Miracle-dz/UniFAR-FTUs huggingface dataset:
Binding of TATA Binding Protein to a Naturally Positioned Nucleosome Is Facilitated by Histone Acetylation

ABSTRACT The TATA sequence of the human, estrogen-responsive pS2 promoter is complexed in vivo with a rotationally and translationally positioned nucleosome (NUC T). Using a chromatin immunoprecipitation assay, we demonstrate that TATA binding protein (TBP) does not detectably interact with this genomic binding site in MCF-7 cells in the absence of transcriptional stimuli. Estrogen stimulation of these cells results in hyperacetylation of both histones H3 and H4 within the pS2 chromatin encompassing NUC T and the TATA sequence. Concurrently, TBP becomes associated with the pS2 promoter region. The relationship between histone hyperacetylation and the binding of TBP was assayed in vitro using an in vivo-assembled nucleosomal array over the pS2 promoter. With chromatin in its basal state, the binding of TBP to the pS2 TATA sequence at the edge of NUC T was severely restricted, consistent with our in vivo data. Acetylation of the core histones facilitated the binding of TBP to this nucleosomal TATA sequence. Therefore, we demonstrate that one specific, functional consequence of induced histone acetylation at a native promoter is the alleviation of nucleosome-mediated repression of the binding of TBP. Our data support a fundamental role for histone acetylation at genomic promoters in transcriptional activation by nuclear receptors and provide a general mechanism for rapid and reversible transcriptional activation from a chromatin template.
Challenges of parents having developmentally challenged children: An intervention approach using acceptance and commitment therapy

Sir, Neurodevelopmental disorders (NDs) refer to a group of conditions that typically manifest early in development and are characterized by developmental deficits that produce impairments in personal, social, academic, or occupational functioning and the range varies from specific limitations to global impairments. As these problems invariably posit “nonnormative” life‐long conditions and are unlikely to change, at least quickly, those evidently mallet the expectations and create parenting stress ‐ An aversive psychological reaction to the demands of being a parent. [1] They set up long‐lasting reverberations in their relationship with the child and also between themselves and with others who care for and teach the child. Moreover, the child’s need for special nurturance is often inconvenient to the parents and family members, especially provided the socio‐economic scenario and mental health awareness of our country. Acceptance and commitment therapy (ACT)[2] seems well‐suited to address the issue as even widely used behavioral parent training overlook parents’ internal experiences, their ability to learn and implement behavioral parenting techniques and appropriately utilize those in changing contexts. ACT utilizes an eclectic mix of metaphor, paradox, and mindfulness skills, along with a wide range of experiential exercises and values‐guided behavioral intervention that aim to undermine the power of experiential avoidance and cognitive fusion. The ACT practitioner targets six sub‐processes in order to build psychological flexibility[3] using two main components: Acceptance and mindfulness processes (acceptance, defusion, the present moment, and a transcendent sense of self), and commitment and behavioral change processes (values, committed action, the present moment, and a transcendent sense of self).
Ultrasonic evaluation of abdominal aortic thrombus.

Ultrasonograms of 38 patients and computed tomograms of 21 patients with abdominal aortic aneurysms (AAA) were retrospectively reviewed. In 69 per cent of cases in which intraluminal thrombus was demonstrated, sonography revealed a high‐amplitude linear echo along the luminal surface of the thrombus. Although calcification could be easily visualized within the aortic wall by computed tomography, it was seen at the lumen‐‐thrombus interface in only one patient. In addition, a resected aortic aneurysm with thrombus, when scanned in a water bath in vitro, demonstrated this echo pattern at the luminal‐thrombus interface on sonography but revealed no calcification on pathologic examination. An explanation of the source of this echo pattern and a caution against misinterpretation of this echo pattern as the aortic wall in a dissection or leaking aneurysm with hematoma are presented.
The Greater Taurus–Auriga Ecosystem. I. There is a Distributed Older Population

The census of Taurus–Auriga has been assembled over seven decades and inherited the biases and incompleteness of the input studies. The unusual shape of its inferred initial mass function (IMF) and the existence of isolated disk-bearing stars suggest that additional (likely disk-free) members remain to be discovered. We therefore have begun a global reassessment of the census of Taurus–Auriga that exploits new data and better definitions of youth and kinematic membership. As a first step, we reconsider the membership of all disk-free candidate members from the literature with spectral type ≥F0, , and . We combine data from the literature with Keck/HIRES and UH88/SNIFS spectra to test the membership of these candidates using the positions in the Hertzsprung-Russel diagram, proper motions, radial velocities, Hα, lithium, and surface gravity. We find 218 confirmed or likely Taurus members, 160 confirmed or likely interlopers, and only 18 that lack sufficient evidence to draw firm conclusions. A significant fraction of these stars (81/218 = 37%) are not included in the most recent canonical member lists. There are few additional members to the immediate vicinity of the molecular clouds, preserving the IMFs that have been deemed anomalous in past work. Many of the likely Taurus members are instead distributed broadly across the search area. When combined with the known disk hosts, our updated census reveals two regimes: a high-density population with a high disk fraction (indicative of youth) that broadly traces the molecular clouds, and a low-density population with low disk fraction (hence likely older) that most likely represents previous generations of star formation.
A Respiratory Syncytial Virus Replicon That Is Noncytotoxic and Capable of Long-Term Foreign Gene Expression

ABSTRACT Respiratory syncytial virus (RSV) infection of most cultured cell lines causes cell-cell fusion and death. Cell fusion is caused by the fusion (F) glycoprotein and is clearly cytopathic, but other aspects of RSV infection may also contribute to cytopathology. To investigate this possibility, we generated an RSV replicon that lacks all three of its glycoprotein genes and so cannot cause cell-cell fusion or virus spread. This replicon includes a green fluorescent protein gene and an antibiotic resistance gene to enable detection and selection of replicon-containing cells. Adaptive mutations in the RSV replicon were not required for replicon maintenance. Cells containing the replicon could be cloned and passaged many times in the absence of antibiotic selection, with 99% or more of the cells retaining the replicon after each cell division. Transient expression of the F and G (attachment) glycoproteins supported the production of virions that could transfer the replicon into most cell lines tested. Since the RSV replicon is not toxic to these cultured cells and does not affect their rate of cell division, none of the 8 internal viral proteins, the viral RNA transcripts, or the host response to these molecules or their activities is cytopathic. However, the level of replicon genome and gene expression is controlled in some manner well below that of complete virus and, as such, might avoid cytotoxicity. RSV replicons could be useful for cytoplasmic gene expression in vitro and in vivo and for screening for compounds active against the viral polymerase.
Quorum-sensing Salmonella selectively trigger protein expression within tumors

Significance Nonpathogenic Salmonella localize to tumors and can be engineered to secrete anticancer proteins, but tumor-specific expression is essential to prevent systemic toxicity. To reduce unwanted side effects in healthy tissue, we integrated Salmonella with a quorum-sensing (QS) switch that only initiates drug expression in the tightly packed colonies present within tumors. Using an in vitro 3D-tumor-on-a-chip device and in vivo mouse models, we show that QS Salmonella specifically initiates protein expression within cancerous tissue while remaining uninduced in livers. Protein expression was triggered when inducer molecules from enough close neighbors reached a critical concentration. Because of these selective qualities, QS Salmonella are a promising tool for tumor-specific delivery of therapeutic proteins. Salmonella that secrete anticancer proteins have the potential to eliminate tumors, but nonspecific expression causes damage to healthy tissue. We hypothesize that Salmonella, integrated with a density-dependent switch, would only express proteins in tightly packed colonies within tumors. To test this hypothesis, we cloned the lux quorum-sensing (QS) system and a GFP reporter into nonpathogenic Salmonella. Fluorescence and bacterial density were measured in culture and in a tumor-on-a-chip device to determine the critical density necessary to initiate expression. QS Salmonella were injected into 4T1 tumor-bearing mice to quantify GFP expression in vivo using immunofluorescence. At densities below 0.6 × 1010 cfu/g in tumors, less than 3% of QS Salmonella expressed GFP. Above densities of 4.2 × 1010 cfu/g, QS Salmonella had similar expression levels to constitutive controls. GFP expression by QS colonies was dependent upon the distance to neighboring bacteria. No colonies expressed GFP when the average distance to neighbors was greater than 155 µm. Calculations of autoinducer concentrations showed that expression was sigmoidally dependent on density and inversely dependent on average radial distance. Based on bacterial counts from excised tissue, the liver density (0.0079 × 1010 cfu/g) was less than the critical density (0.11 × 1010 cfu/g) necessary to initiate expression. QS Salmonella are a promising tool for cancer treatment that will target drugs to tumors while preventing damage to healthy tissue.
A C‐index for recurrent event data: Application to hospitalizations among dialysis patients

We propose a C‐index (index of concordance) applicable to recurrent event data. The present work addresses the dearth of measures for quantifying a regression model's ability to discriminate with respect to recurrent event risk. The data which motivated the methods arise from the Dialysis Outcomes and Practice Patterns Study (DOPPS), a long‐running prospective international study of end‐stage renal disease patients on hemodialysis. We derive the theoretical properties of the measure under the proportional rates model (Lin et al., 2000), and propose computationally convenient inference procedures based on perturbed influence functions. The methods are shown through simulations to perform well in moderate samples. Analysis of hospitalizations among a cohort of DOPPS patients reveals substantial improvement in discrimination upon adding country indicators to a model already containing basic clinical and demographic covariates, and further improvement upon adding a relatively large set of comorbidity indicators.
Isolation of milk leucocytes and their nuclei.

Abstract Addition of ethylenediaminetetraacetate to 2% concentration increased the recovery of leucocytes in milk by centrifugation. Leucocyte nuclei were isolated by homogenization of milk leucocytes with a Waring Blendor in pH 5.9 citrate buffer and by differential centrifugation of the homogenate. Chemical composition of the leucocyte nuclei was similar to those of somatic cells. The leucocyte nuclei isolated in pH 5.9 citrate buffer formed thick gel with the California Mastitis Test reagent.
Effect of pH on Hydride Transfer by Escherichia coli Dihydrofolate Reductase

The kinetic isotope effect (KIE) on hydride transfer in the reaction catalysed by dihydrofolate reductase from Escherichia coli (EcDHFR) is known to be temperature dependent at pH 7, but essentially independent of temperature at elevated pH. Here, we show that the transition from the temperature‐dependent regime to the temperature‐independent regime occurs sharply between pH 7.5 and 8. The activation energy for hydride transfer is independent of pH. The mechanism leading to the change in behaviour of the KIEs is not clear, but probably involves a conformational change in the enzyme brought about by deprotonation of a key residue (or residues) at high pH. The KIE on hydride transfer at low pH suggests that the rate constant for the reaction is not limited by a conformational change to the enzyme under these conditions. The effect of pH on the temperature dependence of the rate constants and KIEs for hydride transfer catalysed by EcDHFR suggests that enzyme motions and conformational changes do not directly influence the chemistry, but that the reaction conditions affect the conformational ensemble of the enzyme prior to reaction and control the reaction though this route.
Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins

Bacterial microcompartments (MCPs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. MCPs carrying out three different metabolic functions have been characterized in some detail, while gene expression and bioinformatics studies have implicated other types, including one believed to perform glycyl radical‐based metabolism of 1,2‐propanediol (Grp). Here we report the crystal structure of a protein (GrpN), which is presumed to be part of the shell of a Grp‐type MCP in Rhodospirillum rubrum F11. GrpN is homologous to a family of proteins (EutN/PduN/CcmL/CsoS4) whose members have been implicated in forming the vertices of MCP shells. Consistent with that notion, the crystal structure of GrpN revealed a pentameric assembly. That observation revived an outstanding question about the oligomeric state of this protein family: pentameric forms (for CcmL and CsoS4A) and a hexameric form (for EutN) had both been observed in previous crystal structures. To clarify these confounding observations, we revisited the case of EutN. We developed a molecular biology‐based method for accurately determining the number of subunits in homo‐oligomeric proteins, and found unequivocally that EutN is a pentamer in solution. Based on these convergent findings, we propose the name bacterial microcompartment vertex for this special family of MCP shell proteins.
Signal processing for the multistate myoelectric channel

In the multistate myoelectric channel, a single myoelectric signal source is used to control a multifunction powered prosthesis. The selection of a prosthesis function requires a receiver to process the myoelectric signal, contaminated with noise, and to decide on the basis of the received signals which function is desired. Thus the channnel cleady presents a problem of choice of receiver and of decision strategy. Previous sotutions to this problem have been basically empirical. In this paper we seek the optimum receiver where optimum is in the minimum probability of error sense. First a model is developed for the bipolar myoelectric signal to provide information about the relevant signal parameters and statistics. Using this information the Bayes minimum probability of error receiver is derived for an orbitrary signal parameter set. The optimum signal parameter set is then found for the Bayes receiver, and the receiver performance calculated. The receiver performance is measured and compared with the calculated performance. A significant performance improvement is seen in the optimum receiver over a more conventional receiver.
Environmental Impacts of Rice Cultivation

This paper describes the major environmental aspects related to the cultivation of rice. Rice is one of the most important agricultural products and it is cultivated in almost all countries in the world. Its production requires usually large flooded areas. Under these conditions, many greenhouse gases are generated, such as carbon dioxide, methane, nitrogen oxides and its derivatives. Cultivation of rice is responsible by the release of relevant amounts of these gases and contributes decisively to global warming. In this sense, the major points described here are general environmental aspects, the mechanisms of production of greenhouse gases, bioremediation, mitigation using other techniques and possible improvements of the cultivation by fertilizers and chemicals.
Modifying a breast cancer risk factor survey for African American women.

PURPOSE/OBJECTIVES To evaluate a breast cancer risk factor survey for use with African American women. DESIGN Two focus groups consisting of women randomly selected from the patient population of Henry Ford Health System in Detroit, MI. SETTING A large, vertically integrated, private, nonprofit health system. SAMPLE Focus Group I consisted of 11 African American women aged 18-50, with a mean age of 41 years. Focus Group II consisted of nine African American women aged 51 and older, with a mean age of 60.9 years. METHODS A qualitative approach was used to gather and interpret the focus group data. MAIN RESEARCH VARIABLES Perceptions of a breast cancer risk factor survey and perceptions of breast cancer risk factors. FINDINGS The focus group participants suggested ways to improve the survey. Women in the younger age group appeared to lack awareness regarding breast cancer risk factors. Women in the older age group reported not knowing their family health histories. CONCLUSIONS Based on comments made by the focus group participants, the survey was modified substantially. Breast cancer risk factors were perceived differently by women in the two age groups. IMPLICATIONS FOR NURSING Results of a survey of a large, ethnically diverse sample of women could inform the development of culturally and age-appropriate nursing interventions designed to address breast cancer risk perceptions and enhance the likelihood of adherence to recommended mammography screening guidelines.
Weightedhomogeneity and robustness of slidingmode control Automatica , 72 ( 10 ) , pp . 186 – 193 , 2016

General features of finite-time-stable (FTS) homogeneous differential inclusions (DIs) are investigated in the context of slidingmode control (SMC). The continuity features of the settling-time functions of FTS homogeneous DIs are considered, and the system asymptotic accuracy is calculated in the presence of disturbances, noises and delays. Performance of output-feedback multi-input multi-output homogeneous SMC systems is studied in the presence of relative degree fluctuations. The bifurcation of the kinematic-car-model relative degree is analyzed as an example.
Content-based Image Hiding Method for Secure Network Biometric Verification

For secure biometric verification, most existing methods embed biometric information directly into the cover image, but content correlation analysis between the biometric image and the cover image is often ignored. In this paper, we propose a novel biometric image hiding approach based on the content correlation analysis to protect the network-based transmitted image. By using principal component analysis (PCA), the content correlation between the biometric image and the cover image is firstly analyzed. Then based on particle swarm optimization (PSO) algorithm, some regions of the cover image are selected to represent the biometric image, in which the cover image can carry partial content of the biometric image. As a result of the correlation analysis, the unrepresented part of the biometric image is embedded into the cover image by using the discrete wavelet transform (DWT). Combined with human visual system (HVS) model, this approach makes the hiding result perceptually invisible. The extensive experime.
Are Dangerous Offenders Different From Other Offenders? A Clinical Profile

The Canadian dangerous offender (DO) statute requires the assistance of psychiatrists and psychologists in evaluating offenders’ potential danger and risk of future offenses, without substantive supporting empirical clinical research on the topic. The present study compared 62 men facing Canadian DO applications to 2,414 non-DO sexual and violent offenders (ACs) and 62 non-DO offenders matched on offense type (MCs). DOs differed significantly from ACs on 30 of 45 variables and from MCs only on 6. More DOs than MCs had an extensive criminal history, were psychopaths, and had more school truancy. Compared with ACs, DOs had less education and more school adjustment problems, more disturbed childhoods, and more often were diagnosed with sadism, psychopathy, and substance abuse problems. Total sexual and violent offense convictions provided the best but weak distinction of DOs from ACs. The “three strikes” law is noted and early intervention in DOs’ criminal careers is discussed.
Accelerated Accumulation of Misfolded Prion Protein and Spongiform Degeneration in a Drosophila Model of Gerstmann–Sträussler–Scheinker Syndrome

Prion diseases are CNS disorders that can occur in sporadic, infectious, and inherited forms. Although all forms of prion disease are associated with the accumulation of pathogenic conformers of the prion protein, collectively termed PrPSc, the mechanisms by which PrPSc molecules form and cause neuronal degeneration are unknown. Using the bipartite galactosidase-4–upstream activating sequence expression system, we generated transgenic Drosophila melanogaster heterologously expressing either wild-type (WT) or mutant, disease-associated (P101L) mouse PrP molecules in cholinergic neurons. Transgenic flies expressing neuronal P101L PrP molecules exhibited severe locomotor dysfunction and premature death as larvae and adults. These striking clinical abnormalities were accompanied by age-dependent accumulation of misfolded PrP molecules, intracellular PrP aggregates, and neuronal vacuoles. In contrast, transgenic flies expressing comparable levels of WT PrP displayed no clinical, pathological, or biochemical abnormalities. These results indicate that transgenic Drosophila expressing neuronal P101L PrP specifically exhibit several hallmark features of human Gerstmann–Sträussler–Scheinker (GSS) syndrome. Because the rates of abnormal PrP accumulation and clinical progression are highly accelerated in Drosophila compared with the rates of these processes in rodents or humans, the P101L mutant may be used for future genetic and pharmacologic studies as a novel invertebrate model of GSS.
Encoding-Retrieval Relationships in Episodic Memory: A Functional Neuroimaging Perspective

Encoding-Retrieval Relationships in Episodic Memory: A Functional Neuroimaging Perspective by Erik Atkins Wing Department of Psychology and Neuroscience Duke University Date:_______________________ Approved: ___________________________ Roberto Cabeza, Supervisor ___________________________ Elizabeth Marsh ___________________________ Tobias Egner ___________________________ David Madden An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Psychology and Neuroscience in the Graduate School of Duke University 2015 Copyright by Erik Atkins Wing 2015