Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA damage and repair system in spinal cord ischemia.

BACKGROUND AND PURPOSE Spinal cord ischemia-reperfusion injury may be initiated by a number of mediators, including reactive oxygen species. Recent studies have shown that human MutY homologue (hMYH), human 8-oxo-7,8-dihydrodeoxyguanine (8-oxoG) glycosylase (hOGG1), and human MutS homologue 2 (hMSH2) are important DNA mismatch repair genes. We hypothesized that ischemia-reperfusion injury in spinal cord causes DNA damage manifested by 8-oxoG production and activates the DNA repair system involving hMYH, hOGG1, and hMSH2. METHODS Spinal cords of rabbits were removed at 1, 3, 6, 24, and 48 hours after 30 minutes of infrarenal aortic occlusion. DNA damage was determined with 8-oxoG staining. The expression and localization of DNA repair enzymes, such as hMYH, hOGG1, and hMSH2, were studied with Western blot analysis and immunohistochemical staining. The level of apoptosis was determined with TUNEL study. Activation of caspase-3, an enzyme induced by cellular injury that leads to apoptosis by degrading cellular structural proteins, was also studied. RESULTS DNA damage monitored with 8-oxoG level was significantly present from 1 hour to 6 hours after reperfusion in gray matter neurons of ischemic spinal cord. The levels of hMYH, hOGG1, and hMSH2 were markedly increased in gray matter neurons at 6 hours after reperfusion. Caspase-3 was also induced at 6 hours to 24 hours after reperfusion in ischemic spinal cord. However, the peak level of TUNEL reactivity was found at 48 hours after reperfusion in spinal cord neurons. CONCLUSION This study has shown, for the first time, the rapid expression of DNA damage-repair processes associated with spinal cord ischemia and subsequent reperfusion.
An implantable guide-screw system for brain tumor studies in small animals.

OBJECT To overcome the problems associated with using stereotactic techniques to establish intracranial xenografts in nude mice and to treat engrafted tumors with intratumoral therapies (such as gene or viral therapies), the authors developed an implantable guide-screw system. In this study, they describe the guide-screw system, its method of implantation, and their experience with establishing xenografts and delivering intratumoral therapy. METHODS The system consists of a 2.6-mm guide screw with a central 0.5-mm diameter hole that accepts the 26-gauge needle of a Hamilton syringe. The screw is implanted into a small drill hole made 2.5 mm lateral and 1 mm anterior to the bregma. A stylet is used to cap the screw between treatments. Tumor cells or therapeutic agents are injected in a freehand fashion by using a Hamilton syringe and a 26-gauge needle fitted with a cuff to determine the depth of injection. To test this system, guide screws were successfully implanted in 44 (98%) of 45 nude mice. After 1 to 2 weeks of recovery, 38 mice were inoculated with U87MG cells and killed 5 days later. On histological studies in 37 (97%) of these animals, xenografts were evident within the caudate nucleus (mean diameter 2.5 mm). To determine whether injections into the center of an established xenograft could be reproducibly achieved with the guide-screw system, an adenovirus vector containing the beta-galactosidase gene was injected 3 days after cell implantation in 15 of the mice. All of these animals demonstrated transduced cells within the tumor. To demonstrate that engrafted animals have a uniform survival time that is indicative of reproducible tumor growth, the survival of six mice was assessed after engraftment with U87MG cells. All six animals died within 28 to 35 days. CONCLUSIONS The guide-screw system allows a large number of animals to be rapidly and reproducibly engrafted and for intratumoral treatments to be accurately delivered into established xenografts.
HIGH CAPACITY IMAGE STEGANOGRAPHY IN THE SPATIAL DOMAIN USING LEHMER CODE

Steganography is one of the modern techniques for covert communication through the internet. In addition to providing confidentiality, it also enables the communication of large amounts of data without raising suspicion. This paper presents a novel technique for image steganography using Lehmer code that provides high capacity and better performance. Lehmer code is a way of encoding each possible permutation of a sequence of
Allicin, the active component of garlic, prevents immune‐mediated, concanavalin A‐induced hepatic injury in mice

Abstract: Background/Aim: Allicin, the immunologically active component of garlic, has been found to affect oxidative stress and immune response in several experimental systems. In the present study, we examined the ability of allicin to prevent immune‐mediated, concanavalin A (Con A)‐induced liver damage in mice.
The development and release of maize fortified with provitamin A carotenoids in developing countries

ABSTRACT Micronutrient deficiencies have been identified as major public health problems affecting a large part of the world's population. Biofortification of staple crops like maize has been proposed as one of the most cost effective and feasible approaches to combat micronutrient deficiencies. Studies have shown that provitamin A from biofortified crops is highly bioavailable and has the capacity to improve vitamin A status of vulnerable groups. Most people in sub-Saharan Africa subsist on maize and many people may benefit from consumption of provitamin A carotenoid biofortified maize, especially women and children. With the exception of transgenic golden rice, biofortified crops have received considerable acceptance by most communities. Negative perceptions associated with yellow maize do not affect orange maize, which is, for example, well-liked in rural Zambia. With proper policy frameworks and full commercialization, provitamin A maize can address the problem of vitamin A deficiencies among poor nations with maize-based diets.
Audit of Physicians’ Adherence to the Antibiotic Policy Guidelines in Kuwait

Objective: To audit physicians’ adherence to the local antibiotic policy guidelines in government hospitals in Kuwait. Materials and Methods: The study was a retrospective review of patient records in nine hospitals between July 1 and December 31, 2008. Clinical notes and medication charts of the latest hospital admissions were checked for antibiotic prescribing. On the audit form, aspects of the prescribed antibiotic were benchmarked to the hospital antibiotic policy guidelines to evaluate adherence. Results: Of 2,232 reviewed records, 1,112 (49.8%) patients had 1,528 antibiotic prescriptions. Patients who received antibiotics were significantly younger than those who did not (median age: 26.3 vs. 29.8 years, p < 0.001) and their hospital stay was significantly longer (median: 4 vs. 2 days, p < 0.001). The choice of an antibiotic was appropriate and matched the policy in 806 (52.7%) prescriptions. Of such appropriate antibiotics, adherence to route of administration was observed in 768/806 (95.3%), to dose in 758 (94%), to frequency in 746 (92.6%) and to duration in 608 (75.4%). Full adherence to all aspects of antibiotic choice, dose, route, frequency and duration was achieved in 464 (30.4%) prescriptions. In 382 (25%), the antibiotics administered were not indicated. Conclusion: There was low adherence to the local antibiotic policy guidelines. Physicians’ antibiotic prescribing practices should be optimized. Adherence to, and update of, the policy is recommended.
NADPH Oxidase–Independent Formation of Extracellular DNA Traps by Basophils

Basophils are primarily associated with a proinflammatory and immunoregulatory role in allergic diseases and parasitic infections. Recent studies have shown that basophils can also bind various bacteria both in the presence and the absence of opsonizing Abs. In this report, we show that both human and mouse basophils are able to produce mitochondrial reactive oxygen species and to form extracellular DNA traps upon IL-3 priming and subsequent activation of the complement factor 5 a receptor or FcεRI. Such basophil extracellular traps (BETs) contain mitochondrial, but not nuclear DNA, as well as the granule proteins basogranulin and mouse mast cell protease 8. BET formation occurs despite the absence of any functional NADPH oxidase in basophils. BETs can be found in both human and mouse inflamed tissues, suggesting that they also play a role under in vivo inflammatory conditions. Taken together, these findings suggest that basophils exert direct innate immune effector functions in the extracellular space.
A RETROSPECTIVE HISTOLOGICAL STUDY OF 669 CASES OF PRIMARY CUTANEOUS MALIGNANT MELANOMA IN CLINICAL STAGE I

A selected series of 669 primary cutaneous malignant melanomas, stage I, was studied. The series includes 86 lentigo maligna melanomas, 259 superficial spreading malignant melanomas, 194 nodular malignant melanomas and 130 unclassifiable malignant melanomas. The cross‐sectional profile, level of invasion, ulceration and vascular invasion were graded. The relation of these features to each other and to tumour type was studied by X2 tests. The prognostic value was also studied. The most common finding was a slightly elevated surface, level III of invasion, no ulceration and no vascular invasion. Most of these tumours were superficial spreading malignant melanomas. A good prognosis was associated with a flat cross‐sectional profile, level II of invasion, no ulceration and no vascular invasion. A poor prognosis was associated with marked protrusion of the surface, level IV–V of invasion, ulceration and vascular invasion. Lentigo maligna melanomas tended to be more benign while nodular malignant melanomas tended to be more malignant than the average. A superficial spreading malignant melanoma could vary in either direction. The prognostic value of level of invasion and ulceration was found to be greater than that of tumour type. The prognostic importance of invasion no further than level III is stressed. Level of invasion ought to be reported to the clinician as well as the tumour type.
Combined double CK5/P63 stain: Useful adjunct test for diagnosing pulmonary squamous cell carcinoma

Increasing demand for accurate differentiation of pulmonary squamous cell carcinoma (SQCC) from other subtypes can be challenging for pathologists. This is more so in fine‐needle aspirations (FNA) since the sample is small and SQCC may show degenerative changes and necrosis that distort the cellular features. Immunohistochemistry (IHC) is a valuable adjunct, and CK5/6 and P63 immunoreactivity is found to be basically restricted to SQCC. In our study, we evaluated the efficiency of CK5/P63 double staining in the diagnosis of pulmonary SQCC in cell blocks (CB) of lung FNA. We used a cohort including 24 CB of lung SQCC and 34 CB of lung adenocarcinomas (ADC). IHC was performed for CK5/P63 double stain. Seventeen of 24 (70%) lung SQCC were positive for the double stain CK5/P63. Two (8%) were positive for CK5 alone and two (8%) were positive for P63 alone. Thus, a total 19 of 24(79%) SQCC of the lung were positive for CK5 and P63 each. In ADC, no immunoreactivity was detected for CK5 alone or combined CK5/P63. Three of 34(8%) ADC were positive for P63. This first study of double staining of CK5/P63 in FNA CB shows a sensitivity of 70% and specificity of 100% for SQCC of the lung. When each marker staining alone is included, the sensitivity for CK5 and P63 increases to 79% each. This double stain can help in the diagnosis of pulmonary SQCC with an accuracy of 88% and a positive predictive value of 100%. Diagn. Cytopathol. 2012. © 2011 Wiley Periodicals, Inc.
Apoptotic death in epithelial cells: cleavage of DNA to 300 and/or 50 kb fragments prior to or in the absence of internucleosomal fragmentation.

To date, apoptosis has been characterized biochemically by the production of 180–200 bp internucleosomal DNA fragments resulting from the activation of an endonuclease(s). The principal morphological feature of apoptosis is the condensation of chromatin and it has been assumed that this may reflect the oligonucleosomal fragmentation pattern. We have re‐examined this dogma by comparing the biochemical and morphological features of cell death in several epithelial cell types (HT‐29‐I1 colon adenocarcinoma, CC164 mink lung, DU‐145 human prostatic carcinoma and MCF‐7 human breast adenocarcinoma) and one mesenchymal cell line (H11ras‐R3 ras‐transformed rat fibroblasts). Cell death was induced either by serum deprivation, TGF‐beta 1 or etoposide, or by leaving cells to reach confluence. Cell death was assessed with respect to detachment from monolayers, morphological changes and DNA integrity. The DNA‐binding fluorophore Hoechst 33258 revealed chromatin condensation patterns consistent with apoptotic cell death in all cell types except MCF‐7 cells. Using field inversion gel electrophoresis in conjunction with conventional 2% agarose gel electrophoresis, cleavage of DNA to 50 kbp fragments was observed in all cases except MCF‐7 cells. This preceded the appearance of oligonucleosomal fragments in HT‐29‐I1, CC164 and H11ras‐R3 cells. Although the DNA of DU‐145 cells fragmented into 50 kbp units, and although the cells exhibited classical apoptotic morphology, no subsequent internucleosomal cleavage was observed. These results suggest that changes in the integrity of DNA indicative of the release of chromatin loop domains occur before cleavage at internucleosomal sites is initiated and that the latter is not an essential step in the apoptotic process.
Surface PD evolution of conventional and nanocomposite enamels

The stator motor windings of low voltage rotating electrical machines are usually insulated by organic enamel. When the motors are supplied by power electronic converters, the stator insulation system is subjected to pulsed voltage waveform and a fast degradation of the insulating system could occur. In fact, it is possible that partial discharge (PD) activity incepts leading to the deterioration of the insulating system. In this work the evolution of partial discharges is monitored when twisted pairs of copper enameled wires are subjected to sinusoidal and pulsed PWM-like voltage waveform. Conventional and nanocomposite enamels have been considered monitoring the behavior during the degradation processes evidencing the main peculiarities of each enamel when subjected to the PD action.
Language Barriers and Immigrant Health Production

We study the impact of language deficiency on the health production of childhood migrants to Australia. Our identification strategy relies on a quasi-experiment comparing immigrants arriving at different ages and from different linguistic origins by utilising a measure of differences along a continuous range of linguistic distances. Our main results indicate a large negative effect of English deficiency on physical health that is robust to a range of different specifications.In the presence of considerable non-classical measurement error in self-reported language proficiency, our results provide lower and upper bounds for the true effect of English deficiency on health of one half and a full standard deviation in the health score respectively. The empirical analysis is framed in terms of a Grossman model which indicates a twofold role of language skills in health production: language deficiency directly affects the efficiency of health production and indirectly affects access to health inputs. We provide some suggestive evidence on the relative importance of these distinct roles.
Ultrasound phase velocities in SonoVue™ as a function of pressure and bubble concentration

This work investigates the effects of insonating pressure on ultrasound phase velocity in the SonoVue™ microbubble suspension. Ultrasound transmission measurements were carried out using a single element transducer and calibrated needle hydrophone, for a range of SonoVue™ concentrations from 50 to 800µl/l. Phase velocity was calculated using an established method based on the phase difference between pulses transmitted through the contrast agent and reference pulses for a range of insonating pressures from 13 to 128 kPa. Phase velocity was shown to be dependent on frequency, insonating pressure and SonoVue™ concentration. The relationship between pressure and phase velocity was found to be approximately linear, with the pressure-velocity gradient increasing with concentration. These results may have significant implications for contrast-enhanced ultrasonography, for example in understanding artifact generation and quantitative applications such as estimating local bubble concentration.
Genetics of Coagulation: Considerations for Cardiac Surgery

Genetic variants in the coagulation system have been known since antiquity. Today, because of modern improvements in diagnosis and medical management, the clinician is likely to encounter a spectrum of coagulation factor deficiencies and identified polymorphic variants in the surgical population. Because perioperative hemorrhagic and thrombotic complications are potentially serious, it is important to understand the role that these defects and variants may play in predicting risk and optimizing patient management. The implications of coagulation genetics on the perioperative management of the cardiac surgery patient are reviewed.
Epigenetic approach of Prader-Willi syndrome diagnosis in Romanian population

This work aimed to compare the clinical validity of a newly developed assay for Prader-Willi syndrome diagnosis in Romanian population, as compared to an existing assay. This syndrome is a complex multisystem, genetic and epigenetic disorder, which arises from a defect in imprinted genes regulation and contribution. So far, a molecular cytogenetic method (fluorescence in situ hybridization) has been the most frequently used assay in primary diagnosis, but because it is targeted towards genetic factors it only covers deletional cases in this pathology. However, gene expression control is realized both through physical presence of the corresponding DNA sequence and through specific methylation patterns on parental alleles of the given gene: normal healthy state is defined by unmethylated (expressed) paternal allele, in the presence of methylated (repressed) maternal allele; by contrast, the pathological condition is defined by the presence of only methylated (repressed) maternal allele, thus the lack of unmethylated (contributing) paternal allele. This is the first report presenting a methylation mapping assay, based on methylation specific amplification, for Prader-Willi syndrome in Romanian population, suggesting it might be used as primary diagnosis tool based on its cost-efficiency and covering ability of almost entire Prader-Willi syndrome etiology (deletions, unimaternal disomy, imprinting defect).
BBMerge – Accurate paired shotgun read merging via overlap

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highly sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.
Landmine feature extraction in GPR(SFCW) data

This paper shows an algorithm based on linear geostatistics in ground penetrating radar (GPR) data for extracting landmine features. That is a major problem for civilian population in different rural areas in Colombia. Because linear geostatistics has a main difference respect to classic statistics, this technique can be used to detect, to create a signal with object information, and to extract information about physical parameters of buried object such as a landmine as Improvised Explosive Device (IED). Consecutive acquired signals provide a correlated relationship useful for both clutter reduction (background and test lane limits) by using Principal Component Analysis (PCA) and separation of object information by using geostatistics. The samples of resulting signal are compared with a threshold value to obtain a signal with features related to position and object size. The experimental data have been collected by using frequency stepped GPR system covering a range from 700[MHz] to 10[GHz] in a Military Base with real conditions.
Body-Image Correlates of Anxiety in a Sample of Male Alcoholics

Body-image testing of 10 male alcoholics with and 7 without anxiety disorders showed those with panic disorder had low barrier scores. Those with phobias emphasized their hearts and those with Posttraumatic Stress Disorder emphasized their backs. The barrier score correlated positively with both intensity of physical symptoms and with sense of blocked body openings.
IS IMPAIRED FASTING GLUCOSE ASSOCIATED WITH INCREASED RISK OF CORONARY ATEROSCLEROSIS

Impaired fasting glucose identifies individuals at high risk of progression to diabetes but the role of IFG as a coronary artery disease risk factor, independent of its progression to diabetes and its association with other coronary artery disease risk factors ,is unclear. A cross-sectional study was conducted to evaluate the hypothesis that impaired fasting glucose increased the likelihood of atherosclerotic plaque formation. Blood chemistry data as well as traditional coronary artery disease risk factors from 812 patients referred for coronary angiography to heart centers in Shahid- Chamran and Sina hospital, Isfahan, Iran were recorded. The population were stratified into three groups according to American Diabetes Association criteria: normal fasting glucose (n=608), impaired fasting glucose(n=92) and diabetes mellitus(n=112). We use extent, Vessel and stenosis scores to indicate the coronary artery involvement. KrusKal-Wallis test showed that the means of extent, Vessel and stenosis scores are not significantly different between three groups(P> 0.05). Multivariate linear regression analysis, using extent score of coronary artery disease as dependent variable and traditional risk factors and impaired fasting glucose as independent variables did not show any significant difference either. Our data suggested that impaired fasting glucose is not associated with increased risk of coronary atherosclerosis.