Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulating genes with electromagnetic response elements

A 900 base pair segment of the c‐myc promoter, containing eight nCTCTn sequences, is required for the induction of c‐myc expression by electromagnetic (EM) fields. Similarly, a 70 bp region of the HSP70 promoter, containing three nCTCTn sequences, is required for the induction of HSP70 expression by EM fields. Removal of the 900 base pair segment of the c‐myc promoter eliminates the ability of EM fields to induce c‐myc expression. Similarly, removal of the 70 bp region of the HSP70 promoter, with its three nCTCTn sequences, eliminates the response to EM fields. The nCTCTn sequences apparently act as electromagnetic field response elements (EMRE). To test if introducing EMREs imparts the ability to respond to applied EM fields, the 900 bp segment of the c‐myc promoter (containing eight EMREs) was placed upstream of CAT or luciferase reporter constructs that were otherwise unresponsive to EM fields. EMREs‐reporter constructs were transfected into HeLa cells and exposed to 8 μT 60 Hz fields. Protein extracts from EM field‐exposed transfectants had significant increases in activity of both CAT and luciferase, compared with identical transfectants that were sham‐exposed. Transfectants with CAT or luciferase constructs lacking EMREs remained unresponsive to EM fields, i.e., there was no increase in either CAT or luciferase activity. These data support the idea that EMREs can be used as switches to regulate exogenously introduced genes in gene therapy. J. Cell. Biochem. 81:143–148, 2001. © 2001 Wiley‐Liss, Inc.
RAPID SYMPATRY EXPLAINS GREATER COLOR PATTERN DIVERGENCE IN HIGH LATITUDE BIRDS

Latitudinal variation in patterns of evolution has fascinated biologists for over a century, but our understanding of latitudinal differences in evolutionary processes—such as selection and drift—remains limited. Here, we test for, and find, accelerated evolution of color patterns in bird taxa that breed at higher latitudes compared with those breeding in the tropics, analyzing data from seven diverse avian families. Most important, we show that the extent of overlap of species’ breeding ranges (degree of sympatry) explains the elevated rate of color pattern evolution at higher latitudes. We suggest that the dynamic shifts in breeding ranges that accompanied climatic changes during the last 3 million years (Milankovitch Oscillations) resulted in more rapid and more frequent secondary contact at high latitudes. We argue that sympatry among diverging clades causes greater divergence of color traits in birds at higher latitudes through sexual, social, or ecological character displacement that accelerate rates of evolution, and through the selective elimination of weakly differentiated lineages that hybridize and fuse in sympatry (differential fusion).
Hexavalent chromium‐induced multiple biomarker responses in liver and kidney of goldfish, Carassius auratus

Hexavalent chromium [Cr (VI)] is a constituent of chromite ore. Although it is known to have several industrial and technological applications, its release into the aquatic environment as a result of chemical spill or inadequate waste discharge may hamper the health of aquatic organisms. In this study, we have investigated the effects of Cr (VI) on multiple biomarkers responses in goldfish under subchronic exposure conditions. Laboratory‐acclimatized fish were exposed to 4.25 ppm and 8.57 ppm Cr (VI) for four weeks using a continuous flow‐through system. During exposure, fish samples were collected on a weekly basis and analyzed for multiple biomarkers including catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), metallothionein (MT), and total protein in liver and kidney. Study results indicated that the CAT activity and total protein levels in Cr (VI) ‐ treated goldfish did not significantly differ (P > 0.05) from their respective controls during experimentation. However, highly significant up‐regulations (P < 0.05) of SOD, GPx, and MT expression in Cr (VI) ‐ treated goldfish were recorded at different exposure times depending on Cr (VI) concentration, test organ, and/or biomarker of interest. For example, significantly higher liver GPx levels were found at weeks 2 and 3 in the 4.25 ppm concentration, and at weeks 3 and 4 in the 8.57 ppm, while kidney GPx levels were significantly higher at weeks 1, 2 and 3 in the 4.25 ppm concentration, and at weeks 2, 3 and 4 in the 8.57 ppm concentration. In summary, Cr (VI)‐induced oxidative stress was characterized by statistically significant increases in SOD, GPx, and MT expression in goldfish tissues; with the kidney showing a relatively higher sensitivity to Cr (VI) toxicity compared with the liver. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Atomic and molecular adsorption on Rh(111)

Due to the wide use of copper-based catalysts in industrial chemical processes, fundamental understanding of the interactions between copper surfaces and various reaction intermediates is highly desired. Here, we performed periodic, self-consistent density functional theory (DFT-GGA) calculations to study the adsorption of five atomic species (H, C, N, O, and S), seven molecular species (NH3, CH4, N2, CO, HCN, NO, and HCOOH), and 13 molecular fragments (CH, CH2, CH3, NH, NH2, OH, CN, COH, HCO, COOH, HCOO, NOH, and HNO) on the Cu(111) surface at a coverage of 0.25 monolayer. The preferred binding site, binding energy, and the corresponding surface deformation energy of each species were determined, as well as the estimated diffusion barrier and diffusion pathway. The binding strengths calculated using the PW91 functional decreased in the following order: CH > C > O > S > CN > NH > N > CH2 > OH > HCOO > COH > H > NH2 > NOH > COOH > HNO > HCO > CH3 > NO > CO > NH3 > HCOOH. No stable binding structures were observed for N2, HCN, and CH4. The adsorbate–surface and intramolecular vibrational modes of all the adsorbates at their preferred binding sites were deternined. Using the calculated adsorption energetics, potential energy surfaces were constructed for the direct decomposition of CO, CO2, NO, N2, NH3, and CH4 and the hydrogen-assisted decomposition of CO, CO2, and NO.
Dopamine-Dependent Sensitization of Rod Bipolar Cells by GABA Is Conveyed through Wide-Field Amacrine Cells

The vertebrate retina has the remarkable ability to support visual function under conditions of limited illumination, including the processing of signals evoked by single photons. Dim-light vision is regulated by several adaptive mechanisms. The mechanism explored in this study is responsible for increasing the light sensitivity and operational range of rod bipolar cells, the retinal neurons operating immediately downstream of rod photoreceptors. This sensitization is achieved through the sustained dopamine-dependent GABA release from other retinal neurons. Our goals were to identify the cell type responsible for the GABA release and the site of its modulation by dopamine. Previous studies have suggested the involvement of amacrine and/or horizontal cells. We now demonstrate, using mice of both sexes, that horizontal cells do not participate in this mechanism. Instead, sustained GABA input is provided by a subpopulation of wide-field amacrine cells, which stimulate the GABAC receptors at rod bipolar cell axons. We also found that dopamine does not act directly on either of these cells. Rather, it suppresses inhibition imposed on these wide-field cells by another subpopulation of upstream GABAergic amacrine cells, thereby sustaining the GABAC receptor activation required for rod bipolar cell sensitization. SIGNIFICANCE STATEMENT The vertebrate retina has an exquisite ability to adjust information processing to ever-changing conditions of ambient illumination, from bright sunlight to single-photon counting under dim starlight. Operation under each of these functional regimes requires an engagement of specific adaptation mechanisms. Here, we describe a mechanism optimizing the performance of the dim-light channel of vision, which consists of sensitizing rod bipolar cells by a sustained GABAergic input originating from a population of wide-field amacrine cells. Wide-field amacrine cells span large segments of the retina, making them uniquely equipped to normalize and optimize response sensitivity across distant receptive fields and preclude any bias toward local light-intensity fluctuations.
A Multicenter Multinational Registry for Assessing Ventriculoperitoneal Shunt Infections for Hydrocephalus

BACKGROUND:Reported infection rates after ventriculoperitoneal shunt surgery vary from 1 to 25%. Antibiotic-impregnated (AI) catheters may reduce shunt infection rates, but this is uncertain. OBJECTIVE:To establish a prospective shunt registry to evaluate short-term (3-month) infection rates associated with ventriculoperitoneal shunts and standard or AI catheters during surgical treatment of hydrocephalus. METHODS:A prospective, multicenter, noncontrolled, open-label registry investigated patients with de novo catheter implantation or catheter replacement of an existing ventriculoperitoneal shunt. The primary outcome was shunt infection. RESULTS:A total of 440 patients were entered into the registry at 10 sites: 3 in North America, 2 in Singapore, 4 in China and 1 in India. Seven patients were excluded. Of the 433 remaining patients, 314 had new shunts and 119 were revisions. Shunt infections occurred in 14 of 433 patients (3.2%) overall and in 2 of 37 infants (5.2%) younger than 1 year. AI catheters were used in 46 of 433 patients at 7 centers. The shunt infection rate was 0 of 46 for shunts with AI catheters and 14 of 387 (3.6%) without AI catheters. Infection rates were similar with AI catheters, adjusting for age and catheter type. CONCLUSION:The overall shunt infection rate was lower than in previous multicentered studies. The low infection rate and low rate of AI catheter use precludes any meaningful statement regarding the value of AI catheters in reducing the infection rate. Consideration should be given to performing a well designed, adequately powered, prospective randomized controlled trial to determine whether AI catheters reduce shunt infection rates.
Contributing factors to the development of childhood asthma: working toward risk minimization

Asthma is the most common chronic disease in childhood, and considerable research has been undertaken to find ways to prevent its development and reduce its prevalence. For such interventions to be successful, risk factors for asthma emergence should be identified and clearly defined. Data are robust for some of them, including atopy, viral infections and exposure to airborne irritants, whereas it is less conclusive for others, such as aeroallergen exposure and bacterial infections. Several interventions for asthma prevention, including avoidance and pharmacotherapy, have been attempted. However, most of them have furnished equivocal results. Various issues hinder the establishment of risk factors for asthma development and reduce the effectiveness of interventions, including the complexity of the disease and the fluidity of the developing systems in childhood. In this review, we revisit the evidence on pediatric asthma risk factors and prevention and discuss issues that perplex this field.
An Improved Distribution-free EWMA Mean Chart

Control charts are effective tools for signal detection in both manufacturing processes and service processes. Much service data come from a process with variables having nonnormal or unknown distributions. The commonly used Shewhart variable control charts, which depend heavily on the normality assumption, should not be properly used here. In this article, we propose an improved asymmetric EWMA mean chart based on a simple statistic to monitor process mean shift. We explored the sampling properties of the new monitoring statistic and calculated the average run lengths of the proposed asymmetric EWMA mean chart. We recommend the proposed improved asymmetric EWMA mean chart because the average run lengths of the modified charts are more accurate and reasonable than those of the five existed mean charts. A numerical example of service times with a right skewed distribution from a service system of a bank branch is used to illustrate the application of the improved asymmetric EWMA mean chart and to compare it with the five existing mean charts. The proposed chart showed better detection performance than those of the five existing mean charts in monitoring and detecting shifts in the process mean.
Deletion of the murine scavenger receptor CD68[S]

Scavenger receptors (ScRs) are a structurally unrelated family of receptors with the ability to bind modified low density lipoprotein (LDL) as well as a broad range of polyanionic ligands. CD68, whose expression is restricted to mononuclear phagocytes, is a unique ScR family member, owing to its lysosome associated membrane protein (LAMP)-like domain and predominant endosomal distribution. Knockout (ko) mice were generated to directly evaluate the role murine CD68 may play in oxidized LDL (Ox-LDL) uptake. However, CD68−/− macrophages took up Ox-LDL robustly. Likewise, no defects were observed in the ability of CD68−/− mononuclear phagocytes to take up or mount an effective innate response against a number of microbes. Curiously, CD68−/− mononuclear phagocytes exhibited a trend toward enhanced antigen presentation to CD4+ T-cells, raising the possibility that CD68 may function either to negatively regulate antigen uptake, loading, or major histocompatibility complex class II (MHC-II) trafficking.
Dietary intake exposure to sulphites in Italy - analytical determination of sulphite-containing foods and their combination into standard meals for adults and children

The theoretical risk of exceeding the Acceptable Daily Intake (ADI) for sulphites has mostly been examined on the basis of a worst-case scenario. In order to examine the real situation the determination of residue sulphite levels in ready-to-consume foods is required. The aim of this paper is to assess the actual sulphite content of diets obtained from a combination of realistic meals high in sulphite-containing foods. Food products available in Italy containing added sulphites were identified. Overall, 211 samples of foods and beverages (including 85 samples of wine) were collected. The determination of sulphite residues was carried out on the foods which were prepared according to normal domestic practice. It was shown that the diets obtained from these foods would lead to an intake of 23mg/day in children and 50mg/day in adults (both slightly above the ADI for respectively a 30kg child and a 60kg adult). Among all sulphite-containing foods, the highest contributors to the intake were dried fruit and wine, both ingested without further treatment. The analysis of specific consumption data confirmed the existence of a risk of exceeding the ADI related to sulphite residue levels in wine.
The Value of Patients' Handwritten Comments on HCAHPS Surveys

EXECUTIVE SUMMARY Some patients write comments on their Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) surveys, but survey vendors do not record them, and the value of this anecdotal information is not well understood. However, many rating websites contain both numerical ratings and anecdotal comments from consumers who wish to share their experiences, and the option to write comments enhances the appeal of these survey forums. Recent research shows that numerical ratings do not sufficiently capture the range of consumer experiences and that comments contain additional information that complements survey responses. In this study, we investigate the contribution of anecdotal comments on HCAHPS surveys to the prediction of two global outcome measures: overall hospital rating and intention to recommend. HCAHPS surveys were collected retrospectively from 589 inpatients at two community hospitals, whose answers to the HCAHPS questions plus any handwritten comments were entered into a database. Nearly 20% of the surveys contained at least one written comment. A content analysis was performed, and comments were classified as positive, negative, neutral, or mixed. Regression analyses showed that negative comments significantly affected patients' overall hospital rating with and intention to recommend the hospital. After adjusting for their quantitative ratings on the HCAHPS questions, we found that patients who wrote negative comments gave the hospitals significantly lower satisfaction and intention scores. Consistent with prior research, our study showed that the information contained in numerical HCAHPS composite measures was enhanced by patients' commentary. In addition, quantitative HCAHPS ratings appear to underestimate the feelings of people who write negative comments, validating practices at hospitals that use surveys containing negative anecdotes in quality improvement initiatives.
Optimal reception of signals propagating in media with absorption and dispersion

The features of optimal reception of signals propagating in media with the absorption and dispersion are considered. It is shown that in this case bandwidth of emission-reception should be adapted to the desired range of distances, as well as to compensate the phase distortion is introduced by medium of propagation. It is proposed using of the modified correlation functions for signal analysis in such cases.
Regulation of the Il4 Gene Is Independently Controlled by Proximal and Distal 3′ Enhancers in Mast Cells and Basophils

ABSTRACT Mast cells and basophils are known to be a critical interleukin 4 (IL-4) source for establishing Th2 protective responses to parasitic infections. Chromatin structure and histone modification patterns in the Il13/Il4 locus of mast cells were similar to those of IL-4-producing type 2 helper T cells. However, using a transgenic approach, we found that Il4 gene expression was distinctly regulated by individual cis regulatory elements in cell types of different lineages. The distal 3′ element contained conserved noncoding sequence 2 (CNS-2), which was a common enhancer for memory phenotype T cells, NKT cells, mast cells, and basophils. Targeted deletion of CNS-2 compromised production of IL-4 and several Th2 cytokines in connective-tissue-type and immature-type mast cells but not in basophils. Interestingly, the proximal 3′ element containing DNase I-hypersensitive site 4 (HS4), which controls Il4 gene silencing in T-lineage cells, exhibited selective enhancer activity in basophils. These results indicate that CNS-2 is an essential enhancer for Il4 gene transcription in mast cell but not in basophils. The transcription of the Il4 gene in mast cells and basophils is independently regulated by CNS-2 and HS4 elements that may be critical for lineage-specific Il4 gene regulation in these cell types.
Autoimmune hepatitis with incidental histologic features of bile duct injury

Bile duct changes are atypical of autoimmune hepatitis. Our aims were to assess the frequency and significance of these changes in classical disease. Liver biopsy specimens were reviewed under code from 84 patients who satisfied international scoring criteria for autoimmune hepatitis, and the findings were correlated with clinical features and outcome. Twenty patients (24%) had biliary changes, including 6 with destructive cholangitis, 4 with ductopenia, and 10 with nondestructive cholangitis. Patients with and without bile duct changes had similar laboratory findings. Diagnostic scores for autoimmune hepatitis were lower in patients with bile duct changes (16.6 ± 0.6 vs. 19.1 ± 0.2, P < .0001). The frequencies of scores sufficient for a definite (80% vs. 97%, P = .03) or probable diagnosis (20% vs. 3%, P = .03) were also less in this group. Patients with destructive cholangitis and/or ductopenia responded as well to therapy as patients with nondestructive cholangitis, and outcomes in each group were similar to those of patients without biliary changes. We concluded that biliary changes can occur in classic autoimmune hepatitis, and they are not associated with distinctive clinical features or treatment response. They may be coincidental findings associated with classic disease or weak expressions of a variant syndrome. In the absence of a cholestatic clinical syndrome, they do not compel a different management strategy.
Inspiratory muscle strength and endurance during hyperinflation and histamine induced bronchoconstriction.

BACKGROUND: This study investigated whether the inspiratory muscles are susceptible to fatigue during acute airway narrowing because of increased airway resistance and hyperinflation. METHODS: Asthmatic subjects performed up to four series (on separate days) of 18 maximal static inspiratory efforts of 10 seconds' duration with 10 second rest intervals (50% duty cycle; total duration six minutes): at functional residual capacity (FRC) (control); after histamine induced bronchoconstriction, which decreased forced expiratory volume in one second (FEV1) to a mean of 55% (SD 11%) of the initial value; at a voluntarily increased lung volume (initial volume held at 140% control); and after inhalation of histamine at a voluntarily increased lung volume. RESULTS: For the group of subjects the mean (SD) maximal inspiratory pressure (MIP) in the control experiments was 114 (22) cmH2O and the initial volume was 3.5 (1.2) 1. After histamine inhalation the initial lung volume for contractions increased to 118% (5%) of the control volume. In the high lung volume experiments initial volumes were 140% (12%) of the control (volume without histamine) and 140% (15%) (with histamine). The relation between MIP and initial absolute lung volume was determined for each subject before fatigue developed. When the inspiratory pressures for each contraction in the endurance test were normalised to the pressure expected for that lung volume, no significant differences were found between the four experimental conditions for MIP, or between pressures sustained over the 18 contractions. CONCLUSIONS: Histamine induced bronchoconstriction and hyperinflation had no detectable effect on inspiratory muscle strength or endurance in these asthmatic subjects.
Transfusion in the Critically Ill: Does It Affect Outcome?

Anemia and red blood cell (RBC) transfusions are common in critically ill and injured, trauma, and surgical patients. Tolerance of anemia is highly variable, depending on the presence of cardiovascular and other comorbid diseases that may diminish the hemodynamic response to a lower hemoglobin (Hb) level. The quest to define a minimum threshold Hb concentration at which patients achieve significant benefit to improve outcome has not yet been identified. Complications related to RBC transfusion are related to RBC storage and intrinsic properties of donor allogeneic RBCs, including bacterial contamination, transfusion-related acute lung injury, and transfusion-related immunomodulation. The best evidence related to transfusion-related outcome involves titrating transfusion requirements to parameters of severity of illness rather than arbitrarily defined Hb levels.