bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explanation of Molecular Processes without Tracking Mechanism Operation
Authors: Brigandt Ingo 
Published: July 2018

AbstractPhilosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism’s operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems in which the explanatory understanding does not consist in tracking a mechanism’s operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, articulating the distinctive way in which explanatory understanding is provided, especially about the reversibility or irreversibility of molecular processes.
On the estimation of the incidence and prevalence in two-phase longitudinal sampling design
Authors: Banerjee Prithish , Ghosh Samiran 
Published: July 2018

SUMMARY
Two-phase sampling design is a common practice in many medical studies. Generally, the first-phase classification is fallible but relatively cheap, while the accurate second phase state-of-the-art medical diagnosis is complex and rather expensive to perform. When constructed efficiently it offers great potential for higher true case detection as well as for higher precision at a limited cost. In this article, we consider epidemiological studies with two-phase sampling design. However, instead of a single two-phase study, we consider a scenario where a series of two-phase studies are done in a longitudinal fashion on a cohort of interest. Another major design issue is non-curable pattern of certain disease (e.g. Dementia, Alzheimer’s etc.). Thus often the identified disease positive subjects are removed from the original population under observation, as they require clinical attention, which is quite different from the yet unidentified group. In this article, we motivated our methodology development from two real-life studies. We consider efficient and simultaneous estimation of prevalence as well incidence at multiple time points from a sampling design-based approach. We have explicitly shown the benefit of our developed methodology for an elderly population with significant burden of home-health care usage and at the high risk of major depressive disorder.
Feeling Old, Body and Soul: The Effect of Aging Body Reminders on Age Identity
Authors: Barrett Anne E , Gumber Clayton 
Published: July 2018

Abstract

Objectives
Although changes in body functioning and appearance signal the aging process to ourselves and others, studies give limited attention to the effect of bodily experiences of aging on age identity. Our study examines the effect on age identity of 3 categories of aging body reminders: everyday body problems, body repairs, and body aids.

Methods
Hierarchical linear models are run using 5 waves of the National Health and Aging Trends Study (2011–2015). Models predict the effect on age identity of change in the count of everyday body problems (e.g., pain), body repairs (i.e., surgeries and medications), and body aids (e.g., hearing aids).

Results
Increases in everyday body problems and body repairs (in particular, medications) predict older identities, with the strongest average effect found for everyday body problems. These results are observed in models controlling on health, suggesting that body reminders exert independent effects.

Discussion
Our study reveals a realm of aging experiences—bodily experiences—that influence age identity. Avenues for further research include examinations of other aging body reminders, as well as variation across individuals.
Does health literacy mediate the relationship between socioeconomic status and health disparities? Integrative review
Authors: Stormacq Coraline , Van den Broucke Stephan , Wosinski Jacqueline 
Published: July 2018

Summary
While socioeconomic disparities are among the most fundamental causes of health disparities, socioeconomic status (SES) does not impact health directly. One of the potential mediating factors that link SES and health is health literacy (HL). Yet although HL can be considered a modifiable risk factor of socioeconomic disparities in health, the relationship between SES, HL and health disparities is not well understood. This study reviewed the evidence regarding the mediating role of HL in the relationship between socioeconomic and health disparities. Medline, Cinahl, Embase, PsychInfo, Eric, Web of Science, Google, Google Scholar, Mednar, Doaj and Worldcat were used to retrieve studies that specifically addressed socioeconomic and socio-demographic factors related to low HL levels, as well as the mediating role of HL in the relationship between SES and disparities in health outcomes. Selected studies were assessed for methodological quality. Sixteen published studies were retained for inclusion and content analyzed using the constant comparison method. The review indicates that disadvantaged social and socioeconomic conditions contribute to low HL levels, whereby low SES, and particularly educational attainment, is the most important determinant of HL, and that HL mediates the relationship between SES and health status, quality of life, specific health-related outcomes, health behaviors and use of preventive services. HL can be considered as a modifiable risk factor of socioeconomic disparities in health. Enhancing the level of HL in the population or making health services more accessible to people with low HL may be a means to reach a greater equity in health.
Ibrutinib Therapy and Mycobacterium chelonae Skin and Soft Tissue Infection
Authors: Dousa Khalid M , Babiker Ahmed , Van Aartsen Daniel , Shah Neel , Bonomo Robert A , Johnson John L , Skalweit Marion J 
Published: July 2018

Abstract
Ibrutinib is an irreversible inhibitor of Bruton’s tyrosine kinase approved for the treatment of B-cell malignancies. There is growing concern about the risk of opportunistic infections following ibrutinib therapy. Herein, we describe the first case of Mycobacterium chelonae skin and soft tissue infection in a patient receiving ibrutinib and recount the challenges in treating this infection.
‘The Only Trouble is the Dam’ Heroin’: Addiction, Treatment and Punishment at the Fort Worth Narcotic Farm
Authors: Karibo Holly M 
Published: July 2018

Summary
In 1929, the U.S. federal government approved two ground-breaking programs designed to treat drug addiction. Emerging at a time when many began to worry about a supposed rising tide of drug use across the country, the establishment of narcotic hospitals at Lexington, Kentucky and Fort Worth, Texas marked a watershed moment in the treatment of addiction. This article traces the institutional history of one of those facilities, the Fort Worth Narcotic Farm, and the experiences of the men who found themselves under its care. It argues that, on the surface, the creation of the farm model seemed like a hopeful alternative to strict incarceration models. Its creation reflected shifting notions of addiction: namely, that addiction is not simply a crime, but it is also a disease with serious public health implications. Yet, the establishment of the hospital as places to both treat and punish addicts was their inherent and fundamental flaw. Central to this was the concept of the “prisoner-patient,” a person forced to undergo treatment as a result of criminal charges. Not only did patients express their frustration with the prison-like setting at Fort Worth, but recidivism rates remained high throughout the facility’s operation. Ultimately, lawmakers and politicians would use these recidivism rates as part of a broader push for more punitive drug legislation in the post-World War II period. By placing the history of addiction into conversation with mass incarceration studies, this article shows that the roots of the punishment model employed in the last quarter of the twentieth century were interwoven into seemingly “progressive” treatment models dating back to at least the 1930s. Indeed, the very failures of early addiction treatment models that arose by mid-century helped to justify an expanding criminal justice model in the post-1960s era.
Uncommon Histopathological Variants of Malignant Melanoma: Part 1
Authors: Cota Carlo , Saggini Andrea , Lora Viviana , Kutzner Heinz , Rütten Arno , Sangüeza Omar , Requena Luis , Cerroni Lorenzo 
Published: July 2018

Abstract:Despite new horizons opened by recent advances in molecular pathology, histological evaluation still remains the diagnostic gold standard regarding cutaneous melanocytic neoplasms. Several histological variants of melanoma have been described, and their knowledge is crucial for accurate diagnosis and classification of cases with unusual clinicopathological features. Uncommon histological variants of melanoma have been described based on a broad constellation of features, including architectural pattern, stromal alterations, cytological attributes, and other morphological properties. This review is aimed at providing an extensive discussion of unusual but distinctive histopathological variants of melanoma.
The Extended Fetal Cardiac Examination: Is It Feasible in a High-Risk Practice?
Authors: McGahan John P. , Cheang Ellen C. , Sekhon Simran , Gerscovich Eugenio O. , James Gina , Boe Nina M. , Wilson Machelle D. 
Published: July 2018

Abstract
The aims of this study were to demonstrate the feasibility of obtaining additional cardiac views as proposed on an extended fetal cardiac examination and to see if there was any variation in individual components of that examination stratified by sonographer training, patient body habitus, or equipment. We retrospectively reviewed 200 consecutive detailed second-trimester high-risk fetal obstetric sonograms that included additional extended cardiac views. We analyzed the percentage of the time individual views were obtained, with variation based on (1) a sonographer with greater than 3 years of training compared with a group with 6 to 12 months of training, (2) 2 different ultrasound units, and (3) different body mass indices. Overall, the highest rate of visualization was achieved with the 4-chamber view (98.2%), whereas the 3-vessel tracheal view had the lowest percentage of visualization (40.2%), among the less experienced sonographers. Differences in successful completion of the extended cardiac views were not statistically different between the sonographer with a level of training greater than 3 years as compared with those with 6 to 12 months' training except for the 3-vessel tracheal view (P < 0.001). There is no statistically significant difference in our ultrasound equipment, when considering only inexperienced sonographers. Increasing body mass index had an inverse relationship with obtaining the components of the detailed cardiac examination. Using state-of-the-art ultrasound equipment and with focused additional training of obstetric sonographers, the majority of extended cardiac views can be obtained. There are exceptions.
Hepatitis C–Associated B-cell Non-Hodgkin Lymphoma
Authors: Iliescu Laura , Mercan-Stanciu Adriana , Ioanitescu Elena Simona , Toma Letitia 
Published: July 2018

Background and Purpose
Hepatitis C virus (HCV) can induce both hepatic and extrahepatic malignancies. A strong association between HCV and non-Hodgkin lymphomas (NHLs) has been demonstrated. The purpose of this article is to give emphasis on the clinical and imagistic particularities of the hepatitis C–associated NHL, revealing the importance of ultrasonography in discovering and characterizing splenic masses.

Methods
We present the cases of 3 women (aged 72, 61, and 56 years, respectively), all of which had a history of chronic hepatitis C and were subsequently diagnosed with different forms of lymphoma. In all 3 cases, conventional ultrasound exploration showed inhomogeneous splenomegaly. Contrast-enhanced ultrasound and computerized tomography were performed soon after admission, both clinical and imaging findings leading to the suspicion of lymphoma. The bone marrow biopsy was relevant for the diagnosis lymphoma in 2 patients, whereas the third woman only presented age-related changes in cellularity. Splenectomy was later performed in this case, for both diagnostic and therapeutic purposes; histopathological examination and immunohistochemistry revealed malignant non-Hodgkin diffuse large B-cell lymphoma.

Conclusions
The cooccurrence of HCV infection and splenic lymphoma is a frequently encountered scenery. Ultrasonography, both conventional and contrast-enhanced, plays an important role in the exploration of the spleen, representing a first-line imagistic method and a valuable means of characterizing different types of splenic lesions.

Implications for Practice
This article states the importance of ultrasonographic evaluation regarding the splenic pathology, by revealing clinical and imagistic findings in 3 cases of hepatitis C–associated lymphoma.
Transient Elastography Identifies the Risk of Esophageal Varices and Bleeding in Patients With Hepatitis B Virus–Related Liver Cirrhosis
Authors: Zhu Qingjing , Wang Weijun , Zhao Jinfang , AL-Asbahi Afnan Ahmed Mohamed , Huang Ying , Du Fan , Zhou Jianning , Song Yuhu , Xu Keshu , Ye Jin , Yang Ling 
Published: July 2018

Abstract
This study aimed to analyze the diagnostic accuracy of liver stiffness for predicting esophageal variceal grading and the risk of esophageal variceal bleeding (EVB) in cases of cirrhosis. Hematological and biochemical parameters were measured and transient elastography was performed in 88 patients with hepatitis B–related cirrhosis undergoing endoscopy for esophageal varices. Esophageal varices grade was highly correlated with liver stiffness measurement (LSM) and the liver stiffness spleen diameter-to-platelet score in cirrhosis. Compared with those from endoscopy, the LSM and the liver stiffness spleen diameter-to-platelet score for the absence of esophageal varices were as follows: area under the receiver operating characteristic curve (AUROC), 0.894/0.926; sensitivity, 0.836/0.818; and specificity, 0.875/1.000, respectively. The AUROC and the sensitivity and specificity of LSM and the liver stiffness spleen diameter-to-platelet score for predicting grade III esophageal varices were 0.954 and 0.901, respectively. The AUROCs of LSM and the liver stiffness spleen diameter-to-platelet score for discriminating grades II and III from grade I or the absence of esophageal varices were 0.958 and 0.941, respectively. We also found that EVB was closely associated with LSM and spleen diameter. The AUROC, sensitivity, and specificity were 0.855/0.819, 0.857/0.875, and 0.747/0.780, respectively. Meanwhile, LSM and spleen diameter were 2 independent factors for predicting EVB. These data suggest that LSM and the liver stiffness spleen diameter-to-platelet score could accurately rule out cirrhosis without esophageal varices and differentiate high- and low-risk patients. Furthermore, LSM and spleen diameter had excellent abilities to predict EVB.
Ultra-sensitive proteome profiling of FACS-isolated cell populations by data-independent acquisition-MS: Application to human hematopoietic stem and progenitor cells
Authors: Amon Sabine , Meier-Abt Fabienne , Gillet Ludovic C , Dimitrieva Slavica , Theocharides Alexandre PA , Manz Markus G , Aebersold Ruedi 
Published: July 2018

ABSTRACTPhysiological processes in multicellular organisms depend on the function and interactions of a multitude of specialized cell types operating in context. Fluorescence-activated cell sorting (FACS) provides a powerful tool to determine the cell type composition of complex mixtures and to purify highly homogeneous cell populations using a small number of differentially expressed marker proteins. These populations can be further characterized, e.g. by phenotypic or molecular analyses.We describe an ultra-sensitive mass spectrometric method for the robust quantitative and reproducible proteomic analysis of cohorts of FACS-isolated cell samples. It uses a minimum of post-sorting sample processing steps prior to data-independent acquisition MS on a current generation Orbitrap hybrid mass spectrometer. The method provides highly accurate and reproducible quantitative proteome profiles across the cohort with an average coefficient of variance <15% from as little as 150 ng of total peptide mass. We quantified the proteome of 25,000 sorted human hematopoietic stem/multipotent progenitor cell and three committed progenitor cell subpopulations (common myeloid progenitors, megakaryocyte-erythrocyte progenitors and granulocyte-macrophage progenitors) isolated from five healthy donors. On average, 5,851 protein groups were identified per sample. After stringent filtering, a subset of 4,131 protein groups (≥2 peptides) was used for differential comparison across the 20 samples, defining unique proteomic signatures for each cell type tested. A comparison of proteomic and transcriptomic profiles of the four cell types indicated hematopoietic stem/multipotent progenitor cell-specific divergent regulation of biochemical processes that are essential for maintaining stemness and were detected at the proteome rather than the transcriptome level.The technology supports the generation of extensive and accurate quantitative proteomic profiles from low numbers of FACS-purified cells providing new information about the biochemical state of the analyzed cell types that is essential for basic and translational research.
Using GPUs to accelerate computational diffusion MRI: From microstructure estimation to tractography and connectomes
Authors: Hernandez-Fernandez Moises , Reguly Istvan , Jbabdi Saad , Giles Mike , Smith Stephen , Sotiropoulos Stamatios N. 
Published: July 2018

AbstractThe great potential of computational diffusion MRI (dMRI) relies on indirect inference of tissue microstructure and brain connections, since modelling and tractography frameworks map diffusion measurements to neuroanatomical features. This mapping however can be computationally highly expensive, particularly given the trend of increasing dataset sizes and the complexity in biophysical modelling. Limitations on computing resources can restrict data exploration and methodology development. A step forward is to take advantage of the computational power offered by recent parallel computing architectures, especially Graphics Processing Units (GPUs). GPUs are massive parallel processors that offer trillions of floating point operations per second, and have made possible the solution of computationally-intensive scientific problems that were intractable before. However, they are not inherently suited for all problems. Here, we present two different frameworks for accelerating dMRI computations using GPUs that cover the most typical dMRI applications: a framework for performing biophysical modelling and microstructure estimation, and a second framework for performing tractography and long-range connectivity estimation. The former provides a front-end and automatically generates a GPU executable file from a user-specified biophysical model, allowing accelerated non-linear model fitting in both deterministic and stochastic ways (Bayesian inference). The latter performs probabilistic tractography, it can generate whole-brain connectomes and supports new functionality for imposing anatomical constraints, such as inherent consideration of surface meshes (GIFTI files) along with volumetric images. We validate the frameworks against well-established CPU-based implementations and we show that despite the very different challenges for parallelising these problems, GPU-based designs can offer accelerations of more than two orders of magnitude in both cases.
Complementary topology of maintenance and manipulation brain networks in working memory
Authors: Davis S.W. , Crowell C.A. , Beynel L. , Deng L. , Lakhlani D. , Hilbig S.A. , Lim W. , Palmer H. , Nguyen D. , Peterchev A. V. , Luber B. , Lisanby S.H. , Appelbaum L.G. , Cabeza R. 
Published: July 2018

AbstractWorking memory (WM) is assumed to consist of a process that sustains memory representations in an active state (maintenance) and a process that operates on these activated representations (manipulation). Prior fMRI studies have examined maintenance and manipulation in separate task conditions, whereas in real life these processes operate simultaneously. In the current study, the neural mechanisms of maintenance and manipulation were disentangled during the same task by parametrically varying these processes. During fMRI, participants maintained consonant letters in WM while sorting them in alphabetical order. Maintenance was investigated by varying the number of letters held in WM and manipulation by varying the number of moves required to sort the list alphabetically. The study yielded three main findings. First, the degree of both maintenance and manipulation demand had significant effects on behavior that were associated with different cortical regions: maintenance was associated with bilateral prefrontal and left parietal cortex, and manipulation with right parietal activity, a link that is consistent with the role of parietal cortex in symbolic computations. Second, univariate fMRI and tractography based on diffusion-weighted imaging showed that maintenance and manipulation regions are supported by two dissociable structural networks. Finally, maintenance and manipulation functional networks became increasingly segregated with increasing demand, possibly reflecting the protection of information held in WM from interference generated by manipulation operations. These results represent a novel approach to study the brain as an adaptive system that coordinates multiple ongoing cognitive processes.Significance StatementDespite the importance of working memory (WM) in everyday life, little is known about how the brain is able to simultaneously maintain and manipulate information stored in short-term memory buffers. We examined evidence for two distinct, concurrent cognitive functions supporting maintenance and manipulation abilities by testing brain activity as participants performed a WM alphabetization task. We found behavioral and neural evidence in support of dissociable cognitive functions associated with these two operations. Furthermore, we found that connectivity between these networks was increasingly segregated as difficulty increased, and that this effect was positively related to individual WM ability. These results provide evidence that network segregation may act as a protective mechanism to enable successful performance under increasing WM demand.