Miracle-dz/UniFAR-FTUs huggingface dataset:
The Acquisition of hMLH 1 Methylation in Plasma DNA after Chemotherapy Predicts Poor Survival for Ovarian Cancer Patients

Aberrant epigenetic regulation, such as CpG island methylation and associated transcriptional silencing of genes, has been implicated in a variety of human diseases, including cancer. Methylation of genes involved in apoptosis, including the DNA mismatch repair (MMR) gene hMLH1, can occur in tumor models of resistance to chemotherapeutic drugs. However, the relevance for acquired resistance to chemotherapy of patients’ tumors remains unsubstantiated. Plasma DNA from cancer patients, including those with ovarian cancer, often contains identical DNA changes as the tumor and provides a means to monitor CpG island methylation changes. We have examined plasma DNA of patients with epithelial ovarian cancer enrolled in the SCOTROC1 Phase III clinical trial for methylation of the hMLH1 CpG island before carboplatin/taxoid chemotherapy and at relapse. Methylation of hMLH1 is increased at relapse, and 25% (34 of 138) of relapse samples have hMLH1 methylation that is not detected in matched prechemotherapy plasma samples. Furthermore, hMLH1 methylation is significantly associated with increased microsatellite instability in plasma DNA at relapse, providing an independent measure of function of the MMR pathway. Acquisition of hMLH1 methylation in plasma DNA at relapse predicts poor overall survival of patients, independent from time to progression and age (hazard ratio, 1.99; 95% confidence interval, 1.20–3.30; P 0.007). These data support the clinical relevance of acquired hMLH1 methylation and concomitant loss of DNA MMR after chemotherapy of ovarian cancer patients. DNA methylation changes in plasma provide the potential to define patterns of methylation during therapy and identify those patient populations who would be suitable for novel epigenetic therapies.
IOT Perception Layer Security and Privacy

One of the current challenges in Internet of Things (IOT) security is the choice cryptography algorithms and key management mechanism to be used in the perception (hardware) layer. The purpose of this paper is to study the various security algorithms to achieve security standards (confidentiality, integrity, privacy) on the perception layer of IOT. The study is based on comparing the different characteristics of these algorithms, such as the degree of security of the algorithm, its speed, its achievement of various security standards, and determination of which algorithms are easy to apply to physical devices such as sensors.
Lipid-dependent Targeting of G Proteins into Rafts*

Domains rich in sphingolipids and cholesterol, or rafts, may organize signal transduction complexes at the plasma membrane. Raft lipids are believed to exist in a state similar to the liquid-ordered phase. It has been proposed that proteins with a high affinity for an ordered lipid environment will preferentially partition into rafts (Melkonian, K. A., Ostermeyer, A. G., Chen, J. Z., Roth, M. G., and Brown, D. A. (1999)J. Biol. Chem. 274, 3910–3917). We investigated the possibility that lipid-lipid interactions between lipid-modified proteins and raft lipids mediate targeting of proteins to these domains. G protein monomers or trimers were reconstituted in liposomes, engineered to mimic raft domains. Assay for partitioning of G proteins into rafts was based on Triton X-100 insolubility. Myristoylation and palmitoylation of Gαi were necessary and sufficient for association with liposomes and partitioning into rafts. Strikingly, the amount of fatty-acylated Gαi in rafts was significantly reduced when myristoylated Gαi was thioacylated withcis-unsaturated fatty acids instead of saturated fatty acids such as palmitate. Prenylated βγ subunits were excluded from rafts, whether reconstituted alone or with fatty-acylated α subunits. These results suggest that the structural difference between lipids that modify proteins is one basis for the selectivity of protein targeting to rafts.
LIFE‐HISTORY DIFFERENTIATION AND THE MAINTENANCE OF MONOECY AND DIOECY IN SAGITTARIA LATIFOLIA (ALISMATACEAE)

Abstract The existence of monoecious and dioecious populations within plant species is rare. This limits opportunities to investigate the ecological mechanisms responsible for the evolution and maintenance of these contrasting sexual systems. In Sagittaria latifolia, an aquatic flowering plant, monoecious and dioecious populations exist in close geographic proximity but occupy distinct wetland habitats differing in the relative importance of disturbance and competition, respectively. Life‐history theory predicts contrasting evolutionary responses to these environmental conditions. We propose that the maintenance of monoecy and dioecy in S. latifolia is governed by ecological selection of divergent life‐history strategies in contrasting habitats. Here we evaluate this hypothesis by comparing components of growth and reproduction between monoecious and dioecious populations under four conditions: natural populations, a uniform glasshouse environment, a common garden in which monoecious and dioecious populations and their F1 progeny were compared, and a transplant experiment using shaded and unshaded plots in a freshwater marsh. Plants from dioecious populations were larger in size and produced heavier corms in comparison with monoecious populations. Monoecious populations flowered earlier and produced more flowers, clonal ramets, and corms than dioecious populations. The life‐history differences between the sexual systems were shown to have a quantitative genetic basis, with F1 progeny generally exhibiting intermediate trait values. Survival was highest for each sexual system in field plots that most closely resembled the habitats in which monoecious (unshaded) and dioecious (shaded) populations grow. These results demonstrate that monoecious and dioecious populations exhibit contrasting patterns of investment in traits involved with growth and reproduction. Selection for divergent life histories between monoecious and dioecious populations of S. latifolia appears to be the principal mechanism maintaining the integrity of the two sexual systems in areas of geographic overlap.
Associations between lower extremity muscle mass and metabolic parameters related to obesity in Japanese obese patients with type 2 diabetes

Background. Age-related loss of muscle mass (sarcopenia) increases the incidence of obesity in the elderly by reducing physical activity. This sarcopenic obesity may become self-perpetuating, increasing the risks for metabolic syndrome, disability, and mortality. We investigated the associations of two sarcopenic indices, the ratio of lower extremity muscle mass to body weight (L/W ratio) and the ratio of lower extremity muscle mass to upper extremity muscle mass (L/U ratio), with metabolic parameters related to obesity in patients with type 2 diabetes and obesity. Methods. Of 148 inpatients with type 2 diabetes treated between October 2013 and April 2014, we recruited 26 with obesity but no physical disability. Daily physical activity was measured by a triaxial accelerometer during a period of hospitalization, and which was also evaluated by our previously reported non-exercise activity thermogenesis questionnaire. We measured body composition by bioelectrical impedance and investigated the correlations of L/W and L/U ratios with body weight, body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), visceral fat area, subcutaneous fat area, serum lipid profile, and daily physical activity. Results. The L/W ratio was significantly and negatively correlated with BMI, WC, WHR, body fat mass, body fat percentage, subcutaneous fat area, and serum free fatty acid concentration, was positively correlated with daily physical activity: the locomotive non-exercise activity thermogenesis score, but was not correlated with visceral fat area. The L/U ratio was significantly and positively correlated with serum high-density lipoprotein cholesterol. Conclusions. High L/W and L/U ratios, indicative of relatively preserved lower extremity muscle mass, were predictive of improved metabolic parameters related to obesity. Preserved muscle fitness in obesity, especially of the lower extremities, may prevent sarcopenic obesity and lower associated risks for metabolic syndrome and early mortality.
Immunosuppressive effect of 2'-deoxycoformycin (Pentostatin) for rat islet allotransplantation.

Adenosine deaminase (ADA) is an important enzyme for proper function of lymphocytes and congenital absence of ADA results in a form of severe combined immunodeficiency syndrome. 2'-Deoxycoformycin (Pentostatin, DCF) irreversibly inhibits ADA and therefore has been suggested as an immunosuppressive drug. The present study evaluated the immunosuppressive effect of DCF for islet allotransplantation in rats. Isolated islets (1,500 islets) from Lewis rats were transplanted into the kidney subcapsular space of streptozotocin-induced diabetic Wistar-Furth rats. DCF was administered IP either as a single injection at 1 mg/kg/wk, 1 mg/kg twice weekly, 5 mg/kg/twice weekly or 1 mg/kg/day, or as a continuous infusion at 0.8 or 1 mg/kg/day. Daily administration of DCF at 0.8 mg/kg in both methods, single daily injection or continuous infusion, resulted in a lymphopenia and a decrease in concanavalin A stimulation of splenic lymphocytes. However, DCF (in all doses) was not effective in preventing islet allograft rejection as evaluated by measuring the duration of normoglycemia following islet transplantation and by microscopic examination of the islet grafts. In fact, the duration of normoglycemia following islet transplantation was 7.5 +/- 0.9 and 9.0 +/- 1.0 days in rats receiving DCF in single daily injection or continuous infusion, respectively. This was not significantly different from control nontreated transplanted rats (8.5 +/- 0.7 days). Increasing the dose of DCF to 1 mg/kg, administered by continuous infusion, resulted in 100% mortality. For comparison, cyclosporine A (20 mg/kg, IP daily injection for 14 days) prolonged islet allograft survival to 27.3 +/- 1.5 days (p < 0.001). (ABSTRACT TRUNCATED AT 250 WORDS)
Complex Permittivity and Permeability Measurements and Finite-Difference Time-Domain Simulation of Ferrite Materials

A methodology to efficiently design products based on magneto-dielectric (ferrite) materials with desirable frequency responses that satisfy electromagnetic compatibility and signal integrity requirements over RF and microwave bands is presented here. This methodology is based on an analytical model of a composite magneto-dielectric material with both frequency-dispersive permittivity and permeability. A procedure for extracting complex permittivity and permeability of materials from experimental data is based on transmission line measurements. The genetic algorithm is applied for approximating both permittivity and permeability of materials by series of Debye frequency dependencies, so that they are represented as “double-Debye materials” (DDM). The DDM is incorporated in the finite-difference time-domain numerical codes by the auxiliary differential equation approach.
Fiber Optic Surface Fluorometry-Reflectometry Technique in the Renal Physiology of Rats

Most current knowledge on events in the mitochondria leading to acute renal failure originates from studies in which indirect methods were used. The disadvantage of these methods is that they cannot measure the turnover rate of various metabolites, and only one result per animal can be obtained. Chance et al. /9/ developed a method using optical techniques for continuously monitoring the fluorescence of intramitochondrial NADH, which has been applied mainly to the brain. This optical method has not yet been examined quantitatively in the kidney and no attempt has been made to adapt this method for routine measurement in kidney tissue. The purpose of this study was to adapt the surface fluorometry method for monitoring renal NADH redox state in situ, and to determine whether the hemodynamic artifacts involved in fluorometric studies of the renal surface in situ could be eliminated by using a correction factor. Another purpose was to understand the relationship between the changes in reflectance and blood volume in the rat kidney. This was achieved by measuring the reflectance after: a) blood exchange by FC-43 emulsion; b) intrarenal saline flush; c) occlusion of the renal vein, renal artery and reopening of the renal vein; d) calculation of the correlation between changes in kidney weight after renal artery occlusion, and the reflectance. Our results suggest that in the rat kidney, as opposed to the brain, a correction factor of 1:1 is not always applicable. This factor may vary between animals, and it is therefore necessary to adjust it electronically for each rat kidney. This observation contradicts the view suggesting a constant correction factor of 1:1 in the kidney. The results reported herein indicate that changes in the reflectance in the ischemic rat kidney are due to changes in blood volume. In conclusion, it seems that optical techniques for monitoring fluorescence are suitable for localized, continuous and non-invasive recording of tissue mitochondrial NADH redox states under various conditions in the rat kidney.
BLOOD BRAIN BARRIER IN RIGHT- AND LEFT-PAWED FEMALE RATS ASSESSED BY A NEW STAINING METHOD

The asymmetrical breakdown of the blood-brain barrier (BBB) was studied in female rats. Paw preference was assessed by a food reaching test. Adrenaline-induced hypertension was used to destroy the BBB, which was evaluated using triphenyltetrazolium (TTC) staining of the brain slices just after giving adrenaline for 30 s. In normal rats, the whole brain sections exhibited complete staining with TTC. After adrenaline infusion for 30 s, there were large unstained areas in the left brain in right-pawed animals, and vice versa in left-pawed animals. Similar results were obtained in seizure-induced breakdown of BBB. These results were explained by an asymmetric cerebral blood flow depending upon the paw preference in rats. It was suggested that this new method and the results are consistent with contralateral motor control that may be important in determining the dominant cerebral hemisphere in animals.
Flavopiridol, fludarabine, and rituximab in mantle cell lymphoma and indolent B-cell lymphoproliferative disorders.

PURPOSE Flavopiridol downmodulates antiapoptotic proteins associated with resistance to fludarabine and rituximab and is effective against p53-mutated chronic lymphocytic leukemia (CLL). We conducted a phase I study of flavopiridol, fludarabine, and rituximab (FFR) in patients with mantle-cell lymphoma (MCL), indolent B-cell non-Hodgkin's lymphomas (B-NHL), and CLL to determine the activity of FFR. PATIENTS AND METHODS Therapy included fludarabine 25 mg/m(2) intravenously (IV) days 1 to 5 and rituximab 375 mg/m(2) day 1 every 28 days for 6 cycles. We administered flavopiridol 50 mg/m(2) by 1-hour IV bolus (IVB) day 1 (n = 15); day 1 to 2 (n = 6); 20 mg/m(2) 30-minute IVB + 20 mg/m(2) 4-hour IV infusion (n = 3); or 30 mg/m(2) + 30 mg/m(2) (n = 14). RESULTS Thirty-eight patients (median age, 62 years) with MCL (n = 10); indolent B-NHL including follicular (n = 9), marginal zone (n = 4), lymphoplasmacytic (n = 1), or small lymphocytic lymphoma (n = 3); and CLL (n = 11), were enrolled. Twenty-two patients were previously untreated; 16 had received one to two prior therapies. Two patients in cohort 2 developed grade 3 dose-limiting toxicity (seizures, renal insufficiency). The median number of treatment cycles was 4, with cytopenias (n = 10) and fatigue (n = 3) the most common reasons for early discontinuation. Overall response rate was 82% (complete response, 50%; unconfirmed complete response, 5%; partial response, 26%), including 80% of patients with MCL (median age, 68; seven complete responses, one partial response). Median progression-free survival (PFS) was 25.6 months. Median PFS of patients with nonblastoid variant MCL (n = 8) was 35.9 months. CONCLUSION FFR was active in MCL, indolent B-NHL, and CLL and should be studied for older patients with MCL who are not candidates for aggressive chemotherapy.
Functional Role of the PE Domain and Immunogenicity of the Mycobacterium tuberculosis Triacylglycerol Hydrolase LipY

ABSTRACT PE and PPE proteins appear to be important for virulence and immunopathogenicity in mycobacteria, yet the functions of the PE/PPE domains remain an enigma. To decipher the role of these domains, we have characterized the triacylglycerol (TAG) hydrolase LipY from Mycobacterium tuberculosis, which is the only known PE protein expressing an enzymatic activity. The overproduction of LipY in mycobacteria resulted in a significant reduction in the pool of TAGs, consistent with the lipase activity of this enzyme. Unexpectedly, this reduction was more pronounced in mycobacteria overexpressing LipY lacking the PE domain [LipY(ΔPE)], suggesting that the PE domain participates in the modulation of LipY activity. Interestingly, Mycobacterium marinum contains a protein homologous to LipY, termed LipYmar, in which the PE domain is substituted by a PPE domain. As for LipY, overexpression of LipYmar in Mycobacterium smegmatis significantly reduced the TAG pool, and this was further pronounced when the PPE domain of LipYmar was removed. Fractionation studies and Western blot analysis demonstrated that both LipY and LipY(ΔPE) were mainly present in the cell wall, indicating that the PE domain was not required for translocation to this site. Furthermore, electron microscopy immunolabeling of LipY(ΔPE) clearly showed a cell surface localization, thereby suggesting that the lipase may interact with the host immune system. Accordingly, a strong humoral response against LipY and LipY(ΔPE) was observed in tuberculosis patients. Together, our results suggest for the first time that both PE and PPE domains can share similar functional roles and that LipY represents a novel immunodominant antigen.
Influence of ENSO on Regional Indian Summer Monsoon Precipitation—Local Atmospheric Influences or Remote Influence from Pacific

Using CMIP5 model outputs in different El Nino-Southern Oscillation (ENSO) phases, this work investigates the indicator that could be used as an Index to characterise regional Indian Summer Monsoon (ISM) precipitation. Dividing the Indian subcontinent into five arbitrarily chosen regions, viz. Central North East (CNE) (18°N–31°N, 86°E–75°E), Hilly (H) (28°N–38°N, 85°E–70°E), North West (NW) (21°N–31°N, 79°E–67°E), North East (NE) (21°N–31°N, 86°E–97°E) and Southern India (S) (18°N–7°N, 73°E–85°E), local wind field and remote influences from the tropical Pacific are considered to improve understanding of regional monsoon rainfall. Results are also compared with observations/reanalysis data to pinpoint areas of shortcomings and agreements. Model results suggest that regional wind velocity, viz. meridional wind component (V) at 850 mb level (V850) and zonal component at 200 mb (U200) and 850 mb (U850) can yield better estimation of local precipitation in regions CNE, H and NW, agreeing well with earlier proposed monsoon Indices. Such observations are independent of different subcategories of ENSO phases and models show good correspondence with observations. Analyses with V at 200 mb (V200) indicate circulation of the upper branch of Hadley cells in regions CNE and S, though suggest the best agreement among models in comparison with other fields, but there are some deviations from observations, indicating a missing mechanism in the models. Using models, this study identified the best parameter in different regions that could be used for the regional monsoon Index, irrespective of various ENSO subcategories; for CNE it is the U200, for H it is U200 and U850, and for NW it is U850. The current analysis, however, fails to indicate anything clearly about the NE region. When focusing on the remote influence from the eastern Pacific region, it is found that atmospheric contribution to regional ISM precipitation fails to indicate consistent roles among models, but sea surface temperature suggests strong connection. However, remote influence from the Central Pacific is captured uniformly in models via zonal components of wind in the H and NW regions.
Constructing Financial Sentiment Lexicons by Integrating Textual and Time-Series Data

This paper describes an approach to constructing sentiment lexicons in the financial domain. The approach takes advantages of news headlines and a given financial variable, such as stock prices, so as to generate candidates of sentiment expressions by fusing the two data resources. The candidates are then filtered based on their co-occurrences with financial seed words and are subsequently expanded by analogical reasoning by using distributed representation of words. Evaluative experiments on real-world news and stock price data show that the resulting lexicons are mostly reasonable and capture the characteristics of the target financial variables.
Neurotrophin-3 Antibodies Disrupt the Normal Development of the Chick Retina

When chick embryos are treated with a monoclonal antibody specifically blocking the activity of neurotrophin-3 (NT-3), the development of the retina is profoundly affected. Fewer axons are found in the optic nerve, and the retina shows abnormalities in all layers. Early during retinogenesis, the proportion of dividing cells is higher in NT-3-deprived embryos compared with age-matched controls and that of differentiated neurons is smaller. The NT-3 receptor trkC is expressed early by a majority of retinal cells, and NT-3 is present in the retina at the earliest stage studied. Initially, it is located mainly in the pigmented epithelium, with a shift toward the neural retina as development proceeds. Thus, NT-3 seems to be an essential intrinsic signal acting early in development to promote the differentiation and survival of many retinal neurons.
Similarity and denoising

We can discover the effective similarity among pairs of finite objects and denoise a finite object using the Kolmogorov complexity of these objects. The drawback is that the Kolmogorov complexity is not computable. If we approximate it, using a good real-world compressor, then it turns out that on natural data the processes give adequate results in practice. The methodology is parameter-free, alignment-free and works on individual data. We illustrate both methods with examples.
Knoxia hookeri (Rubiaceae): A New Species from India

Abstract. A new species, Knoxia hookeri (Rubiaceae), is proposed here, and a discussion about the invalidity of the three previously published names is presented. A dichotomous key is provided to distinguish the two Knoxia species: K. hookeri from K. sumatrensis. The synonymy of both species is presented with comments on typification.