bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clofarabine-fludarabine-busulfan in HCT for pediatric leukemia: an effective, low toxicity, TBI-free conditioning regimen
Authors: Versluijs A. Birgitta , de Koning Coco C. H. , Lankester Arjan C. , Nierkens Stefan , Kollen Wouter J. , Bresters Dorine , Lindemans Caroline A. , Boelens Jaap Jan , Bierings Marc 
Published: November 2021

Abstract
We prospectively studied clofarabine-fludarabine-busulfan (CloFluBu)-conditioning in allogeneic hematopoietic cell therapy (HCT) for lymphoid and myeloid malignancies and hypothesized that CloFluBu provides a less toxic alternative to conventional conditioning regimens, with adequate antileukemic activity. All patients receiving their first HCT, from 2011-2019, were included and received CloFluBu. The primary endpoint was event-free survival (EFS). Secondary endpoints were overall survival (OS), graft-versus-host disease (GvHD)-relapse-free survival (GRFS), treatment-related mortality (TRM), cumulative incidence of relapse (CIR), acute and chronic GvHD (aGvHD and cGvHD), and veno-occlusive disease (VOD). Cox proportional hazard and Fine and Gray competing-risk models were used for data analysis. One hundred fifty-five children were included: 60 acute lymphoid leukemia (ALL), 69 acute myeloid leukemia (AML), and 26 other malignancies (mostly MDS-EB). The median age was 9.7 (0.5 to 18.6) years. Estimated 2-year EFS was 72.0% ± 6.0 in ALL patients, and 62.4% ± 6.0 in AML patients. TRM in the whole cohort was 11.0% ± 2.6, incidence of aGvHD 3 to 4 at 6 months was 12.3% ± 2.7, extensive cGvHD at 2 years was 6.4% ± 2.1. Minimal residual disease-positivity prior to HCT was associated with higher CIR, both in ALL and AML. CloFluBu showed limited toxicity and encouraging EFS. CloFluBu is a potentially less toxic alternative to conventional conditioning regimens. Randomized prospective studies are needed.
Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle
Authors: Li Jiyuan , Mukiibi Robert , Wang Yining , Plastow Graham S. , Li Changxi 
Published: November 2021

Abstract
Background
Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle.

Results
Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10−5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules.

Conclusions
This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.
Molecular detection, not extended culture incubation, contributes to diagnosis of fungal infection
Authors: Zhu Alex , Zembower Teresa , Qi Chao 
Published: November 2021

Abstract
Background
Despite its low sensitivity, fungal culture remains one of the key methods for diagnosis and treatment of fungal infections, as it identifies the etiology at the genus and species level and affords the opportunity for susceptibility testing. The Manual of Clinical Microbiology recommends that fungal culture screening for all pathogens should routinely be held for 4 weeks to maximize the recovery of slow-growing species. Information on the optimal fungal culture time in this era of expansion of immunocompromised populations and availability of molecular diagnostics is lacking. We reviewed our experience with fungal culture to determine the optimal culture incubation time. In addition, our experience of broad-range ITS PCR for diagnosis of culture-negative fungal infections was also reviewed.

Methods
Fungal culture and ITS PCR results from January 1, 2013, to December 31, 2017, were reviewed.

Results
This study included 4234 non-duplicated positive cultures. Ninety-six percent (4058) of the positive cultures were detected in the first 7 days of incubation. During the second week of incubation, 111 (2.8%) positives were detected from day 8 to day 10, and 71 (1.7%) were detected from day 11 to day 14. Only 6 (0.1%) positive cultures were detected in the third week of incubation, and no positive culture was detected in the fourth week of incubation. No clinically significant fungal isolates were recovered after 14 days. Clinically significant pathogens were detected in 16 (0.2%) culture-negative samples by ITS PCR.

Conclusion
Extending culture incubation beyond 2 weeks did not generate clinically relevant results. When culture failed to make a laboratory diagnosis, broad-range internal transcribed spacer (ITS) rRNA gene PCR followed by sequencing produced clinically significant results.
Antibiotics prescription for targeted therapy of pediatric invasive pneumococcal diseases in China: a multicenter retrospective study
Authors: Chen Tian-ming , Li Wen-hui , Wang Fang , Tan Kun , Zhu Qing-xiong , Zhou Kai , Liu Shi-hua , Liu Jing , Bi Jing , Deng Hui-ling , Chen Xue-xia , Li Juan , Wang Yu-min , Zhao Qing , Zhu Liang , Ma Hui-xuan , Li Zhi , Deng Ji-kui , Zhu Chun-hui , Wu Kang-kang , Lin Ai-wei , Li Shuang-jie , Wang Dong-meng , Cai Hui-jun , Zhao Shi-yong , Lu Xu-dong , Ye Lan , Dong Fang , Zhang Wen-shuang , Yang Yong-hong , Liu Gang 
Published: November 2021

Abstract
Background
Streptococcus pneumoniae (S. pneumoniae) is a major cause of bacterial meningitis, septicemia and pneumonia in children. Inappropriate choice of antibiotic can have important adverse consequences for both the individual and the community. Here, we focused on penicillin/cefotaxime non-susceptibility of S. pneumoniae and evaluated appropriateness of targeted antibiotic therapy for children with IPD (invasive pneumococcal diseases) in China.

Methods
A multicenter retrospective study was conducted in 14 hospitals from 13 provinces in China. Antibiotics prescription, clinical features and resistance patterns of IPD cases from January 2012 to December 2017 were collected. Appropriateness of targeted antibiotics therapy was assessed.

Results
806 IPD cases were collected. The non-susceptibility rates of S. pneumoniae to penicillin and cefotaxime were 40.9% and 20.7% respectively in 492 non-meningitis cases, whereas those were 73.2% and 43.0% respectively in 314 meningitis cases. Carbapenems were used in 21.3% of non-meningitis cases and 42.0% of meningitis cases for targeted therapy. For 390 non-meningitis cases with isolates susceptible to cefotaxime, vancomycin and linezolid were used in 17.9% and 8.7% of cases respectively for targeted therapy. For 179 meningitis cases with isolates susceptible to cefotaxime, vancomycin and linezolid were prescribed in 55.3% and 15.6% of cases respectively. Overall, inappropriate targeted therapies were identified in 361 (44.8%) of 806 IPD cases, including 232 (28.8%) cases with inappropriate use of carbapenems, 169 (21.0%) cases with inappropriate use of vancomycin and 62 (7.7%) cases with inappropriate use of linezolid.

Conclusions
Antibiotic regimens for IPD definite therapy were often excessive with extensive prescription of carbapenems, vancomycin or linezolid in China. Antimicrobial stewardship programs should be implemented to improve antimicrobial use.
Expression of early growth responsive gene-1 in the visual cortex of monocular form deprivation amblyopic kittens
Authors: Fan Haobo , Wang Ying , Tang Xiuping , Yang Liyuan , Song Weiqi , Zou Yunchun 
Published: November 2021

Abstract
Purpose
The present study compared the expression of early growth responsive gene-1 (Egr-1) in visual cortex between amblyopia kittens and normal kittens, and to explore the role of Egr-1 in the pathogenesis of amblyopia.

Methods
A total of 20 healthy kittens were randomly divided into deprivation group and control group with 10 kittens in each group. Raised in natural light, and covered the right eye of the deprived kittens with a black opaque covering cloth. Pattern visual evoked potentials (PVEP) were measured before and at the 1st, 3rd and 5th week after covering in all kittens. After the last PVEP test, all kittens were killed. The expression of Egr-1 in the visual cortex of the two groups was compared by immunohistochemistry and in situ hybridization.

Results
PVEP detection showed that at the age of 6 and 8 weeks, the P100 wave latency in the right eye of deprivation group was higher than that in the left eye of deprivation group (P < 0.05) and the right eye of control group (P < 0.05), while the amplitude decreased (P < 0.05). The number of positive cells (P < 0.05) and mean optical density (P < 0.05) of Egr-1 protein expression in visual cortex of 8-week-old deprivation group were lower than those of normal group, as well as the number (P < 0.05) and mean optical density of Egr-1 mRNA-positive cells (P < 0.05).

Conclusions
Monocular form deprivation amblyopia can lead to the decrease of Egr-1 protein and mRNA expression in visual cortex, and then promote the occurrence and development of amblyopia.
Differences in verbal and spatial working memory in patients with bipolar II and unipolar depression: an MSI study
Authors: Li Zhinan , Chen Junhao , Feng Yigang , Zhong Shuming , Tian Shui , Dai Zhongpeng , Lu Qing , Guan Yufang , Shan Yanyan , Jia Yanbin 
Published: November 2021

AbstractBackgroundDepressive symptoms could be similarly expressed in bipolar and unipolar disorder. However, changes in cognition and brain networks might be quite distinct. We aimed to find out the difference in the neural mechanism of impaired working memory in patients with bipolar and unipolar disorder.MethodAccording to diagnostic criteria of bipolar II disorder of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) and assessments, 13 bipolar II depression (BP II), 8 unipolar depression (UD) patients and 15 healthy controls (HC) were recruited in the study. We used 2-back tasks and magnetic source imaging (MSI) to test working memory functions and get the brain reactions of the participants.ResultsCompared with HC, only spatial working memory tasks accuracy was significantly worse in both UD and BP II (p = 0.001). Pearson correlation showed that the stronger the FCs’ strength of MFG-IPL and IPL-preSMA, the higher accuracy of SWM task within left FPN in patients with UD (r = 0.860,p = 0.006;r = 0.752,p = 0.031). However, the FC strength of IFG-IPL was negatively correlated with the accuracy of SWM task within left FPN in patients with BP II (r = − 0.591,p = 0.033).ConclusionsOur study showed that the spatial working memory of patients with whether UD or BP II was impaired. The patterns of FCs within these two groups of patients were different when performing working memory tasks.
Magnesium isoglycyrrhizinate inhibits airway inflammation in rats with chronic obstructive pulmonary disease
Authors: Yang Ye , Huang Lei , Tian Chongchong , Qian Bingjun 
Published: November 2021

Abstract
Background
Chronic obstructive pulmonary disease (COPD) is a kind of chronic lung diseases with the characteristics of airway remodeling and airflow obstruction. Magnesium isoglycyrrhizinate (MgIG) is an anti-inflammatory glycyrrhizic acid preparation for treating hepatitis. However, whether MgIG can treat other diseases and its action mechanism is still obscure. In this study, we evaluated the anti-inflammatory effect of MgIG in rats with COPD and investigated the underlying mechanisms.

Methods
Rat model of COPD was constructed by endotracheal-atomized lipopolysaccharide exposure and cigarette smoke induction. Rats were randomly divided into 5 groups: control group, COPD model group, salmeterol fluticasone comparator group, low dose of MgIG group, and high dose of MgIG group. Except for normal control group, the other four groups received sensitization treatment by cigarette smoking and endotracheal-atomization of endotoxin lipopolysaccharide to construct COPD rats model. After model established successfully, the COPD rats in each group received corresponding dose of endotracheal-atomized normal saline, salmeterol fluticasone, and MgIG every day prior to exposure of cigarette smoke from days 30 to 45. Normal control group were treated with normal saline. Finally, All rats were euthanatized. Pulmonary function was measured. Cells in bronchoalveolar lavage fluid were classified, inflammatory factors IL-6 and TNF-α were determined, histopathological analysis was performed by HE staining, and expression of NLRP3 and cleaved caspase-1 in the lung tissue was also determined by Western blotting.

Results
It showed that MgIG treatment (0.40 or 0.80 mg/kg/day) could recover the weight and the clinical symptoms of rats with COPD, accompanied with lung inflammation infiltration reduction, airway wall attenuation, bronchial mucus secretion reduction. Additionally, MgIG administration reduced inflammatory cells (white blood cells, neutrophils, lymphocytes and monocytes) accumulation in bronchoalveolar lavage fluid and decreased IL-6 and TNF-α production in the serum of COPD rats. Furthermore, MgIG treatment also reduced the expression level of NLRP3 and cleaved caspase-1.

Conclusion
It indicate that MgIG might be an alternative for COPD treatment, and its mechanism of action might be related to the suppression of NLRP3 inflammasome.
Using patient feedback to adapt intervention materials based on acceptance and commitment therapy for people receiving renal dialysis
Authors: Elander James , Kapadi Romaana , Coyne Emma , Taal Maarten W. , Selby Nicholas M. , Stalker Carol , Mitchell Kathryn 
Published: November 2021

AbstractBackgroundTheory-based intervention materials must be carefully adapted to meet the needs of users with specific physical conditions. Acceptance and Commitment Therapy (ACT) has been adapted successfully for cancer, chronic pain, diabetes, irritable bowel syndrome, multiple sclerosis, and a range of other conditions, but not so far for people receiving renal haemodialysis. This paper presents findings from a study to adapt ACT-based intervention materials specifically for renal dialysis.MethodsDraft written materials consisting of four stories depicting fictitious individuals who used ACT-related techniques to help overcome different challenges and difficulties related to dialysis were adapted using a systematic patient consultation process. The participants were 18 people aged 19–80 years, with chronic kidney disease and receiving renal dialysis. Individual, semi-structured interviews were conducted to elicit participants’ views about how the content of the draft materials should be adapted to make them more realistic and relevant for people receiving renal dialysis and about how the materials should be presented and delivered to people receiving renal dialysis. The interview transcripts were analysed using a qualitative adaptation of the Delphi method in which themes are used as a framework for translating feedback into proposals for modifications.ResultsThe analysis of patient feedback supported the use of patient stories but suggested they should be presented by video and narrated by real dialysis patients. They also indicated specific adaptations to make the stories more credible and realistic. Participant feedback was translated into proposals for change that were considered along with clinical, ethical and theoretical factors. The outcome was a design for a video-based intervention that separated the stories about individuals from the explanations of the specific ACT techniques and provided greater structure, with material organised into smaller chunks. This intervention is adapted specifically for people receiving renal dialysis while retaining the distinctive theoretical principles of ACT.ConclusionsThe study shows the value of consulting patients in the development of intervention materials and illustrates a process for integrating patient feedback with theoretical, clinical and practical considerations in intervention design.
Comparison of vacuum-assisted sheaths and normal sheaths in minimally invasive percutaneous nephrolithotomy: a systematic review and meta-analysis
Authors: Zhu Ling , Wang Zhenghao , Zhou Ye , Gou Liping , Huang Yan , Zheng Xiaofeng 
Published: November 2021

Abstract
Background
A systematic review and meta-analysis was conducted to compare the safety and efficacy of vacuum-assisted sheaths and conventional sheaths in minimally invasive percutaneous nephrolithotomy (MPCNL) in the treatment of nephrolithiasis.

Methods
PubMed, Web of Science, Embase, EBSCO, and Cochrane Library databases (updated March 2021) were used to search for studies assessing the effect of vacuum-assisted sheaths in patients who underwent MPCNL. The search strategy and study selection processes were implemented in accordance with the PRISMA statement.

Result
Three randomized controlled trials and two case-controlled trials that satisfied the inclusion criteria were enrolled in this meta-analysis. Overall, the stone-free rate (SFR) in patients who underwent vacuum-assisted sheaths was significantly higher than that in patients who underwent conventional sheaths (RR 1.23, 95% CI 1.04, 1.46, P = 0.02), with significant heterogeneity among the studies (I2 = 72%, P = 0.03). In terms of the outcome of complications, vacuum-assisted sheath could bring a benefit to the postoperative infection rate (RR 0.48, 95% CI 0.33, 0.70, P < 0.00001) with insignificant heterogeneity among the studies (I2 = 0%, P = 0.68). There was no significant difference in the blood transfusion rate (RR 0.35, 95% CI 0.07, 1.73, P = 0.17), with significant heterogeneity (I2 = 66%, P = 0.35). Three studies contained operative time data, and the results indicated that the vacuum-assisted sheath led to a shorter operative time (MD = − 15.74; 95% CI − 1944, − 12.04, P < 0.00001) with insignificant heterogeneity (I2 = 0%, P = 0.91).

Conclusion
The application of a vacuum-assisted sheath in MPCNL improves the safety and efficiency compared to the conventional sheath. A vacuum-assisted sheath significantly increases the SFR while reducing operative time and postoperative infection.
CRISPR and KRAS: a match yet to be made
Authors: Bender Guzide , Fahrioglu Yamaci Rezan , Taneri Bahar 
Published: November 2021

AbstractCRISPR (clustered regularly interspaced short palindromic repeats) systems are one of the most fascinating tools of the current era in molecular biotechnology. With the ease that they provide in genome editing, CRISPR systems generate broad opportunities for targeting mutations. Specifically in recent years, disease-causing mutations targeted by the CRISPR systems have been of main research interest; particularly for those diseases where there is no current cure, including cancer. KRAS mutations remain untargetable in cancer. Mutations in this oncogene are main drivers in common cancers, including lung, colorectal and pancreatic cancers, which are severe causes of public health burden and mortality worldwide, with no cure at hand. CRISPR systems provide an opportunity for targeting cancer causing mutations. In this review, we highlight the work published on CRISPR applications targeting KRAS mutations directly, as well as CRISPR applications targeting mutations in KRAS-related molecules. In specific, we focus on lung, colorectal and pancreatic cancers. To date, the limited literature on CRISPR applications targeting KRAS, reflect promising results. Namely, direct targeting of mutant KRAS variants using various CRISPR systems resulted in significant decrease in cell viability and proliferation in vitro, as well as tumor growth inhibition in vivo. In addition, the effect of mutant KRAS knockdown, via CRISPR, has been observed to exert regulatory effects on the downstream molecules including PI3K, ERK, Akt, Stat3, and c-myc. Molecules in the KRAS pathway have been subjected to CRISPR applications more often than KRAS itself. The aim of using CRISPR systems in these studies was mainly to analyze the therapeutic potential of possible downstream and upstream effectors of KRAS, as well as to discover further potential molecules. Although there have been molecules identified to have such potential in treatment of KRAS-driven cancers, a substantial amount of effort is still needed to establish treatment strategies based on these discoveries. We conclude that, at this point in time, despite being such a powerful directed genome editing tool, CRISPR remains to be underutilized for targeting KRAS mutations in cancer. Efforts channelled in this direction, might pave the way in solving the long-standing challenge of targeting the KRAS mutations in cancers.