Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

Homologs of the phosphatidylinositol‐4‐phosphate‐5‐kinase (PIP5K), which controls a multitude of essential cellular functions, contain a 8 aa insert in a conserved region that is specific for the Saccharomycetaceae family of fungi. Using structures of human PIP4K proteins as templates, structural models were generated of the Saccharomyces cerevisiae and human PIP5K proteins. In the modeled S. cerevisiae PIP5K, the 8 aa insert forms a surface exposed loop, present on the same face of the protein as the activation loop of the kinase domain. Electrostatic potential analysis indicates that the residues from 8 aa conserved loop form a highly positively charged surface patch, which through electrostatic interaction with the anionic portions of phospholipid head groups, is expected to play a role in the membrane interaction of the yeast PIP5K. To unravel this prediction, molecular dynamics (MD) simulations were carried out to examine the binding interaction of PIP5K, either containing or lacking the conserved signature insert, with two different membrane lipid bilayers. The results from MD studies provide insights concerning the mechanistic of interaction of PIP5K with lipid bilayer, and support the contention that the identified 8 aa conserved insert in fungal PIP5K plays an important role in the binding of this protein with membrane surface. Proteins 2017; 85:1454–1467. © 2017 Wiley Periodicals, Inc.
A cortical potential imaging analysis of the P300 and Novelty P3 components

The P300 and Novelty P3 are positive components of the event related brain potential (ERP) with a latency of at least 300 ms, which are manifestations of brain activity evoked by deviant events. Spencer et al. [ 1999 , 2001 ] demonstrated that these are two distinct components, both of which may be elicited, with different amplitudes, by both rare and novel events. However, the locations of the intracranial sources of the components remain unknown. We describe the application of cortical potential imaging (CPI) analysis to the data described by Spencer et al. [ 1999 ]. The ERPs were recorded from 15 healthy subjects presented with auditory oddball sequences. Cortical potential maps (CPMs) were reconstructed from the scalp potential maps (SPMs) corresponding to the P300 and Novelty P3 components by deblurring the smoothing effect of the head volume conductor. The reconstructed CPMs, derived from the SPMs by means of the CPI, showed localized areas of activity distributed in both the frontal and parietal lobes; the parietal region was active throughout the period of the late positivities. The reconstructed CPMs associated with novel events showed prominent activity at the frontal lobe (Novelty P3) followed by progressively pronounced parietal lobe activity (P300), and these two components can be well separated by the CPMs. These analyses show how the CPI can be used to relate the scalp electrical recordings to the underlying brain activity. Hum. Brain Mapping 12:120–130, 2001. © 2001 Wiley‐Liss, Inc.
Adriamycin stimulates proliferation of human lymphoblastic leukaemic cells via a mechanism of hydrogen peroxide (H2O2) production

It is becoming clear that adriamycin cytotoxicity may be mediated by semiquinone‐free radicals derived from the drug itself and reactive oxygen species (ROS). Recent evidence supports the concept that low concentrations of ROS are able to stimulate cell proliferation, and, based on the observation that subtoxic concentrations of adriamycin can also induce cell proliferation, we hypothesize that low concentrations of adriamycin stimulate cell proliferation by a ROS generation mechanism. We have employed spin‐trapping and electron spin resonance (ESR) spectroscopy to investigate the nature of the adriamycin‐generated ROS. The spin trap 3,5‐dibromo‐4‐nitrosobenzenesulphonate (DBNBS), which is oxidized in the presence of H2O2 and peroxidase enzymes, was used to produce a characteristic three‐line spectrum, and it was found that an identical spectrum was produced by human lymphoblastic leukaemic cells (CCRF‐CEM cells) after exposure to adriamycin. We tested our hypothesis further by exposing CCRF‐CEM cells to subtoxic concentrations of adriamycin (10−8, 10−9 and 10−10 M) and low concentrations of H2O2 (10−8, 10−9 and 10−10 M) and subsequently monitored cell proliferation. We found that low concentrations of both adriamycin and H2O2 significantly stimulate CCRF‐CEM cell proliferation. We therefore conclude that subtoxic concentrations of adriamycin are likely to induce cell proliferation via an H2O2 mediated mechanism.
Benefit of a 2-month treatment with a micronized, purified flavonoidic fraction on venous ulcer healing. A randomized, double-blind, controlled versus placebo trial.

OBJECTIVE To assess the efficacy of a micronized purified flavonoid fraction (Daflon 500 mg = Dios) in venous leg ulcer healing, in addition to compression therapy and standardized local care. DESIGN Double-blind, multicentre, randomized, parallel groups, controlled versus placebo trial; stratification according to ulcer size. SUBJECTS 107 patients, with venous ulcer of the leg for at least 3 months, and accepting bandaging therapy. RESULTS 105 patients (Dios = 53, placebo = 52) were available for an intention to treat (ITT) analysis. Age (mean +/- SD, 71+/-11 years), gender (M = 33, F = 74) and ulcer size were evenly distributed among both groups. 99 patients completed the protocol (Dios = 51, placebo = 48). Among the 91 patients with ulcer size < or = 100 cm (Dios = 44, placebo = 47), a significantly higher number of patients had complete ulcer healing at 2 months in the Dios group (n = 14) in comparison to the placebo group (n = 6) after ITT analysis (32 vs. 13%, p = 0.028) and after per protocol analysis (32 vs. 14%, p = 0.048), and a shorter time duration of healing (p = 0.037). Among the 14 patients with ulcer size > 10 cm (Dios = 9, placebo = 5), no ulcer healed. CONCLUSION This study showed that a 2-month course of purified micronized flavonoid fraction (2 tablets/day), in addition to conventional treatment, is of benefit in patients by accelerating complete healing of venous leg ulcers which are < or = 10 cm in diameter.
Development of 4-axis soft deformable sensor for humanoid sensor flesh

In order to achieve tactile sensing exterior for humanoid robots expected to have close interaction with humans or environments, not only the distribution of the sensors, but also softness of the sensor element itself and detection capability for multi-axis deformation are crucial. Although there's some studies on developing tactile sensor with both softness and multi-axis deformation, few of them can be applicable to humanoid exterior from viewpoint of embedding them inside the soft thick exterior. In our previous works, 20mm-cube 3-axis soft deformable sensor is developed. However, there is enough room to improve. In this paper, 4-axis soft deformable sensor unit is proposed. Proposed sensor can detect 3-axis rotational change including twisting direction, and 1-axis normal direction force. 3D rotation of the sensor is estimated by a pair of MEMS IMU boards. Although each of the outputs of IMUs are affected by motions or vibrations of the attached link, rotational deformation of the sensor can robustly estimated by monitoring the difference between them. Also, we have developed a prototype sensor flesh embedded with this deformation sensor for a humanoid robot, and the result of implemented reactive behavior against tactile sensation shows the feasibility of the proposed tactile sensor system.
A Cluster-Based Model for Object Detecting with Wireless Sensor Networks

A system model for wireless sensor networks is presented for efficiently realizing objective detecting. By self-organizing mechanism based on the maximum number of neighboring nodes, a data-gathering algorithm is proposed that partitions network nodes deployed in the detected region into several clusters for the fusion of the sensed objective data. Each cluster consists of a head node and several member nodes, taking responsibility for the fusion and transmitting to base station (BS) of sensed data through multihop communication and being responsible for sensing data respectively. In the process of data gathering, the energy efficiency-aware mechanism insure each node stand for one of four conditions including sleep, passive, test, and active, which are determined by the neighbor node number threshold (NT) and the average data loss rate (DL). Simulations prove that the proposed scheme is valid through put ratio, mean time delay, and packet loss ratio.
A Cysteine-Rich Extracellular Protein Containing a PA14 Domain Mediates Quorum Sensing in Dictyostelium discoideum

ABSTRACT Much remains to be understood about quorum-sensing factors that allow cells to sense their local density. Dictyostelium discoideum is a simple eukaryote that grows as single-celled amoebae and switches to multicellular development when food becomes limited. As the growing cells reach a high density, they begin expressing discoidin genes. The cells secrete an unknown factor, and at high cell densities the concomitant high levels of the factor induce discoidin expression. We report here the enrichment of discoidin-inducing complex (DIC), an ∼400-kDa protein complex that induces discoidin expression during growth and development. Two proteins in the DIC preparation, DicA1 and DicB, were identified by sequencing proteolytic digests. DicA1 and DicB were expressed in Escherichia coli and tested for their ability to induce discoidin during growth and development. Recombinant DicB was unable to induce discoidin expression, while recombinant DicA1 was able to induce discoidin expression. This suggests that DicA1 is an active component of DIC and indicates that posttranslational modification is dispensable for activity. DicA1 mRNA is expressed in vegetative and developing cells. The mature secreted form of DicA1 has a molecular mass of 80 kDa and has a 24-amino-acid cysteine-rich repeat that is similar to repeats in Dictyostelium proteins, such as the extracellular matrix protein ecmB/PstA, the prespore cell-inducing factor PSI, and the cyclic AMP phosphodiesterase inhibitor PDI. Together, the data suggest that DicA1 is a component of a secreted quorum-sensing signal regulating discoidin gene expression during Dictyostelium growth and development.
Uptake of dexamethasone incorporated into liposomes by macrophages and foam cells and its inhibitory effect on cellular cholesterol ester accumulation

To confirm the efficacy of dexamethasone incorporated into liposomes in the treatment of atherosclerosis, the uptake of dexamethasone‐liposomes by macrophages and foam cells and its inhibitory effect on cellular cholesterol ester accumulation in these cells were investigated in‐vitro. Dexamethasone‐liposomes were prepared with egg yolk phosphatidylcholine, cholesterol and dicetylphosphate in a lipid molar ratio of 7/2/1 by the hydration method. This was adjusted to three different particle sizes to clarify the influence of particle size on the uptake by the macrophages and foam cells, and the inhibitory effect on cellular cholesterol ester accumulation. The distribution of particle sizes of dexamethasone‐liposomes were 518.7 ± 49.5nm (L500), 202.2± 23.1 nm (L200), and 68.6 ± 6.5 nm (L70), respectively. For each size, dexamethasone concentration and dexamethasone/lipid molar ratio in dexamethasone‐liposome suspension were 1 mg dexamethasone mL−1 and 0.134 mol dexamethasone mol−1 total lipids, respectively. The zeta potential was approximately −70 mV for all sizes. Dexamethasone‐liposomes or free dexamethasone were added to the macrophages in the presence of oxidized low density lipoprotein (oxLDL) and foam cells, and then incubated at 37°C. The uptake amount of dexamethasone by the macrophages and foam cells after a 24‐h incubation was L500 > L200 > free dexamethasone > L70. The macrophages in the presence of oxLDL and foam cells were incubated with dexamethasone‐liposomes or free dexamethasone for 24 h at 37°C to evaluate the inhibitory effect on the cellular cholesterol ester accumulation. The cellular cholesterol ester level in the macrophages treated with oxLDL was significantly increased compared with that in macrophages without additives. L500, L200 and free dexamethasone significantly inhibited this cholesterol ester accumulation. L500, L200 and free dexamethasone also significantly reduced cellular cholesterol ester accumulation in foam cells. In addition, the relationship between the area under the uptake amount of dexamethasone‐time curve (AUC) and the inhibition rate of cholesterol ester accumulation in macrophages and foam cells was evaluated. The inhibition rate of cholesterol ester accumulation (%) was related to the AUC in both types of cell. These results suggested that dexamethasone‐liposomes would be a useful approach to the development of a novel drug delivery system for atherosclerotic therapy. Furthermore, the prediction of the inhibitory effect of dexamethasone on cellular cholesterol ester accumulation may become possible by using the results of this study.
Sex Differences in Application, Success, and Funding Rates for NIH Extramural Programs

Purpose The authors provide an analysis of sex differences in National Institutes of Health (NIH) award programs to inform potential initiatives for promoting diversity in the research workforce. Method In 2010, the authors retrieved data for NIH extramural grants in the electronic Research Administration Information for Management, Planning, and Coordination II database and used statistical analysis to determine any sex differences in securing NIH funding, as well as subsequent success of researchers who had already received independent NIH support. Results Success and funding rates for men and women were not significantly different in most award programs. Furthermore, in programs where participation was lower for women than men, the disparity was primarily related to a lower percentage of women applicants compared with men, rather than decreased success rates or funding rates. However, for subsequent grants, both application and funding rates were generally higher for men than for women. Conclusions Cross-sectional analysis showed that women and men were generally equally successful at all career stages, but longitudinal analysis showed that men with previous experience as NIH grantees had higher application and funding rates than women at similar career points. On average, although women received larger R01 awards than men, men had more R01 awards than women at all points in their careers. Therefore, while greater participation of women in NIH programs is under way, further action will be required to eradicate remaining sex differences.
Association of symptoms of depression with progression of CKD.

BACKGROUND Depression is related to morbidity and mortality in patients with kidney failure treated by dialysis, but its influence on patients with earlier stages of chronic kidney disease (CKD) is uncertain. This study investigates the association of depressive symptoms with clinical outcomes in patients with CKD not requiring dialysis. STUDY DESIGN Prospective observational cohort study. SETTING & PARTICIPANTS 568 participants with CKD not requiring maintenance dialysis were recruited consecutively at a tertiary hospital in Southern Taiwan and followed up for 4 years. PREDICTORS Baseline status of depressive symptoms. OUTCOMES The primary outcome is a composite of progression to end-stage renal disease (ESRD), defined as requiring maintenance dialysis treatment, or all-cause mortality; and secondary outcome was first hospitalization. MEASUREMENTS Depressive symptoms were assessed by Beck Depression Inventory. Estimated glomerular filtration rate (eGFR) was computed using the 4-variable MDRD (Modification of Diet in Renal Disease) Study equation. RESULTS 428 participants completed the questionnaires and 160 (37%) had depressive symptoms. During a mean follow-up of 25.2 ± 11.9 months, 136 participants (32%) reached the primary outcome (119 reached ESRD and 17 died) and 110 participants (26%) were hospitalized. High depressive symptoms increased the risk of progression to ESRD or death (HR, 1.66; 95% CI, 1.14-2.44) and first hospitalization (HR, 1.59; 95% CI, 1.03-2.47). Participants with high depressive symptoms had more rapid GFR decrease (eGFR slopes of -2.3 [25th-75th percentile, -5.3 to -0.4] vs -1.2 [25th-75th percentile, -3.5 to 0.3] mL/min/1.73 m(2) per year; P = 0.001) and initial dialysis treatment at a higher eGFR (OR for initiation of dialysis at eGFR >5 mL/min/1.73 m(2), 4.45; 95% CI, 1.44-13.78). LIMITATIONS A single-center study of Taiwanese, Beck Depression Inventory evaluates only depressive symptom burden. CONCLUSIONS Depressive symptoms in CKD are independent predictors of adverse clinical outcomes, including faster eGFR decrease, dialysis therapy initiation, death, or hospitalization. Depression should be evaluated early and treated in patients with CKD.
THE MIAMI HERALD AND THE MILLER EFFECT: LITERARY JOURNALISM IN THE 1980S

A process of preparing a branched (co)polycarbonate resin is disclosed. The process entails using at least one compound conforming to formulae 1a or 1b in which R1, R2 and R3 independently denote linear or branched C1-C10-alkyl, R4 and R5 independently denote hydrogen or linear or branched C1-C10-alkyl, p1 and p2 independently of one another denote a whole number between 3 and 10, as a branching agent.
A New Black Hole Detection Scheme for Vanets

In this paper, we address a key topic in the field of computer networking security which is the detection of black hole nodes in VANETs "Vehicular Ad Hoc Networks" that are vulnerable to security attacks due to its infrastructureless nature. The black hole attack is a form of a denial of service attack that makes a gap for data traffic in a VANET. Our solution is suitable for a low density network where each car moves in a straight line and delivers packets to other neighboring cars using a geographic routing protocol. Road side units are placed in the intersection of roads and may accept to transfer packets when a car encounters a problem of packet delivery. The black hole attack is considered at the network layer and each car maintains a trust table in order to evaluate the reliability of neighboring cars. Each sender updates the trust value of each neighbor according to the acknowledgement received by the destination and uses jointly this value with the progress to select the best neighbor. More specifically, IEEE 802.11 is the communication standard that is used and guarantees the functions of the physical and the data link layers and solves the common problems of wireless communication between the cars since our focus is related to the network layer. Omnet++ is the simulation tool which is used to design and simulate our proposed scheme. Our results demonstrate the routing and the detection process and the impact of the density on the required time for the detection.
High plasma fatty acid concentrations were present in non-diabetic patients with coronary heart disease.

BACKGROUND Free fatty acids (FFAs) are reported to be related to coronary heart disease (CHD); however, some case subjects in those reports suffered from CHD and diabetes mellitus. The aim of this research was to reveal the FFAs as the independent discriminators in non-diabetic CHD patients. The association between FFA concentrations and DNA methylation of carbohydrate response element binding protein (ChREBP) was also investigated, since ChREBP acted as an important regulatory factor in the FFA synthesis. METHODS Blood samples were collected after an overnight fast from 60 controls and 68 non-diabetic patients with CHD. Plasma concentrations of glucose, cholesterol (TC), triglycerides (TG), high density lipoprotein cholesterol (HDL-C), and low density lipoprotein cholesterol (LDL-C) were measured by standard techniques in an automatic biochemical analyzer. Plasma concentrations of nine types of FFAs were determined by high performance liquid chromatography (HPLC). The DNA methylation of ChREBP was detected by direct bisulfate sequencing. RESULTS In the case group, the concentrations of glucose and HDL-C decreased, while the concentrations of TC, TG, and each FFA significantly increased compared with controls (p < 0.05). By logistic regression analysis, all FFAs except C14:0 were found to be independent risk factors for CHD in non-diabetic patients. No significant differences of clinical chemistry indicators were found between the methylated and unmethylated case groups. CONCLUSIONS Plasma concentrations of FFAs are higher in non-diabetic patients with CHD and are emerging independent discriminators for CHD. High FFA concentrations are expected to play a role even in non-diabetic patients with CHD.
Determinants of a Blunted Carotid-to-Radial Pulse Wave Velocity Decline in Response to Hyperemia

Carotid—radial pulse wave velocity (PWV) decreases in normal healthy individuals following hyperemia provoked by release of arterial cuff occlusion. To determine the effects of specific cardiovascular (CV) risk factors on the hyperemic PWV response, we measured PWV before and after brachial artery (BA) occlusion in 218 participants (66% males, age 56 ± 19 years), with and without CV risk factors/disease. ΔPWV ranged from -46% to +35% and values were normally distributed. On univariate analyses, ΔPWV correlated with age, hypertension (Htn), hypercholesterolemia, diabetes mellitus (DM), coronary disease, congestive heart failure (CHF), smoking, and mean arterial pressure (MAP). On multivariate analysis, ΔPWV was independently related to Htn (B = 4.56, P = .03) and CHF (B = 7.34, P = .008) and trended toward a higher MAP (B = .113, P = .067), DM (B = 4.01, P = .11), and hypercholesterolemia (B = 3.36, P = .12). In conclusion, hyperemic changes in carotid—radial PWV values are independently related to Htn and CHF and possibly DM and hyperlipidemia.
DNA Sequence Analysis of a 23 002 bp DNA Fragment of the Right Arm of Saccharomyces cerevisiae Chromosome VII

We report the sequence of a 23 002 bp fragment located on the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of this region revealed 14 complete open reading frames (ORFs) with more than 300 base pairs. Six of them correspond to previously known genes. G7164 is the QCR9 gene coding for subunit 9 of the cytochrome c reductase; G7168 is UBR1, encoding an ubiquitin protein ligase; G7522 is the TYS1 gene, which encodes for the tyrosyl tRNA synthetase; G7526 is TFG1, the gene coding for the RNA polymerase transcription initiation factor TFIIF (factor G); G7538 is the gene HGH1 which encodes a protein related to the mammalian HMG1 and HMG2 proteins. G7542 is the BUB1 gene which encodes a ser/thr protein kinase involved in spindle assembly during the cell cycle. One of the ORFs, G7553, shares significant homologies with the gene UTR2 from S. cerevisiae. None of the seven remaining ORFs shows similarity to any of the sequences within the public databases. Three ORFs are internal ORFs of the above‐described known genes, and two small ORFs are completely contained in larger ORFs on the complementary strand, and therefore probably do not correspond to real genes. This region also contains three genes specifying tRNAs for Leu, Lys and Trp, and several LTR elements. The sequence described in this paper has been deposited in the EMBL data library under the Accession Number X99074. © 1997 John Wiley & Sons, Ltd.