bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute Myeloid Leukemia in the Elderly: Assessment of Multidrug Resistance (MDR1) and Cytogenetics Distinguishes Biologic Subgroups With Remarkably Distinct Responses to Standard Chemotherapy. A Southwest Oncology Group Study
Authors: Leith Catherine P. , Kopecky Kenneth J. , Godwin John , McConnell Thomas , Slovak Marilyn L. , Chen I-Ming , Head David R. , Appelbaum Frederick R. , Willman Cheryl L. 
Published: April 2020

AbstractCompared with younger patients, elderly patients with acute myeloid leukemia (AML) respond poorly to conventional chemotherapy. To determine if this poor response is due to differences in the biologic characteristics of AML in the elderly, we studied 211 patients (161 de novo, 50 secondary AML) over 55 years of age (median, 68 years) registered to a single clinical trial for previously untreated AML (SWOG 9031, Phase III randomized trial of standard dose cytosine arabinoside and daunomycin ± rhG-CSF ). Pretreatment leukemic blasts were karyotyped and were also analyzed for intrinsic drug resistance by quantitating expression of the multidrug resistance glycoprotein MDR1 and functional drug efflux using sensitive flow cytometric techniques. Results were correlated with clinical variables and outcome. These elderly AML patients had a high frequency of unfavorable cytogenetics (32%), MDR1 protein expression (71%), and functional drug efflux (58%); each of these factors occurred at high frequencies in both de novo and secondary AML patients and was associated with a significantly poorer complete remission (CR) rate. In multivariate analysis, secondary AML (P = .0035), unfavorable cytogenetics (P = .0031), and MDR1 (P = .0041) were each significantly and independently associated with lower CR rates. Resistant disease was associated with unfavorable cytogenetics (P = .017) and MDR1 expression (P = .0007). Strikingly, elderly MDR1(−) de novo AML patients with favorable/intermediate cytogenetics had a CR rate of 81%; with increasing MDR1 expression, CR rate decreased in this cytogenetic group. MDR1(+) secondary AML patients with unfavorable cytogenetics had a CR rate of only 12%. Thus, AML in the elderly is associated with an increased frequency of unfavorable cytogenetics and MDR1 expression, both of which independently contribute to poor outcomes. The high frequencies of these features in both de novo and secondary elderly AML patients suggest a common biologic mechanism for these leukemias distinct from that in younger patients. Investigation of biologic parameters at diagnosis in AML in the elderly may help identify patients with a high likelihood of achieving CR with conventional regimens, as well as those who may require alternate regimens designed to overcome therapy resistance.
Glycoprotein VI Is a Major Collagen Receptor for Platelet Activation: It Recognizes the Platelet-Activating Quaternary Structure of Collagen, Whereas CD36, Glycoprotein IIb/IIIa, and von Willebrand Factor Do Not
Authors: Kehrel Beate , Wierwille Sonja , Clemetson Kenneth J. , Anders Olaf , Steiner Michael , Graham Knight C. , Farndale Richard W. , Okuma Minoru , Barnes Michael J. 
Published: April 2020

AbstractSimple collagen-related peptides (CRPs) containing a repeat Gly-Pro-Hyp sequence are highly potent platelet agonists. Like collagen, they must exhibit tertiary (triple-helical) and quaternary (polymeric) structure to activate platelets. Platelet signaling events induced by the peptides are the same as most of those induced by collagen. The peptides do not recognize the α2β1 integrin. To identify the signaling receptor involved, we have evaluated the response to the CRP, Gly-Lys-Hyp(Gly-Pro-Hyp)10-Gly-Lys-Hyp-Gly of platelets with defined functional deficiencies. These studies exclude a primary recognition role for CD36, von Willebrand factor (vWF), or glycoprotein (GP) IIb/IIIa. Thus, both CD36 and vWF-deficient platelets exhibited normal aggregation, normal fibrinogen binding, and normal expression of CD62 and CD63, measured by flow cytometry, in response to the peptide, and there was normal expression of CD62 and CD63 on thrombasthenic platelets. In contrast, GPVI-deficient platelets were totally unresponsive to the peptide, indicating that this receptor recognizes the Gly-Pro-Hyp sequence in collagen. GPVI-deficient platelets showed some fibrinogen binding in response to collagen but failed to aggregate and to express CD62 and CD63. Collagen, but not CRP-XL, contains binding sites for α2β1. Therefore, it is possible that collagen still induces some signaling via α2β1, leading to activation of GPIIb/IIIa. Our findings are consistent with a two-site, two-step model of collagen interaction with platelets involving recognition of specific sequences in collagen by an adhesive receptor such as α2β1 to arrest platelets under flow and subsequent recognition of another specific collagen sequence by an activatory receptor, namely GPVI.
Molecular Analysis of the ERGIC-53 Gene in 35 Families With Combined Factor V-Factor VIII Deficiency
Authors: Neerman-Arbez M. , Johnson K.M. , Morris M.A. , McVey J.H. , Peyvandi F. , Nichols W.C. , Ginsburg D. , Rossier C. , Antonarakis S.E. , Tuddenham E.G.D. 
Published: April 2020

AbstractCombined factor V-factor VIII deficiency (F5F8D) is a rare, autosomal recessive coagulation disorder in which the levels of both coagulation factors V and VIII are diminished. The F5F8D locus was previously mapped to a 1-cM interval on chromosome 18q21. Mutations in a candidate gene in this region, ERGIC-53, were recently found to be associated with the coagulation defect in nine Jewish families. We performed single-strand conformation and sequence analysis of the ERGIC-53 gene in 35 F5F8D families of different ethnic origins. We identified 13 distinct mutations accounting for 52 of 70 mutant alleles. These were 3 splice site mutations, 6 insertions and deletions resulting in translational frameshifts, 3 nonsense codons, and elimination of the translation initiation codon. These mutations are predicted to result in synthesis of either a truncated protein product or no protein at all. This study revealed that F5F8D shows extensive allelic heterogeneity and all ERGIC-53 mutations resulting in F5F8D are “null.” Approximately 26% of the mutations have not been identified, suggesting that lesions in regulatory elements or severe abnormalities within the introns may be responsible for the disease in these individuals. In two such families, ERGIC-53 protein was detectable at normal levels in patients’ lymphocytes, raising the further possibility of defects at other genetic loci.
Diazoxide affects mitochondrial bioenergetics by the opening of mKATP channel on submicromolar scale
Authors: Akopova Olga , Kolchinskaya Liudmila , Nosar Valentina , Mankovska Iryna , Sagach Vadim 
Published: April 2020

Abstract
Background
Cytoprotection afforded by mitochondrial ATP-sensitive K+-channel (mKATP-channel) opener diazoxide (DZ) largely depends on the activation of potassium cycle with eventual modulation of mitochondrial functions and ROS production. However, generally these effects were studied in the presence of Mg∙ATP known to block K+ transport. Thus, the purpose of our work was the estimation of DZ effects on K+ transport, K+ cycle and ROS production in rat liver mitochondria in the absence of Mg∙ATP.

Results
Without Mg·ATP, full activation of native mKATP-channel, accompanied by the increase in ATP-insensitive K+ uptake, activation of K+-cycle and respiratory uncoupling, was reached at ≤0.5 μM of DZ,. Higher diazoxide concentrations augmented ATP-insensitive K+ uptake, but not mKATP-channel activity. mKATP-channel was blocked by Mg·ATP, reactivated by DZ, and repeatedly blocked by mKATP-channel blockers glibenclamide and 5-hydroxydecanoate, whereas ATP-insensitive potassium transport was blocked by Mg2+ and was not restored by DZ. High sensitivity of potassium transport to DZ in native mitochondria resulted in suppression of mitochondrial ROS production caused by the activation of K+-cycle on sub-micromolar scale. Based on the oxygen consumption study, the share of mKATP-channel in respiratory uncoupling by DZ was found.

Conclusions
The study of mKATP-channel activation by diazoxide in the absence of MgATP discloses novel, not described earlier, aspects of mKATP-channel interaction with this drug. High sensitivity of mKATP-channel to DZ results in the modulation of mitochondrial functions and ROS production by DZ on sub-micromolar concentration scale. Our experiments led us to the hypothesis that under the conditions marked by ATP deficiency affinity of mKATP-channel to DZ can increase, which might contribute to the high effectiveness of this drug in cardio- and neuroprotection.
Campylobacter jejuni and Campylobacter coli autotransporter genes exhibit lineage-associated distribution and decay
Authors: Mehat Jai W. , La Ragione Roberto M. , van Vliet Arnoud H. M. 
Published: April 2020

Abstract
Background
Campylobacter jejuni and Campylobacter coli are major global causes of bacterial gastroenteritis. Whilst several individual colonisation and virulence factors have been identified, our understanding of their role in the transmission, pathogenesis and ecology of Campylobacter has been hampered by the genotypic and phenotypic diversity within C. jejuni and C. coli. Autotransporter proteins are a family of outer membrane or secreted proteins in Gram-negative bacteria such as Campylobacter, which are associated with virulence functions. In this study we have examined the distribution and predicted functionality of the previously described capC and the newly identified, related capD autotransporter gene families in Campylobacter.

Results
Two capC-like autotransporter families, designated capC and capD, were identified by homology searches of genomes of the genus Campylobacter. Each family contained four distinct orthologs of CapC and CapD. The distribution of these autotransporter genes was determined in 5829 C. jejuni and 1347 C. coli genomes. Autotransporter genes were found as intact, complete copies and inactive formats due to premature stop codons and frameshift mutations. Presence of inactive and intact autotransporter genes was associated with C. jejuni and C. coli multi-locus sequence types, but for capC, inactivation was independent from the length of homopolymeric tracts in the region upstream of the capC gene. Inactivation of capC or capD genes appears to represent lineage-specific gene decay of autotransporter genes. Intact capC genes were predominantly associated with the C. jejuni ST-45 and C. coli ST-828 generalist lineages. The capD3 gene was only found in the environmental C. coli Clade 3 lineage. These combined data support a scenario of inter-lineage and interspecies exchange of capC and subsets of capD autotransporters.

Conclusions
In this study we have identified two novel, related autotransporter gene families in the genus Campylobacter, which are not uniformly present and exhibit lineage-specific associations and gene decay. The distribution and decay of the capC and capD genes exemplifies the erosion of species barriers between certain lineages of C. jejuni and C. coli, probably arising through co-habitation. This may have implications for the phenotypic variability of these two pathogens and provide opportunity for new, hybrid genotypes to emerge.
DolphinNext: a distributed data processing platform for high throughput genomics
Authors: Yukselen Onur , Turkyilmaz Osman , Ozturk Ahmet Rasit , Garber Manuel , Kucukural Alper 
Published: April 2020

AbstractBackgroundThe emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks.Several platforms currently exist for the design and execution of complex pipelines. Unfortunately, current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen. We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platform will simplify robust and reproducible workflow creation for non-technical users as well as provide a robust platform to maintain pipelines for large organizations.ResultsTo simplify development, maintenance, and execution of complex pipelines we created DolphinNext. DolphinNext facilitates building and deployment of complex pipelines using a modular approach implemented in a graphical interface that relies on the powerful Nextflow workflow framework by providing 1. A drag and drop user interface that visualizes pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. Modules to execute and monitor pipelines in distributed computing environments such as high-performance clusters and/or cloud 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Modular process design with process revisioning support to increase reusability and pipeline development efficiency. 5. Pipeline sharing with GitHub and automated testing 6. Extensive reports with R-markdown and shiny support for interactive data visualization and analysis.ConclusionDolphinNext is a flexible, intuitive, web-based data processing and analysis platform that enables creating, deploying, sharing, and executing complex Nextflow pipelines with extensive revisioning and interactive reporting to enhance reproducible results.
Incidence of heart failure among diabetic patients with ischemic heart disease: a cohort study
Authors: Abdissa Senbeta Guteta , Deressa Wakgari , Shah Amit J. 
Published: April 2020

Abstract
Background
In population studies of heart failure (HF), diabetes has been shown to be an independent risk factor. However, the evidence evaluating diabetes mellitus (DM) as an independent risk factor in incident HF in patients with ischemic heart disease (IHD) is scarce. Our study aimed to assess the incidence of HF in diabetic IHD patients compared to non-diabetic IHD patients in Ethiopia.

Methods
A retrospective cohort study was conducted among 306 patients with IHD followed-up at Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia. The IHD patients who did not have HF at baseline were followed for 24 months beginning from November 30, 2015. We assessed the incidence of HF in patients with diabetic IHD versus the non-diabetic IHD. Cox proportional hazards models were used to assess the association between diabetic IHD and HF after controlling for important covariates. Hypertension was examined as a possible effect modifier as well.

Results
The mean age was 56.8 years, 69% were male, and 31% were diabetic. During the 24 months follow-up period, 196 (64.1%) had incident HF. On multivariate Cox regression, DM was significantly associated with incident HF [Hazard Ratio = 2.04, 95% confidence interval (CI): 1.32–3.14, p = 0.001]. Furthermore, when the patients were stratified by hypertension (HTN), DM was associated with worse prognosis, the strongest association being in those with co-existing DM and HTN [HR = 2.57,95% CI =1.66–3.98, p <  0.0001] followed by the presence of DM without HTN [HR 2.27, 95% CI = 1.38–3.71, p = 0.001] (compared to those with neither).

Conclusion
DM is the strongest predictor of incident HF, compared to other traditional risk factors, in Ethiopian patients with IHD. Those with both DM and HTN are at the highest risk.
Patients without colonoscopic follow-up after abnormal fecal immunochemical tests are often unaware of the abnormal result and report several barriers to colonoscopy
Authors: Cusumano Vivy T. , Corona Edgar , Partida Diana , Yang Liu , Yu Christine , May Folasade P. 
Published: April 2020

Abstract
Background
The fecal immunochemical test (FIT) is the second most commonly used colorectal cancer (CRC) screening modality in the United States; yet, follow-up of abnormal FIT results with diagnostic colonoscopy is underutilized. Our objective was to determine patient-reported barriers to diagnostic colonoscopy following abnormal FIT in an academic healthcare setting.

Methods
We included patients age 50–75 with an abnormal FIT result between 1/1/2015 and 10/31/2017 and no documented follow-up diagnostic colonoscopy. We abstracted demographic data from the electronic health record (EHR). Study personnel conducted telephone surveys with patients to confirm colonoscopy completion and elicit data on notification of FIT results and barriers to colonoscopy. We also provided brief verbal education about diagnostic colonoscopy. We calculated frequencies of demographic data and survey responses and compared survey responses by interest in colonoscopy after education.

Results
We surveyed 67 patients. Fifty-one were aware of the abnormal FIT result, and a majority learned of the abnormal FIT result by direct communication with providers (19, 37.3%) or EHR messaging (11, 21.6%). Overall, fifty-three patients (79.1%) confirmed lack of colonoscopy, citing provider-related (19, 35.8%), patient-related (16, 30.2%), system-related (1, 1.9%), or multifactorial (17, 32.1%) reasons. Lack of knowledge of FIT result (14, 26.4%) was most common. After brief education, 20 (37.7%) patients requested colonoscopy.

Conclusion
Patients with an abnormal FIT reported various multi-level barriers to diagnostic colonoscopy after abnormal FIT, including knowledge of FIT results. When provided with brief education, participants expressed interest in diagnostic colonoscopy. Future efforts will evaluate interventions to improve colonoscopy follow-up.
Performance of TGSE BLADE DWI compared with RESOLVE DWI in the diagnosis of cholesteatoma
Authors: Sheng Yaru , Hong Rujian , Sha Yan , Zhang Zhongshuai , Zhou Kun , Fu Caixia 
Published: April 2020

Abstract
Background
Based on its high resolution in soft tissue, MRI, especially diffusion-weighted imaging (DWI), is increasingly important in the evaluation of cholesteatoma. The purpose of this study was to evaluate the role of the 2D turbo gradient- and spin-echo (TGSE) diffusion-weighted (DW) pulse sequence with the BLADE trajectory technique in the diagnosis of cholesteatoma at 3 T and to qualitatively and quantitatively compare image quality between the TGSE BLADE and RESOLVE methods.

Method
A total of 42 patients (23 males, 19 females; age range, 7–65 years; mean, 40.1 years) with surgically confirmed cholesteatoma in the middle ear were enrolled in this study. All patients underwent DWI (both a prototype TGSE BLADE DWI sequence and the RESOLVE DWI sequence) using a 3-T scanner with a 64-channel brain coil.
Qualitative imaging parameters (imaging sharpness, geometric distortion, ghosting artifacts, and overall imaging quality) and quantitative imaging parameters (apparent diffusion coefficient [ADC], signal-to-noise ratio [SNR], contrast, and contrast-to-noise ratio [CNR]) were assessed for the two diffusion acquisition techniques by two independent radiologists.

Result
A comparison of qualitative scores indicated that TGSE BLADE DWI produced less geometric distortion, fewer ghosting artifacts (P < 0.001) and higher image quality (P < 0.001) than were observed for RESOLVE DWI. A comparison of the evaluated quantitative image parameters between TGSE and RESOLVE showed that TGSE BLADE DWI produced a significantly lower SNR (P < 0.001) and higher parameter values (both contrast and CNR (P < 0.001)) than were found for RESOLVE DWI.
The ADC (P < 0.001) was significantly lower for TGSE BLADE DWI (0.763 × 10− 3 mm2/s) than RESOLVE DWI (0.928 × 10− 3 mm2/s).

Conclusion
Compared with RESOLVE DWI, TGSE BLADE DWI significantly improved the image quality of cholesteatoma by reducing magnetic sensitive artifacts, distortion, and blurring. TGSE BLADE DWI is more valuable than RESOLVE DWI for the diagnosis of small-sized (2 mm) cholesteatoma lesions. However, TGSE BLADE DWI also has some disadvantages: the whole image intensity is slightly low, so that the anatomical details of the air-bone interface are not shown well, and this shortcoming should be improved in the future.
Correlation between gene polymorphism in angiotensin II type 1 receptor and type 2 diabetes mellitus complicated by hypertension in a population of Inner Mongolia
Authors: Hou Lina , Quan Xiaohong , Li Xian , Su Xiulan 
Published: April 2020

Abstract
Background
The role of angiotensin II type 1 receptor (AT1R) as a key player in type 2 diabetes mellitus (T2DM) complicated with hypertension remains controversial. The present case-control study systematically investigated the association between gene the correct variation type in the angiotensin II type 1 receptor (AT1R) gene and type 2 diabetes mellitus complicated with hypertension in the Han population from the Inner Mongolia region, China.

Method
Here, state which variants were analysis, including age, occupation, triglyceride, systolic, diastolic, sex, culture, marital status, smoking, alcohol, BMI (body mass index), SBP (systolic blood pressure), DBP (diastolic blood pressure), TG (triglyceride), TC (total cholesterol), HDL-C (high-density lipoprotein cholesterol), LDL-C (low-density lipoprotein cholesterol), FPG (fasting plasma glucose). Genomic DNA was extracted from samples from 202 type 2 diabetic patients with hypertension and 216 type 2 diabetic patients without hypertension.

Results
Non-conditional regression analysis showed that in comparison with the TT genotype, the presence of the CC genotype for the T573 site of the AT1R gene increased the risk for diabetes mellitus complicated with hypertension by 3.219-fold (OR = 3.219, 95% CI: 1.042–9.941, P = 0.042). The results from multivariate linear regression analysis suggested the rs5182 polymorphism in the AT1R gene to be associated with diastolic blood pressure (P = 0.032). No other associations were found between the incidence of disease and the correct variation type at other sites of the AT1R gene.

Conclusions
Our results suggest that the rs5182 polymorphism in the AT1R gene is associated with diabetes complicated by hypertension in the Han population of Inner Mongolia.