Miracle-dz/UniFAR-FTUs huggingface dataset:
Debridement and wound bed preparation

ABSTRACT: Debridement can play a vital role in wound bed preparation and the removal of barriers that impair wound healing. In accordance with the TIME principles, debridement can help remove nonviable tissue, control inflammation or infection, decrease excess moisture, and stimulate a nonadvancing wound edge. There are many types of debridement, each with a set of advantages and disadvantages that must be clearly understood by the healthcare team. Failure to use the correct debridement method for a given type of wound may lead to further delays in healing, increase patient suffering, and unnecessarily increase the cost of care. This review article discusses the various methods of debridement, describes currently available debriding agents, evaluates the clinical data regarding their efficacy and safety, and describes strategies for the management of problematic nonhealing wounds.
Characterization of a cell line, NKL, derived from an aggressive human natural killer cell leukemia.

Cell line NKL was established from the the peripheral blood of a patient with CD3-CD16+CD56+ large granular lymphocyte (LGL) leukemia. The neoplastic LGL of this patient mediated natural killing and antibody-dependent cellular cytotoxicity (ADCC) and exhibited proliferative responses similar to normal CD16+CD56dim natural killer (NK) cells. The Morphology of NKL cells resembles that of normal activated NK cells. The karyotype of NKL is 47, XY, add (1) (q42), +6 del (6) (q15 q23), del (17) (p11). NKL cells express CD2, CD6, CD11a, CD26, CD27, CD29, CD38, CD43, CD58, CD81, CD94, CD95, class II MHC, and the C1.7. 1 antigen, but do not express detectable levels of CD3, CD4, CD5, CD8, CD14, CD19, CD20, CD28, alpha/beta or gamma/delta T cell receptors on the cell surface. The density of the CD16, CD56, and CD57 antigens declined markedly on NKL cells during prolonged im vitro culture. Nevertheless, NKL cells can mediate ADCC as well as natural killing. NKL cells are strictly dependent on interleukin-2 (IL-2) for sustained growth and die if deprived of IL-2 for more than 7 days. NKL cells proliferate in response to concentrations of IL-2 as low as 1 pM, but an optimal proliferative response requires approximately 100 pM IL-2. NKL cells growing in the presence of IL-2 express abundant IL-2R alpha with little or no detectable IL-2 beta or gamma chain on the cell surface; NKL cells deprived of IL-2 express high levels of both IL-2R alpha and beta. IL-4, IL-7, and IL-12, unlike IL-2, do not maintain the viability of NKL cells. Furthermore, IL-1, IL-4, IL-6, IL-7, IL-12, tumor necrosis factor-alpha (TNF-alpha), interferon-alpha (IFN-alpha) and IFN-gamma do not support the growth of NKL cells. The NKL cell line may prove useful for studies of human NK cell biology.
Comparison of multiplex ligation dependent probe amplification to immunohistochemistry for assessing HER-2/neu amplification in invasive breast cancer

The HER-2/neu transmembrane tyrosine kinase receptor is both a prognostic marker and a therapeutic target for breast cancer. Accurate determination of HER-2/neu status is a prerequisite for selecting breast tumors for HER-2/neu immunotherapy or for taxan based chemotherapy. Unfortunately, there is no consensus concerning how this determination should be reached. We compared assessment of HER-2/neu status using Multiplex ligation-dependent probe amplification (MLPA) and immunohistochemistry (IHC). The patient group comprised 60 Indonesian breast cancers patients. IHC was performed on paraffin sections using the CB11 antibody from Novocastra. Results were scored according to the Hercept test. For MLPA, DNA was extracted from frozen samples, PCR amplified with a probe set containing three hemi-primer sets for the HER-2 locus and another nine control probes spread over chromosome 17 and other chromosomes, and analyzed on a gene scanner. A ratio above two for at least two HER-2 locus probes compared to the control probes was regarded as amplification. IHC for HER-2/neu was negative in 36 cases, and 24 cases (40%) showed expression. Seven, eight and nine of the latter cases were 1+, 2+ and 3+ positive, respectively. Forty-seven cases showed no amplification by MLPA, and 13 cases (22%) were amplified. Comparison of IHC and MPLA showed that none of the 36 IHC-negative or seven IHC 1+ cases was amplified. Five of the eight (63%) 2+ cases were amplified, and eight of nine (89%) of the IHC 3+ tumors showed gene amplification by MLPA assay. For HER-2/neu, there is a good correlation between gene amplification detected by MLPA and overexpression by IHC in invasive breast cancer. It appears that MLPA can detect the HER-2 amplified cases in the IHC 2+ class. Because MLPA is quick and inexpensive, it is an attractive method for detecting HER-2/neu amplification in daily laboratory practice.
BENCHMARKING DEEP LEARNING FRAMEWORKS FOR THE CLASSIFICATION OF VERY HIGH RESOLUTION SATELLITE MULTISPECTRAL DATA

Abstract. In this paper we evaluated deep-learning frameworks based on Convolutional Neural Networks for the accurate classification of multispectral remote sensing data. Certain state-of-the-art models have been tested on the publicly available SAT-4 and SAT-6 high resolution satellite multispectral datasets. In particular, the performed benchmark included the AlexNet, AlexNet-small and VGG models which had been trained and applied to both datasets exploiting all the available spectral information. Deep Belief Networks, Autoencoders and other semi-supervised frameworks have been, also, compared. The high level features that were calculated from the tested models managed to classify the different land cover classes with significantly high accuracy rates i.e., above 99.9%. The experimental results demonstrate the great potentials of advanced deep-learning frameworks for the supervised classification of high resolution multispectral remote sensing data.
Evaluation of Vitamin D Standardization Program protocols for standardizing serum 25-hydroxyvitamin D data: a case study of the program's potential for national nutrition and health surveys.

BACKGROUND The Vitamin D Standardization Program (VDSP) has developed protocols for standardizing procedures of 25-hydroxyvitamin D [25(OH)D] measurement in National Health/Nutrition Surveys to promote 25(OH)D measurements that are accurate and comparable over time, location, and laboratory procedure to improve public health practice. OBJECTIVE We applied VDSP protocols to existing ELISA-derived serum 25(OH)D data from the Irish National Adult Nutrition Survey (NANS) as a case-study survey and evaluated their effectiveness by comparison of the protocol-projected estimates with those from a reanalysis of survey serums by using liquid chromatography-tandem mass spectrometry (LC-tandem MS). DESIGN The VDSP reference system and protocols were applied to ELISA-based serum 25(OH)D data from the representative NANS sample (n = 1118). A reanalysis of 99 stored serums by using standardized LC-tandem MS and resulting regression equations yielded predicted standardized serum 25(OH)D values, which were then compared with LC-tandem MS reanalyzed values for all serums. RESULTS Year-round prevalence rates for serum 25(OH)D concentrations <30, <40, and <50 nmol/L were 6.5%, 21.9%, and 40.0%, respectively, via original ELISA measurements and 11.4%, 25.3%, and 43.7%, respectively, when VDSP protocols were applied. Differences in estimates at <30- and <40-nmol/L thresholds, but not at the <50-nmol/L threshold, were significant (P < 0.05). A reanalysis of all serums by using LC-tandem MS confirmed prevalence estimates as 11.2%, 27.2%, and 45.0%, respectively. Prevalences of serum 25(OH)D concentrations >125 nmol/L were 1.2%, 0.3%, and 0.6% by means of ELISA, VDSP protocols, and LC-tandem MS, respectively. CONCLUSION VDSP protocols hold a major potential for national nutrition and health surveys in terms of the standardization of serum 25(OH)D data.
CD44 expression indicates favorable prognosis in epithelial ovarian cancer.

PURPOSE The purpose of this study was to investigate the expression and prognostic significance of CD44 in epithelial ovarian cancer. EXPERIMENTAL DESIGN We analyzed the expression of CD44 by immunohistochemistry in 307 epithelial ovarian cancers and evaluated its relation to hyaluronan, clinicopathological factors, and prognosis. RESULTS Fifty-one percent of the tumors had a high proportion of CD44-positive cells (i.e., >/==" BORDER="0">10%), and this high CD44 expression was significantly associated with cancer cell-associated hyaluronan, well-differentiated tumor, mucinous histological type, and early stage of the tumor. High CD44 expression predicted better 5-year overall survival (50% versus 22%) and recurrence-free survival (70% versus 34%) in the univariate analyses (P < 0.00005 for both). In the Cox multivariate analyses, the independent predictors of overall survival at 5 years were primary residual tumor (P < 0.0005), International Federation of Gynecologists and Obstetricians (FIGO) stage (P = 0.001), histological grade (P = 0.014), adjuvant chemotherapy (P = 0.004), and stromal hyaluronan level (P < 0.0005), but not CD44. However, the expression of CD44 (P = 0.04) and stromal hyaluronan (P = 0.005) were both independent predictors of recurrence-free survival at 5 years, together with the size of the primary residual tumor (P < 0.0005) and histological type (P = 0.043). CONCLUSIONS The relatively frequent ectopic expression of CD44 on ovarian cancer cells is thus related to well-differentiated, early-stage tumor and long survival of the patients. Thus, whereas CD44-expressing cancer cells may adhere and implant to the hyaluronan-positive mesothelium, at least in model systems, high expression of CD44 in the tumor does not bring about an unfavorable prognosis.
The Northern Ireland dietary survey and related studies

The 1980s heralded an increased consciousness of the potential relationships between diet, lifestyles and health. Northern Ireland had a poor health record, having one of the highest death rates from ischaemic heart disease in the world, and there was a paucity of information on the lifestyle and dietary characteristics of its population. In contrast Great Britain and the Republic of Ireland had been monitoring food and nutrient intake through household food surveys, thereby providing time-series trends in food consumption and nutrient intake. For these reasons the Northern Ireland Diet and Health Study (NIDHS) was undertaken; it had the primary objective of obtaining baseline information on the dietary behaviour of the population and the secondary objective to relate these to information on health and nutritional status.
DNA Topoisomerases Regulate R-loop Formation during Transcription of the rrnB Operon in Escherichia coli *

Recent in vivo and in vitro studies have suggested an important role for DNA topoisomerases in regulating R-loop formation during transcription inEscherichia coli. In the present report we present genetic and biochemical evidence strongly suggesting that R-loop formation can occur during transcription of a portion of the rrnB operon and that it is regulated by DNA topoisomerase activity. We found that a multicopy plasmid (pBR322) carrying an heavily transcribed portion of the rrnB operon cannot be transformed in topAmutants unless RNase H is overproduced. Transcription of the 567-base pair HindIII fragment from the rrnB operon allows the extraction of large amount of R-looped plasmid DNAs from atopA mutant, in a manner that depends on the intracellular level of RNase H activity. When DNA gyrase is sufficiently active, hypernegatively supercoiled plasmid DNA is produced if the same DNA fragment is transcribed in a topA mutant. The formation of such topoisomers most likely reflect the presence of extensive R-loops since it is sensitive to the intracellular level of RNase H activity. Finally, the formation of R-looped plasmid DNAs in an in vitro transcription system using phage RNA polymerases is also detected when the 567-base pair HindIII fragment is transcribed on a negatively supercoiled DNA template.
Complications and outcomes following rectal pull-through surgery in dogs with rectal masses: 74 cases (2000-2013).

OBJECTIVE To evaluate the incidence of and factors associated with complications following rectal pull-through (RPT) surgery and the outcome for dogs with rectal tumors. DESIGN Retrospective case series. ANIMALS 74 dogs with rectal masses. PROCEDURES Information regarding signalment, history, diagnostic testing, type of rectal disease, surgical details, and postoperative complications, treatments, and outcomes was obtained from medical records and follow-up communications. Survival times were calculated. Descriptive statistics were generated. Regression analyses were used to evaluate the effect of various variables on the development of postsurgical complications and survival time. RESULTS 58 (78.4%) dogs developed postsurgical complications, the most common of which was fecal incontinence with 42 (56.8%) dogs affected, of which 23 (54.8%) developed permanent incontinence. Other complications included diarrhea (n = 32), tenesmus (23), stricture formation (16), rectal bleeding (8), constipation (7), dehiscence (6), and infection (4). The rectal tumor recurred in 10 dogs. The median survival time was 1,150 days for all dogs and 726 days for dogs with malignant tumors. The 2 most common rectal masses were rectal carcinoma and rectal carcinoma in situ, and the dogs with these tumors had median survival times of 696 and 1,006 days, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Dogs with rectal diseases that underwent RPT surgery had a high incidence of complications; however, those dogs had good local tumor control and survival times. The risk and impact of postsurgical complications on the quality of life and oncological outcomes should be discussed with owners before RPT surgery is performed in dogs with rectal masses.
Contributions of Viral Splice Sites andcis-Regulatory Elements to Lentivirus Vector Function

ABSTRACT The mobile transgene constructs of most human immunodeficiency virus (HIV)-based lentivirus vectors currently in use contain viral long terminal repeats, a 5′ untranslated region, gagsequences, and env sequences that include the Rev-responsive element (RRE). In this study, we examined the possibility of deleting HIV splice sites and gag andenv sequences from an HIV type 1 recombinant vector established in our laboratory as part of our ongoing efforts to improve this vector system. Mutations in the major splice donor site (SD) markedly reduced viral RNA expression but had little effect on vector titer. Deletion of gag or env sequences, excluding RRE, led to a moderate reduction in vector titer. Interestingly, deletion of RRE slightly reduced viral RNA expression but markedly impaired vector function. Combined deletions of RRE,gag (except for the first 40 nucleotides), env, and the SD mutation resulted in a twofold increase in cytoplasmic viral RNA expression and a recovery of vector efficiency to ∼50% of the wild-type level. This increase in cytoplasmic RNA levels is likely to be due, at least in part, to effects of the TE671 host cells, a human rhabdomyosarcoma cell line used for vector production in our system, on the cytoplasmic distribution of spliced and unspliced viral RNA. These results show that optimal lentivirus vector function can be maintained in the absence of multiple essential viral elements.
ELATE: an open-source online application for analysis and visualization of elastic tensors

We report on the implementation of a tool for the analysis of second-order elastic stiffness tensors, provided with both an open-source Python module and a standalone online application allowing the visualization of anisotropic mechanical properties. After describing the software features, how we compute the conventional elastic constants and how we represent them graphically, we explain our technical choices for the implementation. In particular, we focus on why a Python module is used to generate the HTML web page with embedded Javascript for dynamical plots.
The effects of cigarette smoking on hemoglobin levels compared between smokers and non-smokers

Background : Smoking is one of the global problems causing different disease. Smoking cause variation in different parameters of blood among which hemoglobin is believed to be increased due to smoking. Objective : To compare the effect of cigarette smoking on hemoglobin levels between smokers and non smokers. Materials and methods : A cross-sectional comparative study was conducted in Department of Pathology, Hematology Laboratory, B.P. Koirala Institute of Health Sciences, Dharan, Nepal. Total of 100 sample size which compromised of 50 smokers and 50 non smokers were included the study. Hemoglobin was estimated by Cyanmethemoglobin method. Student ‘t’ test was applied for parametric data and Chi- Square test was applied for categorical data. A p-value less than 0.05 was considered statistically significant. Results : Mean±SD of hemoglobin for smokers was 14.14±1.3 g/dl and for non smokers was 12.37±2.36 g/dl. The awareness about smoking effect in both smokers and non smokers group was not significantly different (p=0.15). Similarly the mean±SD age was 32.78±9.27 years for smokers and 35.68±11.11 years for non smokers, and was not significantly different (p=0.18). Conclusion : The present study showed that the hemoglobin level of smoker group was higher than the non-smoker group. Further substantial studies in large population should be conducted to generalize this findings. DOI: http://dx.doi. org/10.3126/stcj.v1i1. 7985 Sunsari Technical College Journal Vol.1(1) 2012 42-44
Hyperactivation of Rhizomucor miehei lipase by hydrophobic xerogels

Although a variety of approaches exist for the immobilization of enzymes, the “science” of enzyme immobilization is still in its infancy. In recent years, considerable interest has developed regarding the use of xerogels for enzyme immobilization. There are several advantages to xerogels for enzyme immobilization, including the opportunity to produce them in defined shapes or thin films and the ability to manipulate their physical characteristics (e.g., porosity, hydrophobicity, and optical properties). In this study we examined the effect of xerogel hydrophobicity on the activity of lipase (EC 3.2.2.3) from Rhizomucor miehei. The hydrophobicity of the xerogels was manipulated by generating xerogels with various molar ratios of propyltrimethoxysilane (PTMS) to tetramethoxysilane (TMOS), from 1:1 to 10:1. The belief was that, by increasing the proportion of propyl groups, the hydrophobicity of the resulting xerogel would be increased. Differences in the hydrophobicity of the resulting xerogels were confirmed using water‐affinity studies. Two approaches were taken for water‐affinity determinations by examining the ability of the xerogels to remove water from air (controlled humidity) and from water‐saturated isopropyl ether. Xerogels with higher propyl content showed a reduced affinity for water. A crude lipase preparation from Rhizomucor miehei was then contacted with sized xerogel particulates and the effect of the xerogel on lipase activity was determined. The presence of the xerogel resulted in hyperactivation of the lipase. Analysis of the protein adsorption revealed changes in the profile of proteins adsorbed to the xerogel based on the hydrophobicity of the xerogel. Based on estimations of the specific activity of the hyperactivated lipase, a minimum hyperactivation of 207% was observed. Part of the hyperactivation may be attributable to xerogel–lipase interactions, but also to the adsorption of a component from the crude lipase preparation that may complex with the lipase and the xerogel producing a stabilizing effect. Further improvements in hyperactivation and selectivity of the xerogels is likely possible by working at lower PTMS:TMOS ratios than those investigated in this study. © 2004 Wiley Periodicals, Inc.
NMR and neutron-scattering experiments on the cuprate superconductors: A critical re-examination.

We show that it is possible to reconcile NMR and neutron scattering experiments on both LSCO and YBCO, by making use of the Millis-Monien-Pines mean field phenomenological expression for the dynamic spin-spin response function, and reexamining the standard Shastry-Mila-Rice hyperfine Hamiltonian for NMR experiments. The recent neutron scattering results of Aeppli et al on LSCO (x=14%) are shown to agree quantitatively with the NMR measurements of $^{63}T_1$ and the magnetic scaling behavior proposed by Barzykin and Pines. The reconciliation of the $^{17}T_1$ relaxation rates with the degree of incommensuration in the spin fluctuation spectrum seen in neutron experiments is achieved by introducing a new transferred hyperfine coupling $C'$ between oxygen nuclei and their next nearest neighbor $Cu^{2+}$ spins; this leads to a near-perfect cancellation of the influence of the incommensurate spin fluctuation peaks on the oxygen relaxation rates of LSCO. The inclusion of the new $C'$ term also leads to a natural explanation, within the one-component model, the different temperature dependence of the anisotropic oxygen relaxation rates for different field orientations, recently observed by Martindale $et~al$. The measured significant decrease with doping of the anisotropy ratio, $R= ^{63}T_{1ab}/^{63}T_{1c}$ in LSCO system, from $R =3.9$ for ${\rm La_2CuO_4}$ to $R ~ 3.0$ for LSCO (x=15%) is made compatible with the doping dependence of the shift in the incommensurate spin fluctuation peaks measured in neutron experiments, by suitable choices of the direct and transferred hyperfine coupling constants $A_{\beta}$ and B.
Tanycyte‐like cells form a blood–cerebrospinal fluid barrier in the circumventricular organs of the mouse brain

Tanycytes are highly specialized ependymal cells that form a blood–cerebrospinal fluid (CSF) barrier at the level of the median eminence (ME), a circumventricular organ (CVO) located in the tuberal region of the hypothalamus. This ependymal layer harbors well‐organized tight junctions, a hallmark of central nervous system barriers that is lacking in the fenestrated portal vessels of the ME. The displacement of barrier properties from the vascular to the ventricular side allows the diffusion of blood‐borne molecules into the parenchyma of the ME while tanycyte tight junctions control their diffusion into the CSF, thus maintaining brain homeostasis. In the present work, we combined immunohistochemical and permeability studies to investigate the presence of tanycyte barriers along the ventricular walls of other brain CVOs. Our data indicate that, unlike cuboidal ependymal cells, ependymal cells bordering the CVOs possess long processes that project into the parenchyma of the CVOs to reach the fenestrated capillary network. Remarkably, these tanycyte‐like cells display well‐organized tight junctions around their cell bodies. Consistent with these observations, permeability studies show that this ependymal layer acts as a diffusion barrier. Together, our results suggest that tanycytes are a characteristic feature of all CVOs and yield potential new insights into their involvement in regulating the exchange between the blood, the brain, and the CSF within these “brain windows. ” J. Comp. Neurol. 521:3389‐3405, 2013. © 2013 Wiley Periodicals, Inc.