bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of interim FDG-PET in diffuse large cell lymphoma: results from the CALGB 50303 Clinical Trial
Authors: Schöder Heiko , Polley Mei-Yin C. , Knopp Michael V. , Hall Nathan , Kostakoglu Lale , Zhang Jun , Higley Howard R. , Kelloff Gary , Liu Heshan , Zelenetz Andrew D. , Cheson Bruce D. , Wagner-Johnston Nina , Kahl Brad S. , Friedberg Jonathan W. , Hsi Eric D. , Leonard John P. , Schwartz Lawrence H. , Wilson Wyndham H. , Bartlett Nancy L. 
Published: March 2020

Abstract
As part of a randomized, prospective clinical trial in large cell lymphoma, we conducted serial fluorodeoxyglucose positron emission tomography (FDG-PET) at baseline, after 2 cycles of chemotherapy (interim PET [i-PET]), and at end of treatment (EoT) to identify biomarkers of response that are predictive of remission and survival. Scans were interpreted in a core laboratory by 2 imaging experts, using the visual Deauville 5-point scale (5-PS), and by calculating percent change in FDG uptake (change in standardized uptake value [ΔSUV]). Visual scores of 1 through 3 and ΔSUV ≥66% were prospectively defined as negative. Of 524 patients enrolled in the parent trial, 169 agreed to enroll in the PET substudy and 158 were eligible for final analysis. In this selected population, all had FDG-avid disease at baseline; by 5-PS, 55 (35%) remained positive on i-PET and 28 (18%) on EoT PET. Median ΔSUV on i-PET was 86.2%. With a median follow-up of 5 years, ΔSUV, as continuous variable, was associated with progression-free survival (PFS) (hazard ratio [HR] = 0.99; 95% confidence interval [CI], 0.97-1.00; P = .02) and overall survival (OS) (HR, 0.98; 95% CI, 0.97-0.99; P = .03). ΔSUV ≥66% was predictive of OS (HR, 0.31; 95% CI, 0.11-0.85; P = .02) but not PFS (HR, 0.47; 95% CI, 0.19-1.13; P = .09). Visual 5-PS on i-PET did not predict outcome. ΔSUV, but not visual analysis, on i-PET predicted OS in DLBCL, although the low number of events limited the statistical analysis. These data may help guide future clinical trials using PET response-adapted therapy. This trial was registered at www.clinicaltrials.gov as #NCT00118209.
An intestinal organoid–based platform that recreates susceptibility to T-cell–mediated tissue injury
Authors: Matsuzawa-Ishimoto Yu , Hine Ashley , Shono Yusuke , Rudensky Eugene , Lazrak Amina , Yeung Frank , Neil Jessica A. , Yao Xiaomin , Chen Ying-Han , Heaney Thomas , Schuster Samantha L. , Zwack Erin E. , Axelrad Jordan E. , Hudesman David , Tsai Jennifer J. , Nichols Katherine , Dewan M. Zahidunnabi , Cammer Michael , Beal Allison , Hoffman Sandra , Geddes Brad , Bertin John , Liu Chen , Torres Victor J. , Loke P’ng , van den Brink Marcel R. M. , Cadwell Ken 
Published: March 2020

Abstract
A goal in precision medicine is to use patient-derived material to predict disease course and intervention outcomes. Here, we use mechanistic observations in a preclinical animal model to design an ex vivo platform that recreates genetic susceptibility to T-cell–mediated damage. Intestinal graft-versus-host disease (GVHD) is a life-threatening complication of allogeneic hematopoietic cell transplantation. We found that intestinal GVHD in mice deficient in Atg16L1, an autophagy gene that is polymorphic in humans, is reversed by inhibiting necroptosis. We further show that cocultured allogeneic T cells kill Atg16L1-mutant intestinal organoids from mice, which was associated with an aberrant epithelial interferon signature. Using this information, we demonstrate that pharmacologically inhibiting necroptosis or interferon signaling protects human organoids derived from individuals harboring a common ATG16L1 variant from allogeneic T-cell attack. Our study provides a roadmap for applying findings in animal models to individualized therapy that targets affected tissues.
Clonal hematopoiesis and measurable residual disease assessment in acute myeloid leukemia
Authors: Hasserjian Robert P. , Steensma David P. , Graubert Timothy A. , Ebert Benjamin L. 
Published: March 2020

Abstract
Current objectives regarding treatment of acute myeloid leukemia (AML) include achieving complete remission (CR) by clinicopathological criteria followed by interrogation for the presence of minimal/measurable residual disease (MRD) by molecular genetic and/or flow cytometric techniques. Although advances in molecular genetic technologies have enabled highly sensitive detection of AML-associated mutations and translocations, determination of MRD is complicated by the fact that many treated patients have persistent clonal hematopoiesis (CH) that may not reflect residual AML. CH detected in AML patients in CR includes true residual or early recurrent AML, myelodysplastic syndrome or CH that is ancestral to the AML, and independent or newly emerging clones of uncertain leukemogenic potential. Although the presence of AML-related mutations has been shown to be a harbinger of relapse in multiple studies, the significance of other types of CH is less well understood. In patients who undergo allogeneic hematopoietic cell transplantation (HCT), post-HCT clones can be donor-derived and in some cases engender a new myeloid neoplasm that is clonally unrelated to the recipient’s original AML. In this article, we discuss the spectrum of CH that can be detected in treated AML patients, propose terminology to standardize nomenclature in this setting, and review clinical data and areas of uncertainty among the various types of posttreatment hematopoietic clones.
Prediction of Leakage from an Axial Piston Pump Slipper with Circular Dimples Using Deep Neural Networks
Authors: Özmen Özkan , Sinanoğlu Cem , Caliskan Abdullah , Badem Hasan 
Published: March 2020

AbstractOil leakage between the slipper and swash plate of an axial piston pump has a significant effect on the efficiency of the pump. Therefore, it is extremely important that any leakage can be predicted. This study investigates the leakage, oil film thickness, and pocket pressure values of a slipper with circular dimples under different working conditions. The results reveal that flat slippers suffer less leakage than those with textured surfaces. Also, a deep learning-based framework is proposed for modeling the slipper behavior. This framework is a long short-term memory-based deep neural network, which has been extremely successful in predicting time series. The model is compared with four conventional machine learning methods. In addition, statistical analyses and comparisons confirm the superiority of the proposed model.
Butterfly eyespot color pattern formation requires physical contact of the pupal wing epithelium with extracellular materials for morphogenic signal propagation
Authors: Otaki Joji M. 
Published: March 2020

AbstractBackgroundEyespot color pattern formation on butterfly wings is sensitive to physical damage and physical distortion as well as physical contact with materials on the surface of wing epithelial tissue at the pupal stage. Contact-mediated eyespot color pattern changes may imply a developmental role of the extracellular matrix in morphogenic signal propagation. Here, we examined eyespot responses to various contact materials, focusing on the hindwing posterior eyespots of the blue pansy butterfly,Junonia orithya.ResultsContact with various materials, including both nonbiological and biological materials, induced eyespot enlargement, reduction, or no change in eyespot size, and each material was characterized by a unique response profile. For example, silicone glassine paper almost always induced a considerable reduction, while glass plates most frequently induced enlargement, and plastic plates generally produced no change. The biological materials tested here (fibronectin, polylysine, collagen type I, and gelatin) resulted in various responses, but polylysine induced more cases of enlargement, similar to glass plates. The response profile of the materials was not readily predictable from the chemical composition of the materials but was significantly correlated with the water contact angle (water repellency) of the material surface, suggesting that the surface physical chemistry of materials is a determinant of eyespot size. When the proximal side of a prospective eyespot was covered with a size-reducing material (silicone glassine paper) and the distal side and the organizer were covered with a material that rarely induced size reduction (plastic film), the proximal side of the eyespot was reduced in size in comparison with the distal side, suggesting that signal propagation but not organizer activity was inhibited by silicone glassine paper.ConclusionsThese results suggest that physical contact with an appropriate hydrophobic surface is required for morphogenic signals from organizers to propagate normally. The binding of the apical surface of the epithelium with an opposing surface may provide mechanical support for signal propagation. In addition to conventional molecular morphogens, there is a possibility that mechanical distortion of the epithelium that is propagated mechanically serves as a nonmolecular morphogen to induce subsequent molecular changes, in accordance with the distortion hypothesis for butterfly wing color pattern formation.
Molecular dissection of Secale africanum chromosome 6Rafr in wheat enabled localization of genes for resistance to powdery mildew and stripe rust
Authors: Li Guangrong , Tang Lingrong , Yin Yan , Zhang Ahui , Yu Zhihui , Yang Ennian , Tang Zongxiang , Fu Shulan , Yang Zujun 
Published: March 2020

Abstract
Background
Introgression of chromatin from Secale species into common wheat has for decades been a successful strategy for controlling the wheat diseases. The wild Secale species, Secale africanum Stapf., is a valuable source for resistance to foliar disease of wheat. A wheat-S. africanum chromosome 6Rafr substitution line displayed resistance to both powdery mildew and stripe rust at the adult-plant stage.

Results
Wheat-S. africanum chromosome 6Rafr deletion and translocation lines were produced and identified by sequential non-denaturing fluorescence in situ hybridization (ND-FISH) using multiple Oligo-based probes. Different ND-FISH patterns were observed between S. cereale 6R and S. africanum 6Rafr. With reference to the physical map of the draft genome sequence of rye inbred line Lo7, a comprehensive PCR marker analysis indicated that insertions and deletions had occurred by random exchange between chromosomes 6R and 6Rafr. A survey of the wheat- S. africanum 6Rafr lines for disease resistance indicated that a powdery mildew resistance gene(s) was present on the long arm of 6Rafr at FL0.85–1.00, and that a stripe rust resistance gene(s) was located in the terminal region of 6RafrS at FL0.95–1.00. The wheat-S. africanum 6Rafr introgression lines also displayed superior agronomic traits, indicating that the chromosome 6Rafr may have little linkage drag in the wheat background.

Conclusions
The combination of molecular and cytogenetic methods allowed to precisely identify the chromosome rearrangements in wheat- S. africanum 6Rafr substitution, deletion and translocation lines, and compare the structural difference between chromosomes 6R and 6Rafr. The wheat- S. africanum 6Rafr lines containing gene(s) for powdery mildew and stripe rust resistance could be used as novel germplasm for wheat breeding by chromosome engineering.
Obesity-associated poor muscle quality: prevalence and association with age, sex, and body mass index
Authors: Valenzuela Pedro L. , Maffiuletti Nicola A. , Tringali Gabriella , De Col Alessandra , Sartorio Alessandro 
Published: March 2020

Abstract
Background
Muscle quality (i.e., the expression of muscle function per unit of muscle mass) has been proposed as a clinically-relevant measure to detect individuals at risk of functional incapacity. Individuals with obesity might be at an increased risk of having poor muscle quality. Thus, we aimed to analyze the prevalence of poor muscle quality in obese individuals, to determine associated variables, and to provide normative values for this population.

Methods
203 individuals with obesity (103 women, age: 18–75 years, body mass index (BMI): 35–64 kg·m− 2) participated in this cross-sectional study. Their muscle strength (handgrip dynamometry), muscle power (sit-to-stand test) and muscle mass (bioelectrical impedance analysis) were measured, and muscle quality (strength/power to muscle mass ratio) was compared with reference values obtained in young healthy individuals. Muscle quality was individually categorized as normal, low or poor based on specific muscle strength and power (i.e., strength and power per unit of muscle mass, respectively). Sex and age-specific normative values of specific muscle strength and power were computed for the whole cohort.

Results
Age and being a woman were inversely associated with specific muscle strength, with age being also inversely associated with specific muscle power. A small proportion of participants (6%) presented with an impaired (i.e., low/poor) specific muscle power while most of them (96%) had impaired specific muscle strength. Eventually, 84% of the participants were deemed to have poor muscle quality. Being a woman (odds ratio [OR]: 18.09, 95% confidence intervals [CI]: 4.07–80.38), age (OR: 1.06, 95%CI: 1.03–1.10) and BMI (OR: 1.22, 95%CI: 1.07–1.38) were independently associated with a higher risk of poor muscle quality in adjusted analyses.

Conclusions
These findings show a high prevalence of poor muscle quality among individuals with obesity, with age, sex and BMI being independent predictors.
System reliability analysis of the scoliosis disorder
Authors: Nouri Fatemeh , Ghasemi S. Hooman , Lee Ji Yun 
Published: March 2020

Abstract
Background
Scoliosis is a spine abnormal deviation, which is an idiopathic disorder among children and adolescents. As a matter of the fact, distribution of loads on the patient’s spine and load-carrying capacity of the vertebral column are both random variables. Therefore, the probabilistic approach may consider as a sophisticated method to deal with this problem.

Method
Reliability analysis is a probabilistic-based approach to consider the uncertainties of load and resistance of the vertebral column. The main contribution of this paper is to compare the reliability level of a normal and scoliosis spinal. To do so, the numerical analyses associated with the inherent random parameters of bones and applied load are performed. Then, the reliability indices for all vertebrae and discs are determined. Accordingly, as the main innovation of this paper, the system reliability indices of the spinal column for both normal and damaged backbone systems are represented.

Results
Based on the required reliability index for normal spinal curvature the target system reliability level for scoliosis disorder is proposed.

Conclusion
Since the proposed target reliability index is based on the strength limit state of the vertebral column, it can be considered as a reliability level for any proposed treatment approaches.
“The best thing is that you are doing it for yourself” – perspectives on acceptability and feasibility of HPV self-sampling among cervical cancer screening clients in Tanzania: a qualitative pilot study
Authors: Bakiewicz Aleksandra , Rasch Vibeke , Mwaiselage Julius , Linde Ditte S. 
Published: March 2020

Abstract
Background
Cervical cancer is the most common type of cancer in sub-Saharan Africa, and it is also the cancer disease that most women die from. The high mortality rate is partly due to low attendance rates to screening services and low sensitivity of visual inspection with acetic acid, which is the standard screening method used in screening programs in sub-Saharan Africa. In order to overcome of the burden of disease new screening strategies and methods are warranted. This study aims to explore the acceptability and feasibility of HPV self-sampling compared to provider-based sampling among cervical cancer screening clients living in Dar es Salaam.

Methods
Women attending cervical cancer screening at Ocean Road Cancer Institute in Dar es Salaam, Tanzania between February – April 2017 were invited into the study. The participants had (1) a provider-collected sample, and (2) a self-sample for HPV on top of the regular cervical cancer screening. 50% of the participants conducted the self-sample after receiving a written instruction guide of how to collect the sample (written). The other 50% received both the written and an oral introduction to self-sampling (written+). All participants could ask for nurse assistance during self-sample collection if needed. Individual semi-structured interviews were conducted with the participants post sample collection. Data collection stopped when saturation was reached. Data were analysed using a thematic content analysis.

Results
Twenty-one women participated in the study. Regardless of how women were introduced to the self-sample (written or written+), there was a high demand for nurse presence as they felt uncertain of their personal capabilities to collect the self-sample correctly. However, as long as nurse assistance was an option most women perceived self-sampling as easy and comfortable though few experienced bleeding and pain. The majority of women preferred self-sampling over provider-sampling primarily due to the method being more private than the provider-sampling.

Conclusions
HPV self-sampling was well-perceived and accepted, however, for the method to be feasible a nurse needed to be present. HPV Self-sampling may be an alternative method to increase uptake of cervical cancer screening. Larger quantitative studies are recommended to support the study findings.
Self-regulated learning: the effect on medical student learning outcomes in a flipped classroom environment
Authors: Zheng Binbin , Zhang Yining 
Published: March 2020

Abstract
Background
The flipped-classroom model is increasingly being adopted in competency-based medical education. However, it poses a major challenge to students who have not mastered self-regulated learning strategies. This study explores which self-regulated learning skills affect student learning performance in the first 2 years of medical school at a university in the midwestern United States.

Methods
Survey data were used to assess how 146 first- and second-year medical students’ use of self-regulated learning strategies affected their performance on standardized tests.

Results
Based on the results of regression analysis and content analysis, it was found that the use of peer learning and help-seeking positively affected the performance of first- and second-year students, respectively; whereas the use of rehearsal had a negative effect on student learning outcomes.

Conclusions
The study findings imply that during the transition period from traditional lecture-intensive learning to flipped-classroom learning, promoting peer learning and help-seeking could significantly improve students’ academic achievement.
Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome: insights from the LUNG SAFE study
Authors:   for the LUNG SAFE Investigators and the ESICM Trials Group, Madotto Fabiana , Rezoagli Emanuele , Pham Tài , Schmidt Marcello , McNicholas Bairbre , Protti Alessandro , Panwar Rakshit , Bellani Giacomo , Fan Eddy , van Haren Frank , Brochard Laurent , Laffey John G. 
Published: March 2020

Abstract
Background
Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study.

Methods
In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia).

Results
Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55–100 mmHg) patients (P = 0.47).

Conclusions
Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort.

Trial registration
LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families
Authors: Fernandes Jason D. , Zamudio-Hurtado Armando , Clawson Hiram , Kent W. James , Haussler David , Salama Sofie R. , Haeussler Maximilian 
Published: March 2020

Abstract
Background
Nearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of which play important biological roles. However repeat elements pose several unique challenges to current bioinformatic analyses and visualization tools, as short repeat sequences can map to multiple genomic loci resulting in their misclassification and misinterpretation. In fact, sequence data mapping to repeat elements are often discarded from analysis pipelines. Therefore, there is a continued need for standardized tools and techniques to interpret genomic data of repeats.

Results
We present the UCSC Repeat Browser, which consists of a complete set of human repeat reference sequences derived from annotations made by the commonly used program RepeatMasker. The UCSC Repeat Browser also provides an alignment from the human genome to these references, uses it to map the standard human genome annotation tracks, and presents all of them as a comprehensive interface to facilitate work with repetitive elements. It also provides processed tracks of multiple publicly available datasets of particular interest to the repeat community, including ChIP-seq datasets for KRAB Zinc Finger Proteins (KZNFs) – a family of proteins known to bind and repress certain classes of repeats. We used the UCSC Repeat Browser in combination with these datasets, as well as RepeatMasker annotations in several non-human primates, to trace the independent trajectories of species-specific evolutionary battles between LINE 1 retroelements and their repressors. Furthermore, we document at https://repeatbrowser.ucsc.edu how researchers can map their own human genome annotations to these reference repeat sequences.

Conclusions
The UCSC Repeat Browser allows easy and intuitive visualization of genomic data on consensus repeat elements, circumventing the problem of multi-mapping, in which sequencing reads of repeat elements map to multiple locations on the human genome. By developing a reference consensus, multiple datasets and annotation tracks can easily be overlaid to reveal complex evolutionary histories of repeats in a single interactive window. Specifically, we use this approach to retrace the history of several primate specific LINE-1 families across apes, and discover several species-specific routes of evolution that correlate with the emergence and binding of KZNFs.