Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Campylobacter jejuni Biofilms under Defined Growth Conditions

ABSTRACT Campylobacter jejuni is a major cause of human diarrheal disease in many industrialized countries and is a source of public health and economic burden. C. jejuni, present as normal flora in the intestinal tract of commercial broiler chickens and other livestock, is probably the main source of human infections. The presence of C. jejuni in biofilms found in animal production watering systems may play a role in the colonization of these animals. We have determined that C. jejuni can form biofilms on a variety of abiotic surfaces commonly used in watering systems, such as acrylonitrile butadiene styrene and polyvinyl chloride plastics. Furthermore, C. jejuni biofilm formation was inhibited by growth in nutrient-rich media or high osmolarity, and thermophilic and microaerophilic conditions enhanced biofilm formation. Thus, nutritional and environmental conditions affect the formation of C. jejuni biofilms. Both flagella and quorum sensing appear to be required for maximal biofilm formation, as C. jejuni flaAB and luxS mutants were significantly reduced in their ability to form biofilms compared to the wild-type strain.
A large scale screen for neural stem cell markers in Xenopus retina

Neural stem cell research suffers from a lack of molecular markers to specifically assess stem or progenitor cell properties. The organization of the Xenopus ciliary marginal zone (CMZ) in the retina allows the spatial distinction of these two cell types: stem cells are confined to the most peripheral region, while progenitors are more central. Despite this clear advantage, very few genes specifically expressed in retinal stem cells have been discovered so far in this model. To gain insight into the molecular signature of these cells, we performed a large‐scale expression screen in the Xenopus CMZ, establishing it as a model system for stem cell gene profiling. Eighteen genes expressed specifically in the CMZ stem cell compartment were retrieved and are discussed here. These encode various types of proteins, including factors associated with proliferation, mitotic spindle organization, DNA/RNA processing, and cell adhesion. In addition, the publication of this work in a special issue on Xenopus prompted us to give a more general illustration of the value of large‐scale screens in this model species. Thus, beyond neural stem cell specific genes, we give a broader highlight of our screen outcome, describing in particular other retinal cell markers that we found. Finally, we present how these can all be easily retrieved through a novel module we developed in the web‐based annotation tool XenMARK, and illustrate the potential of this powerful searchable database in the context of the retina. © 2011 Wiley Periodicals, Inc. Develop Neurobiol 72: 491–506, 2012
Elucidation of the molecular mechanism and the efficacy in vivo of a novel 1,4‐benzoquinone that inhibits 5‐lipoxygenase

1,4‐Benzoquinones are well‐known inhibitors of 5‐lipoxygenase (5‐LOX, the key enzyme in leukotriene biosynthesis), but the molecular mechanisms of 5‐LOX inhibition are not completely understood. Here we investigated the molecular mode of action and the pharmacological profile of the novel 1,4‐benzoquinone derivative 3‐((decahydronaphthalen‐6‐yl)methyl)‐2,5‐dihydroxycyclohexa‐2,5‐diene‐1,4‐dione (RF‐Id) in vitro and its effectiveness in vivo.
Endothelial Nitric Oxide Synthase–Independent Protective Action of Statin Against Angiotensin II–Induced Atrial Remodeling via Reduced Oxidant Injury

Activation of the renin-angiotensin system exacerbates atrial remodeling, leading to atrial fibrillation and thrombosis, especially in a condition with decreased NO bioavailability. Recently, it has been reported that statins reduce the incidence of atrial fibrillation through attenuation of atrial remodeling; however, the mechanisms have not been completely elucidated. Therefore, we aimed to clarify the beneficial effect of statin on atrial remodeling in condition with reduced NO bioavailability. Endothelial NO synthase−/− mice were sham operated or infused with angiotensin II (Ang II) via an osmotic minipump for 2 weeks, and Ang II–infused mice were divided into 3 treatment groups: pitavastatin, Tempol (a free radical scavenger), or vehicle. Echocardiography and electrocardiography showed that Ang II infusion caused left atrial enlargement and a high incidence of atrial fibrillation, whereas pitavastatin and Tempol prevented these abnormalities. In histological analysis, Ang II–induced atrial interstitial fibrosis, perivascular fibrosis, and cardiomyocyte hypertrophy were all attenuated by pitavastatin and Tempol. Immunohistochemical staining showed that Ang II downregulated thrombomodulin and tissue factor pathway inhibitor and upregulated tissue factor and plasminogen activator inhibitor 1 in the left atrium and that pitavastatin and Tempol corrected the thrombogenic condition. Moreover, pitavastatin and Tempol reduced Ang II–induced atrial superoxide production and atrial transforming growth factor-&bgr;1 expression and Smad 2/3 phosphorylation. Atrial rac1-GTPase activity, known to activate NADPH oxidase, was attenuated by pitavastatin but not by Tempol. In conclusion, pitavastatin exerts endothelial NO synthase–independent protective actions against Ang II–induced atrial remodeling and atrial fibrillation with enhanced thrombogenicity through suppression of oxidant injury.
[Identification of differentially expressed genes in familial acute myelogenous leukemia by suppression subtractive hybridization].

OBJECTIVE To isolate genes expressed differentially from the bone marrow cells of patients with familial acute myelocytic leukemia and to explain the molecular mechanisms of the disease at the gene level. METHODS Bone marrow cells were obtained from a family with cases of familial acute myelocytic leukemia for successive 4 generations. Super SMART cDNA synthesis and suppression subtractive hybridization (SSH) were performed to set up a subtractive cDNA library of specially or highly expressed genes. The white clones were screened and identified by modified differential screening technique in which the probes were labeled with digoxin/deoxyuridine 5'-triphosphate. Positive clones were sequenced and compared with the known sequences in the public databases of GenBank/EMBL/DDBJ using NCBI BLAST for homology analysis. The unknown fragments were then submitted to GenBank. RESULTS A subtractive library of differentially expressed genes for the family with cases of familial acute myelocytic leukemia was constructed successfully. After differential screening, 28 effective sequences were confirmed to be positive differentially expressed gene fragments and were submitted to GenBank for homology analysis. Then 17 sequences were identified as a part of known genes, and the rests were verified as unknown fragments. CONCLUSION SSH is an effective approach to isolate differentially expressed genes. Some genes related to cell proliferation and differentiation has been acquired by SSH. Eleven novel expressed sequence tags related to library have been successfully isolated and accepted by GenBank.
Screening for metastasis from choroidal melanoma: the Collaborative Ocular Melanoma Study Group Report 23.

PURPOSE To describe the predictive value of liver function tests (LFTs), chest x-ray, and diagnostic imaging for detecting melanoma metastasis during routine follow-up after treatment for choroidal melanoma. MATERIALS AND METHODS Prospective longitudinal follow-up of patients enrolled onto two randomized trials was conducted by the Collaborative Ocular Melanoma Study (COMS) Group. Baseline and annual or semiannual systemic and laboratory evaluations were performed according to a standard protocol for 2320 patients enrolled on the COMS. RESULTS COMS patients were screened annually for metastasis and new cancers using LFTs (alkaline phosphatase, AST, ALT, or bilirubin). Elevated findings (1.5 to 2 times upper limit of normal) on LFT prompted a diagnostic or imaging test to confirm or rule out cancer recurrence. Of 714 patients with clinical reports of metastasis, 675 patients died. Of these 675 patients, all but four had either histopathologically confirmed or clinically suspected metastatic melanoma present at the time of death. Among all patients, the 5-year cumulative diagnosis rate of metastatic melanoma was 24% (95% CI, 22% to 27%). Based on all patients with reported metastasis, the sensitivity, specificity, positive predictive value and negative predictive value associated with at least one abnormal LFT before first diagnosis of metastasis at any site was 14.7%, 92.3%, 45.7% and 71.0%, respectively. CONCLUSION Use of LFTs results followed by diagnostic tests has high specificity and predictive values but low sensitivity. Better tests are needed to identify earlier metastatic disease associated with choroidal melanoma.
The effects of different doses of 670 nm diode laser on skin flap survival in rats.

PURPOSE To investigate the effects of different low-level laser therapy (LLLT) doses on random skin flap rats. METHODS Forty Wistar rats were randomly divided in four groups. The control group (CG) was not irradiated. The experimental groups were irradiated with a diode laser 670 nm with different energies per point: group 2 (G2) with 0.06 J; group 3 (G3) 0.15 J and group 4 (G4) 0.57 J. The three groups were irradiated in 12 equally distributed points in the cranial skin flap portion. They were submitted to the irradiation during the immediate, first and second postoperative days. The necrosis area was evaluated in the seventh postoperative day. RESULTS The CG shows 49.35% of necrosis area in the skin flap; G2, 39.14%; G3, 47.01% and G4, 29.17% respectively. There was a significantly difference when G4 was compared with CG`s skin flap necrosis area. CONCLUSION The low-level laser therapy diode 670 nm with 0.57 J energy per point increases the survival in randomic skin flap rats.
Scalable critical-path analysis and optimization guidance for hybrid MPI-CUDA applications

The use of accelerators in heterogeneous systems is an established approach in designing petascale applications. Today, Compute Unified Device Architecture (CUDA) offers a rich programming interface for GPU accelerators but requires developers to incorporate several layers of parallelism on both the CPU and the GPU. From this increasing program complexity emerges the need for sophisticated performance tools. This work contributes by analyzing hybrid MPI-CUDA programs for properties based on wait states, such as the critical path, a metric proven to identify application bottlenecks effectively. We developed a tool to construct a dependency graph based on an execution trace and the inherent dependencies of the programming models CUDA and Message Passing Interface (MPI). Thereafter, it detects wait states and attributes blame to responsible activities. Together with the property of being on the critical path, we can identify activities that are most viable for optimization. To evaluate the global impact of optimizations to critical activities, we predict the program execution using a graph-based performance projection. The developed approach has been demonstrated with suitable examples to be both scalable and correct. Furthermore, we establish a new categorization of CUDA inefficiency patterns ensuing from the dependencies between CUDA activities.
Electronic monitoring and monitoring probation: The case of Ireland

Set against an environment of diverse reforms across the domestic criminal justice system, including new oversight arrangements, the current article considers how probation in Ireland has almost entirely escaped notice. A case for probation oversight is made on the basis of its caseload size but also a decade of unaccounted use of electronic monitoring (EM). Global EM use highlights questions about domestic probation standards, research and planning. Shortcomings within the legislative consultation process around the tool’s role, the lack of any evaluation of EM suppliers and increasing focus on data management to date also bolster a case for oversight of Irish probation. A principal issue within this set of challenges for probation is how EM might adjust traditional agency values. Overall, the contention is made that the assumed exceptionalism of Republic of Ireland’s criminal justice system, that which acts as a buffer to change, may no longer be valid.
Preliminary treatment results of intensity-modulated radiotherapy for prostate cancer.

BACKGROUND To review the initial treatment results of intensity-modulated radiotherapy (IMRT) for prostate cancer. METHODS Ninety-two patients treated with IMRT before July 2003 were included in this study. The median follow-up was 32 months. The indications for IMRT included primary, adjuvant, and salvage treatment. Combined treatment with androgen suppression therapy was variable. The primary study endpoints were chronic adverse events which were subjectively reported. Only patients with an adenocarcinoma and who had been treated by primary radiotherapy were included in the analysis of disease relapse. RESULTS At the time of analysis, 89 patients were still alive, and only 2 patients had died of prostate cancer. In the survival analysis, the 30-month failure-free survival rates were 100%, 89.2%, and 67.3% for the low-, intermediate-, and high-risk groups of patients, respectively. Pretreatment PSA level, Gleason score, risk classification, and adjuvant hormone therapy were significantly associated with relapse according to the univariate analysis, while only risk classification remained significant in the multivariate analysis. During follow-up, 5 (6%) patients developed grade 2 gastrointestinal (GI) adverse events (AE). Sixteen (18%) and 7 (8%) patients developed grade 2 and 3 urinary AE, respectively. Development of severe urinary adverse events was closely related to previous surgical treatment. No factor was identified as being correlated with the GI adverse events. The preservation rate of sexual function was 25.7%. CONCLUSIONS Seventy-two Grays of irradiation, administered by IMRT, is a safe method as the primary treatment for prostate cancer. However, severe urinary toxicity was related to previous surgical treatment. There is a need for longer follow-up periods to verity the benetit of this dosage level.
Mechanisms of formation of chromosomal aberrations: insights from studies with DNA repair-deficient cells

In order to understand the mechanisms of formation of chromosomal aberrations, studies performed on human syndromes with genomic instability can be fruitful. In this report, the results from studies in our laboratory on the importance of the transcription-coupled repair (TCR) pathway on the induction of chromosomal damage and apoptosis by ultraviolet light (UV) are discussed. UV61 cells (hamster homologue of human Cockayne’s syndrome group B) deficient in TCR showed a dramatic increase in the induction of chromosomal aberrations and apoptosis following UV treatment. At relatively low UV doses, the induction of chromosomal aberrations preceded the apoptotic process. Chromosomal aberrations probably lead to apoptosis and most of the cells had gone through an S phase after the UV treatment before entering apoptosis. At higher doses of UV, the cells could go into apoptosis already in the G1 phase of the cell cycle. Abolition of TCR by treatment with α-amanitin (an inhibitor of RNA polymerase II) in the parental cell line AA8 also resulted in the induction of elevated chromosomal damage and apoptotic response similar to the one observed in UV61 cells treated with UV alone. This suggests that the lack of TCR is responsible for the increased frequencies of chromosomal aberrations and apoptosis in UV61 cells. Hypersensitivity to the induction of chromosomal damage by inhibitors of antitopoisomerases I and II in Werner’s syndrome cells is also discussed in relation to the compromised G2 phase processes involving the Werner protein.
Continuous low-level heatwrap therapy for treating acute nonspecific low back pain.

OBJECTIVE To evaluate the efficacy of 8 hours of continuous low-level heatwrap therapy for the treatment of acute nonspecific low back pain (LBP). DESIGN Prospective, randomized, parallel, single-blind (investigator), placebo-controlled, multicenter clinical trial. SETTING Five community-based research facilities. PARTICIPANTS Two-hundred nineteen subjects, aged 18 to 55 years, with acute nonspecific LBP. INTERVENTION Subjects were stratified by baseline pain intensity and gender and randomized to one of the following groups: evaluation of efficacy (heatwrap, n=95; oral placebo, n=96) and blinding (oral ibuprofen, n=12; unheated back, wrap n=16). All treatments were administered for 3 consecutive days with 2 days of follow-up. MAIN OUTCOME MEASURES Primary: day 1 mean pain relief (0- to 5-point verbal response scale). Secondary: muscle stiffness (101-point numeric rating scale), lateral trunk flexibility (fingertip-floor distance), and Roland-Morris Disability Questionnaire over 3 days of treatment and 2 days of follow-up. RESULTS Heatwrap therapy was shown to provide significant therapeutic benefits when compared with placebo during both the treatment and follow-up period. On day 1, the heatwrap group had greater pain relief (1.76+/-.10 vs 1.05+/-.11, P <.001), less muscle stiffness (43.1+/-1.21 vs 47.6+/-1.21, P=.008), and increased flexibility (18.6+/-.44 cm vs 16.5+/-.45 cm, P=.001) compared with placebo. Disability was also reduced in the heatwrap group (5.3 vs 7.4, P=.0002). Adverse events were mild and infrequent. CONCLUSION Continuous low-level heatwrap therapy was shown to be effective for the treatment of acute, nonspecific LBP.
Temporal Changes in the Toxicity of Pentachlorophenol to Chlorella pyrenidosa Algae

The toxicity of pentachlorophenol (PCP) on Chlorella pyrenidosa algae was investigated with specific attention given to possible variation of toxic effects with time. A concentration‐effect relationship was observed in which there was significant inhibition of PCP on cell density and chlorophyll A content. The inhibition rate of PCP on cell density was dependent on exposure time. The IC50 values after exposure times of 2, 4 and 6 days for cell growth were 4.18 ± 0.49, 3.49 ± 0.40 and 3.30 ± 0.26 mg/L, respectively. There was also inhibition of chlorophyll A production, which appeared to increase marginally with exposure time for a given concentration of PCP. The corresponding IC50values on day 2, 4 and 6 were 2.30 ± 0.12, 2.63 ± 0.38 and 3.30 ± 0.34 mg/L, respectively. The effect of PCP on nitrate reductase (NR), was first stimulation followed by an inhibition phase. It is postulated that the observed temporal changes in the activity of nitrate reductase (NR) may occur through the addition or loss of phosphorus in the NR protein.
Neuropeptide Y expression and endogenous leptin concentrations in a dietary model of obesity.

OBJECTIVE To determine how leptin concentrations and neuropeptide (NPY) are regulated in a model of dietary obesity in relation to relative growth (RG) and relative food consumption (RFC). RESEARCH METHODS AND PROCEDURES Sprague-Dawley rats were fed a moderately high-fat diet for 14 weeks over which time animals diverged into obesity-prone (OP) and obesity-resistant (OR) populations. RG rates and RFC were calculated weekly. Following the study, an adiposity index was calculated and arcuate nucleus (ARC) NPY expression was determined by in situ hybridization (ISH) or ribonuclease protection (RPA) assays. RESULTS Body weights were greater in OP rats after 2 weeks on the diet compared to OR rats and remained different throughout the study. RG and RFC were greater in OP rats compared to OR rats only during the first 2 weeks of the study. Leptin concentrations rose in both groups during the experiment, but the increase was greater in OP rats than in OR rats. Insulin changes paralleled those for leptin. ARC NPY mRNA expression was not different between OP and OR rats as measured by ISH and RPA. DISCUSSION Although NPY expression has been reported to be different initially in OP and OR rats, this difference dissipates following divergence of body weight. RFC and RG data suggest the initial NPY elevation may contribute to increased weight gain of OP rats during the first 2 weeks of the diet. Higher relative leptin concentrations in OP rats may be necessary to normalize differences in adiposity and apparent leptin and insulin resistance of OP rats.
Facial allergic granulomatous reaction and systemic hypersensitivity associated with microneedle therapy for skin rejuvenation.

IMPORTANCE Microneedle therapy includes skin puncture with multiple micro-sized needles to promote skin rejuvenation or increase transdermal delivery of topical medications. In cosmetic practices, various cosmeceuticals are applied before microneedling to enhance the therapeutic effects. This results in intradermal tattooing of the topical product. Despite rapid increase in the use of microneedles in dermatology, there are few data about their safety. OBSERVATIONS We describe 3 women, aged 40s to 60s, who developed open [corrected] facial granulomas following microneedle therapy for skin rejuvenation. Two patients had undergone microinjection of the same branded topical moisturizer (Vita C Serum; Sanítas Skincare) during microneedle therapy. Biopsy in all cases showed foreign body-type granulomas. Results of tissue cultures were negative. Chest radiography and serum angiotensin-converting enzyme findings were normal. The first 2 patients had a positive patch test reaction to Vita C Serum. Initial treatment with topical and oral corticosteroids was ineffective. Therapy with doxycycline hydrochloride and minocycline hydrochloride led to partial improvement in one case and resolution in another. CONCLUSIONS AND RELEVANCE Application of topical products prior to microneedling can introduce immunogenic particles into the dermis and potentiate local or systemic hypersensitivity reactions. Because the microneedle therapy system is accessible for home use, health care providers need to be aware of its potential consequences.
Interventions targeted toward patients to increase mammography use.

The objective of this study was to determine the effects of patient-based mammography screening strategies. We performed a meta-analysis and included United States studies that met the following criteria: (a) randomized or concurrent control design; (b) defined outcomes; and (c) data available for reanalysis. Interventions were classified as behavioral, cognitive, or sociological and further categorized by the type of control group (active versus usual care), number of interventions, and mode of intervention (interactive versus static). Data were combined using DerSimonian and Laird random effects models to yield summary effect sizes. A total of 63 interventions in 43 studies met the inclusion criteria. Behavioral interventions increased screening by 13.2% [95% confidence interval (CI), 4.7-21.2] compared with usual care, and by 13.0% (95% CI, 8.7-17.4) when using multiple strategies and 5.6% (95% CI, 0.6-10.6) when using a single intervention compared to active controls. Cognitive interventions using generic education strategies had little impact on screening, but those that used theory-based education (e.g., health belief model) increased rates by 23.6% (95% CI, 16.4-30.1) compared with usual care. Sociological interventions also increased screening rates. Interventions using a theoretical framework were the most effective in increasing screening rates. The ability of these interventions to increase screening among subgroups and improve rates of ongoing screening, as well as the costs of these strategies, is unknown and is an important area for future research.