Miracle-dz/UniFAR-FTUs huggingface dataset:
MOLECULAR APPROACH TO MATERIAL DETACHMENT MECHANISM DURING CHEMICAL MECHANICAL PLANARIZATION

Mechanistic numerical analysis and molecular dynamics (MD) simulation are employed to understand the material detachment mechanism associated with chemical mechanical polishing. We investigate the mechanics of scratch intersection mechanism to obtain a characteristic length scale and compare the theoretical predictions with previous experimental observations on ductile copper discs at the micro-scale. First, an analytical model is developed based on mechanics of materials approach. The analytical model includes the effects of strain hardening during material removal as well as the geometry of indenter tip. In the next step, molecular simulations of the scratch intersection are performed at the atomistic scale. The embedded atom method (EAM) is utilized as the force field for workpiece material and a simplified tool-workpiece interaction is assumed to simulate material removal through scratch intersection mechanism. Both models are utilized to predict a characteristic length of material detachment related to material removal during scratch intersection. The predictions from two approaches are compared with experimental observations in order to draw correlations between experiment and simulation. The insights obtained from this work may assist in understanding the mechanism for chemical mechanical planarization (CMP), and even be applied to other different machining and polishing events.
Elastic ankle muscle–tendon interactions are adjusted to produce acceleration during walking in humans

ABSTRACT Humans and other cursorial mammals have distal leg muscles with high in-series compliance that aid locomotor economy. This muscle–tendon design is considered sub-optimal for injecting net positive mechanical work. However, humans change speed frequently when walking and any acceleration requires net positive ankle work. The present study unveiled how the muscle–tendon interaction of human ankle plantar flexors are adjusted and integrated with body mechanics to provide net positive work during accelerative walking. We found that for accelerative walking, a greater amount of active plantar flexor fascicle shortening early in the stance phase occurred and was transitioned through series elastic tissue stretch and recoil. Reorientation of the leg during early stance for acceleration allowed the ankle and whole soleus muscle–tendon complex to remain isometric while its fascicles actively shortened, stretching in-series elastic tissues for subsequent recoil and net positive joint work. This muscle–tendon behaviour is fundamentally different from constant-speed walking, where the ankle and soleus muscle–tendon complex undergo a period of negative work to store energy in series elastic tissues before subsequent recoil, minimizing net joint work. Muscles with high in-series compliance can therefore contribute to net positive work for accelerative walking and here we show a mechanism for how in human ankle muscles. Summary: A novel mechanism is presented by which human ankle muscles use their elastic tendons to contribute mechanical work and produce acceleration during walking gait.
Gauss or Bernoulli?

This Monte Carlo study compares performance of the linear and the logistic mixed-model analyses of simulated community trials having event rates of 37%, 13%, or 5%, intraclass correlations between 0.01 and 0.05, and 17 or 5 denominator degrees of freedom. Type I or Type II error rates showed no essential difference between the two analysis methods. They showed depressed error rates when the event rate or the denominator degrees of freedom were small. The authors conclude that in studies with adequate denominator degrees of freedom, the researcher may use either method of analysis but should accept negative estimates of components of variance to avoid depression of error rates.
Parallel Partial Order Reduction with Topological Sort Proviso

Partial order reduction and distributed-memory processing are the two essential techniques to fight the well-known state space explosion problem in explicit state model checking. Unfortunately, these two techniques have not been integrated yet to a satisfactory degree. While for verification of safety properties, there are a few rather successful approaches to parallel partial order reduction, for LTL model checking all suggested approaches are either too technically involved to be smoothly incorporated with the existing parallel algorithms, or they are simply weak in the sense that the achieved reduction in the size of the state space is minor. The main source of difficulties is the cycle proviso that requires one fully expanded state on every cycle in the reduced state space graph. This can be easily achieved in the sequential case by employing depth-first search strategy for state space generation. Unfortunately, this strategy is incompatible with parallel (hence distributed-memory) processing, which limits application of partial order reduction technique to the sequential case. In this paper we suggest a new technique that guarantees correct construction of the reduced state space graph w.r. t. the cycle proviso. Our new technique is fully compatible with the parallel graph traversal procedure while at the same time it provides competitive reduction of the state space if compared to the serial case. The new technique has been implemented within the parallel and distributed-memory LTL model checker DiVinE and its performance is reported in this paper.
Information Privacy: Measuring Individuals' Concerns About Organizational Practices

Information privacy has been called one of the most important ethical issues of the informa1 Alien Lee was the accepting senior for this paper. tion age. Public opinion polls show rising levels of concer about privacy among Americans. Against this backdrop, research into issues associated with information privacy is increasing. Based on a number of preliminary studies, it has become apparent that organizational practices, individuals' perceptions of these practices, and societal responses are inextricably linked in many ways. Theories regarding these relationships are slowly emerging. Unfortunately, researchers attempting to examine such relationships through confirmatory empirical approaches may be impeded by the lack of validated instruments for measuring individuals' concerns about organizational information privacy practices. To enable future studies in the information privacy research stream, we developed and validated an instrument that identifies and measures the primary dimensions of individuals' concers about organizational information privacy practices. The development process included examinations of privacy literature; experience surveys and focus groups; and the use of expert judges. The result was a parsimonious 15-item instrument with four subscales tapping into dimensions of individuals' concerns about organizational information privacy practices. The instrument was rigorously tested and validated across several heterogenous populations, providing a high degree of confidence in the scales' validity, reliability, and generalizability.
Biomedical Diagnostics and Clinical Technologies: Applying High-Performance Cluster and Grid Computing

Product or company names used in this set are for identification purposes only. Inclusion of the names of the products or companies does not indicate a claim of ownership by IGI Global of the trademark or registered trademark. Biomedical diagnostics and clinical technologies : applying high-performance cluster and grid computing / Manuela Pereira and Mario Freire, editors. p. ; cm. Includes bibliographical references and index. Summary: "This book disseminates knowledge regarding high performance computing for medical applications and bioinformatics"-All work contributed to this book is new, previously-unpublished material. The views expressed in this book are those of the authors, but not necessarily of the publisher. intrODUctiOn What is texture? Even when the concept of texture is intuitive, no single unifying definition has been given by the image analysis community. Most of the numerous definitions that are present in the literature have some common elements that emerge from the etymology of the word: texture comes from the Latin textura, the past participle of the verb texere, to weave (Webster, 2004). This implies that a texture will exhibit a certain structure created by common elements, repeated in a regular way, as in the threads that form a fabric. Three ingredients of texture were identified in (Hawkins, 1970): abstract In recent years, the development of new and powerful image acquisition techniques has lead to a shift from purely qualitative observation of biomedical images towards more a quantitative examination of the data, which linked with statistical analysis and mathematical modeling has provided more interesting and solid results than the purely visual monitoring of an experiment. The resolution of the imaging equipment has increased considerably and the data provided in many cases is not just a simple image , but a three-dimensional volume. Texture provides interesting information that can characterize anatomical regions or cell populations whose intensities may not be different enough to discriminate between them. This chapter presents a tutorial on volumetric texture analysis. The chapter begins with different definitions of texture together with a literature review focused on the medical and biological applications of texture. A review of texture extraction techniques follows, with a special emphasis on the analysis of volumetric data and examples to visualize the techniques. By the end of the chapter, a review of advantages and disadvantages of all techniques is presented together with some important considerations regarding the classification of the measurement space. • some local 'order' is repeated …
Evaluation of gene expression signatures predictive of cytogenetic and molecular subtypes of pediatric acute myeloid leukemia

Background Pediatric acute myeloid leukemia is a heterogeneous disease characterized by non-random genetic aberrations related to outcome. The genetic subtype is currently detected by different diagnostic procedures which differ in success rate and/or specificity. Design and Methods We examined the potential of gene expression profiles to classify pediatric acute myeloid leukemia. Gene expression microarray data of 237 children with acute myeloid leukemia were collected and a double-loop cross validation approach was used to generate a subtype-predictive gene expression profile in the discovery cohort (n=157) which was then tested for its true predictive value in the independent validation cohort (n=80). The classifier consisted of 75 probe sets, representing the top 15 discriminating probe sets for MLL-rearranged, t(8;21)(q22;q22), inv(16)(p13q22), t(15;17)(q21;q22) and t(7;12)(q36;p13)-positive acute myeloid leukemia. Results These cytogenetic subtypes represent approximately 40% of cases of pediatric acute myeloid leukemia and were predicted with 92% and 99% accuracy in the discovery and independent validation cohort, respectively. However, for NPM1, CEBPA, MLL(-PTD), FLT3(-ITD), KIT, PTPN11 and N/K-RAS gene expression signatures had limited predictive value. This may be caused by a limited frequency of these mutations and by underlying cytogenetics. This latter is exemplified by the fact that different gene expression signatures were discovered for FLT3-ITD in patients with normal cytogenetics and in those with t(15;17)(q21;q22)-positive acute myeloid leukemia, which pointed to HOXB-upregulation being specific for FLT3-ITD+ cytogenetically normal acute myeloid leukemia. Conclusions In conclusion, gene expression profiling correctly predicted the most prevalent cytogenetic subtypes of pediatric acute myeloid leukemia with high accuracy. In clinical practice, this gene expression signature may replace multiple diagnostic tests for approximately 40% of pediatric acute myeloid leukemia cases whereas only for the remaining cases (predicted as ‘acute myeloid leukemia-other’) are additional tests indicated. Moreover, the discriminative genes reveal new insights into the biology of acute myeloid leukemia subtypes that warrants follow-up as potential targets for new therapies.
Association of AKI with adverse outcomes in burned military casualties.

BACKGROUND AND OBJECTIVES Although associated with increased morbidity and mortality, AKI has not been systematically examined in military personnel injured from combat operations in Iraq and Afghanistan. DESIGN, SETTINGS, PARTICIPANTS, & MEASUREMENTS Patients evacuated from Iraq and Afghanistan to a burn unit were examined. AKI was classified by the Acute Kidney Injury Network (AKIN) and Risk-Injury-Failure-Loss-End Stage (RIFLE) schemas. Age, sex, percentage of total body surface area burned (TBSA), percentage of full-thickness burn, inhalation injury, and injury severity score were recorded. Additional data that could be associated with poor outcomes were recorded for patients with TBSA ≥20%. Multivariate logistic regression analyses were performed to determine factors associated with morbidity and mortality. RESULTS AKI prevalence rates by the RIFLE and AKIN criteria were 23.8% and 29.9%, respectively. After logistic regression, RIFLE categories of risk (odds ratio [OR], 15.34; 95% confidence interval [CI], 1.75-134; P=0.01), injury (OR, 46.28; 95% CI, 5.02-427; P<0.001), and failure (OR, 126; 95% CI, 13.39->999; P<0.001); AKIN-2 (OR, 23.70; 95% CI, 2.32-242; P=0.008); and AKIN-3 (OR, 130; 95% CI, 13.38->999; P<0.001) were significantly associated with death. AKIN-3, injury, and failure remained significant in the subset of patients with ≥20% TBSA. There was also a strong interaction between TBSA and the stage of AKI with respect to ventilator and intensive care unit days. CONCLUSIONS AKI is prevalent in military casualties with burn injury and is independently associated with morbidity and mortality after adjustment for factors associated with injury severity.
Linoleic Acid-Induced Mitochondrial Ca2+ Efflux Causes Peroxynitrite Generation and Protein Nitrotyrosylation

It is well known that excessive non-esterified fatty acids in diabetes contribute to the pathogenesis of renal complications although the mechanism remains elusive. Enhanced oxidative stress has been hypothesized as a unified factor contributing to diabetic complications and increased protein nitrotyrosylation has been reported in the kidneys of diabetic patients. In the current manuscript we described that linoleic acid (LA) caused mitochondrial Ca2+ efflux and peroxynitrite production, along with increased nitrotyrosine levels of cellular proteins in primary human mesangial cells. The peroxynitrite production by LA was found to depend on mitochondrial Ca2+ efflux. Downregulation of hsp90β1, which has been previously shown to be essential for polyunsaturated fatty acid-induced mitochondrial Ca2+ efflux, significantly diminished LA-responsive mitochondrial Ca2+ efflux and the coupled peroxynitrite generation, implicating a critical role of hsp90β1 in the LA responses. Our results further demonstrated that mitochondrial complexes I and III were directly involved in the LA-induced peroxynitrite generation. Using the well established type 2 diabetic animal model db/db mice, we observed a dramatically enhanced LA responsive mitochondrial Ca2+ efflux and protein nitrotyrosylation in the kidney. Our study thus demonstrates a cause-effect relationship between LA and peroxynitrite or protein nitrotyrosylation and provides a novel mechanism for lipid-induced nephropathy in diabetes.
A randomness-efficient sampler for matrix-valued functions and applications

In this paper we give a randomness-efficient sampler for matrix-valued functions. Specifically, we show that a random walk on an expander approximates the recent Chernoff-like bound for matrix-valued functions of Ahlswede and Winter [2002], in a manner which depends optimally on the spectral gap. The proof uses perturbation theory, and is a generalization of Gillman's and Lezaud's analyses of the Ajtai-Komlos-Szemeredi sampler for real-valued functions [Gillman, 1993]. Derandomizing our sampler gives a few applications, yielding deterministic polynomial time algorithms for problems in which derandomizing independent sampling gives only quasi-polynomial time deterministic algorithms. The first (which was our original motivation) is to a polynomial-time derandomization of the Alon-Roichman theorem [Alon and Roichman, 1994]: given a group of size n, find O(log n) elements which generate it as an expander. This implies a second application - efficiently constructing a randomness-optimal homo-morphism tester, significantly improving the previous result of Shpilka and Wigderson [2004]. A third application, which derandomizes a generalization of the set cover problem, is deferred to the full version of this paper.
Prenatal Exposure to Perfluoroalkyl Acids and Serum Testosterone Concentrations at 15 Years of Age in Female ALSPAC Study Participants

Background Exposure to perfluorooctane sulfonic acid (PFOS) or to perfluorooctanoic acid (PFOA) increases mouse and human peroxisome proliferator–activated receptor alpha (PPARα) subtype activity, which influences lipid metabolism. Because cholesterol is the substrate from which testosterone is synthesized, exposure to these substances has the potential to alter testosterone concentrations. Objectives We explored associations of total testosterone and sex hormone–binding globulin (SHBG) concentrations at age 15 years with prenatal exposures to PFOS, PFOA, perfluorohexane sulfonic acid (PFHxS), and perfluoronanoic acid (PFNA) in females. Methods Prenatal concentrations of the perfluoroalkyl acids (PFAAs) were measured in serum collected from pregnant mothers at enrollment (1991–1992) in the Avon Longitudinal Study of Parents and Children (ALSPAC). The median gestational age when the maternal blood sample was obtained was 16 weeks (interquartile range, 11–28 weeks). Total testosterone and SHBG concentrations were measured in serum obtained from their daughters at 15 years of age. Associations between prenatal PFAAs concentrations and reproductive outcomes were estimated using linear regression models (n = 72). Results Adjusted total testosterone concentrations were on average 0.18-nmol/L (95% CI: 0.01, 0.35) higher in daughters with prenatal PFOS in the upper concentration tertile compared with daughters with prenatal PFOS in the lower tertile. Adjusted total testosterone concentrations were also higher in daughters with prenatal concentrations of PFOA (β = 0.24; 95% CI: 0.05, 0.43) and PFHxS (β = 0.18; 95% CI: 0.00, 0.35) in the upper tertile compared with daughters with concentrations in the lower tertile. We did not find evidence of associations between PFNA and total testosterone or between any of the PFAAs and SHBG. Conclusions Our findings were based on a small study sample and should be interpreted with caution. However, they suggest that prenatal exposure to some PFAAs may alter testosterone concentrations in females. Citation Maisonet M, Calafat AM, Marcus M, Jaakkola JJ, Lashen H. 2015. Prenatal exposure to perfluoroalkyl acids and serum testosterone concentrations at 15 years of age in female ALSPAC study participants. Environ Health Perspect 123:1325–1330; http://dx.doi. org/10.1289/ehp.1408847
Eliciting community perspectives on research with older adults living with HIV through focus groups

Abstract Approximately half of all people living with HIV in the US are age 50 and older. Existing research highlights the health challenges of these individuals, but little work has focused on gathering input about concerns in participating in HIV and aging research. Prior to designing a prospective cohort study on HIV and aging, we elicited feedback from potential participants on general attitudes toward participation in a prospective HIV cohort study, and perspectives on important research topics relevant to older adults living with HIV. Three qualitative focus groups were formed. Three focus groups (5–7 participants each; N = 18) were held with older adults living with HIV. All discussions were audiorecorded and transcribed. Transcripts were analyzed using content analysis. Participants emphasized the importance of data confidentiality, shared concerns about study biases arising from sponsored research, and suggested that conflicts of interest should be independently assessed by “representative” boards made of community members. They urged researchers to be mindful of research “burnout,” because many people with HIV participate in multiple research studies. A number of priority research areas emerged, including the gap in provision of end-of-life services. Many older adults with HIV are knowledgeable about the research process and offer valuable insights to researchers. Addressing participant concerns can facilitate inclusion and enhance HIV research success.
Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity

There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating environment) selection for single environmental variables such as temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of Escherichia coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H2O2) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness‐correlation with tolerance to pH, NaCl or H2O2. Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy‐dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad‐spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public health.