Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of gene expression in ductal carcinoma in situ of the breast.

PURPOSE The risk of recurrence and progression of ductal carcinoma in situ (DCIS) of the breast is best designated by morphological indicators, including the presence of necrosis. Our purpose was to identify molecular alterations underlying progression of DCIS. EXPERIMENTAL DESIGN We have compared gene expression within a cohort of six cases of DCIS with necrosis (DCIS(necrosis+)) and four cases without necrosis (DCIS(necrosis-)) using microdissection and cDNA microarray. RESULTS A set of 69 cDNAs from a group of 1,181 was identified that were consistently differentially expressed. Among this set, the mRNA for angio-associated migratory cell protein and a serine threonine protein kinase, nuclear Dbf2 related, were consistently higher in DCIS(necrosis+) and were also found to be overexpressed in the T47D breast cancer cell line subjected to hypoxia. Further study of angio-associated migratory cell protein by quantitative reverse transcriptase-PCR and in situ hybridization analysis of 37 cases of DCIS confirmed higher mRNA expression in DCIS(necrosis+) (P = 0.0095). CONCLUSIONS This study shows that although levels of gene expression are mostly similar between morphologically different DCIS, consistent differences in expression of a subset of genes can be identified between DCIS with and without necrosis.
The Relationship between Land Use and Vulnerability to Nitrogen and Phosphorus Pollution in an Urban Watershed.

Characterization of the vulnerability of water bodies to pollution from natural and anthropogenic sources requires understanding the relationship between land use and water quality. This study aims (i) to explore the influence of upstream land use on annual stream water concentrations and loads of total nitrogen (TN) and phosphorus (TP) and (ii) to characterize the vulnerability of water bodies to TN and TP pollution as a function of land use under varying climatic conditions. Multiple linear regression models were used across 23 stream locations within the Jordan Lake watershed in North Carolina between 1992 and 2012 to explore land use–water quality relationships. The percentage of urban land use and wastewater treatment plant capacity were the most important factors with strong (R2 > 0.7) and significant (p < 0.01) positive correlations with annual TN and TP concentrations and loads. Percent agricultural land was negatively correlated with TN in 18 out of 21 yr of the study period. Using analysis of covariance, significant (p < 0.01) differences were determined between models developed for urban land use with TN and TP loads based on annual precipitation. Using concentrations instead of loads resulted in a nonsignificant difference between models for average and wet years. Finally, a procedure was developed to characterize the vulnerability to TN and TP pollution, computed as the probability of exceeding the nutrient standard limits. Results indicated that the vulnerability to TN and TP was controlled primarily by urban land use, with higher values in dry years than normal and wet years. The Relationship between Land Use and Vulnerability to Nitrogen and Phosphorus Pollution in an Urban Watershed
Comparison study of the average transfer matrix of first- and second-order PMD

This paper presents numerical simulations of the transfer matrix of polarization-mode dispersion (PMD) in long optical fibers, wherein the average frequency dependence of this matrix is calculated conditioned on various given values of the differential group delay that is introduced between signal components in the two principal states of polarization (PSPs) and the second-order PMD parameter that characterizes frequency-dependent cross coupling between the PSPs. The results are then compared with four popular models of first- and second-order PMDs (F&SO-PMD), and it is found that none of them describes the average Jones matrix of F&SO-PMD with acceptable accuracy over the entire range of PMD parameters and optical bandwidth of interest. The differences between the various models and the simulation results are particularly large when the frequency-dependent cross coupling is large.
Pro- and Retrospective Memory in Late Adulthood

Everyday tasks, such as getting groceries en route from work, involve two distinct components, one prospective (i.e., remembering the plan) and the other retrospective (i.e., remembering the grocery list). The present investigation examined the size of the age-related performance declines in these components, as well as the relationship between these components and age-related differences in processing resources. The subjects were 133 community-dwelling adults between 65 and 95 years of age. They completed a large battery of tests, including tests of pro- and retrospective memory as well as tests for indexing processing resources. The results showed similar age-related declines in pro- and retrospective memory. There was only a weak relationship between pro- and retrospective memory, and the age-related decline in processing resources was related more strongly to retro- than prospective memory.
Assessment of susceptibility of olive cultivars to the Bactrocera oleae (Gmelin, 1790) and Camarosporium dalmaticum (Thüm.) Zachos & Tzav.-Klon. attacks in Calabria (Southern Italy)

Within the framework of research concerning the application of techniques alternative to chemical pesticides for control of parasites, the C.R. A. Experimental Institute for Olive Growing for many years has been performing a large investigation in order to detect sources of genetic resistance in olive germplasm. In the present study we observed the behavior related to the olive fly (Bactrocera oleae) infestation and Camarosporium dalmaticum infection of ten olive cultivars farmed under the same agronomic and climatic conditions in Calabria, Southern Italy. The sampling and the data collecting were carried out in three different ripening times.The drupe amount of oleuropein and cyanidine was detected by laboratory analyses in order to verify a possible correlation between these molecules and the level of infestation/infection of the above-mentioned parasites. The obtained data were submitted to analysis of variance. In relation to the fungal infection the results displayed that cvs Tonda nera dolce showed the lowest susceptibility, while the cv Giarraffa turned out to be the most susceptible. The less susceptible cultivars to the phytophagous were Tonda nera dolce and Bhardi Tirana. Since the less susceptible cultivar to olive fly attacks are the same observed in relation to the susceptibility to olive fruit rot, it is suggested a relation between the olive fly infestation and the fungal infection. It suggests the utility to achieve these results both to transfer directly to the farmers' world and to emphasize ecosystem health and biodiversity conservation.
Late-breaking clinical trials at the American Heart Association's scientific sessions 2001.

The PRoject of Ex-vivo Vein graft ENgineering via Transfection (PREVENT) II trial found that a double-stranded piece of DNA called the E2F duplex decoy significantly reduced failure of vein grafts after coronary artery bypass surgery (CABG), according to Eberhard Grube, MD, of the Heart Center in Sieburg, Germany, during the American Heart Association’s 2001 Scientific Sessions in Anaheim, Calif. During the Late-Breaking Clinical Trials Plenary Session on November 12, 2001, Dr Grube said that his decoy blocks vascular smooth muscle proliferation, which is the core problem in vein graft failure. Eberhard Grube, MD (photo by Paul C. SoRelle) The graft is treated during CABG after the vein has been removed from the leg. A solution containing the E2F decoy is placed in a tube with a stopcock on one side and a syringe at the other, which is used to apply pressure. The vein is placed in the tube and pressure is applied via the syringe to ≈6 lbs/in2 for 10 minutes, Dr Grube said. That is enough to insure that 80% of the cells in the graft will take up the decoy. The transfected graft then is used to bypass blocked coronary arteries. In the study, 101 patients who had undergone CABG were randomly assigned to the treatment group, and 99 were assigned to placebo. In angiographic studies performed on 61 placebo patients and 75 treated patients who received a total of 309 grafts, the E2F decoy was associated with a 30% relative reduction in a composite index of vein graft failure and death, said Dr Grube. In addition, there was a 30% reduction in the size of vessel wall volume. According to Dr Grube, the results are similar to those in the PREVENT I trial, which used E2F to treat bypass veins in peripheral artery disease. He …
Catheter-Related Bacteremia Due to Gordonia sputi in a Patient with Acute Lymphocytic Leukemia: a Case Report.

Accepted January 4, 2016. J-STAGE Advance Publication February 19, 2016. DOI: 10.7883/yoken.JJID. 2015.487 *Corresponding author: Mailing address: Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto 390-8621, Japan. Tel: +81-263-373493, Fax: +81-263-34-5316, E-mail: ggatcc@shinshu-u. ac.jp **Present address: Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-Machi, Maebashi, Gunma 371-8514, Japan. Tel: +81-27-220-8940, E-mail: tmatumoto@ gunma-u.ac.jp Jpn. J. Infect. Dis. , 69, 342–343, 2016
Deeply virtual vector meson electroproduction at small Bjorken‐x

It is reported on an analysis of vector meson electroproduction at small Bjorken‐x (xBj) within the handbag approach. Using a model for the generalized parton distributions (GPDs) and calculating the partonic subprocess, electroproduction off gluons, within the modified perturbative approach, cross sections and spin density matrix elements (SDME) are evaluated. The numerical results of this analysis agree fairly well with recent HERA data.
Drifting field‐aligned density structures in the night‐side polar cap

Spatio‐temporal properties of density irregularities in the night‐side polar cap are inferred from multi‐point observations of auroral hiss at a radial distance of 5 Earth radii. In this case study, we use high resolution data of the wave instruments onboard the four Cluster spacecraft to estimate the local plasma density, obtaining values close to 1 cm−3 with density depletions decreasing down to 0.15 cm−3. Combined analysis in different points in space conclusively shows for the first time that these density structures are field‐aligned and that they predominantly drift in the anti‐sunward direction at speeds of a few km/s. This corresponds to a dawn‐to‐dusk convection electric field of approximately 1 mV/m. The transverse dimension of the observed density depletions, mapped down to the ionospheric heights, is of the order of a few tens of km. Their lifetime is probably longer than tens of seconds.
Delayed lupus onset in (NZB x NZW)F1 mice expressing a human C-reactive protein transgene.

OBJECTIVE Human C-reactive protein (CRP) binds apoptotic cells and alters blood clearance of injected chromatin in mice. To test whether CRP participates in the pathogenesis of systemic lupus erythematosus (SLE), we examined disease development in lupus-prone (NZB x NZW)F(1) (NZB/NZW) mice expressing a human CRP transgene (hCRPtg/BW). METHODS Mortality was monitored, proteinuria was determined by dipstick, and serum levels of human CRP and anti-double-stranded DNA (anti-dsDNA) were determined by enzyme-linked immunosorbent assay in NZB/NZW and hCRPtg/BW mice. Thin sections of kidneys were analyzed by immunofluorescence microscopy to compare deposition of IgG, IgM, C3, and human CRP, and electron microscopy was used to reveal differences in ultrastructure. In situ hybridization was performed to detect human CRP messenger RNA expression. RESULTS The hCRPtg/BW mice had less proteinuria and longer survival than NZB/NZW mice. They also had lower IgM and higher IgG anti-dsDNA titers than NZB/NZW mice, although the differences were transient and small. In hCRPtg/BW mice, accumulation of IgM and IgG in the renal glomeruli was delayed, reduced, and more mesangial than in NZB/NZW mice, while end-stage accumulation of IgG, IgM, and C3 in the renal cortex was prevented. There was less glomerular podocyte fusion, basement membrane thickening, mesangial cell proliferation, and occlusion of capillary lumens in hCRPtg/BW mice, but dense deposits in the mesangium were increased. With disease progression in hCRPtg/BW mice, there was little rise in the plasma CRP level, but CRP in the kidneys became increasingly apparent due to local, disease-independent, age-related expression of the transgene. CONCLUSION In hCRPtg/BW mice, CRP protects against SLE by increasing blood and mesangial clearance of immune complexes and by preventing their accumulation in the renal cortex.
Pharmacokinetic interactions between protease inhibitors and statins in HIV seronegative volunteers: ACTG Study A5047

Objective Lipid lowering therapy is used increasingly in persons with HIV infection in the absence of safety data or information on drug interactions with antiretroviral agents. The primary objectives of this study were to examine the effects of ritonavir (RTV) plus saquinavir soft-gel (SQVsgc) capsules on the pharmacokinetics of pravastatin, simvastatin, and atorvastatin, and the effect of pravastatin on the pharmacokinetics of nelfinavir (NFV) in order to determine clinically important drug–drug interactions. Design Randomized, open-label study in healthy, HIV seronegative adults at AIDS Clinical Trials Units across the USA. Methods Three groups of subjects (arms 1, 2, and 3) received pravastatin, simvastatin or atorvastatin (40 mg daily each) from days 1–4 and 15–18. In these groups, RTV 400 mg and SQVsgc 400 mg twice daily were given from days 4–18. A fourth group (arm 4) received NFV 1250 mg twice daily from days 1–14 with pravastatin 40 mg daily added from days 15–18. Statin and NFV levels were measured by liquid chromatography/tandem mass spectrometry. Results Fifty-six subjects completed both pharmacokinetic study days. In arms 1–3, the median estimated area under the curves (AUC)0−−24 for the statins were: pravastatin (arm 1, n = 13), 151 and 75 nguu.h/ml on days 4 and 18 (decline of 50% in presence of RTV/SQVsgc), respectively (P = 0.005); simvastatin (arm 2, n = 14), 17 and 548 nguu.h/ml on days 4 and 18 (increase of 3059% in the presence of RTV/SQVsgc), respectively (P < 0.001); and total active atorvastatin (arm 3, n = 14), 167 and 289 nguu.h/ml on days 4 and 18 (increase of 79% in the presence of RTV/SQVsgc), respectively (P < 0.001). In arm 4, the median estimated AUC0−−8 for NFV (24 319 versus 26 760 nguu.h/ml;P = 0.58) and its active M8 metabolite (15 565 versus 14 571 nguu.h/m;P = 0.63) were not statistically different from day 14 to day 18 (without or with pravastatin). Conclusions Simvastatin should be avoided and atorvastatin may be used with caution in persons taking RTV and SQVsgc. Dose adjustment of pravastatin may be necessary with concomitant use of RTV and SQVsgc. Pravastatin does not alter the NFV pharmacokinetics, and thus appears to be safe for concomitant use.
The development of psychiatric concepts in traditional Chinese medicine.

The development of psychiatric conceptualization in traditional Chinese medicine is traced by reviewing the descriptions of psychiatric maladies appearing in Chinese medical documents of various periods. The theory of mental illness has gone through a sequence of supernatural, natural, somatic, and psychological stages. Psychiatric illness has been recognized in medical literature in the following order: organic mental illness, excited psychosis, hysteria, depression, and minor psychiatric illness. This is discussed in comparison with the development of psychiatric concepts in the West in an attempt to understand how the perception and interpretation of mental illness, associated with the increase of man's knowledge, have changed and developed through time in different sociocultural environments.
Prescribing for Hyperopia in Childhood and Teenage by Academic Optometrists

Purpose. The purpose of this study was to examine the prescribing patterns of academic optometrists for infants, children, and teenagers with hyperopia and the factors that affected the decision to prescribe. A comparison was made to published guidelines for prescribing for hyperopia in children. Methods. The Waterloo Eye Study (WatES) database is a database of all patients attending the Primary Care Clinic or the Pediatric Clinic at the School of Optometry, University of Waterloo, between February 2007 and January 2008. Records for 698 patients aged from birth to 19 years with hyperopia but without strabismus or significant anisometropia were extracted. They were analyzed to determine the factors that predicted whether a child was prescribed spectacles and the 50% prescribing points for hyperopia and astigmatism according to age. Results. Univariate analysis showed that the level of hyperopia, astigmatism, age, distance, and near phoria and presence of symptoms were associated with the prescription of spectacles (p < 0.05). Multivariate analysis showed that the prescription of spectacles was predicted by age, highest sphere (either right or left eye), highest cylinder, the presence of symptoms, and distance phoria. Among 0 to 3 year olds, all the children with 5 D or more of hyperopia had been prescribed spectacles. Among the 4 to 6 year olds, this point was 3.25 D; and for the 7 to 19 year olds, it was 2.25 D. The levels at which 50% of the population had been prescribed spectacles was 3.7, 1.8, and 1.1 D for the 0 to 3 year olds, 4 to 6 year olds, and 7 to 19 year olds, respectively. There was frequently a difference between the refraction and the prescription such that the younger children, in particular, were often under corrected for both hyperopia and astigmatism. Conclusions. The optometrists in this academic setting appear to follow the available optometric guidelines for prescribing for hyperopia. They tend to prescribe for lower levels of hyperopia than U.S. ophthalmologists.
Comparison of the Intubating Laryngeal Mask Airway with the Fiberoptic Intubation in Anticipated Difficult Airway Management

Background The intubating laryngeal mask airway (ILMA; Fastrach ™; Laryngeal Mask Company, Henley-on-Thames, UK) may provide an alternative technique to fiberoptic intubation (FIB) to facilitate the management of the anticipated difficult airway. The authors therefore compared the effectiveness of the ILMA with FIB in patients with anticipated difficult intubation. Methods One hundred patients, with at least one difficult intubation criteria (Mallampati class III or IV, thyromental distance < 65 mm, interincisor distance < 35 mm) were enrolled (FIB group, n = 49; ILMA group, n = 51) in this prospective randomized study. Anesthesia was induced with propofol and maintained with alfentanil and propofol after an efficient mask ventilation has been demonstrated. The success of the technique (within three attempts), the number of attempts, duration of the successful attempt, and adverse events (oxygen saturation < 90%, bleeding) were recorded. Results The rate of successful tracheal intubation with ILMA was 94% and comparable with FIB (92%). The number of attempts and the time to succeed were not significantly different between groups. In case of failure of the first technique, the alternative technique always succeeded. Failures in FIB group were related to oxygen desaturation (oxygen saturation < 90%) and bleeding, and to previous cervical radiotherapy in the ILMA group. Adverse events occurred significantly more frequently in FIB group than in ILMA group (18 vs. 0%, P < 0.05). Conclusion The authors obtained a high success rate and comparable duration of tracheal intubation with ILMA and FIB techniques. In patients with previous cervical radiotherapy, the use of ILMA cannot be recommended. Nevertheless, the use of the ILMA was associated with fewer adverse events.
Oestrogen receptors and breast cancer

Breast cancer is marked by great clinical and biological diversity. Some women can be cured, while others die rapidly over just a few months. Systemic treatments can have gratifying and possibly curative effects for some, while for others they add only misery and financial hardship. Given this great heterogeneity, are women with breast cancer best served by therapeutic approaches emphasising homogeneity or ones that reflect the variability of the disease in individual choices of treatment? A case in point is the use of oestrogen receptor status in making decisions about endocrine therapy. Oestrogen receptors are required for oestrogen stimulated growth and proliferation of breast cancer. They are found to some degree in 50-80% of breast tumours. Endocrine treatments are designed to antagonise the effects of oestrogen. Oophorectomy, luteinising hormone releasing hormone agonists, and aromatase inhibition all reduce the level of oestrogen, while antioestrogens such as tamoxifen competitively block binding of oestrogen to receptors and thus antagonise transcriptional activation of genes required for tumour growth. Twenty five years ago it was first hypothesised that the response to such endocrine treatments would depend on the presence of oestrogen receptors in the tumours. And indeed, 50-60% of receptor positive metastatic tumours do respond.1 For tumours that test negative for oestrogen and progesterone receptors, the response rate (in terms of tumour …
Expression of vitreoscilla hemoglobin improves growth and levels of extracellular enzyme in yarrowia lipolytica

Enhancement in oxygen uptake by high‐cell‐density cultivations has been achieved previously by expression of the bacterial hemoglobin gene from Vitreoscilla. The Vitreoscilla hemoglobin (VHb) gene was expressed in the yeast Yarrowia lipolytica to study the effect of expression in this commercially important yeast. The expression of VHb in this yeast was found to enhance growth, contrary to reported observations in wild‐type Saccharomyces cerevisiae in which there was no significant growth enhancement. VHb‐expressing Y. lipolytica exhibited higher specific growth rate, enhanced oxygen uptake rate, and higher respiratory activity. We report the beneficial effects of VHb expression on growth under microaerobic as well as under nonlimiting dissolved oxygen conditions. Earlier studies in Y. lipolytica have demonstrated inhibition of mycelia formation by respiratory inhibitors and poor nitrogen source, conditions poor for growth. VHb+ Y. lipolytica cells were more efficient at forming mycelia, indicating better utilization of available oxygen as compared with the VHb− cells. Expression of VHb was also found to increase the levels of enzyme ribonuclease secreted into the medium, a property that may be beneficial for producing heterologous proteins in Y. lipolytica. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 658–666, 2003.