Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Aminoglycoside Resistance Genes by Multiplex PCR among Coagulase Negative Staphylococci Isolated from Ventriculoperitoneal Shunt Infections

A Ventriculoperitoneal (VP) shunt infection is a cause of significant morbidity causing shunt malfunction and chronic ill health. This study was carried out to detect the causative pathogens associated with VP shunt infections, to assess the frequency of Coagulase negative Staphylococci (CoNS) as well as study their phenotypic resistance pattern to methicillin and different aminoglycosides (AGs), and genotypic pattern for gene encoding aminoglycosides modifying enzymes (AMEs) by multiplex PCR. This study was carried out in Medical Microbiology & Immunology and Neurosurgery Departments, Faculty of Medicine, Zagazig University during the period from June 2008 to June 2010. During this period 240 shunt procedures were carried on 175 infants and children with hydrocephalus. CoNS were identified using standard microbiological laboratory techniques. Antimicrobial susceptibility testing was performed using disc diffusion method with 4 aminoglycosides and methicillin. Multiplex PCR assay was used to identify AMEs encoding genes. 58 out of 240 shunt procedures cases showed shunt infections, (64%) caused by CoNS, (28%) by Gram negative rods (5%) by Staph. aureus and (3%) by candida. 26 (70%) of CoNS isolates were methicillin resistant (MRCoNS). 25 (67.5%) isolates of CoNS were resistant to at least one of the tested AGs and the highest resistance was to gentamicin and tobramycin (67.5%) for both, followed by amikacin (27%) and streptomycin (19%). As regard results of multiplex PCR aac(6`)Ie+aph(2``) gene encoding for the bifunctional enzyme was the most common (54%) followed by ant(4`)Ia gene encoding for the ANT(4`) – Ia enzyme (46%) and the aph(3`)-IIIa gene encoding APH(3`) – IIIa enzyme (40.5%). In conclusion this study increased our knowledge about the causative pathogens of VP shunt infections, the phenotypic pattern of CoNS susceptibility to different AGs and the distribution of AMEs encoding genes in relation to methicillin susceptibility. The usage of appropriate antibiotic according to antimicrobial susceptibility testing at the probable time and the removal of the shunt apparatus are essential for successful treatment of VP shunt infection. Continued surveillance at both phenotypic and genotypic levels are recommended for monitoring the presence of other variant of the genes or new AGs resistance genes that may be produced within CoNS population.
Long‐term survival in post‐transplant lymphoproliferative disorders with a dose‐adjusted ACVBP regimen

Post‐transplant lymphoproliferative disorders (PTLD) are severe complications after solid organ transplantation with no consensus on best treatment practice. Chemotherapy is a therapeutic option with a high response and a significant relapse rate leading to a low long‐term tolerance rate. Currently, most centres use anthracycline‐based drug combinations, such as CHOP (cyclophosphamide, doxorubicin, vincristine and prednisone). We assessed the efficacy and safety of a dose‐adjusted ACVBP (doxorubicin reduced to 50 mg/m2, cyclophosphamide adjusted to renal function, vindesine, bleomycin, prednisone) regimen in patients failing to respond to a reduction in immunosuppressive therapy. Favourable responses were observed in 24 (73%) of the 33 treated patients. Fourteen (42%) patients died, mostly from PTLD progression. Actuarial survival was 60% at 5 years and 55% at 10 years. Survival prognostic factors were: number of involved sites (P = 0·007), clinical stage III/IV (P = 0·004), bulky tumour (P < 0·0001), B symptoms (P = 0·03), decreased serum albumin (P = 0·03) and poor performance status (P = 0·06). Both the international and the PTLD prognostic index were predictive for survival (P = 0·001 and P = 0·002, respectively). Overall 128 cycles were given. Grade 3 or 4 neutropenia was recorded after 26 (20%) chemotherapy cycles in 19 (58%) patients. Forty‐one (32%) infections were recorded in 26 (79%) patients. This study demonstrated that an individual dose‐adjustment of ACVBP regimen was manageable in PTLD patients and favourably impacted on long‐term survival.
Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms

Chlamydia trachomatis is an obligate intracellular pathogen responsible for ocular and genital infections of significant public health importance. C. trachomatis undergoes a biphasic developmental cycle alternating between two distinct forms: the infectious elementary body (EB), and the replicative but non‐infectious reticulate body (RB). The molecular basis for these developmental transitions and the metabolic properties of the EB and RB forms are poorly understood as these bacteria have traditionally been difficult to manipulate through classical genetic approaches. Using two‐dimensional liquid chromatography – tandem mass spectrometry (LC/LC‐MS/MS) we performed a large‐scale, label‐free quantitative proteomic analysis of C. trachomatis LGV‐L2 EB and RB forms. Additionally, we carried out LC‐MS/MS to analyse the membranes of the pathogen‐containing vacuole (‘inclusion’). We developed a label‐free quantification approaches to measure protein abundance in a mixed‐proteome background which we applied for EB and RB quantitative analysis. In this manner, we catalogued the relative distribution of > 54% of the predicted proteins in the C. trachomatis LGV‐L2 proteome. Proteins required for central metabolism and glucose catabolism were predominant in the EB, whereas proteins associated with protein synthesis, ATP generation and nutrient transport were more abundant in the RB. These findings suggest that the EB is primed for a burst in metabolic activity upon entry, whereas the RB form is geared towards nutrient utilization, a rapid increase in cellular mass, and securing the resources for an impending transition back to the EB form. The most revealing difference between the two forms was the relative deficiency of cytoplasmic factors required for efficient type III secretion (T3S) in the RB stage at 18 h post infection, suggesting a reduced T3S capacity or a low frequency of active T3S apparatus assembled on a ‘per organism’ basis. Our results show that EB and RB proteomes are streamlined to fulfil their predicted biological functions: maximum infectivity for EBs and replicative capacity for RBs.
EVALUATION OF ANTI PARKINSON ’ S ACTIVITY OF NIGELLA SATIVA ( KALONJI ) SEEDS IN CHLORPROMAZINE INDUCED EXPERIMENTAL ANIMAL MODEL

The present study was carried out to evaluate Anti Parkinson’s Activity of Ethanolic Extract of Nigella sativa seeds (EENS) in Chlorpromazine (CPZ) induced experimental animal model. The effects of ethanolic extracts of Nigella sativa (200 and 400 mg/kg, p.o) was studied using in-vivo parameter like catalepsy. Alongwith it effect of EENS on Neurochemical parameters (TBARS, GSH, Nitrite and Total Protein) were also assessed. Catalepsy was measured using block method. For neurochemical estimations all groups were given CPZ dosing for 21 days to induce Parkinson’s Disease (PD). The cataleptic scores was significantly (P<0.001) found to be reduced, with the Nigella sativa (200 and 400 mg/kg, p.o.). Levodopa + Carbidopa and Nigella sativa increase the depleted level of Reduced Glutathione (GSH) (P<0.001) and Total Protein (P<0.001) and decrease the elevated levels of TBARS (P<0.001) and Nitrite (P<0.001) preferably at higher dose(400 mg/kg) as compared to group II receiving Chlorpromazine. Our results suggest the Anti Parkinson’s activity of Nigella Sativa due to its Anti Cataleptic and Neurochemical responses.
DEVELOPMENT OF AHP BASED MODEL FOR DECISION MAKING ON E-LEARNING IMPLEMENTATION

Strategic planning of e-learning implementation includes decision making about the most suitable form of implementing e-learning on different levels. Decision making about e-learning implementation has been covered as consisting of four phases: (1) intelligence, (2) design, (3) choice and (4) implementation. During the Intelligence phase we have precisely identified our central decision problem and have conducted situation analysis. In the Design phase we have developed alternatives and established criteria and subcriteria. Then, we have created the questionnaire about the importance of the advantages and goals of e-learning implementation and about criteria and subcriteria essential for decision making. The survey has been conducted on the sample of 90 elearning experts in Croatia. Further, we connected these findings with the results of the factor analysis which was performed on the complete survey. The results of the factor analysis have served as input in the multicriteria decision model (AHP) that we have developed in the Choice phase. The AHP model will be presented in the article and qualitative and quantitative evaluation of the model will be indicated.
Directed Test Generation for Improved Fault Localization

Fault-localization techniques that apply statistical analyses to execution data gathered from multiple tests are quite effective when a large test suite is available. However, if no test suite is available, what is the best approach to generate one? This paper investigates the fault-localization effectiveness of test suites generated according to several test-generation techniques based on combined concrete and symbolic (concolic) execution. We evaluate these techniques by applying the Ochiai fault-localization technique to generated test suites in order to localize 35 faults in four PHP Web applications. Our results show that the test-generation techniques under consideration produce test suites with similar high fault-localization effectiveness, when given a large time budget. However, a new, “directed” test-generation technique, which aims to maximize the similarity between the path constraints of the generated tests and those of faulty executions, reaches this level of effectiveness with much smaller test suites. On average, when compared to test generation based on standard concolic execution techniques that aims to maximize code coverage, the new directed technique preserves faultlocalization effectiveness while reducing test-suite size by 86.1% and test-suite generation time by 88.6%.
Augmentation of antibody dependent cell mediated cytotoxicity following in vivo therapy with recombinant interleukin 2.

Monoclonal antibodies (mAB) with tumor specificity are able to enhance the immunological specificity of interleukin 2 (IL-2)-activated lymphokine activated killer (LAK) cells. Antibodies may also be used to broaden the range of tumor types susceptible to immune mediated cytotoxicity by the activated LAK cells. In these studies, mAB with relative tumor specificity were used to target immunologically activated effector cells in an in vitro antibody dependent cell mediated cytotoxicity (ADCC) assay. The mAB included: 3F8 and 14.G2a, which are both specific for neuroblastoma and melanoma and recognize ganglioside GD2, and mAB ING-1, a mouse-human chimeric antibody with constant regions from human IgG1 and kappa chains and variable regions from a mouse mAB that binds to a broad range of human adenocarcinomas. Each of these mAB was able to mediate ADCC with fresh effector cells and antibody binding targets. When peripheral blood mononuclear cells were obtained from cancer patients prior to and following in vivo therapy with interleukin 2, a significant increase was noted in ADCC activity by peripheral blood mononuclear cells obtained following IL-2 therapy. Inclusion of IL-2 in the medium during the cytotoxic assay with mAB further boosted ADCC. The total activity seen was often greater than the sum of the independent LAK activity and standard ADCC activity. The cells responsible for this ADCC had the CD16+ Fc receptor. Combining IL-2 with mAB in clinical tumor therapy may lead to a wider range of tumor types being responsive to immunotherapy and may also enhance the efficacy of therapy by specifically targeting activated effector cells to tumor cells recognized by mAB. Our results provide strong support for the testing of these hypotheses in clinical trials by combining in vivo treatment with IL-2 and mAB able to mediate ADCC.
Development of a Scale to Evaluate the Depressive State among Elderly Patients in General Wards

This study aims to develop a scale to evaluate depressive states among elderly patients in general wards, and verify the reliability and validity of the scale. Based on the results of interviews with nurses, we developed a draft of a scale comprised of 48 questions (NDE48). The Geriatric Depression Scale short version (GDS15), and the Zung Self-rating Depression Scale (SDS) were administered to 54 elderly patients. Two groups of nurses completed the NDE48 on different days. After performing an explanatory factor analysis, the NDE48 was simplified to a 16 question item scale (NDE16), comprising three factors. The correlation coefficient between GDS15 and NDE16 was 0.41 (p = 0.00191), and between SDS and NDE16 was 0.30 (p = 0.02633). Alpha coefficient of the total score of NDE16 was 0.88. For inter-rater reliability, the correlation coefficient was 0.57 (p = 0.00005). The findings suggest that the NDE16 will be highly useful when nurses evaluate depressive states among elderly inpatients.
CORROSION PERFORMANCE OF STAINLESS STEEL CLAD REBAR IN SIMULATED PORE WATER AND CONCRETE

The corrosion performance of stainless steel clad reinforcing bar (SCR) was investigated. Corrosion potential of SCR in various alkaline media as a function of time was measured periodically and corrosion rates were estimated using Electrochemical Impedance Spectroscopy (EIS). At room temperature, SCR without cladding breaks was free of corrosion for up to one year in all the testing conditions: saturated Ca(OH)2 solutions (SCS, pH ~12.6), simulated pore solution (SPS, pH ~13.6), simulated carbonated concrete pore solution (CPS, pH <10) (each with 15 wt% chloride by the end of test), and concrete with chloride up to 8% chloride by weight of cement. SCR without cladding breaks also remained passive at 40 o C in SCS with 15% chloride and in concrete with 8% chloride. SCR with a 1 mm hole corroded actively in SCS with 15% chloride. The results suggest that carbon steel exposed by the small hole was corroding actively at a high local rate. A model for SCR with a single cladding break at one cut-end in concrete was modeled using a finite differences appr oach. Calculations indicated that the resistivity of concrete and size of cladding breaks were critical parameters in establishing the rate of corrosion, and that corrosion of SCR with sub-millime ter breaks in high qualit y concrete would cause concrete cracking only after long service times.
Health care provider recommendation, human papillomavirus vaccination, and race/ethnicity in the US National Immunization Survey.

OBJECTIVES Human papillomavirus (HPV) is a common sexually transmitted infection in the United States, yet HPV vaccination rates remain relatively low. We examined racial/ethnic differences in the prevalence of health care provider recommendations for HPV vaccination and the association between recommendation and vaccination. METHODS We used the 2009 National Immunization Survey-Teen, a nationally representative cross-section of female adolescents aged 13 to 17 years, to assess provider-verified HPV vaccination (≥ 1 dose) and participant-reported health care provider recommendation for the HPV vaccine. RESULTS More than half (56.9%) of female adolescents received a recommendation for the HPV vaccine, and adolescents with a recommendation were almost 5 times as likely to receive a vaccine (odds ratio = 4.81; 95% confidence interval = 4.01, 5.77) as those without a recommendation. Racial/ethnic minorities were less likely to receive a recommendation, but the association between recommendation and vaccination appeared strong for all racial/ethnic groups. CONCLUSIONS Provider recommendations were strongly associated with HPV vaccination. Racial/ethnic minorities and non-Hispanic Whites were equally likely to obtain an HPV vaccine after receiving a recommendation. Vaccine education efforts should target health care providers to increase recommendations, particularly among racial/ethnic minority populations.
CD147 immunohistochemistry discriminates between reactive mesothelial cells and malignant mesothelioma

Malignant mesothelioma (MM) is a rare form of cancer. Its histopathological diagnosis is very difficult, as it exhibits a number of different appearances that can be misinterpreted as metastatic invasion or atypical hyperplasia. Thus, there is an urgent need to identify adequate markers to distinguish between benign and malignant cells, allowing the implementation of appropriate therapies and, possibly, specific directed therapies. MM, like other tumors, show an increase in glucose uptake, due to high rates of glycolysis, inducing an intracellular overload of acids. In this context, monocarboxylate transporters (MCTs) emerge as important players, by mediating the transmembranar co‐transport of lactate with a proton, thereby, regulating pH and allowing continuous glycolysis. Importantly, proper MCT expression and activity depend on its co‐expression with a chaperone, CD147, which is associated with poor prognosis in cancer. Twenty‐two samples including reactive mesothelial cells, MM, and atypical mesothelial hyperplasias were evaluated for immunoexpression of MCT1, MCT4, and CD147. Expression of these proteins was compared with GLUT1 as a new promising marker for MM. Although MCT isoforms were not differentially expressed in the two types of cytological specimens, CD147, as GLUT1, was almost exclusively expressed in MM. Both MCT1 and MCT4 are not able to discriminate between mesothelial reactive cells and mesothelial malignant cells, while CD147 was able to distinguish these two proliferations. If confirmed, besides being a good marker for identification of MM, CD147 may also be a target for therapeutical strategies in this rare type of tumor. Diagn. Cytopathol. 2012;40:478–483. © 2012 Wiley Periodicals, Inc.
APPLICATION AND MEASUREMENT OF ULTRAVIOLET RADIATION.

Abstract Commercially available ultraviolet lamps are mostly mercury vapor lamps, either low-pressure or high-pressure. Low-pressure lamps are used extensively to destroy bacteria. High-pressure lamps are used more for lighting. The power, properties and effectiveness of each type are discussed with precautions for safe use. Methods of measuring the intensity of ultraviolet radiation are reviewed, but there is no simple, inexpensive meter available.
MUC 4 Mucin Interacts with and Stabilizes the HER 2 Oncoprotein in Human Pancreatic Cancer Cells

MUC4, a high–molecular weight transmembrane glycoprotein, is overexpressed in pancreatic cancer and is implicated in its pathogenesis. It is a heterodimeric protein containing a large extracellular, heavily glycosylated subunit, MUC4A, and a transmembrane growth factor–like subunit, MUC4B. In the present study, we have shown the interaction of human MUC4 with the receptor tyrosine kinase HER2 in pancreatic adenocarcinoma cells by reciprocal coimmunoprecipitation and cocapping studies. MUC4 colocalized with HER2 at the cell surface and in the cytoplasm. Silencing of MUC4 by transient or stable expression of MUC4-targeted short-interfering RNA led to the down-regulation of HER2 with a concomitant decrease in its phosphorylated form (pY-HER2). Further analyses revealed that the MUC4-knockdown–mediated decrease in HER2 expression occurred due to the drop in the stability of the receptor. In MUC4-knockdown pancreatic cancer cells, we also observed a reduced phosphorylation of the focal adhesion kinase and p42/44 mitogen-activated protein kinase, which are downstream effector proteins in HER2 signaling. Our findings add a new dimension to MUC4 function as a modulator of cell signaling and provide mechanistic evidence for its role in pancreatic cancer progression. [Cancer Res 2008;68(7):2065–70]
Ocular Manifestations of Whiplash Injury

Introduction: Whiplash or indirect injuries to the neck are a common occurrence because of motor vehicle collisions, in which the frequency of ocular complications is largely unknown. Aim: We aim to review the ocular manifestations, the utility of relevant diagnostic tests, the management, prognosis, and sequelae of whiplash-related ocular complications. Methods: A comprehensive literature search was conducted on Medline®, PubMed®, Google Scholar™, and Cochrane databases. Only articles published or translated into the English language from 1985–2015 were considered and key data from the full article of each paper were extracted and evaluated. Results: The authors’ search yielded 41 articles. Blurring of vision was the most common presenting symptom. Other common presenting symptoms included words and objects moving within the visual field as well as difficulty in concentration. Ocular findings involved: disturbed eye movements; vestibulo-ocular reflex and cervico-ocular reflex dysfunction; anterior segment abnormalities such as accommodative and convergence dysfunction and relative afferent papillary defect; and posterior segment abnormalities such as macular oedema and foveal lesions. The treatment for ophthalmic complications of whiplash injuries is mainly conservative and revolves around neck physiotherapy and oculomotor rehabilitation. The prognosis of the ocular injury depends on the ocular findings as well as the interval between whiplash injury and treatment initiation. Conclusion: Whiplash injuries occur commonly in motor vehicle accidents. While patients may present asymptomatically, a myriad of ophthalmic complications may be detected. Prognosis for ocular complications depends mainly on the severity of complication(s), the time lapse between injury and detection of complication(s), and the initiation of treatment. Ophthalmologists and physicians should be aware and vigilant towards patients following whiplash injury as a small minority of patients may have poor visual outcome and quality of life without treatment and follow-up.