Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein-DNA interactions in soluble telosomes from Saccharomyces cerevisiae.

Telomeric DNA in Saccharomyces is organized into a non-nucleosomal chromatin structure called the telosome that can be released from chromosome ends in soluble form by nuclease digestion (Wright, J. H., Gottschling, D. E. and Zakian, V. A. (1992) Genes Dev. 6, 197-210). The protein-DNA interactions of soluble telosomes were investigated by monitoring isolated telomeric DNA fragments for the retention of bound protein using both gel mobility shift and nitrocellulose filter-binding assays. Telosomal proteins remained associated with telomeric DNA at concentrations of ethidium bromide that dissociated nucleosomes. The protein-DNA interactions in the yeast telosome were also disrupted by much lower salt concentrations than those known to disrupt either the interactions of ciliate terminus-binding proteins with telomeric DNA or the interactions of histones with DNA in nucleosomes. Taken together, these data corroborate previously published nuclease mapping data indicating that telosomes are distinct in structure from conventional nucleosomes. These data also indicate that yeast do not possess telomere binding proteins similar to those detected in ciliates that remain tightly bound to telomeric DNA even in high salt. In addition, the characteristic gel mobility shift of soluble telosomes could be mimicked by complexes formed in vitro with yeast telomeric DNA and recombinant Rap1p suggesting that Rap1p, a known component of soluble yeast telosomes (Wright, J. H., Gottschling, D. E. and Zakian, V. A. (1992) Genes Dev. 6, 197-210; Conrad, M. N. , Wright, J. H. , Wolf, A. J. and Zakian, V. A. (1990) Cell 63, 739-750), is likely to be the major structural protein bound directly to yeast telomeric DNA.
The Elimination of the Unworthy: Credit Men and Small Retailers in Progressive Era Capitalism1

The largest organization of capitalists during the Progressive Era was one that most American historians have never heard of. Motivated primarily by overproduction and ruthless competition, many of the nation's largest manufacturers, distributors, and commercial banks formed the National Association of Credit Men (NACM) in 1896 to reduce the supply of credit available to retailers and consumers. The story of the Credit Men confirms many standard assumptions regarding the rise of corporate America to economic power and cultural legitimacy while challenging others. Advances in technology and salaried organization made possible their mobilization, yet more important was the significant lag in the development of mass retail institutions and consequently mass consumerism behind mass production and distribution. The NACM deployed standardized methods and hungered for administrative efficiency but used these modern tools to instill order and ethical discipline in the nation's business, not to secularize the economy and culture of the new century. America's corporate capitalists seized power by promising moral regulation for unbridled individualism.
Assessment of the Genetic Susceptibility of Sheep to Scrapie by Protein Misfolding Cyclic Amplification and Comparison with Experimental Scrapie Transmission Studies

ABSTRACT The susceptibility of sheep to scrapie is influenced mainly by the prion protein polymorphisms A136V, R154H, and Q171R/H. Here we analyzed the ability of protein misfolding cyclic amplification (PMCA) to model the genetic susceptibility of sheep to scrapie. For this purpose, we studied the efficiency of brain homogenates from sheep with different PrP genotypes to support PrPSc amplification by PMCA using an ARQ/ARQ scrapie inoculum. The results were then compared with those obtained in vivo using the same sheep breed, genotypes, and scrapie inoculum. Genotypes associated with susceptibility (ARQ/ARQ, ARQ/AHQ, and AHQ/ARH) were able to sustain PrPSc amplification in PMCA reactions, while genotypes associated with resistance to scrapie (ARQ/ARR and ARR/ARR) were unable to support the in vitro conversion. The incubation times of the experimental infection were then compared with the in vitro amplification factors. Linear regression analysis showed that the efficiency of in vitro PrPSc amplification of the different genotypes was indeed inversely proportional to their incubation times. Finally, the rare ARQK176/ARQK176 genotype, for which no in vivo data are available, was studied by PMCA. No amplification was obtained, suggesting ARQK176/ARQK176 as an additional genotype associated with resistance, at least to the isolate tested. Our results indicate a direct correlation between the ability of different PrP genotypes to undergo PrPC-to-PrPSc conversion by PMCA and their in vivo susceptibility and point to PMCA as an alternative to transmission studies and a potential tool to test the susceptibility of numerous sheep PrP genotypes to a variety of prion sources.
Security and Control in the Cloud

ABSTRACT Cloud computing is a new IT delivery paradigm that offers computing resources as on-demand services over the Internet. Like all forms of outsourcing, cloud computing raises serious concerns about the security of the data assets that are outsourced to providers of cloud services. To address these security concerns, we show how today's generation of information security management systems (ISMSs), as specified in the ISO/IEC 27001:2005, must be extended to address the transfer of security controls into cloud environments. The resulting virtual ISMS is a standards-compliant management approach for developing a sound control environment while supporting the various modalities of cloud computing. This article addresses chief security and/or information officers of cloud client and cloud provider organizations. Cloud clients will benefit from our exposition of how to manage risk when corporate assets are outsourced to cloud providers. Providers of cloud services will learn what processes and controls they can offer in order to provide superior security that differentiates their offerings in the market.
Suppression of tif-mediated induction of SOS functions in Escherichia coli by an altered dnaB protein

The tif-1 mutation in the Escherichia coli recA gene is known to cause induction of the various "SOS" functions at high temperature, including massive synthesis of the recA protein, lethal filamentation, elevated mutagenesis, and, in lambda lysogens, induction of prophage. It is shown here that the deoxyribonucleic acid initiation mutation dnaB252 suppresses all these manifestations of tif expression. Induction of lambda by ultraviolet irradiation, however, is not affected by the dnaB252 mutation. No similar suppression of tif is observed with other dnaB mutations affecting deoxyribonucleic acid elongation or with other deoxyribonucleic acid initiation mutations at the dnaA and dnaC loci. The fact that an alteration of the dnaB protein specifically suppresses tif-mediated SOS induction implies a role of the replication apparatus in this process, as has been suggested for ultraviolet induction. The induction of lambda is known to proceed via repressor cleavage, presumably promoted by an activated (protease) form of the recA protein. Since lambda induction is normal after ultraviolet irradiation of the tif-1 dnaB252(lambda) strain, tif-mediated induction in this strain may be blocked in a tif-specific step leading to activation of the recA (tif) protein. It is possible that the recA (tif) mutant protein may be directly involved in the replication complex in processes leading to this activation.
Pathogenic Neisseriae Can Use Hemoglobin, Transferrin, and Lactoferrin Independently of the tonBLocus

ABSTRACT Redundant TonB systems which function in iron transport from TonB-dependent ligands have recently been identified in several gram-negative bacteria. We demonstrate here that in addition to the previously described tonB locus, an alternative system exists for the utilization of iron from hemoglobin, transferrin, or lactoferrin in Neisseria meningitidis andNeisseria gonorrhoeae. Following incubation on media containing hemoglobin, N. meningitidis IR3436 (tonB exbB exbD deletion mutant) and N. gonorrhoeae PD3401 (tonB insertional mutant) give rise to colonies which can grow with hemoglobin. Transfer of Hb+ variants (PD3437 or PD3402) to media containing hemoglobin, transferrin, and/or lactoferrin as sole iron sources resulted in growth comparable to that observed for the wild-type strains. Transformation of N. meningitidis IR3436 or N. gonorrhoeae PD3401 with chromosomal DNA from the Hb+ variants yielded transformants capable of growth with hemoglobin. When we inactivated the TonB-dependent outer membrane hemoglobin receptors (HmbR or HpuB) in the NeisseriaHb+ variants, these strains could not grow with hemoglobin; however, growth was observed with transferrin and/or lactoferrin. These results demonstrate that accumulation of iron from hemoglobin, transferrin, and lactoferrin in the pathogenic neisseriae can occur via a system that is independent of the previously describedtonB locus.
Resistencia in vitro a los antifúngicos en Candida albicans de pacientes infectados por el VIH con y sin candidosis oral

El objetivo principal de este trabajo ha sido determinar la sensibilidad in vitroalos antimicoticos de uso clinico mas habitual de aislamientos clinicos deCandidaprocedentes de pacientes infectados por el VIH o con sida, teniendo encuenta si padecian o no candidosis oral. Para ello, se examino la cavidad oralde 307 pacientes y les fue tomada una muestra oral con hisopo esteril que pos-teriormente fue procesada por metodos micologicos convencionales. La sensibi-lidad a anfotericina B, nistatina, fluconazol, itraconazol y ketoconazol, sedetermino por difusion en agar empleando tabletas Neo-Sensitabs® (RoscoDiagnostica, Dinamarca). Se obtuvieron 135 aislamientos de Candida albicans(91 del serotipo A, 38 delserotipo B, tres C. albicansvariedad stellatoideay tres aislamientos no fuerontipificados), tres Candida kruseiy dos Candida glabrata. Ninguno de los 140 ais-lamientos presento resistencia a nistatina o anfotericina B. Sin embargo, seobservaron resistencias in vitroal fluconazol en el 7,9% de los aislamientos y enun 2,9% de los mismos a ketoconazol e itraconazol. Casi todos los aislamientosde C. krusei y C. glabrata, el 31% de los aislamientos de pacientes con candido-sis y el 20% de los de pacientes colonizados por Candida mostraron una sensi-bilidad disminuida a los azoles. El presente estudio muestra que los antifungicospolienicos tienen gran eficacia in vitrosobre los aislamientos de pacientes infec-tados por el VIH y que la resistencia in vitroa los azoles no es tan elevada comola observada en otros paises.Antifungicos, Candida, Sida, Fluconazol, Resistencia
Accurate and efficient loop selections by the DFIRE‐based all‐atom statistical potential

The conformations of loops are determined by the water‐mediated interactions between amino acid residues. Energy functions that describe the interactions can be derived either from physical principles (physical‐based energy function) or statistical analysis of known protein structures (knowledge‐based statistical potentials). It is commonly believed that statistical potentials are appropriate for coarse‐grained representation of proteins but are not as accurate as physical‐based potentials when atomic resolution is required. Several recent applications of physical‐based energy functions to loop selections appear to support this view. In this article, we apply a recently developed DFIRE‐based statistical potential to three different loop decoy sets (RAPPER, Jacobson, and Forrest‐Woolf sets). Together with a rotamer library for side‐chain optimization, the performance of DFIRE‐based potential in the RAPPER decoy set (385 loop targets) is comparable to that of AMBER/GBSA for short loops (two to eight residues). The DFIRE is more accurate for longer loops (9 to 12 residues). Similar trend is observed when comparing DFIRE with another physical‐based OPLS/SGB‐NP energy function in the large Jacobson decoy set (788 loop targets). In the Forrest‐Woolf decoy set for the loops of membrane proteins, the DFIRE potential performs substantially better than the combination of the CHARMM force field with several solvation models. The results suggest that a single‐term DFIRE‐statistical energy function can provide an accurate loop prediction at a fraction of computing cost required for more complicate physical‐based energy functions. A Web server for academic users is established for loop selection at the softwares/services section of the Web site http://theory.med.buffalo.edu/.
Log-logistic Distribution as a Reliability Model: A Bayesian Analysis

Log-logistic distribution is a very important reliability model as it fits well in many practical situations of reliability data analyses. Another important feature with the log-logistic distribution lies in its closed form expression for survival and hazard functions that makes it advantageous over log-normal distribution. It is therefore more convenient in handling censored data than the log-normal, while providing a good approximation to it except in the extreme tails. In this paper an attempt has been made to use Bayesian analytic and simulation methods for fitting the log-logistic reliability model. Real datasets are used for the purpose of illustrations. R code has been provided to implement in censored mechanism. Laplace approximation is implemented for approximating posterior densities of the parameters. Moreover, parallel simulation tools are also implemented with an extensive use of R.
he effects of quantitative skills training on college utcomes and peers

This paper estimates the causal effect of taking a course in quantitative reasoning on students’ academic performance and classroom peer-group composition at a liberal arts college. To identify effects, the paper compares the outcomes of otherwise similar students who barely passed a baseline quantitative skills assessment (not taking the course) with students who barely failed (taking the course). The regression-discontinuity estimates show ollege egression discontinuity uantitative skills emedial eer groups little impact on academic outcomes for student close to the passing cutoff, including grades on subsequent courses with quantitative content, but we are unable to distinguish small from zero effects. Exogenous course assignment does affect the composition of students’ classroom peer groups in subsequent years. The effects can only be generalized to students in the vicinity of the passing threshold (but not students with much worse quantitative e). We skills at the baselin
LvTbx 2 / 3 : a T-box family transcription factor involved in formation of the oral / aboral axis of the sea urchin embryo

Cell-fate specification in the sea urchin embryo is achieved through an initial polarization of the unfertilized egg along the animal/vegetal (A/V) axis and, after fertilization, through cellcell interactions within and between blastomere layers during cleavage and blastula stages. Such polarizations, signaling events and cell-cell interactions activate region-specific genes and segregate the 60-cell stage embryo into five embryonic territories: the small micromeres; the skeletogenic mesenchyme; the vegetal plate endomesoderm; the oral ectoderm; and the aboral ectoderm (Davidson, 1998). Although there is much data about the development of the primary, A/V axis of the embryo (reviewed in Angerer and Angerer, 2000), less is known about the specification of the secondary, O/A axis in the sea urchin. In some species of sea urchins, the O/A axis can be predicted by the plane of first cleavage, whereas in others, the future axis cannot be related to the position of cleavage planes until the third cleavage or later (Cameron et al., 1989; Henry et al., 1992). Signaling events seem also to be involved (Wikramanayake et al., 1995; Wikramanayake and Klein, 1997). Several genes are expressed asymmetrically about the O/A xis in the endoderm, mesoderm and ectoderm, but no genes have yet been identified that reflect the oral/aboral polarity xtending between all three. In the endoderm, asymmetrically 1989 Development 130, 1989-1999 © 2003 The Company of Biologists Ltd doi:10.1242/dev.00409
New computational modeling for solving higher order ODE based on FPGA

In this paper we propose a method for solving complex higher order ordinary differential equations (ODE) based on an emulation of the analog computing paradigm on digital hardware platforms. In this case, we mimic real analog system elements by digital discretized models. Due to the flexibility and reconfigurability of FPGA and also the possibility of system behavioral modeling through hardware description languages (HDL), we are able to create all fundamental elements that are necessary to both simulating complex systems and the modeling of any ordinary differential equations (ODE) or a system simulation based on ODEs. We therefore propose a novel methodology of solving systems and higher order ODEs. This technique is similar to the analog computing but with the key difference that we possess more flexibility and are able to control at will the precision level wanted/needed. Further features are values scaling of both the results and internal variables.
New Roles for Pharmacists in Community Mental Health Care: A Narrative Review

Medicines are a major treatment modality for many mental illnesses, and with the growing burden of mental disorders worldwide pharmacists are ideally positioned to play a greater role in supporting people with a mental illness. This narrative review aims to describe the evidence for pharmacist-delivered services in mental health care and address the barriers and facilitators to increasing the uptake of pharmacist services as part of the broader mental health care team. This narrative review is divided into three main sections: (1) the role of the pharmacist in mental health care in multidisciplinary teams and in supporting early detection of mental illness; (2) the pharmacists’ role in supporting quality use of medicines in medication review, strategies to improve medication adherence and antipsychotic polypharmacy, and shared decision making; and (3) barriers and facilitators to the implementation of mental health pharmacy services with a focus on organizational culture and mental health stigma. In the first section, the review presents new roles for pharmacists within multidisciplinary teams, such as in case conferencing or collaborative drug therapy management; and new roles that would benefit from increased pharmacist involvement, such as the early detection of mental health conditions, development of care plans and follow up of people with mental health problems. The second section describes the impact of medication review services and other pharmacist-led interventions designed to reduce inappropriate use of psychotropic medicines and improve medication adherence. Other new potential roles discussed include the management of antipsychotic polypharmacy and involvement in patient-centered care. Finally, barriers related to pharmacists’ attitudes, stigma and skills in the care of patients with mental health problems and barriers affecting pharmacist-physician collaboration are described, along with strategies to reduce mental health stigma.
Family Lead Poisoning Associated with Occupational Exposure

Lead is a potent poison that affects multiple body systems. It is well documented that children under age 6 years and the fetus are especially vulnerable to neurologic damage affecting learning and behavior with potential for life-long impact. In 1991, the Centers for Disease Control and Prevention (CDC) lowered the blood lead level (BLL) of concern for children from 25 to 10 micrograms per deciliter (μg/dL) (CDC 1991). 1 Efforts to reduce lead in the environment, primarily by eliminating lead from gasoline and paint, have resulted in lowering the overall geometric mean BLL for the general population in the United States from approximately 13 micrograms per deciliter (μg/dL) in the late 1970’s to <2 μg/dL by 1999 (NCHS 1984; CDC 2001). 2,3 Although the average BLL has markedly declined, National Health and Nutrition Examination Survey (NHANES) 1999– 2000 data indicate that 2.2% of U.S. children aged 1 to 5 years had BLLs ≥10 μg/dL (CDC 2003). 4 Recent research suggests that levels once thought safe are considered hazardous as new information emerges about lead’s harmful effects at BLLs less than 10 μg/dL.5,6 Despite success in reducing the number of children with elevated BLLs, some remain at high risk for lead exposure, including those living in homes containing lead-contaminated dust. Invisible toxins may be carried home to household members by inadequately protected workers on their clothes, shoes, or bodies, called “take-home exposure. ” Documented cases of take-home exposure include lead, beryllium, asbestos, pesticides, and other toxic materials.7 In this case series, we describe take-home lead exposure incidents in California from 1992 to 2002. Lead is used in more than 100 industries. Lead dust carried from work settles on surfaces in the vehicle and home where it can be ingested or inhaled by young children with normal mouthing behavior and by household members handling workers’ clothing. Children of lead-exposed workers have disproportionately high BLLs when compared to other children.8-10 One study estimated that 48,000 families have children under age 6 living with household members occupationally exposed to lead.11 Reports of take-home lead exposure include work in mining,8,12 automotive radiator repair,13 battery reclamation,14 construction,9 and antique furniture refinishing.15
Salivary cortisol is related to atherosclerosis of carotid arteries.

BACKGROUND Dysregulation of the hypothalamic-pituitary-adrenal axis has been suggested as an independent risk factor for ischemic heart disease. The aim of our study was to evaluate whether two markers of the hypothalamic-pituitary-adrenal axis activity, the level of salivary cortisol and the diurnal salivary cortisol pattern, are associated with atherosclerosis of the carotid arteries in an elderly population. METHODS AND RESULTS A total of 1866 participants of the Rotterdam Study, a population-based cohort study in the elderly, provided four salivary cortisol samples throughout 1 d, and underwent ultrasonography to examine the presence of plaques in the common, internal, and bifurcation sites of both carotid arteries. Two summary measures of the separate cortisol values were computed: area under the curve (AUC), which is a measure of total cortisol exposure while awake; and the slope, which is a measure of diurnal cortisol decline. RESULTS Total cortisol exposure while awake (AUC) was associated with higher plaque scores (beta = 0.08 per sd of AUC, 95% confidence interval 0.00-0.16; P = 0.04) in a fully adjusted linear regression model. Persons with an AUC in the highest tertile had a higher number of plaques of carotid arteries compared with those in the lowest tertile (3.08 vs. 2.80, 95% confidence interval of difference 0.09-0.48; P = 0.005). There was no relation between diurnal cortisol decline and plaque score. CONCLUSION Our results support the hypothesis that increased total cortisol exposure is independently associated with atherosclerosis of the carotid arteries.