bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing Health Care Financial Burden With an Alternative Measure of Unaffordability
Authors: Kielb Edward S. , Rhyan Corwin N. , Lee James A.
Published: October 2017

Health insurance plans with high deductibles increase exposure to health care costs, raising concerns about how the growth in these plans may be impacting both the financial burden of health care expenditures on families and their access to health care. We find that foregoing medical care is common among low-income, privately insured families, occurring at a greater rate than those with higher incomes or Medicare coverage. To better understand the relationship between out-of-pocket (OOP) spending and access, we used the 2011-2014 Medical Expenditure Panel Survey (MEPS) data and a logistic model to analyze the likelihood of avoiding or delaying needed medical care based on health insurance design and other individual and family characteristics. We find that avoiding or delaying medical care is strongly correlated with coverage under a high-deductible health plan, and with depression, poor perceived health, or poverty. However, it is relatively independent of the percent of income spent on OOP costs, making the percent of income spent on OOP costs by itself a poor measure of health care unaffordability. Individuals who spend a small percentage of their income on health care costs may still be extremely burdened by their health plan when financial concerns prevent access to health care. This work emphasizes the importance of insurance design as a predictor of access and the need to expand the definition of financial barriers to care beyond expenditures, particularly for the low-income, privately insured population.
Beyond Grammar: Tracking Perceptions of Quality in Student E-mail
Authors: Blackburne Brian D. , Nardone Carroll Ferguson
Published: October 2017

This research explores a presumed link between today’s use of digital media and an ever-increasing lack of rhetorical awareness in students. Specifically, the study pilots a method for measuring rhetorical awareness through students’ e-mail transactions with faculty in technical writing service courses, questioning whether rhetorical awareness has decreased in the preceding 10 years. The findings indicate that students might be more rhetorically aware today than they were 10 years ago, but levels remain below expectations.
An Innovative Approach to Pretest Questionnaire: The Analysis of Respondents’ Comments in the Flexible Interview
Authors: Palmieri Marco
Published: October 2017

The researcher, who pretests a questionnaire conventionally, is confident that a small number of interviews reveals numerous problems afflict the questionnaire. The standardized interviewer is asked to observe respondent’s verbal behaviors in order to realize whether respondent misunderstands question. But this strategy fails when respondent does not show any misunderstanding signal. The study, reported in this article, illustrates how to exceed this limit, by means of the analysis of respondent’s comments released in the flexible interview, which researcher uses to unveil incongruities between question and answer; the questions, when many respondents’ misunderstandings occur, should be reworded. This study shows that the number of problems and the number of the problematic questions identified by this unconventional procedure are much higher than the number of problems and the number of problematic questions determined by the conventional pretesting. The strength of respondents’ comments analysis is to discover problems the questionnaire poses for respondents, even when the respondents do not give any misunderstanding signal.
International labor migration and social change in rural Sindh, Pakistan
Authors: Rafique Wassan M , Hussain Zubair , Ali Shah Muhbat , Amin Sara N
Published: October 2017

This study examines why and how labor migration from a village in Sindh, Pakistan to Saudi Arabia has influenced changes for the left-behind families and the community. We find that while migration impacts positively on the material conditions of individual migrants and their families in the village, the potential of migration to impact on other aspects of living conditions, social change and development at community levels is shaped and often limited by existing structures of power, including gender structures and other socio-political structures. In the absence of investment in school infrastructures by the state, remittances from migration have not translated into improved educational outcomes for the children of migrants. We also find that the male migrants are leveraging their new status in the family to exercise more choice in marriage matters with possible negative impact on women.
Variables Associated With Perceived Work Role Performance Among Professionals in Multidisciplinary Mental Health Teams Overall and in Primary Care and Specialized Service Teams, Respectively
Authors: Fleury Marie-Josée , Grenier Guy , Bamvita Jean-Marie , Chiocchio François
Published: October 2017

This study had a dual purpose (1) to identify variables associated with perceived work role performance (WRP) among 315 mental health professionals (MHPs) in Quebec and (2) to compare variables related to WRP in MH primary care teams (PCTs) and specialized service teams (SSTs), respectively. WRP was measured using an adapted version of the work role questionnaire. Variables were organized within five areas: individual characteristics, perceived team attributes, perceived team processes, perceived team emergent states, and geographical and organizational context. Half of the WRP variables were linked to team processes. Knowledge sharing correlated with WRP in both MH PCTs and SSTs. Team attributes had more impact on MH PCTs, while team processes and team emergent states played a larger role among SSTs. The association between WRP and knowledge sharing confirms the need for a systematic training program to promote interdisciplinary collaboration. Integration strategies (e.g., service agreements) could improve collaboration between MH PCTs and SSTs and help MHPs perform more effectively within PCTs.
Proliferative Cartilaginous Lesions in the Calcaneal Tendons of huNOG Mice
Authors: MacLeod Alexandria M. , Treuting Piper M. , Carlson Cathy S.
Published: October 2017

NOD/Shi-scid/IL-2Rγnull (NOG) mice are humanized with CD34+ hematopoietic cells (huNOG mice) and are commonly utilized for biological or medical research on human therapeutics. In the present study, nine 26-week-old, female huNOG mice were utilized for testing proprietary immune–modulating drugs over a 3-week period at the University of Washington. Two of the 9 mice developed unilateral swelling of a tibiotarsal joint with associated paresis of the affected limb. Full necropsies were performed after euthanasia at experimental end point, and routine tissues and affected tibiotarsal joints were evaluated. An expansile, multilobular mass composed primarily of chondroid cells associated with the calcaneal tendon was present within 1 tibiotarsal joint of both mice. A small focus of well-differentiated bone was present within the mass of 1 mouse. In addition, the calcaneal periosteum was expanded by a chondroid mass in 1 mouse. The cartilaginous masses associated with the calcaneal tendon were interpreted as a hyperplastic or low-grade neoplastic process accompanied by endochondral ossification, and the mass associated with the calcaneal periosteum was interpreted as chondroid metaplasia. Although the etiology of these lesions is unclear, their prevalence in 2/9 (22%) huNOG mice is interesting and may have biological significance for future studies involving the huNOG mouse model.
Does the addition of two exercise-focussed home visits to usual care improve outcomes for patients with balance impairments? A randomized controlled trial
Authors: Whitbourne Craig , Shields Nora , Tacey Mark , Koh Kenneth WZ , Lawler Katherine , Hill Keith D
Published: October 2017

Objective:

To investigate whether two additional home visits improve outcomes for rehabilitation outpatients with balance impairments compared to usual care.

Design:

Randomized controlled trial.

Setting:

Outpatient rehabilitation.

Participants:

Fifty with balance impairments.

Interventions:

Both groups received usual care including weekly group exercise over eight weeks. The intervention group received two home visits to individualize home exercises.

Outcome measures:

Primary outcome measure was the Balance Outcome Measure for Elder Rehabilitation (BOOMER) score, and secondary outcomes included force platform measures using the NeuroCom Balance Master®, assessed at baseline, after intervention and three-month follow-up.

Results:

There was no between-group difference for BOOMER score. There were significant between-group differences in favour of the intervention group for limits of stability reaction time at week 9 (mean difference (MD) −0.27, 95% confidence interval (CI) −0.44 to −0.09) and week 22 (MD −0.28, 95% CI −0.45 to −0.10) and for limits of stability maximal excursion at week 9 (MD 8.66, 95% CI 1.67 to 15.65) and week 22 (MD 14.58, 95% CI 7.59 to 21.57). Significant between-group differences favoured the control group for Clinical Test of Sensory Interaction of Balance at week 9 (MD 0.40, 95% CI 0.13 to 0.66) and week 22 (MD 0.45, 95% CI 0.18 to 0.72) and step quick turn time at week 9 (MD 0.56, 95% CI 0.02 to 1.10).

Conclusion:

Two exercise-focussed home visits improved some dynamic balance outcomes in older patients with balance impairments. Some outcomes showed significant improvements with small effect sizes in favour of the control group which may be chance findings or because they completed a standard home exercise programme.
Microvascular decompression or neuromodulation in patients with SUNCT and trigeminal neurovascular conflict?
Authors: Hassan Samih , Lagrata Susie , Levy Andrew , Matharu Manjit , Zrinzo Ludvic
Published: October 2017

Objectives

To assess the effectiveness of neuromodulation and trigeminal microvascular decompression (MVD) in patients with medically-intractable short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT).

Methods

Two patients with medically refractory SUNCT underwent MVD following beneficial but incomplete response to neuromodulation (occipital nerve stimulation and deep brain stimulation). MRI confirmed neurovascular conflict with the ipsilateral trigeminal nerve in both patients.

Results

Although neuromodulation provided significant benefit, it did not deliver complete relief from pain and management required numerous postoperative visits with adjustment of medication and stimulation parameters. Conversely, MVD was successful in eliminating symptoms of SUNCT in both patients with no need for further medical treatment or neuromodulation.

Conclusion

Neuromodulation requires expensive hardware and lifelong follow-up and maintenance. These case reports highlight that microvascular decompression may be preferable to neuromodulation in the subset of SUNCT patients with ipsilateral neurovascular conflict.
HSP60 activity on human bronchial epithelial cells
Authors: Sangiorgi Claudia , Vallese Davide , Gnemmi Isabella , Bucchieri Fabio , Balbi Bruno , Brun Paola , Leone Angelo , Giordano Andrea , Conway de Macario Everly , Macario Alberto JL , Cappello Francesco , Di Stefano Antonino
Published: October 2017

HSP60 has been implicated in chronic inflammatory disease pathogenesis, including chronic obstructive pulmonary disease (COPD), but the mechanisms by which this chaperonin would act are poorly understood. A number of studies suggest a role for extracellular HSP60, since it can be secreted from cells and bind Toll-like receptors; however, the effects of this stimulation have never been extensively studied. We investigated the effects (pro- or anti-inflammatory) of HSP60 in human bronchial epithelial cells (16-HBE) alone and in comparison with oxidative, inflammatory, or bacterial challenges. 16-HBE cells were cultured for 1–4 h in the absence or presence of HSP60, H2O2, lipopolysaccharide (LPS), or cytomix. The cell response was evaluated by measuring the expression of IL-8 and IL-10, respectively, pro- and anti-inflammatory cytokines involved in COPD pathogenesis, as well as of pertinent TLR-4 pathway mediators. Stimulation with HSP60 up-regulated IL-8 at mRNA and protein levels and down-regulated IL-10 mRNA and protein. Likewise, CREB1 mRNA was up-regulated. H2O2 and LPS up-regulated IL-8. Experiments with an inhibitor for p38 showed that this mitogen-activated protein kinase could be involved in the HSP60-mediated pro-inflammatory effects. HSP60 showed pro-inflammatory properties in bronchial epithelial cells mediated by activation of TLR-4-related molecules. The results should prompt further studies on more complex ex-vivo or in-vivo models with the aim to elucidate further the role of those molecules in the pathogenesis of COPD.
Erythropoietin/aloe vera-releasing wet-electrospun polyvinyl alcohol/chitosan sponge-like wound dressing: In vitro and in vivo studies
Authors: Naseri-Nosar Mahdi , Farzamfar Saeed , Salehi Majid , Vaez Ahmad , Tajerian Roksana , Azami Mahmoud
Published: October 2017

This study aimed to develop a recombinant human erythropoietin/aloe vera gel–releasing polyvinyl alcohol/chitosan wound dressing by wet-electrospinning method and investigate the synergistic effects of erythropoietin and aloe vera gel on the excisional wound healing. The polyvinyl alcohol/chitosan (4:1 (w/w)) solution was electrospun into an aloe vera gel–containing water coagulation bath and then coated with the recombinant human erythropoietin–loaded chitosan nanoparticles prepared via ionic gelation technique. The developed sponge-like film was able to release the erythropoietin and aloe vera gel for at least 7 and 1 days, respectively. The dressing was non-toxic to L929 fibroblastic cell line and non-adherent to the wound bed with the contact angle of 67.93° ± 2.31°. It also possessed the water-uptake capacity and water vapor transmission rate of 26.40% ± 3.37% and 2584.00 ± 144.67 g m−2, respectively. The in vivo study demonstrated the synergistic wound-healing effects of aloe vera gel and erythropoietin on the full-thickness excisional wounds of Wistar rats. The erythropoietin/aloe vera gel–releasing dressing had significantly (n = 4, p < 0.005) higher wound closure (92.96% ± 10.09%) than the sterile gauze (73.89% ± 2.61%), as the control group, after 2 weeks. The differences observed between the wound closure percentages of the aloe vera gel–releasing dressing (85.93% ± 6.46%) and the erythropoietin/aloe vera gel–releasing dressing and control group were not statistically significant.
Understanding How Domestic Violence Shelter Rules May Influence Survivor Empowerment
Authors: Gregory Katie , Nnawulezi Nkiru , Sullivan Cris M.
Published: October 2017

Domestic violence shelters have historically gone beyond providing emergency residential space for survivors by assisting in obtaining future housing, employment, health care, child care, or legal services. Domestic violence shelters are expected to operate within an empowerment philosophy, with an understanding that survivors are self-determining, can identify their needs, and know what it takes to meet those needs. Recent research has indicated that, as many shelters have become more rigid in creating rules that survivors must follow to access and retain free temporary housing, the result has been survivors’ feelings of disempowerment, the complete opposite of what was originally intended. This study builds on the small amount of research conducted regarding survivors’ experiences of shelter rules by specifically examining how rules were perceived to affect empowerment. Seventy-three survivors from two domestic violence shelters were asked about their experiences around specific shelter rules relating to curfew, parenting, chores, time limits, food, alcohol, drugs, and medications. A transcendental phenomenological approach was used to analyze the qualitative data, seeking explanations of how survivors made meaning of the rules and how those rules influenced their empowerment. Among those survivors who found the rules problematic, three major themes emerged: (a) rules acted as barriers to carrying out their normal, day-to-day activities; (b) the shelter staff’s flexibility with rules was based on contingencies; and (c) rules negatively affected their psychological well-being, and required them to engage in protective behaviors. Recommendations are made for the reexamination and restructuring of rules within domestic violence shelters.
On Lethal Interactions: Differences Between Expressive and Instrumental Homicides in Mexico City
Authors: Meneses-Reyes Rodrigo , Quintana-Navarrete Miguel
Published: October 2017

Research on violence in Mexico and Latin America suggests that, in part, due to state attempts to fight organized crime and the widespread availability of firearms, violence and homicides in general have experienced a recent shift from expressive to instrumental. Despite this transformation, however, socioeconomically disadvantaged young males continue to be overwhelmingly present in homicide events. We argue that both the use of a firearm and demographic and traditional socioeconomic factors should independently predict instrumental homicide; however, the association between the use of a firearm and instrumentality should be moderated by the level or category of these traditional characteristics (i.e., socioeconomic status, age, and gender). Our findings are broadly consistent with these claims. We show that the relationship between the use of a firearm and instrumental homicides is larger for homicides involving disadvantaged males as victims because this group is more at risk of suffering homicidal violence to begin with, despite the fact that independently (i.e., with no interactions), higher socioeconomic status, age, and female victimhood are positively associated with instrumentality. We discuss the implications of these findings for research on Latin American violence and the expressive/instrumental distinction.
Professional Development for Data-Based Instruction in Early Writing: Tools, Learning, and Collaborative Support
Authors: Lembke Erica S. , McMaster Kristen L. , Smith R. Alex , Allen Abigail , Brandes Dana , Wagner Kyle
Published: October 2017

Few teachers receive adequate preparation to provide effective individualized instruction for children with intensive early writing needs. In this article, the authors describe an attempt to close this learning gap, by developing Data-Based Instruction-Tools, Learning, and Collaborative Support (DBI-TLC), a comprehensive professional development (PD) system that provides tools, learning opportunities, and ongoing collaborative supports for teachers to implement DBI in early writing. They describe the theoretical framework that has guided this work, the teacher population with whom they worked, their approach to assessing important teacher outcomes, and their development process. They highlight key findings that align with their theory of change, and discuss implications for further research and teacher preparation.
The Profound Influence of Unpaid Work on Women’s Lives: An Overview and Future Directions
Authors: Jung Ae-Kyung , O’Brien Karen M.
Published: October 2017

The myriad hours and considerable effort expended by women in unpaid labor at home can have profound effects on their mental, physical, relational, vocational, and economic health. To date, many vocational psychologists have neglected to focus on unpaid work in their research or highlight unpaid work in their theories. Unpaid work in women’s lives is most deserving of increased scholarly attention. Thus, the purposes of this article are to provide an overview of theory and research related to unpaid work, highlight three types of unpaid work, describe the effects of unpaid work on women’s lives, and provide recommendations for future research and practice in vocational psychology to advance understanding regarding unpaid work in women’s lives.
Lateral stability control based on the roll moment distribution using a semiactive suspension
Authors: Yao Jialing , Lv Guangwei , Qv Min , Li Zhihong , Ren Shan , Taheri Saied
Published: October 2017

Existing control schemes which distribute the roll moment by employing the ratio of the damping force of the front axle to the damping force of the rear axle using a semiactive suspension lack a theoretical foundation. Given that a new variable-stiffness variable-damping system configuration may require adjustment of only the damping force of a variable damper, this study considers an ordinary magnetorheological damper semiactive suspension itself as equivalent to a variable-stiffness variable-damping suspension system. The configuration of the semiactive suspension does not need any modifications. A novel control strategy is presented to control the stiffness of the suspension to distribute the roll moment between the front axle and the rear axle, and to regulate the damping force of the suspension to control the attitude of the vehicle body. This strategy considers neutral steering as the control target and minimizes the body accelerations in three directions. A nonlinear controller for the roll moment distribution and three fuzzy controllers for control of the attitude of the vehicle body are designed. The roll moment distribution coefficient is combined with three output control forces from the fuzzy controllers. Using decoupling calculations, the control forces in three directions are decoupled into four control forces generated by four magnetorheological dampers. The simulation results demonstrate that the proposed control strategy can achieve a favorable handling stability while maintaining an acceptable ride comfort.
Facial Width-to-Height Ratio Does Not Predict Self-Reported Behavioral Tendencies
Authors: Kosinski Michal
Published: October 2017

A growing number of studies have linked facial width-to-height ratio (fWHR) with various antisocial or violent behavioral tendencies. However, those studies have predominantly been laboratory based and low powered. This work reexamined the links between fWHR and behavioral tendencies in a large sample of 137,163 participants. Behavioral tendencies were measured using 55 well-established psychometric scales, including self-report scales measuring intelligence, domains and facets of the five-factor model of personality, impulsiveness, sense of fairness, sensational interests, self-monitoring, impression management, and satisfaction with life. The findings revealed that fWHR is not substantially linked with any of these self-reported measures of behavioral tendencies, calling into question whether the links between fWHR and behavior generalize beyond the small samples and specific experimental settings that have been used in past fWHR research.
The field-dependent conductivity of dimorphic magnetorheological gel incorporated with iron nanowire
Authors: Yu Miao , Luo Hongping , Fu Jie , Yang Pingan
Published: October 2017

In this article, iron nanowire is synthesized by reducing Fe2+ ion with excessive sodium borohydride in deionized aqueous solution. A kind of dimorphic magnetorheological gel is prepared by partial substitution of carbonyl iron particles with Fe nanowires. Several experimental devices based on the dimorphic magnetorheological gel were fabricated, and the magneto-resistance characteristics under a magnetic field of those devices are systematically tested to research the influence of the Fe nanowire on the conductivity of magnetorheological gel. The experimental results indicated that by adding a certain amount of Fe nanowire, the conductivity of the dimorphic magnetorheological gel can be greatly improved. Moreover, it can be seen that the conductivity of sample 4 (with 6 wt.% Fe nanowire) is increased by about 100 times than sample 1 (without Fe nanowire). The mechanism of Fe nanowire enhances the conductivity of the dimorphic magnetorheological gel, which is investigated by microstructure analysis.
Anarchist Women and the Politics of Walking
Authors: Ferguson Kathy E.
Published: October 2017

Two anarchist women from the late nineteenth to early twentieth centuries, Alexandra David-Néel and Lily Gair Wilkinson, combined their politics with radical engagement in walking. In both the literal sense, moving their bodies along the earth, and the figurative sense of calling on peripatetic tropes to express their ideas, they found walking to be a constitutive element of freedom. This paper brings the ideas of Whitehead and other process philosophers into conversation with material and semiotic dimensions of walking and with anarchist politics. In the political lives of Wilkinson and David-Néel, I see struggles to live anarchist lives, lives into which one could walk.
Freedom’s Poses
Authors: Marso Lori Jo
Published: October 2017

Kathy Ferguson’s anarchist women enact walking as freedom’s pose. In my response, I ask how the way we imagine poses and postures, comporting our bodies this way or that, alone or together, shapes the way we practice freedom. I worry that the focus on walking, a dominant and frequent metaphor for freedom in many diverse political registers, occludes our ability to see freedom in other poses, registers, and spaces. I argue that highlighting walking as freedom’s preferred pose hovers too close to the replication of the posture (and maybe the perspective too?) of the masculine self. These moves, and this movement, make it harder to discover other sites and kinds of freedom, and to fully appreciate contingency, non-necessity, and the unexpected possibilities available in every encounter. Drawing on the work of Adriana Cavarero, Simone de Beauvoir, and Hannah Arendt, I explore postures of inclination—Beauvoir’s housewives stooped over pots and pans—and consciously chosen inactivity—Arendt lying on her daybed thinking. These postures and poses open up our ability to see freedom in the encounter, an affective and agonistic freedom enacted only with others, and too easily hidden or missed.
Clinical Significance of T-Cell Immunoglobulin Mucin 3 Expression on Peripheral Blood Mononuclear Cells in Pediatric Acute Immune Thrombocytopenia
Authors: Zahran Asmaa M. , Youssef Mervat A. M. , Elsayh Khalid I. , Embaby Mustafa M. , Ibrahim Ahmad I. M.
Published: October 2017

T-cell immunoglobulin mucin 3 (TIM-3) is a transmembrane protein that plays an important role in several autoimmune diseases. The relationship between TIM-3 and excessive immune responses in immune thrombocytopenia (ITP) is still unknown. In this study, we evaluated the relationship between the expression of TIM-3 on peripheral blood mononuclear cells in patients with ITP and the disease severity. The frequency of lymphocyte and monocyte subsets and their TIM-3 expression were evaluated in patients with acute ITP (n = 45) and in healthy control (n = 20) using flow cytometry. Based on bleeding severity, patients were classified into 3 subgroups as mild (n = 12), moderate (n = 25), and severe (n = 8) bleeding. T-helper lymphocytes was found to be significantly decreased in the severe bleeding group compared to the mild and moderate bleeding groups, while CD56high natural killer (NK) cells were significantly expanded in severe bleeding group. In contrast, classical, intermediate, and nonclassical monocytes, natural killer T lymphocyte (NKT), and CD56dim NK cells showed no significant changes among different patient groups. This alteration of lymphocyte and monocyte subsets was associated with significant decrease in TIM-3 expression on CD56high NK cells, T-helper lymphocytes, NKT cells, and nonclassical monocytes in patients with ITP compared to the controls. Lower level of TIM-3 was found in severe bleeding group compared to mild and moderate bleeding groups. These results indicate that TIM-3 may be involved in the pathogenesis of ITP which subsequently can represent an opportunity for new therapeutic plan, moreover. This may have a prognostic value for disease severity.
The Impact of Adult ADHD in the Quality of Life Profile
Authors: Quintero Javier , Morales Isabel , Vera Rosa , Zuluaga Pilar , Fernández Alberto
Published: October 2017

Objective: In this multicenter, cross-sectional study, we aimed to investigate the quality of life (QoL) and the neuropsychological and clinical characteristics of adults with ADHD with different developmental pathways. Method: Our study sample included 25 control (healthy) participants, 31 patients with newly diagnosed ADHD without comorbidities (ADHD-C-D), 31 with newly diagnosed ADHD with comorbidities (ADHD+C-D), and 29 with previously diagnosed ADHD with comorbidities (ADHD+C+D). Results: Compared with controls, ADHDs had little differences in the attentional performance but showed higher impulsivity, more severe symptoms of depression and anxiety, and lower QoL. The ADHD+C-D group showed more severe symptoms of depression and anxiety than the ADHD+C+D group ( p = .037 and p = .008, respectively), and poorer QoL in the psychological health sphere ( p = .003). Conclusion: Differences between ADHD and control subjects were particularly remarkable in mood symptoms and QoL. Previous diagnosis might have a positive impact on mood symptoms and QoL in ADHD adults.
State Authenticity as Fit to Environment: The Implications of Social Identity for Fit, Authenticity, and Self-Segregation
Authors: Schmader Toni , Sedikides Constantine
Published: October 2017

People seek out situations that “fit,” but the concept of fit is not well understood. We introduce State Authenticity as Fit to the Environment (SAFE), a conceptual framework for understanding how social identities motivate the situations that people approach or avoid. Drawing from but expanding the authenticity literature, we first outline three types of person–environment fit: self-concept fit, goal fit, and social fit. Each type of fit, we argue, facilitates cognitive fluency, motivational fluency, and social fluency that promote state authenticity and drive approach or avoidance behaviors. Using this model, we assert that contexts subtly signal social identities in ways that implicate each type of fit, eliciting state authenticity for advantaged groups but state inauthenticity for disadvantaged groups. Given that people strive to be authentic, these processes cascade down to self-segregation among social groups, reinforcing social inequalities. We conclude by mapping out directions for research on relevant mechanisms and boundary conditions.
An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture
Authors: Mironov Vladimir , Moskovsky Alexander , D’Mello Michael , Alexeev Yuri
Published: October 2017

The Hartree–Fock method in the General Atomic and Molecular Structure System (GAMESS) quantum chemistry package represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals and the building of the Fock matrix. These are the central components of the main self consistent field (SCF) loop, the key hot spot in electronic structure codes. By threading the Message Passing Interface (MPI) ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4× to 6× for large systems) but also achieve a significant ([Formula: see text]×) reduction in the overall memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel® Xeon Phi™ supercomputer. Scaling numbers are reported on up to 7680 cores on Intel Xeon Phi coprocessors.
MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL
Authors: Hua Guan-Jie , Hung Che-Lun , Lin Chun-Yuan , Wu Fu-Che , Chan Yu-Wei , Tang Chuan Yi
Published: October 2017

A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists. In this work, a novel parallel Unweighted Pair Group Method with Arithmetic Mean approach on multiple Graphics Processing Units is proposed to construct a phylogenetic tree from extremely large set of sequences. The experimental results present that the proposed approach on a DGX-1 server with 8 NVIDIA P100 graphic cards achieves approximately 3-fold to 7-fold speedup over the implementation of Unweighted Pair Group Method with Arithmetic Mean on a modern CPU and a single GPU, respectively.
Characterising phase variations in MALDI-TOF data and correcting them by peak alignment
Authors: Lin Simon M , Haney Richard P , Campa Michael J , Fitzgerald Michael C , Patz Edward F
Published: October 2017

The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the development of robust data analysis algorithms is the variability in the location of protein ion signals along the x-axis. We studied technical variations of MALDI-TOF measurements in the context of proteomics profiling. By acquiring a benchmark data set with five replicates, we estimated 76% to 85% of the total variance is due to phase variation. We devised a lobster plot, so named because of the resemblance to a lobster claw, to help detect the phase variation in replicates. We also investigated a peak alignment algorithm to remove the phase variation. This operation is analogous to the normalization step in microarray data analysis. Only after this critical step can features of biological interest be clearly revealed. With the help of principal component analysis, we demonstrated that after peak alignment, the differences among replicates are reduced. We compared this approach to peak alignment with a model-based calibration approach in which there was known information about peaks in common among all spectra. Finally, we examined the potential value at each point in an analysis pipeline of having a set of methods available that includes parametric, semiparametric and nonparametric methods; among such methods are those that benefit from the use of prior information.
Novel Approaches to Smoothing and Comparing SELDI TOF Spectra
Authors: Meleth Sreelatha , Eltoum Isam-Eldin , Zhu Liu , Oelschlager Denise , Piyathilake Chandrika , Chhieng David , Grizzle William E.
Published: October 2017

Background

Most published literature using SELDI-TOF has used traditional techniques in Spectral Analysis such as Fourier transforms and wavelets for denoising. Most of these publications also compare spectra using their most prominent feature, ie, peaks or local maximums.

Methods

The maximum intensity value within each window of differentiable m/z values was used to represent the intensity level in that window. We also calculated the ‘Area under the Curve’ (AUC) spanned by each window.

Results

Keeping everything else constant, such as pre-processing of the data and the classifier used, the AUC performed much better as a metric of comparison than the peaks in two out of three data sets. In the third data set both metrics performed equivalently.

Conclusions

This study shows that the feature used to compare spectra can have an impact on the results of a study attempting to identify biomarkers using SELDI TOF data.
Impact of Freeze-thaw Cycles and Storage Time on Plasma Samples Used in Mass Spectrometry Based Biomarker Discovery Projects
Authors: Mitchell Breeana L , Yasui Yutaka , Li Christopher I , Fitzpatrick Annette L. , Lampe Paul D
Published: October 2017

Mass spectrometry approaches to biomarker discovery in human fluids have received a great deal of attention in recent years. While mass spectrometry instrumentation and analysis approaches have been widely investigated, little attention has been paid to how sample handling can impact the plasma proteome and therefore influence biomarker discovery. We have investigated the effects of two main aspects of sample handling on MALDI-TOF data: repeated freeze-thaw cycles and the effects of long-term storage of plasma at –70°C. Repeated freeze-thaw cycles resulted in a trend towards increasing changes in peak intensity, particularly after two thaws. However, a 4-year difference in long-term storage appears to have minimal effect on protein in plasma as no differences in peak number, mass distribution, or coefficient of variation were found between samples. Therefore, limiting freeze/thaw cycles seems more important to maintaining the integrity of the plasma proteome than degradation caused by long-term storage at –70°C.
Tumor Growth Rate Approximation-Assisted Estimation
Authors: An Lihua , Ahmed S. Ejaz , Ali Adnan
Published: October 2017

From tumor to tumor, there is a great variation in the proportion of cancer cells growing and making daughter cells that ultimately metastasize. The differential growth within a single tumor, however, has not been studied extensively and this may be helpful in predicting the aggressiveness of a particular cancer type. The estimation problem of tumor growth rates from several populations is studied. The baseline growth rate estimator is based on a family of interacting particle system models which generalize the linear birth process as models of tumor growth. These interacting models incorporate the spatial structure of the tumor in such a way that growth slows down in a crowded system. Approximation-assisted estimation strategy is proposed when initial values of rates are known from the previous study. Some alternative estimators are suggested and the relative dominance picture of the proposed estimator to the benchmark estimator is investigated. An over-riding theme of this article is that the suggested estimation method extends its traditional counterpart to non-normal populations and to more realistic cases.
Computational Methods for the Analysis of Array Comparative Genomic Hybridization
Authors: Chari Raj , Lockwood William W. , Lam Wan L.
Published: October 2017

Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.
Merging Microarray Data, Robust Feature Selection, and Predicting Prognosis in Prostate Cancer
Authors: Wang Jing , Do Kim Anh , Wen Sijin , Tsavachidis Spyros , Mcdonnell Timothy J. , Logothetis Christopher J. , Coombes Kevin R.
Published: October 2017

Motivation

Individual microarray studies searching for prognostic biomarkers often have few samples and low statistical power; however, publicly accessible data sets make it possible to combine data across studies.

Method

We present a novel approach for combining microarray data across institutions and platforms. We introduce a new algorithm, robust greedy feature selection (RGFS), to select predictive genes.

Results

We combined two prostate cancer microarray data sets, confirmed the appropriateness of the approach with the Kolmogorov-Smirnov goodness-of-fit test, and built several predictive models. The best logistic regression model with stepwise forward selection used 7 genes and had a misclassification rate of 31%. Models that combined LDA with different feature selection algorithms had misclassification rates between 19% and 33%, and the sets of genes in the models varied substantially during cross-validation. When we combined RGFS with LDA, the best model used two genes and had a misclassification rate of 15%.

Availability

Affymetrix U95Av2 array data are available at http://www.broad.mit.edu/cgi-bin/cancer/datasets.cgi . The cDNA microarray data are available through the Stanford Microarray Database ( http://cmgm.stanford.edu/pbrown/ ). GeneLink software is freely available at http://bioinformatics.mdanderson.org/GeneLink/ . DNA-Chip Analyzer software is publicly available at http://biosun1.harvard.edu/complab/dchip/ .
Decentralized Data Sharing of Tissue Microarrays for Investigative Research in Oncology
Authors: Chen Wenjin , Schmidt Cristina , Parashar Manish , Reiss Michael , Foran David J.
Published: October 2017

Tissue microarray technology (TMA) is a relatively new approach for efficiently and economically assessing protein and gene expression across large ensembles of tissue specimens. Tissue microarray technology holds great potential for reducing the time and cost associated with conducting research in tissue banking, proteomics, and outcome studies. However, the sheer volume of images and other data generated from even limited studies involving tissue microarrays quickly approach the processing capacity and resources of a division or department. This challenge is compounded by the fact that large-scale projects in several areas of modern research rely upon multi-institutional efforts in which investigators and resources are spread out over multiple campuses, cities, and states. To address some of the data management issues several leading institutions have begun to develop their own “in-house” systems, independently, but such data will be only minimally useful if it isn't accessible to others in the scientific community. Investigators at different institutions studying the same or related disorders might benefit from the synergy of sharing results. To facilitate sharing of TMA data across different database implementations, the Technical Standards Committee of the Association for Pathology Informatics organized workshops in efforts to establish a standardized TMA data exchange specification. The focus of our research does not relate to the establishment of standards for exchange, but rather builds on these efforts and concentrates on the design, development and deployment of a decentralized collaboratory for the unsupervised characterization, and seamless and secure discovery and sharing of TMA data. Specifically, we present a self-organizing, peer-to-peer indexing and discovery infrastructure for quantitatively assessing digitized TMA's. The system utilizes a novel, optimized decentralized search engine that supports flexible querying, while guaranteeing that once information has been stored in the system, it will be found with bounded costs.
An Empirical Study of Univariate and Genetic Algorithm-Based Feature Selection in Binary Classification with Microarray Data
Authors: Lecocke Michael , Hess Kenneth
Published: October 2017

Background

We consider both univariate- and multivariate-based feature selection for the problem of binary classification with microarray data. The idea is to determine whether the more sophisticated multivariate approach leads to better misclassification error rates because of the potential to consider jointly significant subsets of genes (but without overfitting the data).

Methods

We present an empirical study in which 10-fold cross-validation is applied externally to both a univariate-based and two multivariate- (genetic algorithm (GA)-) based feature selection processes. These procedures are applied with respect to three supervised learning algorithms and six published two-class microarray datasets.

Results

Considering all datasets, and learning algorithms, the average 10-fold external cross-validation error rates for the univariate-, single-stage GA-, and two-stage GA-based processes are 14.2%, 14.6%, and 14.2%, respectively. We also find that the optimism bias estimates from the GA analyses were half that of the univariate approach, but the selection bias estimates from the GA analyses were 2.5 times that of the univariate results.

Conclusions

We find that the 10-fold external cross-validation misclassification error rates were very comparable. Further, we find that a two-stage GA approach did not demonstrate a significant advantage over a 1-stage approach. We also find that the univariate approach had higher optimism bias and lower selection bias compared to both GA approaches.
Heterogeneous Biomedical Database Integration using a Hybrid Strategy: A P53 Cancer Research Database
Authors: Bichutskiy Vadim Y. , Colman Richard , Brachmann Rainer K. , Lathrop Richard H.
Published: October 2017

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html .)
A Mathematical Model for the Onset of Avascular Tumor Growth in Response to the Loss of P53 Function
Authors: Levine Howard A. , Smiley Michael W. , Tucker Anna L. , Nilsen-Hamilton Marit
Published: October 2017

We present a mathematical model for the formation of an avascular tumor based on the loss by gene mutation of the tumor suppressor function of p53. The wild type p53 protein regulates apoptosis, cell expression of growth factor and matrix metalloproteinase, which are regulatory functions that many mutant p53 proteins do not possess. The focus is on a description of cell movement as the transport of cell population density rather than as the movement of individual cells. In contrast to earlier works on solid tumor growth, a model is proposed for the initiation of tumor growth. The central idea, taken from the mathematical theory of dynamical systems, is to view the loss of p53 function in a few cells as a small instability in a rest state for an appropriate system of differential equations describing cell movement. This instability is shown (numerically) to lead to a second, spatially inhomogeneous, solution that can be thought of as a solid tumor whose growth is nutrient diffusion limited. In this formulation, one is led to a system of nine partial differential equations. We show computationally that there can be tumor states that coexist with benign states and that are highly unstable in the sense that a slight increase in tumor size results in the tumor occupying the sample region while a slight decrease in tumor size results in its ultimate disappearance.