Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Thyroid Hormone-Responsive Genes in a Chicken Hepatoma Cell Line, LMH

Abstract Thyroid hormone receptors (TRs) are ligand-dependent transcription factors that regulate the transcription of multiple thyroid hormone (TH)-responsive genes. Our study aimed to identify TH-responsive genes in an estrogen-responsive chicken hepatoma cell line, LMH. RNA was prepared from cells treated with or without 10−8 M 3,3′,5-triiodothyronine (T3) for 24 h and was analyzed by differential display. At least six cDNAs were detected whose transcript increased in the presence of T3, and four of them were cloned. The four candidate TH-responsive genes that were identified had high similarity (>83%) to known chicken or mammalian genes, which included the ribosomal protein L7 gene; the cytoplasmic dynein heavy chain gene; the scaffold attachment factor A (SAF-A) gene, also known as heterogenous nuclear ribonucleoprotein U (hnRNP U); and a gene for an unknown protein. Real-time PCR confirmed that the transcription of the four genes was responsive to T3; their transcript levels increased from four to eleven times with the administration of T3. The amount of TRβ transcript did not change with the administration of T3. The physiological reasons for the activation of these genes and the utility of this cell line are discussed.
Differential type I interferon activation and susceptibility of dendritic cell populations to porcine arterivirus

Dendritic cells (DCs) play a role in anti‐viral immunity by providing early innate protection against viral replication and by presenting antigen to T cells for initiation of the adaptive immune response. Studies show the adaptive response to porcine reproductive and respiratory syndrome virus (PRRSV) is ineffective for complete viral elimination. Other studies describe the kinetics of the adaptive response to PRRSV, but have not investigated the early response by DCs. We hypothesize that there is an aberrant activation of DCs early in PRRSV infection; consequently, the adaptive response is triggered inadequately. The current study characterized a subtype of porcine lung DCs (L‐DCs) and investigated the ability of PRRSV to infect and replicate in L‐DCs and monocyte‐derived DCs (MDDCs). Furthermore, the type I interferon anti‐viral response to PRRSV with and without the addition of recombinant porcine IFN‐α (rpIFN‐α), an important cytokine that signals for anti‐viral mediator activation, was analysed. Results show that PRRSV replicated in MDDCs but not L‐DCs, providing evidence that these cells have followed distinct differentiation pathways. Although both cell types responded to PRRSV with an induction of IFN‐β mRNA, the magnitude and duration of the response differed between cell types. The addition of rpIFN‐α was protective in MDDCs, and mRNA synthesis of Mx (myxovirus resistant) and PKR (double‐stranded RNA dependent protein kinase) was observed in both cell types after rpIFN‐α addition. Overall, PRRSV replicated in MDDCs but not L‐DCs, and rpIFN‐α was required for the transcription of protective anti‐viral mediators. DC response to PRRSV was limited to IFN‐β transcription, which may be inadequate in triggering the adaptive immune response.
Inflammation and Immune System Contribution to the Etiology of Atherosclerosis: Mechanisms and Methods of Assessment

BackgroundImmune system activation and inflammation are intricately involved in the development and progression of atherosclerosis. PurposeThe purposes of this review are to (a) discuss effects of inflammation and the immune system across the lifespan of atherosclerotic plaque, (b) review current recommended testing techniques for assessing inflammation using blood and within the atherosclerotic plaque, and (c) link basic research in inflammation and immunology with ongoing clinical research with potential to impact prevention and treatment interventions in atherosclerotic disease. ResultsThe atherosclerotic process is typically initiated in the presence of endothelial dysfunction by increased uptake, entrapment, and deposition of lipids, especially low-density lipoprotein (LDL). Once inside the intima, LDL can become oxidized (LDLox), which promotes further endothelial cell activation/injury, stimulates adhesion molecule expression, and releases chemotactic factors that promote leukocyte–endothelial interactions. The process of atherogenesis is highly regulated by the innate and adaptive immune systems and systemic inflammatory response. In addition, proinflammatory mediators play a key role in the lifespan of the atherosclerotic plaque and its vulnerability, favoring eventual plaque fissure when exposed to increasing hemodynamic stress. DiscussionThe complex atherosclerotic process involves the innate and adaptive immune systems and systemic inflammatory activation. Incorporation of advances in understanding inflammation and immune system contributions to the etiology of atherosclerosis into intervention research allows the development of novel approaches to prevention and treatment.
The narrow substrate specificity of human tyrosine aminotransferase – the enzyme deficient in tyrosinemia type II

Human tyrosine aminotransferase (hTATase) is the pyridoxal phosphate‐dependent enzyme that catalyzes the reversible transamination of tyrosine to p‐hydrophenylpyruvate, an important step in tyrosine metabolism. hTATase deficiency is implicated in the rare metabolic disorder, tyrosinemia type II. This enzyme is a member of the poorly characterized Iγ subfamily of the family I aminotransferases. The full length and truncated forms of recombinant hTATase were expressed in Escherichia coli, and purified to homogeneity. The pH‐dependent titration of wild‐type reveals a spectrum characteristic of family I aminotransferases with an aldimine pKa of 7.22. I249A mutant hTATase exhibits an unusual spectrum with a similar aldimine pKa (6.85). hTATase has very narrow substrate specificity with the highest enzymatic activity for the Tyr/α‐ketoglutarate substrate pair, which gives a steady state kcat value of 83 s−1. In contrast there is no detectable transamination of aspartate or other cosubstrates. The present findings show that hTATase is the only known aminotransferase that discriminates significantly between Tyr and Phe: the kcat/Km value for Tyr is about four orders of magnitude greater than that for Phe. A comparison of substrate specificities of representative Iα and Iγ aminotransferases is described along with the physiological significance of the discrimination between Tyr and Phe by hTATase as applied to the understanding of the molecular basis of phenylketonuria.
Exploring divergence in soft robot evolution

Divergent search is a recent trend in evolutionary computation that does not reward proximity to the objective of the problem it tries to solve. Traditional evolutionary algorithms tend to converge to a single good solution, using a fitness proportional to the quality of the problem's solution, while divergent algorithms aim to counter convergence by avoiding selection pressure towards the ultimate objective. This paper explores how a recent divergent algorithm, surprise search, can affect the evolution of soft robot morphologies, comparing the performance and the structure of the evolved robots.
State–Society Relations, Institutional Transformation and Economic Development in Sub‐Saharan Africa

This paper examines the nature and origins of state–society relations in sub-Saharan Africa (SSA). It traces the region's predatory state–society relations to slavery and colonialism and the concomitant extractive institutions, which are not conducive to sustainable economic development. Consequently, attempts to achieve sustainable development have been largely futile. The paper proposes a strategy for transforming the region's economic and governance institutions for inclusive and enduring growth and development. This strategy includes the promulgation and enforcement of coherent international codes and guidelines for state–society relations.
Ectodomain Shedding of Preadipocyte Factor 1 (Pref-1) by Tumor Necrosis Factor Alpha Converting Enzyme (TACE) and Inhibition of Adipocyte Differentiation

ABSTRACT Preadipocyte factor 1 (Pref-1), an epidermal growth factor repeat containing transmembrane protein found in the preadipocytes, inhibits adipocyte differentiation in vitro and in vivo. Here, we examined the processing of membrane form of Pref-1A to release the 50-kDa soluble form that inhibits adipocyte differentiation. The ectodomain cleavage of Pref-1 is markedly enhanced by phorbol 12-myristate 13-acetate in a dose- and time-dependent manner. The basal and stimulated cleavage is inhibited by the broad metalloproteinase inhibitor GM6001, a fact that suggests that cleavage of membrane Pref-1A is dependent on a metalloproteinase. Next, we showed that release of soluble Pref-1A is inhibited by TAPI-0 and by a tissue inhibitor of metalloproteinase-3, TIMP-3, that can inhibit tumor necrosis factor alpha converting enzyme (TACE), but not by TIMP-1 or TIMP-2. On the other hand, overexpression of TACE increases Pref-1 cleavage to produce the 50-kDa soluble form. Furthermore, this cleavage was not detected in cells with TACE mutation or with TACE small interfering RNA. TACE-mediated shedding of Pref-1 ectodomain inhibits adipocyte differentiation of 3T3-L1 cells and in Pref-1-null mouse embryo fibroblasts transduced with Pref-1A. Identification of TACE as the major protease responsible for conversion of membrane-bound Pref-1 to the biologically active diffusible form provides a new insight into Pref-1 function in adipocyte differentiation.
Deep affordance learning for single- and multiple-instance object detection

Affordance learning in general, is to identify the purpose, use, and ways to interact with an object, based on information gained from observing the object. Most of the existing affordance learning approaches assume the object target has been cropped individually from images. However, the object could not be easily separated from others due to occlusion or noise. Actually, two or more neighboring objects belong to the same class could be detected as one object target. A fault affordance may thus result. In this paper, we propose an extension of the existing object detection by adding a classifier which can recognize the object to two cases: single instance and multiple instances. By doing so, the concept of affordance learning was introduced to utilize the visual information from detected instances and to understand other properties of the object such as if it is singular or multiple, upright or tilted, rigid or deformable, an even movable or static. The algorithm is implemented in Python to provide a one-stop solution for dataset building and management. Experimental results have been enclosed to show the effectiveness and accuracies of the proposed approach.
Disorganized Infant, Child, and Adult Attachment: Collapse in Behavioral and Attentional Strategies

This presentation focuses on the disorganized/disoriented (Group D) categories of infant, child, and adult attachment. The infant D category is assigned on the basis of interruptions and anomalies in organization and orientation observed during Ainsworth's strange situation procedure. In neurologically normal low-risk samples, D attachment is not substantially related to descriptions of infant temperament, and usually appears with respect to only one parent. At six, former D infants are often found to be role-inverting (D-Controlling) towards the parent, while drawings and separation-related narratives (D-Fearful) suggest continuing states of fear and disorganization. In adults, marked lapses in reasoning and discourse surrounding the discussion of loss or abuse during the Adult Attachment Interview (AAI) causes a transcript to be assigned to Unresolved/disorganized (U/d) adult attachment status, which predicts infant D attachment. Bowlby's theory is extended, with the proposal that certain forms of frightening parental behavior will arouse contradictory biologically channeled propensities to approach and to take flight from the parent. Maltreated infants are therefore highly likely to be disorganized. Also identified are subtler forms of frightening parental behavior (including dissociative behavior and anomalous forms of frightened behavior) that appear to lead to infant disorganization. This suggests that infant D attachment may at times represent a second-generation effect of the parent's own continuing unresolved responses to trauma. Infant D attachment predicts disruptive/aggressive and dissociative disorders in childhood and adolescence, while U/d adult attachment appears frequently in psychiatric and criminal populations. Clinical implications are discussed.
Compliance Externalities and the Role‐Model Effect on Law Abidance: Field and Survey Experimental Evidence

Recent theories of compliance predict that, apart from utilitarian considerations, individual decisions to respect or break the law account for virtuous motives and nonutilitarian willingness to promote the social good. We test whether empirical evidence supports these theories by collecting data on cyclists' decisions to ignore a red traffic light in a natural setting. We consider different situations where noncompliance is costly, but without risk, and where material deterrence incentives from legal sanctions remain constant. The only difference between the situations lies in who is observing the cyclists' decision at the traffic light at the intersection of a footpath with the cycle track. We find that about 68 percent of cyclists ignore the red traffic light when there is the opportunity to do so. This frequency does not change substantially when adult bystanders are observing at the pedestrian traffic light. Interestingly, the violation frequency drops to about 10 percent when children are present. Robustness checks rule out the alternative explanations that this change is driven by concerns for children's unpredictable actions, or by the simultaneous presence of other adult bystanders. In a vignette study, we additionally dissect the cyclists' motives for being compliant. Results suggest a “role‐model effect” on compliance. When asked, the majority of participants report that the willingness to educate and be a good example is the most important reason for their decision to abide by the law, hence supporting the empirical observation that promoting the social good can be an important nonutilitarian motive of compliance decisions.
Evidence for two preferred hairpin folding patterns in d(CGG).d(CCG) repeat tracts in vivo.

Unusual DNA secondary structures have been implicated in the expansion of trinucleotide repeat tracts that has been found to be responsible for a growing number of human inherited disorders and folate-sensitive fragile chromosome sites. By inserting trinucleotide repeat sequences into a palindromic clamp in lambda phage we are able to investigate their tendencies to form hairpins in vivo in any particular alignment and with odd or even numbers of repeat units in the hairpin. We previously showed that with d(CAG). d(CTG) repeat tracts there was a markedly greater tendency to form hairpins with even numbers of repeat units than with odd numbers, whereas d(GAC). d(GTC) repeats showed no such alternation despite having the same base composition. We expected that d(CGG). d(CCG) repeats, might show the same pattern as d(CAG). (CTG) repeats since they are also involved in trinucleotide repeat expansion disorders. The pattern was not so clear and we wondered whether this might be because d(CGG). d(CCG) repeats have more than one possible alignment in which they could self-anneal. We now present results for all three alignments, which suggest that while even-membered hairpins are preferred in the frame d(CGG). d(CCG), hairpins with odd numbers of trinucleotides are more stable in the frame d(GGC). d(GCC). In both cases the base-pair predicted to close the terminal loop of unpaired bases is 5'C.3'G which has previously been found to be a favoured loop-closing pair.
Study and Applications of an Informational Measure of Dependence in Survival Models

Abstract: In survival models, when the factor of interest is a continuous variable or is expressed through a group of several variables, the classical measures of risk, i. e. relative risk and odds ratio, are not appropriate and there is no standard measure of dependence between survival and the considered factor. The Information Gain has been proposed by Linfoot (1957) and Kent (1983), giving any parametric model as a generalization of the squared product-moment correlation coefficient of the linear regression model with normal errors. By using simulation methods, we studied the statistical properties of the information gain as a measure of dependence, in the particular case of survival regression models. We suggest several efficient applications of this informational concept to some classical problems of regression analysis and prognostic analysis. Our ideas are illustrated through an example on the prognosis of idiopathic dilated cardiomyopathy.
Optimal hedging for flexible fuel energy conversion networks

We demonstrate an alternative approach for the hedging of flexible energy conversion networks appropriate for use in campus scale and municipal scale utilities with complex energy requirements, fuel sources, and operational flexibility. This new approach utilizes empirical modeling of price models for alternative commodity fuels coupled with a previously reported class of bilinear models for estimating the efficiency of complex and flexible energy conversion networks. The coupling of financial and operational hedging provides the utility operator with additional mechanisms for mitigating price volatility in the energy markets. In this paper, we use a steady state bilinear model introduced in an earlier paper to model a power plant that can utilize either coal or natural gas. The model demonstrates the complex tradeoff between using a lower cost but less efficient fuel versus a more expensive fuel with higher conversion efficiency. This class of bilinear models incorporates first and second law principles from finite-time thermodynamics to predict energy conversion networks. In the hedging framework, the bilinear models are used to compute deterministic optimal operating conditions which are functions of fuel prices. Historical fuel price data are collected for coal and natural gas, and a stochastic price model is fit to capture the joint distribution of fuel prices. The fit is used to generate a fuel cost uncertainty model. The model is used to project a joint distribution of fuel prices over a single period planning horizon. Economic optimization is performed over many fuel price realizations. These results are aggregated to obtain a distribution of prices of fuels and fuel costs of the energy conversion network on the planning horizon. A fuel 'Cost at Risk' model is suggested, and it shows how one may choose to take position in coal inventory or in natural gas futures in order to reduce 'Cost at Risk'. In summary, this paper presents three main results: (1) A stochastic fuel price model is constructed using historical data. (2) Economic optimal process conditions are determined for a flexible fuel energy conversion network model and realizations of future prices using the uncertain fuel price model. (3) Determination of an optimal hedging strategy for the flexible energy conversion network using Monte Carlo techniques.
Time to Treatment for Women With Chlamydial or Gonococcal Infections: A Comparative Evaluation of Sexually Transmitted Disease Clinics in 3 US Cities

Background: Many women with positive screening tests for chlamydia or gonorrhea are not promptly treated and are at risk for complications and further disease transmission. Improved methods for notifying infected patients might increase timely treatment in this population. Goal: Describe notification procedures at STD clinics in Washington, DC; Los Angeles; and San Diego and compare timeliness of treatment during 2000 to 2002. Study: Interviews were conducted to determine methods for notifying infected patients. Data were abstracted from 327 medical records of women with chlamydia or gonorrhea who had not been treated presumptively. The interval between specimen collection and treatment (“time to treatment”) was calculated. Results: Each clinic had different procedures for notifying untreated infected women. Among those treated, the median time to treatment was 18 days in Washington, DC, and 8 days in Los Angeles. In San Diego, the median time to treatment was initially 14 days, which improved to 7 days after patient-notification procedures were changed. Conclusion: Simple changes in patient notification procedures can decrease time to treatment at STD clinics. STD programs should evaluate time to treatment and institute methods for efficient patient follow-up.
Exercise for overweight or obesity.

BACKGROUND Clinical trials have shown that exercise in adults with overweight or obesity can reduce bodyweight. There has been no quantitative systematic review of this in The Cochrane Library. OBJECTIVES To assess exercise as a means of achieving weight loss in people with overweight or obesity, using randomised controlled clinical trials. SEARCH STRATEGY Studies were obtained from computerised searches of multiple electronic bibliographic databases. The last search was conducted in January 2006. SELECTION CRITERIA Studies were included if they were randomised controlled trials that examined body weight change using one or more physical activity intervention in adults with overweight or obesity at baseline and loss to follow-up of participants of less than 15%. DATA COLLECTION AND ANALYSIS Two authors independently assessed trial quality and extracted data. MAIN RESULTS The 43 studies included 3476 participants. Although significant heterogeneity in some of the main effects' analyses limited ability to pool effect sizes across some studies, a number of pooled effect sizes were calculated. When compared with no treatment, exercise resulted in small weight losses across studies. Exercise combined with diet resulted in a greater weight reduction than diet alone (WMD -1.1 kg; 95% confidence interval (CI) -1.5 to -0.6). Increasing exercise intensity increased the magnitude of weight loss (WMD -1.5 kg; 95% CI -2.3 to -0.7). There were significant differences in other outcome measures such as serum lipids, blood pressure and fasting plasma glucose. Exercise as a sole weight loss intervention resulted in significant reductions in diastolic blood pressure (WMD -2 mmHg; 95% CI -4 to -1), triglycerides (WMD -0.2 mmol/L; 95% CI -0.3 to -0.1) and fasting glucose (WMD -0.2 mmol/L; 95% CI -0.3 to -0.1). Higher intensity exercise resulted in greater reduction in fasting serum glucose than lower intensity exercise (WMD -0.3 mmol/L; 95% CI -0.5 to -0.2). No data were identified on adverse events, quality of life, morbidity, costs or on mortality. AUTHORS' CONCLUSIONS The results of this review support the use of exercise as a weight loss intervention, particularly when combined with dietary change. Exercise is associated with improved cardiovascular disease risk factors even if no weight is lost.