Miracle-dz/UniFAR-FTUs huggingface dataset:
CagA+ H pylori infection is associated with polarization of T helper cell immune responses in gastric carcinogenesis.

AIM To characterize the immune responses including local and systemic immunity induced by infection with H pylori, especially with CagA+ H pylori strains and the underlying immunopathogenesis. METHODS A total of 711 patients with different gastric lesions were recruited to determine the presence of H pylori infection and cytotoxin associated protein A (CagA), the presence of T helper (Th) cells and regulatory T (Treg) cells in peripheral blood mononuclear cells (PBMCs), expression of plasma cytokines, and RNA and protein expression of IFN-gamma and IL-4 in gastric biopsies and PBMCs were determined by rapid urease test, urea [(14)C] breath test, immunoblotting test, flow cytometry , real time RT-PCR and immunohistochemistry. RESULTS Of the patients, 629 (88.47%) were infected with H pylori; 506 (71.16%) with CagA+ and 123 (17.30%) with CagA- strains. Among patients infected with CagA+ H pylori strains, Th1-mediated cellular immunity was associated with earlier stages of gastric carcinogenesis, while Th2-mediated humoral immunity dominated the advanced stages and was negatively associated with an abundance of Treg cells. However, there was no such tendency in Th1/Th2 polarization in patients infected with CagA- H pylori strains and those without H pylori infection. CONCLUSION Polarization of Th cell immune responses occurs in patients with CagA+ H pylori infection, which is associated with the stage and severity of gastric pathology during the progression of gastric carcinogenesis. This finding provides further evidence for a causal role of CagA+ H pylori infection in the immunopathogenesis of gastric cancer.
Comparison of lactoferrin content in colostrum between different cattle breeds.

Lactoferrin content of colostrum obtained from cows within 24 h after parturition was measured using a single radial immunodiffusion test and was compared among cows of two dairy breeds (Holstein-Friesian, Jersey) and two beef breeds (Japanese Black and Japanese Brown). Average lactoferrin content in colostrum of dairy breeds was 2 mg/ml and in colostrum of beef breeds was . 5 mg/ml. Lactoferrin content of colostrum due to lactation number was also different among breeds. In dairy breeds, multiparous cows had lactoferrin content two to three times higher than that of primiparous cows; beef breeds showed no obvious differences between lactation years. Lactoferrin content also varied considerably within breed. In beef breeds, half the cows had values of nearly zero. Transferrin content in colostrum was fairly constant (.9 mg/ml) and was not as variable among and within breeds. There was no correlation between lactoferrin and transferrin contents in colostrum. Examination of cows lacking lactoferrin suggested that transferrin plays an important role as an iron carrier from a cow to her newborn calf.
Successful deep brain stimulation of the nucleus accumbens in severe alcohol dependence is associated with changed performance monitoring

Following recent advances in neuromodulation therapy for mental disorders, we treated one patient with severe alcohol addiction with deep brain stimulation (DBS) of the nucleus accumbens (NAc). Before and one year following the surgery, we assessed the effects of DBS within the NAc on the addiction as well as on psychometric scores and electrophysiological measures of cognitive control. In our patient, DBS achieved normalization of addictive behavior and craving. An electrophysiological marker of error processing (the error‐related negativity) linked to anterior mid‐cingulate cortex (aMCC) functioning was altered through DBS, an effect that could be reversed by periods without stimulation. Thus, this case supports the hypothesis that DBS of the NAc could have a positive effect on addiction trough a normalization of craving associated with aMCC dysfunction.
ToXgene: a template-based data generator for XML

Synthetic collections of XML documents can be useful in many applications, such as benchmarking (e.g., Xmark [4], XOO7 [2]) and algorithm testing and evaluation. We present ToXgene, a template-based tool for facilitating the generation of large, consistent collections of synthetic XML documents. ToXgene was designed with the following requirements in mind: it should be declarative, to speed the data generation up; it should be general enough to generate fairly complex XML content and it should be powerful enough to capture the most common kinds of constraints in popular benchmarks. Preliminary experimental results show that our tool can closely reproduce the data sets for the Xmark and the TPC-H benchmarks [6]. The ToXgene Template Specification Language (TSL) is a subset of the XML Schema notation augmented with annotations for specifying certain properties of the intended data, such as probability distributions, the vocabulary for CDATA content, etc. We use XML Schema as the basis for TSL not only because it is a W3C standard, but also because it provides a more detailed description of XML documents than DTDs; in particular, it allows the specification of datatypes. We note that our tool gives the user total control over the data to be generated; thus, it is intended for the cases when the user knows the structure of the data she wants and requires the data to conform to this structure (however, we note that the structure does not have to be regular). The main features of our tool are:
The structural correlates of climate for change in a multihospital system

This study tests four propositions concerning the relationship among centralization, technological complexity, formalization and stratification, and organizational climate for change. The propositions are based on Jerald Hage's axiomatic theory. Data were collected by questionnaire from 348 respondents from 92 units of a multihospital system. Hage's theory predicts both positive and negative impacts of structure on the organization's capacity for change, with complexity positively related to change and increasing structuring negatively related to change. Findings indicate that, under conditions of technological complexity, aspects of formalization and centralization are functional for climate for change. Critically negative impacts appear to be associated with lack of participation in decision-making and aspects of stratification. The findings are interpreted within the broader theoretical perspective of Weber's theory of bureaucracy
A novel vapor pressure transfusion model for the popcorning analysis of Quad Flat No-lead (QFN) packages

Vapor pressure is caused by moisture vaporizing during the reflow heating process. Most existing models evaluate vapor pressure based on moisture diffusion in solids by adopting Fick's law. Differing from the traditional ones, a novel vapor pressure transfusion model is proposed in this paper with the consideration of moisture transfusion from the encapsulation molding compound into the crack opening zone. Quad Flat No-lead package is employed for demonstration. Based on certain assumptions that can be justified through physical conditions, a simple 1-D moisture transport model is established and a “moisture convection coefficient” is defined. With the “moisture convection” boundary condition, the analytical solution can be derived. In addition to simulation, an experimental study on the same type of package is also performed for model validation. Compared to the experiment results, it is found that the strain energy release rate calculated with the current novel vapor pressure model is more reasonable than those with traditional models. Several key features of the comparison between novel and traditional models are discussed in this paper.
Simultaneous wireless information and power transfer with co-channel interference

Simultaneous wireless information and power transfer (SWIFT) is an appealing solution to balance the energy distribution in wireless networks and improve the energy-efficiency of the entire network. In this paper, we study the optimal policies for SWIPT over the flat-fading channel subject to the co-channel interference. The SWIPT receiver using dynamic power splitting (DPS) is expected to achieve the maximum information rate given an average harvested energy constraint. In the case that channel state information at the transmitter (CSIT) is not available, the optimal power splitting is derived. For the case with CSIT, the joint optimal policy of the transmit power and the power splitting are also provided. Through simulations, we show the optimal rate-energy (R-E) trade-offs of our proposed policies. The case with CSIT achieves better R-E trade-off than the case with no CSIT.
Evaluation of the cardiovascular and subjective effects of rivastigmine in combination with methamphetamine in methamphetamine-dependent human volunteers.

Acetylcholine (ACh) has been implicated in the reinforcing and locomotor-activating effects produced by methamphetamine (Meth). Of interest, recent data suggest that acetylcholinesterase (AChE) inhibitors attenuate Meth-seeking behaviour in rats. We conducted this study in order to determine the safety (adverse events, mood changes, cardiovascular effects) and preliminary efficacy (subjective effects) of the AChE inhibitor rivastigmine (Riv) when tested in combination with Meth. Twenty-three non-treatment-seeking Meth-dependent participants resided in an in-patient unit at UCLA for 2mg i.v. ) and Meth (day 5, 30mg, n=7) or Riv (1.5mg, n=9). On day 11, the subjects received saline and Meth infusions again (randomized to either 11:30 or 14:30 hours), under double-blind conditions. The data analyses compared across-study measures of adverse events and mood, and a post-randomization analysis of cardiovascular and subjective effects (on day 11). The data reveal that rivastigmine was not associated with increased adverse events or alterations in mood. As expected, acute Meth exposure (30mg, significantly attenuated Meth-induced increases in diastolic blood pressure, and self-reports of and (p<0.05). Taken together, the findings in the current report suggest that pharmacological manipulations that enhance brain ACh warrant continued investigation as potential treatments for Meth addiction.
Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure

A well‐designed sampling scheme is critical for obtaining accurate results from population genetic studies. Larval samples contain only the genetic material of successful breeders, often of a single year, and may be biased towards particular families. To quantify the bias of using larval samples to infer population and landscape genetic structure and explore how this bias may be reduced using sibship analysis, we analysed eight microsatellite loci from 484 tissue samples of larvae and adults of Columbia spotted frogs (Rana luteiventris) and long‐toed salamanders (Ambystoma macrodactylum) at nine breeding sites in north Idaho. Differences in allele frequencies between adult and larval samples were not detected after full‐siblings were removed from the larval data set for Columbia spotted frogs; for long‐toed salamanders, these differences remained at two out of four ponds. Data from Columbia spotted frog larvae indicated higher levels of differentiation among populations (median difference in FST = 0.020, P < 0.01), as predicted by population genetic theory, whereas data from larval samples of long‐toed salamanders showed some evidence of lower levels of differentiation among populations (median difference in FST = 0.012, P = 0.06). For both species, removing all but one individual from each full‐sibling family led to parameter estimates that were closer to those calculated from adult samples for both population and landscape genetic measures. Removal of full‐siblings is likely to improve estimates of population genetic parameters; however, knowledge of the species’ breeding system is essential for understanding additional sources of bias when inferring population genetic structure from larval samples.
Accuracy of the Composite Variability Index as a Measure of the Balance Between Nociception and Antinociception During Anesthesia

BACKGROUND:The Composite Variability Index (CVI), derived from the electroencephalogram, was developed to assess the antinociception–nociception balance, whereas the Bispectral Index (BIS) was developed to assess the hypnotic state during anesthesia. We studied the relationships between these indices, level of hypnosis (BIS level), and antinociception (predicted remifentanil effect-site concentrations, CeREMI) before and after stimulation. Also, we measured their association with movement in response to a noxious stimulus. METHODS:We randomized 120 patients to one of 12 groups targeting different hypnotic levels (BIS 70, 50, and 30) and various CeREMI (0, 2, 4, or 6 ng/mL). At pseudo-steady state, baseline values were observed, and a series of stimuli were applied. Changes in BIS, CVI, heart rate (HR), and mean arterial blood pressure (MAP) between baseline and response period were analyzed in relation to level of hypnosis, antinociception, and somatic response to the stimuli. RESULTS:CVI and BIS more accurately correlate with somatic response to an Observer Assessment of Alertness and Sedation-noxious stimulation than HR, MAP, CeREMI, and propofol effect-site concentration (Tukey post hoc tests P < 0.01). Change in CVI is more adequate to monitor response to stimulation than changes in BIS, HR, or MAP (as described by the Mathews Correlation Coefficient with significance level set at P < 0.001). In contrast, none of the candidate analgesic state indices was uniquely related to a specific opioid concentration and is extensively influenced by the hypnotic state as measured by BIS. CONCLUSIONS:CVI appears to correlate with somatic responses to noxious stimuli. However, unstimulated CVI depends more on hypnotic drug effect than on opioid concentration.
Conservation and Function of a Potential Substrate-Binding Domain in the Yeast Clb5 B-Type Cyclin

ABSTRACT Cyclin A contains a region implicated in binding to the p27 inhibitor and to substrates. There is strong evolutionary conservation of surface residues contributing to this region in many cyclins, including yeast B-type cyclins, despite the absence of a yeast p27 homolog. The yeast S-phase B-type cyclin Clb5p interacted with mammalian p27 in a two-hybrid assay. This interaction was disrupted by mutations designed to disrupt hydrophobic interactions (hpmmutation) or hydrogen bonding (Q241A mutation) based on the cyclin A-p27 crystal structure. In contrast, mutation of the Clb5p p27-binding domain only slightly reduced binding and inhibition by the Sic1p Clb-Cdc28p kinase inhibitor. Mutations disrupting the p27-binding domain strongly reduced Clb5p biological activity in diverse assays without reducing Clb5p-associated kinase activity. An analogoushpm mutation in the mitotic cyclin Clb2p reduced mitotic function, but in some assays this mutation increased the ability of Clb2p to perform functions normally restricted to Clb5p. These results support the idea of a modular, structurally conserved cyclin domain involved in substrate targeting.
Making Prudent Recommendations for Return-to-Play in Adult Athletes With Cardiac Conditions

Clinicians who treat millions of adult athletes throughout the world may be faced with participation or return-to-play decisions in individuals with known or suspected cardiac conditions. Here we review existing published participation guidelines and analyze emerging data from ongoing registries and population-based studies pertaining to return-to-play decisions for cardiac conditions specifically affecting adult athletes. Considerations related to return-to-play decisions will vary according to age of the athlete, with inherited disorders being the main consideration in younger adult athletes aged 18 to 40 yr, and coronary artery disease being the main consideration in older adult athletes aged 40 yr and older. Although this arbitrary division is based on the epidemiology of underlying heart disease in these populations, the essential return-to-play decision process for both age groups is quite similar. Among the most widely used guidelines to make return-to-play decisions in this group of athletes are the 36th Bethesda Conference Eligibility Recommendations for Competitive Athletes with Cardiovascular Abnormalities. These have long been considered the "gold standard" for determining return-to-play decisions in young athletes in the United States. Other guidelines are available for unique purposes, including The European Society of Cardiology guidelines, and the American Heart Association published recommendations regarding participation of young patients (younger than 40 yr) with genetic cardiovascular diseases in recreational sports. The latter are consistent with the 36th Bethesda guidelines and cover common genetically based diseases such as inherited cardiomyopathies, channelopathy, and connective tissue disorders like Marfan's syndrome. The consensus on masters athletes (older than 40 yr) provides return-to-play decisions for a wide variety of conditioned states, from elite older athletes to walk-up athletes. For any adult athlete with a cardiac condition, return-to-play decisions following use of medications, ablation procedures, device implantation, corrective surgery, or coronary intervention depend on whether the procedure has sufficiently altered the risk for sudden cardiac events, and whether there is a potential for unfavorable interaction with cardiac performance.
The Phosphotransferase System-Dependent Sucrose Utilization Regulon in Enteropathogenic Escherichia coli Strains Is Located in a Variable Chromosomal Region Containing iap Sequences

The capacity to utilize sucrose as a carbon and energy source (Scr+ phenotype) is a highly variable trait among Escherichia coli strains. In this study, seven enteropathogenic E. coli (EPEC) strains from different sources were studied for their capacity to grow using sucrose. Liquid media cultures showed that all analyzed strains have the Scr+ phenotype and two distinct groups were defined: one of five and another of two strains displaying doubling times of 67 and 125 min, respectively. The genes conferring the Scr+ phenotype in one of the fast-growing strains (T19) were cloned and sequenced. Comparative sequence analysis revealed that this strain possesses the scr regulon genes scrKYABR, encoding phosphoenolpyruvate:phosphotransferase system-dependent sucrose transport and utilization activities. Transcript level quantification revealed sucrose-dependent induction of scrK and scrR genes in fast-growing strains, whereas no transcripts were detected in slow-growing strains. Sequence comparison analysis revealed that the scr genes in strain T19 are almost identical to those present in the scr regulon of prototype EPEC E2348/69 and in both strains, the scr genes are inserted in the chromosomal intergenic region of hypothetical genes ygcE and ygcF. Comparison of the ygcE-ygcF intergenic region sequence of strains MG1655, enterohemorrhagic EDL933, uropathogenic ECFT073 and EPEC T19-E2348/69 revealed that the number of extragenic highly repeated iap sequences corresponded to nine, four, two and none, respectively. These results show that the iap sequence-containing chromosomal ygcE-ygcF intergenic region is highly variable in E. coli.
Gene Structure and Expression of Kaposi's Sarcoma-Associated Herpesvirus ORF56, ORF57, ORF58, and ORF59

ABSTRACT Though similar to those of herpesvirus saimiri and Epstein-Barr virus (EBV), the Kaposi's sarcoma-associated herpesvirus (KSHV) genome features more splice genes and encodes many genes with bicistronic or polycistronic transcripts. In the present study, the gene structure and expression of KSHV ORF56 (primase), ORF57 (MTA), ORF58 (EBV BMRF2 homologue), and ORF59 (DNA polymerase processivity factor) were analyzed in butyrate-activated KSHV+ JSC-1 cells. ORF56 was expressed at low abundance as a bicistronic ORF56/57 transcript that utilized the same intron, with two alternative branch points, as ORF57 for its RNA splicing. ORF56 was transcribed from two transcription start sites, nucleotides (nt) 78994 (minor) and 79075 (major), but selected the same poly(A) signal as ORF57 for RNA polyadenylation. The majority of ORF56 and ORF57 transcripts were cleaved at nt 83628, although other nearby cleavage sites were selectable. On the opposite strand of the viral genome, colinear ORF58 and ORF59 were transcribed from different transcription start sites, nt 95821 (major) or 95824 (minor) for ORF58 and nt 96790 (minor) or 96794 (major) for ORF59, but shared overlapping poly(A) signals at nt 94492 and 94488. Two cleavage sites, at nt 94477 and nt 94469, could be equally selected for ORF59 polyadenylation, but only the cleavage site at nt 94469 could be selected for ORF58 polyadenylation without disrupting the ORF58 stop codon immediately upstream. ORF58 was expressed in low abundance as a monocistronic transcript, with a long 5′ untranslated region (UTR) but a short 3′ UTR, whereas ORF59 was expressed in high abundance as a bicistronic transcript, with a short 5′ UTR and a long 3′ UTR similar to those of polycistronic ORF60 and ORF62. Both ORF56 and ORF59 are targets of ORF57 and were up-regulated significantly in the presence of ORF57, a posttranscriptional regulator.
Rhabditid Nematode-Associated Ophthalmitis and Meningoencephalomyelitis in Captive Asian Horned Frogs (Megophrys Montana)

Between 2006 and 2008, 4 captive Asian horned frogs (Megophrys montana) were diagnosed with ocular and neurologic disease associated with rhabditid nematodiasis. Mortality, either spontaneous or by humane euthanasia, was high (3/4, 75%). Gross and histologic findings included varying degrees of ulcerative keratitis, histiocytic uveitis and retinitis, meningoencephalomyelitis, and epidermal chromatophore (iridophore) hyperplasia with intralesional nematodes. Entry into the host was presumed to be by direct invasion of the skin and the cornea with migration through the optic nerve to the brain and spinal cord. One frog was diagnosed with rhabditid nematodiasis antemortem, and clinical signs and lesions in the frog did not progress after unilateral enucleation and anthelminthic treatment were completed. Gross and tissue morphology of the nematodes were consistent with the order Rhabditida. DNA was extracted separately from 2 individual nematodes that were isolated from frozen and ethanol-preserved eye and brain tissue. These DNA templates were used for polymerase chain reaction amplification and sequencing of nuclear 28S large subunit (LSU) and internal transcribed spacer (ITS) ribosomal DNA regions. Comparison of the LSU and ITS sequences to those deposited in GenBank revealed an exact match for Caenorhabditis elegans.
Adiposity in children and adolescents: correlates and clinical consequences of fat stored in specific body depots

The 2011 Pennington Biomedical Research Center's Scientific Symposium focused on adiposity in children and adolescents. The symposium was attended by 15 speakers and other invited experts. The specific objectives of the symposium were to (i) integrate the latest published and unpublished findings on the laboratory and clinical assessment of depot‐specific adiposity in children and adolescents, (ii) understand the variation in depot‐specific adiposity and related health outcomes associated with age, sex, maturation, ethnicity and other factors and (iii) identify opportunities for incorporating new markers of abdominal obesity into clinical practice guidelines for obesity in children and adolescents. This symposium provided an overview of important new advances in the field and identified directions for future research. The long‐term goal of the symposium is to aid in the early identification of children and adolescents who are at increased health risk because of obesity and obesity‐related conditions.