bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA)
Authors: Hallal Mahmoud , Braga-Lagache Sophie , Jankovic Jovana , Simillion Cedric , Bruggmann Rémy , Uldry Anne-Christine , Allam Ramanjaneyulu , Heller Manfred , Bonadies Nicolas 
Published: July 2021

Abstract
Background
Despite the introduction of targeted therapies, most patients with myeloid malignancies will not be cured and progress. Genomics is useful to elucidate the mutational landscape but remains limited in the prediction of therapeutic outcome and identification of targets for resistance. Dysregulation of phosphorylation-based signaling pathways is a hallmark of cancer, and therefore, kinase-inhibitors are playing an increasingly important role as targeted treatments. Untargeted phosphoproteomics analysis pipelines have been published but show limitations in inferring kinase-activities and identifying potential biomarkers of response and resistance.

Methods
We developed a phosphoproteomics workflow based on titanium dioxide phosphopeptide enrichment with subsequent analysis by liquid chromatography tandem mass spectrometry (LC-MS). We applied a novel Kinase-Activity Enrichment Analysis (KAEA) pipeline on differential phosphoproteomics profiles, which is based on the recently published SetRank enrichment algorithm with reduced false positive rates. Kinase activities were inferred by this algorithm using an extensive reference database comprising five experimentally validated kinase-substrate meta-databases complemented with the NetworKIN in-silico prediction tool. For the proof of concept, we used human myeloid cell lines (K562, NB4, THP1, OCI-AML3, MOLM13 and MV4–11) with known oncogenic drivers and exposed them to clinically established kinase-inhibitors.

Results
Biologically meaningful over- and under-active kinases were identified by KAEA in the unperturbed human myeloid cell lines (K562, NB4, THP1, OCI-AML3 and MOLM13). To increase the inhibition signal of the driving oncogenic kinases, we exposed the K562 (BCR-ABL1) and MOLM13/MV4–11 (FLT3-ITD) cell lines to either Nilotinib or Midostaurin kinase inhibitors, respectively. We observed correct detection of expected direct (ABL, KIT, SRC) and indirect (MAPK) targets of Nilotinib in K562 as well as indirect (PRKC, MAPK, AKT, RPS6K) targets of Midostaurin in MOLM13/MV4–11, respectively. Moreover, our pipeline was able to characterize unexplored kinase-activities within the corresponding signaling networks.

Conclusions
We developed and validated a novel KAEA pipeline for the analysis of differential phosphoproteomics MS profiling data. We provide translational researchers with an improved instrument to characterize the biological behavior of kinases in response or resistance to targeted treatment. Further investigations are warranted to determine the utility of KAEA to characterize mechanisms of disease progression and treatment failure using primary patient samples.

Graphical abstract
Molecular and cellular characterization of two patient-derived ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010
Authors: Samson Julia , Derlipanska Magdalina , Zaheed Oza , Dean Kellie 
Published: July 2021

Abstract
Background
Currently it is unclear how in situ breast cancer progresses to invasive disease; therefore, a better understanding of the events that occur during the transition to invasive carcinoma is warranted. Here we have conducted a detailed molecular and cellular characterization of two, patient-derived, ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010.

Methods
Human DCIS cell lines, ETCC-006 and ETCC-010, were compared against a panel of cell lines including the immortalized, breast epithelial cell line, MCF10A, breast cancer cell lines, MCF7 and MDA-MB-231, and another DCIS line, MCF10DCIS.com. Cell morphology, hormone and HER2/ERBB2 receptor status, cell proliferation, survival, migration, anchorage-independent growth, indicators of EMT, cell signalling pathways and cell cycle proteins were examined using immunostaining, immunoblots, and quantitative, reverse transcriptase PCR (qRT-PCR), along with clonogenic, wound-closure and soft agar assays. RNA sequencing (RNAseq) was used to provide a transcriptomic profile.

Results
ETCC-006 and ETCC-010 cells displayed notable differences to another DCIS cell line, MCF10DCIS.com, in terms of morphology, steroid-receptor/HER status and markers of EMT. The ETCC cell lines lack ER/PR and HER, form colonies in clonogenic assays, have migratory capacity and are capable of anchorage-independent growth. Despite being isogenic, less than 30% of differentially expressed transcripts overlapped between the two lines, with enrichment in pathways involving receptor tyrosine kinases and DNA replication/cell cycle programs and in gene sets responsible for extracellular matrix organisation and ion transport.

Conclusions
For the first time, we provide a molecular and cellular characterization of two, patient-derived DCIS cell lines, ETCC-006 and ETCC-010, facilitating future investigations into the molecular basis of DCIS to invasive ductal carcinoma transition.
The work of managing multiple myeloma and its implications for treatment-related decision making: a qualitative study of patient and caregiver experiences
Authors: Pritlove Cheryl , Jassi Mobin , Burns Bridget , McCurdy Arleigh 
Published: July 2021

Abstract
Background
The evolving nature of multiple myeloma (MM) therapies, including the introduction of novel oral agents, has produced a shift in the delivery of care from hospital to home. Within this context, patients and their caregivers are becoming increasingly engaged in the work of illness management, however the exact nature of this work as well as the ways in which this work informs treatment preferences and decisions within this population has not been explored. This qualitative study sought to develop an in-depth understanding of patient and caregiver experiences with different MM treatments, the work necessitated by MM and treatment management, and the processes of patient/caregiver treatment-related decision making.

Methods
Qualitative interviews were conducted with 16 MM patients and 8 caregivers. Interviews were coded for emergent themes and patterns and a constant comparative approach was used to identify important similarities and differences within and between interviews.

Results
Patient and caregiver participants described four types of work, including the work of accruing and personalizing medical knowledge, illness-related work in the hospital, illness-related work in the home, and psychosocial and relational management. They illuminated the physical, psychological, social and relational toll of this work and traced a pathway through which work informed their treatment-related decisions, sometimes in ways that conflicted with their preferences for treatment.

Conclusions
The work involved in managing MM, its treatment, and side-effects can inform the treatment decisions that patients and caregivers make. We must continue to find meaningful ways for patients and caregivers to discuss goals of care and treatment throughout the cancer trajectory, as well as support health care providers in the delivery of person-centred cancer care. With an increasing emphasis on the importance of shared decision making in MM, an improved understanding of the factors that frame patient’s and caregiver’s treatment decisions will be paramount to ensuring meaningful and high-quality patient-centered care.
Who engages in the arts in the United States? A comparison of several types of engagement using data from The General Social Survey
Authors: Bone Jessica K. , Bu Feifei , Fluharty Meg E. , Paul Elise , Sonke Jill K. , Fancourt Daisy 
Published: July 2021

Abstract
Background
Engaging in the arts is a health-related behavior that may be influenced by social inequalities. While it is generally accepted that there is a social gradient in traditional arts and cultural activities, such as attending classical music performances and museums, previous studies of arts engagement in the US have not adequately investigated whether similar demographic and socioeconomic factors are related to other forms of arts engagement.

Methods
Using cross-sectional data from the General Social Survey (GSS) in the US, we examined which demographic, socioeconomic, residential, and health factors were associated with attendance at arts events, participation in arts activities, membership of creative groups, and being interested in (but not attending) arts events. We combined data from 1993 to 2016 in four analytical samples with a sample size of 8684 for arts events, 4372 for arts activities, 4268 for creative groups, and 2061 for interested non-attendees. Data were analysed using logistic regression.

Results
More education was associated with increased levels of all types of arts engagement. Parental education demonstrated a similar association. Being female, compared to male, was also consistently associated with higher levels of engagement. Attendance at arts events was lower in participants with lower income and social class, poorer health, and those living in less urban areas. However, these factors were not associated with participation in arts activities or creative groups or being an interested non-attendee.

Conclusions
Overall, we found evidence for a social gradient in attendance at arts events, which was not as pronounced in participation in arts activities or creative groups or interest in arts events. Given the many benefits of engagement in the arts for education, health, and wider welfare, our findings demonstrate the importance of identifying factors to reduce barriers to participation in the arts across all groups in society.
Analyzing the paradigmatic cases of two persons with a disorder of consciousness: reflections on the legal and ethical perspectives
Authors: Picozzi Mario , Panzeri Lino , Torri Davide , Sattin Davide 
Published: July 2021

Abstract
Background
Media have increasingly reported on the difficulties associated with end-of-life decision-making in patients with Disorders of Consciousness (DOC), contextualizing such dilemma in detailed accounts of the patient’s life. Two of the first stories debated in the scientific community were those related to the cases of two women, one American, the other Italian, who captured attention of millions of people in the first years of this third millennium.

Methods
Much has been written about the challenges of surrogate decision-making for patients in DOC, but less has been written comparing these challenges across legal systems and cultures. In our paper, we propose a systematic analysis of the final legal documents written by the American and Italian Courts in relation to the two cases, developing our discussion around three areas: the level of certainty/reliability of diagnosis and prognosis, the reconstruction of self-expression, time of illness and time of care. They are examples of the typical issues discussed by legal authors and allow us to understand the link and the difference between the legal and ethical perspectives.

Results
The legal approach to the two cases has some common elements: the need to be certain about the diagnosis and prognosis and the fact that the clinical criteria are necessary in determining the most appropriate treatments, although these criteria are not sufficient unless they are supplemented by the patient’s will. The issue of relations takes on importance both from a legal and an ethical point of view, but from two different perspectives. While ethics safeguards relationships by guaranteeing their differences and makes them reconcilable, law safeguards relationships by guaranteeing the cold forms of respect, equality, impartiality, symmetry, reciprocity, and irreversibility. In this perspective, the link between the time of care and the decision of the family members assumes importance.

Conclusions
The most interesting point that emerges from our analysis is the issue of relationships and how they affect decisions, both from a legal and ethical point of view. For this reason, during the patients’ hospitalization, it is necessary to identify ways in which they might give their opinion about the moral issues underlying their choices.
Validation and minimum important difference of the UCSD Shortness of Breath Questionnaire in fibrotic interstitial lung disease
Authors: Chen Tao , Tsai Amy Po Yu , Hur Seo Am , Wong Alyson W. , Sadatsafavi Mohsen , Fisher Jolene H. , Johannson Kerri A. , Assayag Deborah , Morisset Julie , Shapera Shane , Khalil Nasreen , Fell Charlene D. , Manganas Helene , Cox Gerard , To Teresa , Gershon Andrea S. , Hambly Nathan , Halayko Andrew J. , Wilcox Pearce G. , Kolb Martin , Ryerson Christopher J. 
Published: July 2021

Abstract
Rationale
The University of California, San Diego Shortness of Breath Questionnaire (UCSDSOBQ) is a frequently used domain-specific dyspnea questionnaire; however, there is little information available regarding its use and minimum important difference (MID) in fibrotic interstitial lung disease (ILD). We aimed to describe the key performance characteristics of the UCSDSOBQ in this population.

Methods
UCSDSOBQ scores and selected anchors were measured in 1933 patients from the prospective multi-center Canadian Registry for Pulmonary Fibrosis. Anchors included the St. George’s Respiratory Questionnaire (SGRQ), European Quality of Life 5 Dimensions 5 Levels questionnaire (EQ-5D-5L) and EQ visual analogue scale (EQ-VAS), percent-predicted forced vital capacity (FVC%), diffusing capacity of the lung for carbon monoxide (DLCO%), and 6-min walk distance (6MWD). Concurrent validity, internal consistency, ceiling and floor effects, and responsiveness were assessed, followed by estimation of the MID by anchor-based (linear regression) and distribution-based methods (standard error of measurement).

Results
The UCSDSOBQ had a high level of internal consistency (Cronbach’s alpha = 0.97), no obvious floor or ceiling effect, strong correlations with SGRQ, EQ-5D-5L, and EQ-VAS (|r| > 0.5), and moderate correlations with FVC%, DLCO%, and 6MWD (0.3 < |r| < 0.5). The MID estimate for UCSDSOBQ was 5 points (1–8) for the anchor-based method, and 4.5 points for the distribution-based method.

Conclusion
This study demonstrates the validity of UCSDSOBQ in a large and heterogeneous population of patients with fibrotic ILD, and provides a robust MID estimate of 5–8 points.
Triglyceride-glucose index is associated with in-stent restenosis in patients with acute coronary syndrome after percutaneous coronary intervention with drug-eluting stents
Authors: Zhu Yong , Liu Kesen , Chen Maolin , Liu Yan , Gao Ang , Hu Chengping , Li Hong , Zhu Huagang , Han Hongya , Zhang Jianwei , Zhao Yingxin 
Published: July 2021

Abstract
Background
The triglyceride-glucose (TyG) index is an alternative marker of insulin resistance (IR) and is closely associated with the prevalence and prognosis of atherosclerotic cardiovascular disease (ASCVD). However, the association between the TyG index and in-stent restenosis (ISR) after drug-eluting stent (DES) implantation in patients with acute coronary syndrome (ACS) remains unknown.

Methods
The present study retrospectively recruited patients who were admitted for ACS and underwent coronary angiography at 6 to 24 months after successful DES-based percutaneous coronary intervention (PCI). In addition, we calculated the TyG index with the following formula: Ln(fasting triglyceride [mg/dL] × fasting blood glucose [mg/dL]/2) and divided patients into 3 groups according to the tertile of the TyG index. Most importantly, multivariate logistic regression analysis models were also constructed to assess the association between the TyG index and DES-ISR in patients with ACS.

Results
A total of 1574 patients with ACS (58.4 ± 9.4 years, 77.4% male) were included in this study. At the median follow-up time of 12 (9–14) months, the prevalence of DES-ISR increased stepwise with the increasing tertile of the TyG index (11.6% vs 17.3% vs 19.4%, p = 0.002), and the TyG index was also higher in the ISR group than in the non-ISR group (9.00 ± 0.58 vs 8.84 ± 0.61, p < 0.001). In addition, the positive association between the TyG index and the prevalence of DES-ISR was also determined in the fully adjusted model (TyG, per 1-unit increase: OR 1.424, 95% CI 1.116 to 1.818, p = 0.005; tertile of TyG, the OR (95% CI) values for tertile 2 and tertile 3 were 1.454 (1.013 to 2.087) and 1.634 (1.125 to 2.374), respectively, with tertile 1 as a reference). The association was also reflected in most subgroups. Moreover, adding the TyG index to the predictive model for DES-ISR in patients with ACS could contribute to an increase in C-statistics (0.675 vs 0.659, p = 0.010), categorical net reclassification improvement (0.090, p < 0.001), and integrated discrimination improvement (0.004, p = 0.040).

Conclusion
An elevated TyG index was independently and positively associated with DES-ISR in patients with ACS who underwent PCI. However, the incremental predictive value of the TyG index for DES-ISR was slight. To further confirm our findings, future studies are needed.
LncRNA HAND2-AS1 exerts anti-oncogenic effects on bladder cancer via restoration of RARB as a sponge of microRNA-146
Authors: Shan Liping , Liu Wei , Zhan Yunhong 
Published: July 2021

Abstract
Background
Growing evidence has shown that long noncoding RNA: microRNA: mRNA is implicated in tumor initiation, development, and progression. Long noncoding RNA HAND2-AS1 exhibits anti-cancer effects in diverse cancers. However, the knowledge of HAND-AS1 in bladder cancer development remains unknown.

Methods
LncRNA and miRNA microarray was conducted to explore different expressed RNA in primary bladder cancer specimens. RNA-RNA interaction prediction tools miRcode (http://www.mircode.org/), DIANA-lncBase v2 (https://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex-experimental), DIANA-TarBase v.8 (https://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex) and miRDB (http://www.mirdb.org/) were employed to predict the interactions between RNA. Bladder cancer cell lines were used to perform cell proliferation and apoptosis assays. Western blot and quantitative Real-time Polymerase Chain Reaction were used to determine the expression of protein and RNA separately. Dual-luciferase assay was conducted to determine the activity of three prime untranslated region of retinoic acid receptor beta (RARB). Furthermore, 5637 human bladder cancer mouse models were established to investigate the interactions of lncRNA: miRNA: mRNA in vivo.

Results
Based on the RT2 lncRNA PCR Arrays analysis, we validated HAND2-AS1 declined in bladder cancer and negatively correlated with the depth of invasion and grades. The overexpression of HAND2-AS1 in human bladder cancer cells 5637 and RT4 hampered cell proliferation by provoking Caspase 3-triggered cell apoptosis. Besides, one of the HAND2-AS1 sponges, miR-146, elevated in bladder cancer and targeted the tumor suppressor, retinoic acid receptor beta (RARB). We further demonstrated that the HAND2-AS1: miR-146: RARB complex promoted Caspase 3-mediated apoptosis by suppressing COX-2 expression. Finally, the results gained in mouse xenografts suggested that HAND2-AS1 diminished miR-146 expression, thereby reversing the suppression of miR-146 on RARB-mediated apoptosis and contributing to bladder cancer regression.

Conclusion
The present study sheds light on the fact that lncRNA HAND2-AS1 exerted as a tumor suppressor by releasing RARB from miR-146, leading to tumor proliferation and invasion inhibition. The findings expanded HAND2-AS-mediated regulatory networks' knowledge and provided novel insights to improve the RARB-targeted regimens against bladder cancer.
Assessment of the value of adjuvant radiotherapy for treatment of gastric adenocarcinoma based on pattern of post-surgical progression
Authors: Wang Peng , Zhou Haihua , Han Gaohua , Ni Qingtao , Dai Shengbin , Huang Junxing , Dai Chunlei , Yu Lei 
Published: July 2021

Abstract
Purpose
To assess the value of adjuvant radiotherapy for treatment of gastric adenocarcinoma and to investigate subgroups of patients suitable for adjuvant radiotherapy.

Methods and materials
Data from 785 patients with gastric adenocarcinoma who had undergone D1/D2 radical resection and adjuvant chemotherapy were collected, the site of first progression was determined, and the relationship between the rate of local recurrence and clinicopathologic features was analyzed.

Results
By the end of the follow-up period, progression was observed in 405 patients. Local recurrence was observed as the first progression in 161 cases. The local recurrence rate was significantly lower than the non-local progression rate (20.5% vs 31.5%, p=0.007). Multivariate Cox regression analysis showed a significant relationship among degree of differentiation, T stage, N stage, and rate of local recurrence.

Conclusions
Not all patients with gastric carcinoma required adjuvant radiotherapy. However, patients with poorly differentiated cancer cells, advanced T stage (T3/T4), and positive lymph nodes, which included patients in the T4N1-2M0 subgroup, were recommended for adjuvant radiotherapy.
Inherited unbalanced translocation (4p16.3p15.32 duplication/8p23.3p23.2deletion) in the four generation pedigree with intellectual disability/developmental delay
Authors: Hao Dongmei , Li Yajuan , Chen Lisha , Wang Xiliang , Wang Mengxing , Yu Yuexin 
Published: July 2021

AbstractChromosomal copy number variants (CNVs) are an important cause of congenital malformations and mental retardation. This study reported a large Chinese pedigree (4-generation, 76 members) with mental retardation caused by chromosome microduplication/microdeletion. There were 10 affected individuals with intellectual disability (ID), developmental delay (DD), and language delay phenotypes. SNP array analysis was performed in the proband and eight patients and found all of them had a microduplication of chromosome 4p16.3p15.2 and a microdeletion of chromosome 8p23.3p23.2. The high-resolution karyotyping analysis of the proband had unbalanced karyotype [46, XY, der(8)t(4;8)(p15.2;p23.1)mat], his mother had balanced karyotype [46, XX, t(4;8) (p15.2;p23.1)], whereas his father had normal karyotype [46,XY]. Fluorescence in situ hybridization (FISH) analysis further confirmed that the proband’s mother had a balanced translocation between the short arm terminal segment of chromosome 4 and the short arm end segment of chromosome 8, ish t(4;8)(8p + ,4q + ;4p + ,8q +). In conclusion, all the patients inherited chromosomes 8 with 4p16.3p15.2 duplication and 8p23.3p23.2 deletion from their parental balanced translocation, which might be the cause of the prevalence of intellectual disability. Meanwhile, 8p23.3p23.2 deletion, rather than 4p16.3p15.2 duplication might cause a more severe clinical syndrome.