Miracle-dz/UniFAR-FTUs huggingface dataset:
LymPHOS: Design of a phosphosite database of primary human T cells

Current proteomic technology is capable of producing huge amounts of analytical information, which is often difficult to manage in a comprehensive form. Curation, further annotation and public communication of proteomic data require the development of standard data formats and efficient, multimedia database structures. We have implemented a workflow for the annotation of a phosphopeptide database (LymPHOS) that includes tools for MS data filtering and phosphosite assignation, mass spectrum visualization, experimental description and accurate phosphorylation site assignation. Experimental annotations were fitted to current minimum information about a proteomics experiment guidelines. A new guideline for phosphoprotein sample preparation is also proposed. Currently, the database describes 342 phosphorylation sites mapping to more than 200 gene sequences, and it can be accessed through the net (http://www.lymphos.org).
Clonality and Recombination in Genetically Differentiated Subgroups of Cryptococcus gattii

ABSTRACT Cryptococcus gattii is a pathogenic yeast that together with Cryptococcus neoformans causes cryptococcosis in humans and animals. High numbers of viable C. gattii propagules can be obtained from certain species of Australian Eucalyptus camaldulensis trees, and an epidemiological link between Eucalyptus colonization and human exposure has been proposed. However, the highest prevalence of C. gattii cryptococcosis occurs in Papua New Guinea and in regions of Australia where the eucalypt species implicated to date are not endemic. This study investigated the population structure of three geographically distinct clinical and veterinary populations of C. gattii from Australia and Papua New Guinea. All populations that consisted of a genotype found frequently in Australia (VGI) were strongly clonal and were highly differentiated from one another. Two populations of the less common VGII genotype from Sydney and the Northern Territory had population structures inferring recombination. In addition, there was some evidence of reduced genetic differentiation between these geographically remote regions. In a companion study presented in this issue, VGII isolates were overwhelmingly more fertile than those of the VGI genotype, giving biological support to the indirect assessment of sexual exchange. It appears that the VGI genotype propagates clonally on eucalypts in Australia and on an unknown substrate in Papua New Guinea, with infection initiated by an unidentified infectious propagule. VGII isolates are completing their life cycles and may be dispersed via sexually produced basidiospores, which are also likely to initiate respiratory infection.
Age Discrimination Legislation in the United States

Legislation prohibiting age discrimination in the United States dates back to the decade of the 1960s, when along with the Equal Pay Act and the Civil Rights Act barring discrimination against women and minorities, the U.S. Congress passed the 1967 Age Discrimination in Employment Act. Many critical issues regarding the rationale for or effectiveness of age discrimination legislation have been addressed, and continue to be studied, by researchers in both economics and law, while many questions remain. These questions are likely to become increasingly important as rapidly aging workforces in the United States and other industrialized countries threaten to vastly increase the social costs of any barriers to older workers' employment. This paper provides a summary, critical review, and synthesis of what we know about age discrimination legislation. It first traces out the legislative history and the evolving case law, and discusses implementation of the law. It then moves on to review the existing research on age discrimination legislation research that addresses the rationale for the legislation, evidence on its effectiveness, and criticisms of age discrimination legislation.
Free-variable axiomatic foundations of infinitesimal analysis: A fragment with finitary consistency proof

In treatises or advanced textbooks on theoretical physics, it is apparent that the way mathematics is used is very different from what is to be found in books of mathematics. There is, for example, no close connection between books on analysis, on the one hand, and any classical textbook in quantum mechanics, for example, Schiff, [11], or quite recent books, for example Ryder, [10], on quantum field theory. The differences run a good deal deeper than the fact that the books on theoretical physics are not written in the definition-theorem-proof style characteristic of pure mathematics. Although a good many propositions are proved in the books on physics, there are almost with exception no existential proofs, and consequently there is no really serious systematic use of quantifiers. Another important characteristic is the free use of infinitesimals. In fact, most results would not lose anything, from a physicist's point of view, by leaving them in approximate form, i.e., instead of strict equalities or inequalities, using equalities or inequalities only up to an infinitesimal. The discrepancy between the way mathematics is ordinarily done in theoretical physics and the way it is built up from a foundational standpoint in any of the standard modern views raises the question of whether it might be possible to construct quite directly a rigorous foundation that reflects a significant part of this standard practice in theoretical physics. Other parts of standard practice in physics, for example, the use of physically intuitive but nonrigorous arguments, are not present in our system.
User interfaces for cyber-physical systems

Abstract In this paper, we analyze the specific requirements of interacting with cyber-physical systems and propose a design approach that is driven by user needs and makes use of an expanded toolbox that contains state-of-the-art interaction technologies including Smart Glasses and Wearables. We present several examples of assistance systems in industrial production that use these interaction technologies and discuss the corresponding usability and implementation aspects.
Section A. Physiology. Organ culture techniques and the study of hormone effects on the mammary gland

PAGE PAGE I n t r o d u c t i o n . 419 T h e i n i t i a t i o n a n d m a i n t e n a n c e of s e c r e t o r y a c t i v i t y in v i t r o . 4 2 7 M e t h o d s 4 2 0 Morpho log ica l s t u d i e s . 4 2 7 P r e v e n t i o n of c o n t a m i n a t i o n . 420 B i o c h e m i c a l c h a n g e s . 430 C u l t u r e m e d i a 420 D N A s y n t h e s i s . 4 3 0 T y p e s of c u l t u r e vessel . 4 2 1 R N A s y n t h e s i s . 4 3 2 P r e p a r a t i o n of t i s sues . 4 2 2 P r o t e i n a n d e n z y m e s y n t h e s i s . 433 His to log ica l e x a m u i a t i o n . 4 2 2 C a r b o h y d r a t e a n d l ip id m e t a b o l i s m . 434
Extracts of Cordyceps militaris Lower Blood Glucose via the Stimulation of Cholinergic Activation and Insulin Secretion in Normal Rats

Previous studies have shown that Cordyceps militaris (CM) has a hypoglycemic effect, but the actual mechanism remains unclear. This study explored the hypoglycemic mechanism of aqueous extracts of CM in normal Wistar rats. First, the optimal dose of CM for lowering plasma glucose and insulin secretion was tested. Further, atropine and hemicholinium‐3 (HC‐3) were injected and a western blot was used to investigate insulin signaling. It was found that 10 mg/kg CM extracts had a stronger hypoglycemic effect than a higher dose (100 mg/kg); therefore, a dose of 10 mg/kg was used in subsequent experiments. In normal rats, CM extracts decreased plasma glucose by 21.0% and induced additional insulin secretion by 54.5% after 30 min. When atropine or HC‐3 was injected, CM induced a hypoglycemic effect, but the enhancement of insulin secretion was blocked. By western blotting, significant increases in the insulin receptor substrate 1 (IRS‐1) and glucose transporter 4 (GLUT‐4) were observed after CM feeding. However, the elevation of these signaling proteins was abolished by atropine or HC‐3. Taken together, these findings indicate that CM can lower plasma glucose via the stimulation of insulin secretion and cholinergic activation involved in the hypoglycemic mechanism of normal Wistar rats. Copyright © 2012 John Wiley & Sons, Ltd.
Deep and concordant subdivisions in the self-fertilizing mangrove killifishes (Kryptolebias) revealed by nuclear and mtDNA markers

Author(s): Tatarenkov, A; Lima, SMQ; Earley, RL; Berbel-Filho, WM; Vermeulen, FBM; Taylor, DS; Marson, K; Turner, BJ; Avise, JC | Abstract: We use extensive geographical sampling and surveys of nuclear microsatellite and mitochondrial DNA loci to investigate the phylogeographic structure of the only recognized self-fertilizing vertebrates, the mangrove killifishes, currently thought to comprise two cryptic species, Kryptolebias marmoratus and Kryptolebias hermaphroditus. All genetic markers revealed three concordant main clades. The Northern clade includes populations from Florida, northern Cuba, Bahamas, Belize and Honduras and corresponds to K. marmoratus. The Southern clade encompasses populations from Brazil and corresponds to K. hermaphroditus. This species was considered endemic to southeastern Brazil, but molecular data corroborate its occurrence in northeastern Brazil. The Central clade, not previously resolved with genetic data, includes populations from Panama and Antilles. Despite the geographic proximity of the Northern and Central clades, the latter is genetically closer to the Southern clade. The discovery of the Central clade raises some taxonomic issues - it can either be considered a distinct species or united with the Southern clade into a single species with two subspecies. Another possible taxonomic solution is a single selfing species, K. marmoratus, with three subspecies. We show that the Central and Southern clades are highly selfing (97-100%), whereas selfing rates of the Northern clade populations vary geographically (39-99%). Genetic patterns indicate that populations in SE Brazil are recent, contrary to expectations based on the known distributions of related species.
Antitumor activity in melanoma and anti-self responses in a phase I trial with the anti-cytotoxic T lymphocyte-associated antigen 4 monoclonal antibody CP-675,206.

PURPOSE Cytotoxic T lymphocyte-associated antigen 4 (CTLA4) blockade with CP-675,206, a fully human anti-CTLA4 monoclonal antibody, may break peripheral immunologic tolerance leading to effective immune responses to cancer in humans. A phase I trial was conducted to test the safety of CP-675,206. PATIENTS AND METHODS Thirty-nine patients with solid malignancies (melanoma, n = 34; renal cell, n = 4; colon, n = 1) received an intravenous (IV) infusion of CP-675,206 at seven dose levels. The primary objective was to determine the maximum-tolerated dose and the recommended phase II dose. RESULTS Dose-limiting toxicities and autoimmune phenomena included diarrhea, dermatitis, vitiligo, panhypopituitarism and hyperthyroidism. Two patients experienced complete responses (maintained for 34+ and 25+ months), and there were two partial responses (26+ and 25+ months) among 29 patients with measurable melanoma. There have been no relapses thus far after objective response to therapy. Four other patients had stable disease at end of study evaluation (16, 7, 7, and 4 months). Additionally, five patients had extended periods without disease progression (36+, 35+, 26+, 24+, and 23+ months) after local treatment of progressive metastases. Longer systemic exposure to CP-675,206 achieved in higher dose cohorts predicted for a higher probability of response. CONCLUSION CP-675,206 can be administered safely to humans as a single IV dose up to 15 mg/kg, resulting in breaking of peripheral immune tolerance to self-tissues and antitumor activity in melanoma.
Parahippocampal tau pathology in healthy aging, mild cognitive impairment, and early Alzheimer's disease

Abnormally phosphorylated tau accumulates as neurofibrillary tangles and neuropil threads in older persons with and without Alzheimer's disease. The relationship between neurofibrillary tangles and neuropil threads and how they relate to cognitive function is unknown. This study investigated the relationship between phosphorylated tau lesions and cognitive function in 31 persons participating in the Religious Orders Study, a prospective, longitudinal clinicopathological study of aging and Alzheimer's disease. All subjects underwent detailed neuropsychological performance testing within a year of death and evidenced a spectrum of cognitive performance ranging from normal abilities to mild dementia. Measures of neurofibrillary tangle density and phosphorylated tau immunoreactive structures (predominantly neuropil threads) in the entorhinal and perirhinal cortices by quantitative image analysis were significantly correlated (r = 0.5). In multiple linear regression analyses controlling for age, sex, and education, parahippocampal neurofibrillary tangles and neuropil threads were significantly lower in persons without cognitive impairment compared to those with mild cognitive impairment and/or Alzheimer's disease. Further, neurofibrillary tangles were significantly correlated to measures of episodic memory but not other cognitive abilities; neuropil tangles were not significantly related to memory or other cognitive functions. These data indicate that phosphorylated tau pathology in the ventromedial temporal lobe develop prior to the onset of clinical dementia and their presence is associated with cognitive impairment, particularly impairment of episodic memory.
Convergence of Reweighted ' 1 Minimization Algorithms and Unique Solution of Truncated ' p Minimization

Extensive numerical experiments have shown that the iteratively reweighted ‘1 minimization algorithm (IRL1) is a very e‐cient method for variable selection, signal reconstruction and image processing. However no convergence results have been given for the IRL1. In this paper, we flrst give a global convergence theorem of the IRL1 for the ‘2-‘p (0 < p < 1) minimization problem. We prove that any sequence generated by the IRL1 converges to a stationary point of the ‘2-‘p minimization problem. Moreover, the stationary point is a global minimizer in certain domain and the convergence rate is approximately linear under certain conditions. We derive posteriori error bounds which can be used to construct practical stopping rules for the algorithm. Other contribution of this paper is to prove the uniqueness of solution of the truncated ‘p minimization problem under the truncated null space property which is weaker than the restricted isometry property.
Blocking NK Cell Inhibitory Self-Recognition Promotes Antibody-Dependent Cellular Cytotoxicity in a Model of Anti-Lymphoma Therapy1

Human NK cells lyse Ab-coated target cells through the process of Ab-dependent cellular cytotoxicity (ADCC). Improving ADCC responses is desirable because it is thought to be an important antitumor mechanism for some Abs. NK cell inhibitory receptors, such as killer cell Ig-like receptors, engage with MHC class I molecules on self-cells to block NK cell activation. Accordingly, we enhanced ADCC responses by blocking NK cell inhibitory receptors, thus perturbing induction of the self-recognition signal. In a cell line model of anti-lymphoma therapy, the combination of rituximab with an Ab that blocks inhibitory self-recognition yielded increased NK cell-mediated target cell lysis when compared with rituximab alone. To validate this proof-of-concept, we then used a more representative approach in which an individual’s fresh primary NK cells encountered autologous, EBV-transformed B cells. In this system, rituximab and a combination of Abs that block NK cell inhibitory receptors yielded improved NK cell-mediated lysis over rituximab alone. The results show, for the first time, that disruption of inhibitory self-recognition can efficiently promote ADCC in a human model, applying an autologous system in which physiologic checkpoints are in place. This method provides an alternative approach to potentiate the therapeutic benefit of antitumor Abs that mediate ADCC.
Optimised CSG Tree Evaluation for Space Subdivision

Ray tracing is a well known technique for producing realistic computer images. The computational requirements of this method are such that optimisation techniques, for example space subdivision, must be used if complex scenes are to be rendered in reasonable times. Constructive solid geometry (CSG) is a method for describing the geometry of complex scenes by applying set operations to primitive objects. The status tree approach has been used successfully within ray tracing to evaluate CSG structures. This paper proposes a combination of the status tree and space subdivision techniques as a means to improve further the efficiency of ray tracing.
Guidelines for Conducting Mixed-methods Research: An Extension and Illustration

In this paper, we extend the guidelines of Venkatesh et al. (2013) for mixed-methods research by identifying and integrating variations in mixed-methods research. By considering 14 properties of mixed-methods research (e.g., purposes, research questions, epistemological assumptions), our guidelines demonstrate how researchers can flexibly identify the existing variations in mixed-methods research and proceed accordingly with a study design that suits their needs. To make the guidelines actionable for various situations and issues that researchers could encounter, we develop a decision tree to map the flow and relationship among the design strategies. We also illustrate one possible type of mixed-methods research in information systems in depth and discuss how to develop and validate metainferences as the outcomes of such a study.
Smart Grid Cybersecurity Risk Assessment Experiences with the SGIS Toolbox

As much as possible, it is important that the smart grid is secure from cyber-attacks. A vital part of ensuring the security of smart grids is to perform a cybersecurity risk assessment that methodically examines the impact and likelihood of cyber-attacks. Based on the outcomes of a risk assessment, security requirements and controls can be determined that inform architectural choices and address the identified risks. Numerous high-level risk assessment methods and frameworks are applicable in this context. A method that was developed specifically for smart grids is the Smart Grid Information Security (SGIS) toolbox, which we applied to a voltage control and power flow optimization smart grid use case. The outcomes of the assessment indicate that physical consequences could occur because of cyber-attacks to information assets. Additionally, we provide reflections on our experiences with the SGIS toolbox, in order to support others in the community when implementing their own risk assessment for the smart grid. Keywords—risk assessment; smart grid; SGIS toolbox; cybersecurity
Software Requirement Engineering Risk Prediction Model

Analysis of many software program assignments from 2011 through 2014 shows interesting patterns. When you compare large assignments that have efficiently attained their own cost as well as schedule quotes versus the ones that ran delayed, ended up over spending budget, or maybe ended up, half a dozen popular difficulties ended up noticed: weak requirement analysis and management, weak cost calculating, weak handling of requirement change requests, weak milestone monitoring as well as requirement gold plating habit. By comparison, prosperous local software program assignments tended to be much better than on-site software development and management. Maybe the most interesting part of most of these many problem areas can be like everyone is coordinating project management instead of using technical focus. Author focused over the impact of software requirement change requests and requirement gold plating while dealing with on-site project assignments. Author also evaluated new algorithmic model to avoid global software engineering requirement failure, which in turn curtails the estimated time and budget with client satisfaction.
Validation of a Visual Analog Scale Form of the Pelvic Organ Prolapse/Urinary Incontinence Sexual Function Questionnaire 12

Objective: This study aimed to validate a visual analog scale (VAS) form of the Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire-12 (PISQ-12). Methods: This was a planned secondary analysis of a vaginal anatomy and sexual function study. All women undergoing vaginal reconstruction between October 2008 and December 2009 were asked to participate. We planned for an analysis of 30 women for this validation. Preoperatively, sexually active participants completed a questionnaire containing a PISQ-12 in Likert (0-4) and VAS (0-10) format. Within 30 days, participants completed a PISQ-12 in VAS form only for evaluation of test-retest reliability. At 6 months after surgery, participants completed the PISQ-12 in both the Likert and VAS forms. For each item on the PISQ-12, the Spearman rank correlation coefficient was used to estimate the correlation between the Likert and VAS formats using the responses from the same assessment period (before or after surgery). The intraclass correlation coefficient was estimated to assess the test-retest agreement. Results: A total of 43 women completed the preoperative questionnaire, 25 completed the retest, and 37 completed the postoperative questionnaire. When PISQ-12 scores were compared between the Likert and VAS forms, correlation values were 0.88 preoperatively and 0.91 postoperatively. Test-retest reliability was high with an intraclass correlation coefficient of 0.87. Most women preferred the Likert version (71.4% preoperatively and 55.0% postoperatively). Conclusions: The VAS form of the PISQ-12 is both reliable and reproducible and avoids the limitations of the Likert scale.
Polycation-based nanoparticle delivery for improved RNA interference therapeutics

Small-interfering RNA (siRNA)-mediated silencing of genes implicated in disease by the process of RNA interference offers a novel genetic medicine approach. Polymeric nanoparticles (or polyplexes) formed by self-assembly of polycations with siRNA can be used for site-specific delivery, cellular uptake and intracellular trafficking as a strategy to improve the therapeutic potential of siRNA. This review describes the application of polyplexes for in vivo delivery of synthetic siRNA with focus given to systemic and mucosal routes and in vivo requirements. Issues including use of stimuli-responsive systems for intracellular trafficking of siRNA are discussed as part of neccessary future directives towards the development of RNA-based clinical therapeutics.
A model based method for the quantizer assignment of JPEG-like coders

In most coding systems, for image or audio signals, the bit allocation or quantization assignment problem is one of the important issues to minimize the distortion for a given bit budget. By exploiting the empirical distortion-quantization and rate-quantization relations, we propose a model based bit allocation method for JPEG-like coders. The empirical relations have been established using the regression technique which provides a low computational complexity to construct the preprocessing for the bit allocation. From the empirical relations, we can establish the modeling for the distortion-quantization and rate-quantization relations. Using the model, we simplify the problem of the quantization assignment and then obtain an efficient method for solving the simplified problem.