.49 × 109/L for 9% of the subjects), which is similar to ANCs in severe congenital NP (SCNP). ANCs often normalized during inflammation, even mild. Individuals with ADAN (of 327 observed person-years) showed no cases of myelodysplastic syndrome (MDS), which is frequently encountered in SCNP. Unexpectedly, 22% presented with autoantibodies to neutrophils, compared with &lt;1% in controls. Compared with healthy donors, subjects with ADAN demonstrated significantly lower human cationic antimicrobial protein-18/pro-leucin leucin-37 plasma levels; higher levels of nonclassical, proinflammatory, 6-sulfo LacNac-expressing monocytes; and differentially expressed plasma levels of 28 of the 239 analyzed cytokines related to immunity/inflammation, cell signaling, neutrophil activation, and angiogenesis. Collectively, more severe neutropenia in ADAN than previously assumed may complicate differential diagnoses compared with other SCNPs, and various (auto)immune/inflammatory reactions with a distinct profile may be a cause or consequence of this hereditary neutropenia.
CT-001, a novel fast-clearing factor VIIa, enhanced the hemostatic activity in postpartum samples
Authors: Sim Derek S. , Mallari Cornell R. , Hermiston Terry W. , Bae Daekyeong , Lee Sul , Allen Terrence , Gilner Jennifer , Kim Seung-Chul , James Andra H. 
Published: December 2023

Abstract
The hemostatic system is upregulated to protect pregnant mothers from hemorrhage during childbirth. Studies of the details just before and after delivery, however, are lacking. Recombinant factor VIIa (rFVIIa) has recently been granted approval by the European Medicines Agency for the treatment of postpartum hemorrhage (PPH). A next-generation molecule, CT-001, is being developed as a potentially safer and more efficacious rFVIIa-based therapy. We sought to evaluate the peripartum hemostatic status of pregnant women and assess the ex vivo hemostatic activity of rFVIIa and CT-001 in peripartum blood samples. Pregnant women from 2 study sites were enrolled in this prospective observational study. Baseline blood samples were collected up to 3 days before delivery. Postdelivery samples were collected 45 (±15) minutes after delivery. Between the 2 time points, soluble fibrin monomer and D-dimer increased whereas tissue factor, FVIII, FV, and fibrinogen decreased. Interestingly, the postdelivery lag time and time to peak in the thrombin generation assay were shortened, and the peak thrombin generation capacity was maintained despite the reduced levels of coagulation proteins after delivery. Furthermore, both rFVIIa and CT-001 were effective in enhancing clotting activity of postdelivery samples in activated partial thromboplastin time, prothrombin time, thrombin generation, and viscoelastic hemostatic assays, with CT-001 demonstrating greater activity. In conclusion, despite apparent ongoing consumption of coagulation factors at the time of delivery, thrombin output was maintained. Both rFVIIa and CT-001 enhanced the upregulated hemostatic activity in postdelivery samples, and consistent with previous studies comparing CT-001 and rFVIIa in vitro and in in vivo, CT-001 demonstrated greater activity than rFVIIa.
Effect of Emi1 gene silencing on the proliferation and invasion of human breast cancer cells
Authors: Kuang Ying , Huang Shengwen , Tang Shifan , Zhuo Zhaozhen , Linghu Keyan 
Published: December 2023

AbstractBreast cancer is the most common malignant tumour in women. The early silk-splitting inhibitor protein 1 Emi1 is responsible for mediating ubiquitin protein degradation. The present study investigated the effects of the decreased expression of the Emil gene on the proliferation and invasion of breast cancer cells. The interference efficiency of small interfering ribonucleic acid (siRNA) was quantitatively verified using fluorescence real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting, and the effect of Emi1 gene silencing on cell vitality and invasion was determined using MTT and Transwell assays, respectively. The expression of the proliferation genes programmed cell death receptor 4 (PDCD-4), fatty acid synthase ligand (FasL), PTEN and RhoB, along with the invasive genes Maspin, TIMP3 and RECK, was measured using fluorescence RT-qPCR. In breast cancer cells, siRNA successfully reduced the expression of the Emi1 gene, and the expression level of the cell proliferation genes PDCD-4, FasL, PTEN and RhoB, along with invasive genes Maspin, TIMP3 and RECK, decreased significantly (P < 0.05). Furthermore, Emi1 gene silencing reduced the proliferation and invasion abilities of MDA-MB-231 and SUM149PT cells by reducing the expression of proliferative and invasive genes.
Range of chromatin accessibility configurations are permissive of GABAergic fate acquisition in developing mouse brain
Authors: Kilpinen Sami , Heliölä Heidi , Achim Kaia 
Published: December 2023

AbstractIn recent single-cell -omics studies, both the differential activity of transcription factors regulating cell fate determination and differential genome activation have been tested for utility as descriptors of cell types. Naturally, genome accessibility and gene expression are interlinked. To understand the variability in genomic feature activation in the GABAergic neurons of different spatial origins, we have mapped accessible chromatin regions and mRNA expression in single cells derived from the developing mouse central nervous system (CNS). We first defined a reference set of open chromatin regions for scATAC-seq read quantitation across samples, allowing comparison of chromatin accessibility between brain regions and cell types directly. Second, we integrated the scATAC-seq and scRNA-seq data to form a unified resource of transcriptome and chromatin accessibility landscape for the cell types in di- and telencephalon, midbrain and anterior hindbrain of E14.5 mouse embryo. Importantly, we implemented resolution optimization at the clustering, and automatized the cell typing step. We show high level of concordance between the cell clustering based on the chromatin accessibility and the transcriptome in analyzed neuronal lineages, indicating that both genome and transcriptome features can be used for cell type definition. Hierarchical clustering by the similarity in accessible chromatin reveals that the genomic feature activation correlates with neurotransmitter phenotype, selector gene expression, cell differentiation stage and neuromere origins.
Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize
Authors: Zhu Zhiying , Dai Yan , Yu Guangrun , Zhang Xin , Chen Qi , Kou Xiaobing , Mehareb Eid M. , Raza Ghulam , Zhang Baohong , Wang Baohua , Wang Kai , Han Jinlei 
Published: December 2023

Abstract
Background
Pre-exposing plants to abiotic stresses can induce stress memory, which is crucial for adapting to subsequent stress exposure. Although numerous genes involved in salt stress response have been identified, the understanding of memory responses to salt stress remains limited.

Results
In this study, we conducted physiological and transcriptional assays on maize plants subjected to recurrent salt stress to characterize salt stress memory. During the second exposure to salt stress, the plants exhibited enhanced salt resistance, as evidenced by increased proline content and higher POD and SOD activity, along with decreased MDA content, indicative of physiological memory behavior. Transcriptional analysis revealed fewer differentially expressed genes and variations in response processes during the second exposure compared to the first, indicative of transcriptional memory behavior. A total of 2,213 salt stress memory genes (SMGs) were identified and categorized into four response patterns. The most prominent group of SMGs consisted of genes with elevated expression during the first exposure to salt stress but reduced expression after recurrent exposure to salt stress, or vice versa ([+ / −] or [− / +]), indicating that a revised response is a crucial process in plant stress memory. Furthermore, nine transcription factors (TFs) (WRKY40, WRKY46, WRKY53, WRKY18, WRKY33, WRKY70, MYB15, KNAT7, and WRKY54) were identified as crucial factors related to salt stress memory. These TFs regulate over 53% of SMGs, underscoring their potential significance in salt stress memory.

Conclusions
Our study demonstrates that maize can develop salt stress memory, and the genes identified here will aid in the genetic improvement of maize and other crops.
Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars
Authors: Martins Benoit Renaud , Siani Roberto , Treder Krzysztof , Michałowska Dorota , Radl Viviane , Pritsch Karin , Schloter Michael 
Published: December 2023

Abstract
Background
Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world’s most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome).

Results
Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil.

Conclusions
Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.
Arabidopsis seedlings respond differentially to nutrient efficacy of three rock meals by regulating root architecture and endogenous auxin homeostasis
Authors: Zhang Tianjiao , Zhang Sainan , Yang Shaohui , Zhang Jianchao , Wang Jiehua , Teng H. Henry 
Published: December 2023

Abstract
Background
Plants show developmental plasticity with variations in environmental nutrients. Considering low-cost rock dust has been identified as a potential alternative to artificial fertilizers for more sustainable agriculture, the growth responses of Arabidopsis seedlings on three rock meals (basalt, granite, and marlstone) were examined for the different foraging behavior, biomass accumulation, and root architecture.

Results
Compared to ½ MS medium, basalt and granite meal increased primary root length by 13% and 38%, respectively, but marlstone caused a 66% decrease, and they all drastically reduced initiation and elongation of lateral roots but lengthened root hairs. Simultaneous supply of organic nutrients and trace elements increased fresh weight due to the increased length of primary roots and root hairs. When nitrogen (N), phosphorus (P), and potassium (K) were supplied individually, N proved most effective in improving fresh weight of seedlings growing on basalt and granite, whereas K, followed by P, was most effective for those growing on marlstone. Unexpectedly, the addition of N to marlstone negatively affected seedling growth, which was associated with repressed auxin biosynthesis in roots.

Conclusions
Our data indicate that plants can recognize and adapt to complex mineral deficiency by adjusting hormonal homeostasis to achieve environmental sensitivity and developmental plasticity, which provide a basis for ecologically sound and sustainable strategies to maximize the use of natural resources and reduce the production of artificial fertilizers.
Identification of novel sources of partial and incomplete hypersensitive resistance to rust and associated genomic regions in common bean
Authors: Leitão Susana Trindade , Rubiales Diego , Vaz Patto Maria Carlota 
Published: December 2023

AbstractCommon bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding.