bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blinatumomab in pediatric relapsed/refractory B-cell acute lymphoblastic leukemia: RIALTO expanded access study final analysis
Authors: Locatelli Franco , Zugmaier Gerhard , Mergen Noemi , Bader Peter , Jeha Sima , Schlegel Paul-Gerhardt , Bourquin Jean-Pierre , Handgretinger Rupert , Brethon Benoit , Rössig Claudia , Kormany William N. , Viswagnachar Puneeth , Chen-Santel Christiane 
Published: January 2022

Abstract
The safety and efficacy of blinatumomab, a CD3/CD19-directed bispecific molecule, were examined in an open-label, single-arm, expanded access study (RIALTO). Children (&gt;28 days and &lt;18 years) with CD19+ relapsed/refractory B-cell precursor acute lymphoblastic leukemia (R/R B-ALL) received up to 5 cycles of blinatumomab by continuous infusion (cycle: 4 weeks on/2 weeks off). The primary end point was incidence of adverse events. Secondary end points included complete response (CR) and measurable residual disease (MRD) response within the first 2 cycles and relapse-free survival (RFS), overall survival (OS), and allogeneic hematopoietic stem cell transplant (alloHSCT) after treatment. At final data cutoff (10 January 2020), 110 patients were enrolled (median age, 8.5 years; 88% had ≥5% baseline blasts). A low incidence of grade 3 or 4 cytokine release syndrome (n = 2; 1.8%) and neurologic events (n = 4; 3.6%) was reported; no blinatumomab-related fatal adverse events were recorded. The probability of response was not affected by the presence of cytogenetic/molecular abnormalities. Median OS was 14.6 months (95% confidence interval [CI]: 11.0-not estimable) and was significantly better for MRD responders vs MRD nonresponders (not estimable vs 9.3; hazard ratio, 0.18; 95% CI: 0.08-0.39). Of patients achieving CR after 2 cycles, 73.5% (95% CI: 61.4%-83.5%) proceeded to alloHSCT. One-year OS probability was higher for patients who received alloHSCT vs without alloHSCT after blinatumomab (87% vs 29%). These findings support the use of blinatumomab as a safe and efficacious treatment of pediatric R/R B-ALL. This trial was registered at www.clinicaltrials.gov as #NCT02187354.
The role of polyphenols in overcoming cancer drug resistance: a comprehensive review
Authors: Maleki Dana Parisa , Sadoughi Fatemeh , Asemi Zatollah , Yousefi Bahman 
Published: January 2022

AbstractChemotherapeutic drugs are used to treat advanced stages of cancer or following surgery. However, cancers often develop resistance against drugs, leading to failure of treatment and recurrence of the disease. Polyphenols are a family of organic compounds with more than 10,000 members which have a three-membered flavan ring system in common. These natural compounds are known for their beneficial properties, such as free radical scavenging, decreasing oxidative stress, and modulating inflammation. Herein, we discuss the role of polyphenols (mainly curcumin, resveratrol, and epigallocatechin gallate [EGCG]) in different aspects of cancer drug resistance. Increasing drug uptake by tumor cells, decreasing drug metabolism by enzymes (e.g. cytochromes and glutathione-S-transferases), and reducing drug efflux are some of the mechanisms by which polyphenols increase the sensitivity of cancer cells to chemotherapeutic agents. Polyphenols also affect other targets for overcoming chemoresistance in cancer cells, including cell death (i.e. autophagy and apoptosis), EMT, ROS, DNA repair processes, cancer stem cells, and epigenetics (e.g. miRNAs).
Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs
Authors: Sell-Kubiak Ewa , Knol Egbert F. , Lopes Marcos 
Published: January 2022

Abstract
Background
The genetic background of trait variability has captured the interest of ecologists and animal breeders because the genes that control it could be involved in buffering various environmental effects. Phenotypic variability of a given trait can be assessed by studying the heterogeneity of the residual variance, and the quantitative trait loci (QTL) that are involved in the control of this variability are described as variance QTL (vQTL). This study focuses on litter size (total number born, TNB) and its variability in a Large White pig population. The variability of TNB was evaluated either using a simple method, i.e. analysis of the log-transformed variance of residuals (LnVar), or the more complex double hierarchical generalized linear model (DHGLM). We also performed a single-SNP (single nucleotide polymorphism) genome-wide association study (GWAS). To our knowledge, this is only the second study that reports vQTL for litter size in pigs and the first one that shows GWAS results when using two methods to evaluate variability of TNB: LnVar and DHGLM.

Results
Based on LnVar, three candidate vQTL regions were detected, on Sus scrofa chromosomes (SSC) 1, 7, and 18, which comprised 18 SNPs. Based on the DHGLM, three candidate vQTL regions were detected, i.e. two on SSC7 and one on SSC11, which comprised 32 SNPs. Only one candidate vQTL region overlapped between the two methods, on SSC7, which also contained the most significant SNP. Within this vQTL region, two candidate genes were identified, ADGRF1, which is involved in neurodevelopment of the brain, and ADGRF5, which is involved in the function of the respiratory system and in vascularization. The correlation between estimated breeding values based on the two methods was 0.86. Three-fold cross-validation indicated that DHGLM yielded EBV that were much more accurate and had better prediction of missing observations than LnVar.

Conclusions
The results indicated that the LnVar and DHGLM methods resulted in genetically different traits. Based on their validation, we recommend the use of DHGLM over the simpler method of log-transformed variance of residuals. These conclusions can be useful for future studies on the evaluation of the variability of any trait in any species.
MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal
Authors: Dełeńko Konrad , Nuc Przemysław , Kubiak Dawid , Bielewicz Dawid , Dolata Jakub , Niedojadło Katarzyna , Górka Sylwia , Jarmołowski Artur , Szweykowska-Kulińska Zofia , Niedojadło Janusz 
Published: January 2022

Abstract
Background
Despite the frequent use of protoplast-to-plant system in in vitro cultures of plants, the molecular mechanisms regulating the first and most limiting stages of this process, i.e., protoplast dedifferentiation and the first divisions leading to the formation of a microcallus, have not been elucidated.

Results
In this study, we investigated the function of miRNAs in the dedifferentiation of A. thaliana mesophyll cells in a process stimulated by the enzymatic removal of the cell wall. Leaf cells, protoplasts and CDPs (cells derived from protoplasts) cultured for 24, 72 and 120 h (first cell division). In protoplasts, a strong decrease in the amount of AGO1 in both the nucleus and the cytoplasm, as well as dicing bodies (DBs), which are considered to be sites of miRNA biogenesis, was shown. However during CDPs division, the amounts of AGO1 and DBs strongly increased. MicroRNA transcriptome studies demonstrated that lower amount of differentially expressed miRNAs are present in protoplasts than in CDPs cultured for 120 h. Then analysis of differentially expressed miRNAs, selected pri-miRNA and mRNA targets were performed.

Conclusion
This result indicates that miRNA function is not a major regulation of gene expression in the initial but in later steps of dedifferentiation during CDPs divisions. miRNAs participate in organogenesis, oxidative stress, nutrient deficiencies and cell cycle regulation in protoplasts and CDPs. The important role played by miRNAs in the process of dedifferentiation of mesophyll cells was confirmed by the increased mortality and reduced cell division of CDPs derived from mutants with defective miRNA biogenesis and miR319b expression.
tRNA-derived fragments from wheat are potentially involved in susceptibility to Fusarium head blight
Authors: Sun Zhengxi , Hu Yi , Zhou Yilei , Jiang Ning , Hu Sijia , Li Lei , Li Tao 
Published: January 2022

Abstract
Background
Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating fungal disease of wheat. The mechanism underlying F. graminearum-wheat interaction remains largely unknown. tRNA-derived fragments (tRFs) are RNase-dependent small RNAs derived from tRNAs, and they have not been reported in wheat yet, and whether tRFs are involved in wheat-F. graminearum interactions remains unknown.

Results
Herein, small RNAs from the spikelets inoculated with F. graminearum and mock from an FHB-susceptible variety Chinese Spring (CS) and an FHB-resistant variety Sumai3 (SM) were sequenced respectively. A total of 1249 putative tRFs were identified, in which 15 tRFs was CS-specific and 12 SM-specific. Compared with mock inoculation, 39 tRFs were significantly up-regulated across both wheat varieties after F. graminearum challenge and only nine tRFs were significantly down-regulated. tRFGlu, tRFLys and tRFThr were dramatically induced by F. graminearum infection, with significantly higher fold changes in CS than those in SM. The expression patterns of the three highly induced tRFs were further validated by stem-loop qRT-PCR. The accumulation of tRFs were closely related to ribonucleases T2 family members, which were induced by F. graminearum challenge. The tRFs’ targets in host were predicted and were validated by RNA sequencing.

Conclusion
Integrative analysis of the differentially expressed tRFs and their candidate targets indicated that tRFGlu, tRFLys and tRFThr might negatively regulate wheat resistance to FHB. Our results unvealed the potential roles of tRFs in wheat-F. graminearum interactions.
Endophytic fungus Pseudodidymocyrtis lobariellae KL27 promotes taxol biosynthesis and accumulation in Taxus chinensis
Authors: Cao Xiaoying , Xu Lingxia , Wang Jingyi , Dong Mengmeng , Xu Chunyan , Kai Guoyin , Wan Wen , Jiang Jihong 
Published: January 2022

Abstract
Background
Taxol from Taxus species is a precious drug used for the treatment of cancer and can effectively inhibit the proliferation of cancer cells. However, the growth of Taxus plants is very slow and the content of taxol is quite low. Therefore, it is of great significance to improve the yield of taxol by modern biotechnology without destroying the wild forest resources. Endophytic fungus which symbiosis with their host plants can promote the growth and secondary metabolism of medicinal plants.

Results
Here, an endophytic fungus KL27 was isolated from T. chinensis, and identified as Pseudodidymocyrtis lobariellae. The fermentation broth of KL27 (KL27-FB) could significantly promote the accumulation of taxol in needles of T. chinensis, reaching 0.361 ± 0.082 mg/g·DW (dry weight) at 7 days after KL27-FB treatment, which is 3.26-fold increase as compared to the control. The RNA-seq and qRT-PCR showed that KL27-FB could significantly increase the expression of key genes involved in the upstream pathway of terpene synthesis (such as DXS and DXR) and those in the taxol biosynthesis pathway (such as GGPPS, TS, T5OH, TAT, T10OH, T14OH, T2OH, TBT, DBAT and PAM), especially at the early stage of the stimulation. Moreover, the activation of jasmonic acid (JA) biosynthesis and JA signal transduction, and its crosstalk with other hormones, such as gibberellin acid (GA), ethylene (ET) and salicylic acid (SA), explained the elevation of most of the differential expressed genes related to taxol biosynthesis pathway. Moreover, TF (transcriptional factor)-encoding genes, including MYBs, ethylene-responsive transcription factors (ERFs) and basic/helix-loop-helix (bHLH), were detected as differential expressed genes after KL27-FB treatment, further suggested that the regulation of hormone signaling on genes of taxol biosynthesis was mediated by TFs.

Conclusions
Our results indicated that fermentation broth of endophytic fungus KL27-FB could effectively enhance the accumulation of taxol in T. chinensis needles by regulating the phytohormone metabolism and signal transduction and further up-regulating the expression of multiple key genes involved in taxol biosynthesis. This study provides new insight into the regulatory mechanism of how endophytic fungus promotes the production and accumulation of taxol in Taxus sp.
CRISPR-Cas9-mediated mutagenesis of the SlSRM1-like gene leads to abnormal leaf development in tomatoes
Authors: Tang Yao , Li Huijia , Liu Chunxin , He Yuqing , Wang Hexuan , Zhao Tingting , Xu Xiangyang , Li Jingfu , Yang Huanhuan , Jiang Jingbin 
Published: January 2022

Abstract
Background
Leaves, which are the most important organs of plants, can not only fix carbon sources through photosynthesis, but also absorb nutrients through transpiration. Leaf development directly determines the growth, flowering and fruiting of plants. There are many factors that affect leaf development, such as the growth environment, gene expression, and hormone synthesis. In this study, tomatoes were used to study the role of the transcription factor Solanum lycopersicum salt-related MYB1-like (SlSRM1-like) in the development of tomato leaves.

Results
Loss-of-function of the SlSRM1-like gene mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) resulted in abnormal tomato leaf morphology, including thinner leaves, wrinkled edges, raised veins, disordered edge veins, and left and right asymmetry. An analysis of the transcription levels of genes related to leaf development revealed that the expression of these genes was significantly altered in the SlSRM1-like mutants (SlSRM1-like-Ms). Moreover, the SlSRM1-like gene was expressed at higher transcription levels in young tissues than in old tissues, and its expression was also induced in response to auxin. In addition, the transcription levels of genes related to the auxin pathway, which regulates tomato growth and development, were severely affected in the SlSRM1-like-Ms. Therefore, it is hypothesized that the SlSRM1-like gene functions in the regulation of tomato leaf development through the auxin-related pathway.

Conclusions
In this study, we successfully knocked out the SlSRM1-like gene in the tomato variety Ailsa Craig using CRISPR technology and found that knockout of the SlSRM1-like gene resulted in abnormal development of tomato leaves. Further research indicated that SlSRM1-like regulated tomato leaf development through auxin-related pathways. The results provide an important reference for the functional study of other SRM1-like genes in plants and provide new insights into the regulation of leaf development in tomato and other plants.
The composite risk index based on frailty predicts postoperative complications in older patients recovering from elective digestive tract surgery: a retrospective cohort study
Authors: Li Chun-Qing , Zhang Chen , Yu Fan , Li Xue-Ying , Wang Dong-Xin 
Published: January 2022

Abstract
Background
Limitations exist in available studies investigating effect of preoperative frailty on postoperative outcomes. This study was designed to analyze the association between composite risk index, an accumulation of preoperative frailty deficits, and the risk of postoperative complications in older patients recovering from elective digestive tract surgery.

Methods
This was a retrospective cohort study. Baseline and perioperative data of older patients (age ≥ 65 years) who underwent elective digestive tract surgery from January 1, 2017 to December 31, 2018 were collected. The severity of frailty was assessed with the composite risk index, a composite of frailty deficits including modified frailty index. The primary endpoint was the occurrence of postoperative complications during hospital stay. The association between the composite risk index and the risk of postoperative complications was assessed with a multivariable logistic regression model.

Results
A total of 923 patients were included. Of these, 27.8% (257) developed postoperative complications. Four frailty deficits, i.e., modified frailty index ≥0.27, malnutrition, hemoglobin < 90 g/L, and albumin ≤30 g/L, were combined to generate a composite risk index. Multivariable analysis showed that, when compared with patients with composite risk index of 0, the odds ratios (95% confidence intervals) were 2.408 (1.714–3.383, P <  0.001) for those with a composite risk index of 1, 3.235 (1.985–5.272, P <  0.001) for those with a composite risk index of 2, and 9.227 (3.568–23.86, P <  0.001) for those with composite risk index of 3 or above. The area under receiver-operator characteristic curve to predict postoperative complications was 0.653 (95% confidence interval 0.613–0.694, P <  0.001) for composite risk index compared with 0.622 (0.581–0.663, P <  0.001) for modified frailty index.

Conclusion
For older patients following elective digestive tract surgery, high preoperative composite risk index, a combination of frailty deficits, was independently associated with an increased risk of postoperative complications.
The association of zonulin-related proteins with prevalent and incident inflammatory bowel disease
Authors: Wang Xiao , Memon Ashfaque A. , Palmér Karolina , Hedelius Anna , Sundquist Jan , Sundquist Kristina 
Published: January 2022

Abstract
Background
Current evidence regarding the association of serum zonulin-related proteins (ZRP) levels with prevalent inflammatory bowel disease (IBD) is contradictory. Moreover, the association with the subsequent risk of incident IBD is still unexplored. This study aimed to investigate the association of serum ZRP levels with both prevalent and incident IBD.

Method
The study included a total of 130 women (51–61 years) from the Women’s Health in Lund Area (WHILA) study, which included 18 prevalent IBD (diagnosed before baseline) and 47 incident IBD diagnosed during the 17 years (median) follow-up and age- and sampling time-matched controls. Serum ZRP was tested in all participants by ELISA.

Results
The serum ZRP levels were significantly higher in prevalent IBD compared to their matched controls (63.2 ng/ml vs 57.0 ng/ml, p = 0.02), however, no evidence of a difference in ZRP levels was found between the women who developed IBD during the follow-up period and their matched controls (61.2 ng/ml vs 59.7 ng/ml, p = 0.34). Using linear mixed models, we found that the association between serum ZRP levels and prevalent IBD (β = 6.2, p = 0.01), remained after adjusting for potential confounders. Conditional logistic regression models showed no evidence of an association between ZRP level and incident IBD (OR 1.03, p = 0.34).

Conclusion
Higher serum ZRP levels were associated with prevalent IBD, but not with incident IBD in our study samples.
Brain CT can predict low lean mass in the elderly with cognitive impairment: a community-dwelling study
Authors: Chen Yun-Ting , Yu Chiun-Chieh , Lin Yu-Ching , Chan Shan-Ho , Lin Yi-Yun , Chen Nai-Ching , Lin Wei-Che 
Published: January 2022

Abstract
Background
The coexistence of sarcopenia and dementia in aging populations is not uncommon, and they may share common risk factors and pathophysiological pathways. This study aimed to evaluate the relationship between brain atrophy and low lean mass in the elderly with impaired cognitive function.

Methods
This cross-sectional study included 168 elderly patients who visited the multi-disciplinary dementia outpatient clinic at Kaohsiung Chang Gung Memorial Hospital for memory issues, between 2017 and 2019. The body composition was assessed by dual energy X-ray absorptiometry (DEXA) and CT based skeletal muscle index including L3 skeletal muscle index (L3SMI) and masseter muscle mass index (MSMI). The brain atrophy assessment was measured by CT based visual rating scale. Possible predictors of low lean mass in the elderly with cognitive impairement were identified by binary logistic regression. ROC curves were generated from binary logistic regression.

Results
Among the 81 participants, 43 (53%) remained at a normal appendicular skeletal muscle index (ASMI), whereas 38 (47%) showed low ASMI. Compared with the normal ASMI group, subjects with low ASMI exhibited significantly lower BMI, L3SMI, and MSMI (all p < 0.05), and showed significant brain atrophy as assessed by visual rating scale (p < 0.001). The accuracy of predictive models for low ASMI in the elderly with cognitive impairment were 0.875, (Area under curve (AUC) = 0.926, 95% confidence interval [CI] 0.844–0.972) in model 1 (combination of BMI, GCA and L3SMI) and 0.885, (Area under curve (AUC) = 0.931, [CI] 0.857–0.979) in model 2 (combination of BMI, GCA and MSMI).

Conclusions
Global cortical atrophy and body mass index combined with either L3 skeletal muscle index or masseter skeletal muscle index can predict low lean mass in the elderly with cognitive impairment.
The predictive utility of functional status at discharge: a population-level cohort analysis
Authors: Junek Mats L. , Jones Aaron , Heckman George , Demers Catherine , Griffith Lauren E. , Costa Andrew P. 
Published: January 2022

AbstractBackgroundFunctional status is a patient-important, patient-centered measurement. The utility of functional status measures to inform post-discharge patient needs is unknown. We sought to examine the utility of routinely collected functional status measures gathered from older hospitalized patients to predict a panel of post-discharge outcomes.MethodsIn this population-based retrospective cohort study, Adults 65+ discharged from an acute hospitalization between 4 November 2008 and 18 March 2016 in Ontario, Canada and received an assessment of functional status at discharge using the Health Outcomes for Better Information and Care tool were included. Multivariable regression analysis was used to determine the relationship between functional status and emergency department (ED) re-presentation, hospital readmission, long term care facility (LTCF) admission or wait listing (‘LTCF readiness’), and death at 180 days from discharge.ResultsA total of 80 020 discharges were included. 38 928 (48.6%) re-presented to the ED, 24 222 (30.3%) were re-admitted, 5 037 (6.3%) were LTCF ready, and 9 047 (11.3%) died at 180 days. Beyond age, diminished functional status at discharge was the factor most associated with LTCF readiness (adjusted Odds Ratio [OR] 4.11 for those who are completely dependent for activities of daily living compared to those who are independent; 95% Confidence Interval [CI]: 3.70-4.57) and death (OR 3.99; 95% CI: 3.67-4.35). Functional status also had a graded relationship with each outcome and improved the discriminability of the models predicting death and LTCF readiness (p<0.01) but not ED re-presentation or hospital re-admission.ConclusionRoutinely collected functional status at discharge meaningfully improves the prediction of long term care home readiness and death. The routine assessment of functional status can inform post-discharge care and planning for older adults.