gebhart/patrepeval huggingface dataset:
p<b><i>I</i></b>‐based phosphopeptide enrichment combined with nanoESI‐MS (2007)

IEF is introduced as a new principle for enrichment and separation of phosphopeptides as obtained after digestion of phosphoproteins by trypsin. Tryptic peptides and phosphopeptides exhibit pI values, which overlap in the range of about 4-6. However, after methyl esterification of all carboxyl functions, the pI values of tryptic peptides and phosphopeptides regroup in discrete clusters. In addition, mono- and diphosphorylated peptides show different but very homogeneous pI values, with variations when internal Arg, Lys, or His residues are present. Experimentally, this new concept was applied for separation of model peptides on IPG strips pH 3-10 as used in the first dimension of 2-DE. After IEF of methyl-esterified peptides, the IPG strip was cut into pieces followed by peptide extraction, desalting and MS analysis by nanoESI-MS. Phosphopeptides were found to focus in good agreement with their calculated pI values. This analytical strategy showed a resolution of about 0.2 pI units, and thus turned out to be capable of detecting minor differences in pI values, such as those occurring between pSer, pThr and pTyr residues. Using IPG strips with a pI range of 3-10, methyl esterified nonphosphorylated tryptic peptides are concentrated in the basic part of the IPG strip or even leave the strip. Thus, efficient enrichment of phosphopeptides and their subfractionation according to pI is obtained in one step. Minor hydrolytic side reactions including deamidation of Asn and partial hydrolysis of methyl esters are observed. The results show that IEF opens attractive avenues for the further advancement of analytical phosphoproteomics.
Calixarenes with host-mediated potency in experimental tuberculosis: further evidence that macrophage lipids are involved in their mechanism of action (1996)

Some time ago, it was found that attachment of hydrophilic polyoxyethylene chains to various hydrophobic phenols and alcohols gave water-soluble products which, although inactive in vitro, influenced and experimental tuberculous infection. With short chains the infection was suppressed, and with long chains it was promoted. Later work concentrated on Macrocyclon (short chain) and HOC-60 (long chain), both derived from a hydrophobic, polyphenolic calixarene. Growth of Mycobacterium tuberculosis inside macrophages (M phi) was inhibited by Macrocyclon and stimulated by HOC-60. Also, triglyceride lipase from M phi extracts and an extracellular phospholipase were inhibited by Macrocyclon and stimulated by HOC-60. This suggestion of a mechanism has been strengthened by the finding that M phi cultivated in monolayers and treated with Macrocyclon showed accumulation of lipid and little formation of fatty acid after incubation of killed cells. With HOC-60, lipid was depleted and much fatty acid was found.
Dynamic modelling and control of a hydrogen peroxide bleaching process (2002)

Mathematical models have been developed for a peroxide bleaching plant based on first principles. Responses of the final pulp brightness to changes in chemical charge, incoming pulp properties and operating conditions have been studied by dynamic simulations. It was found that the chemical charge is the most important variable in determining the final pulp brightness. The simulation of different control strategies showed that a combination of feed-forward and feedback control can achieve good brightness control.
A Novel Dispersion and PMD Tolerant Clock Phase Detector for Coherent Transmission Systems (2011)

A novel clock phase detector is presented and shown to be tolerant to chromatic dispersion and PMD. The phase detector can be used in a clock recovery circuit for demodulation of 100 Gb/s coherent transmission system.
CHEMICAL MODIFICATION OF METHIONINES OF RIBONUCLEASE A WITH<i>o</i>‐BENZOQUINONE (1980)

The accessibility of methionines in RNAase A to reaction with OBQ has been studied at highly acidic pH. The differences between the rate constants of reactions of the methionine and methionines of RNAase A with OBQ is a reflection on the limited accessibility of methionines in the protein conformation. Nevertheless, at sufficiently high OBQ concentration, all the four methionines of the enzyme can be modified. At lower concentration of OBQ, a derivative may be prepared in which a specific methionine is modified. The introduced chromophore ionizes at around pH 3 in this derivative. The derivative has partial activity towards RNA which is enhanced on addition of S-protein.
Impact of River Salinity on Fish Diversity i n the South-West Coastal Region of Bangladesh (2008)

ABSTRACT Saline water intrusion is a major problem and conflicting issue in south-west coastal region of Bangladesh. Thepresent study provides an asses sment of changes of fish div ersity with the cha nges of salinity lev el i n the nearby riverover the last thirty years . This study is carried out through semi-structured questionnaire survey i n selected villagesof different salinit y prone areas such as high s aline zone and moderate saline zone , namely Paikgacha a nd Rampal,respectively. The increased salinity has negative impact on fish diversity in this region. Local people’s perception,experts’ judgment was used in detecting decreasing of fish diversity with increasing in river salinity. The study hasrevealed that in Paikgacha, the salinity varies approximately within the range from 20,000 to 45,000 micromhosand in Rampa l it is from 10,000 to 30,000 micro-mhos. D ue to in crea sed sa linity, t he fish spec ies in Paikgacha andRampal have been reduced from 29 to 12 and 24 to 19 species respectively during the period 1975-2005.Dominancy of very few sali nity tolerant species is increasing in both areas but it is more visible in Paikgacha thanRampal.
Genotypic and Drought‐Induced Differences in Carbon Isotope Discrimination and Gas Exchange of Cowpea (1992)

Carbon isotope composition may be useful for selection in plant breeding. Theory predicts that 13 C discrimination (Δ) by leaves can be associated with the ratio of photosynthesis (as indicated by CO 2 assimilation rate, A ) to leaf conductance ( g ) to diffusion of water vapor or CO 2 . In earlier studies with a cowpea ( Vigna unguiculata [L.] Walp.) mutant and parent, drought‐induced differences in Δ were associated with expected differences in A/g based on theory, whereas genotypic differences in Δ were not. Studies were conducted for 2 yr with a broader range of genotypes to determine whether these conclusions are generally valid. Eighteen cowpea accessions were grown under weekly irrigation or stored soil moisture in four randomized split blocks at Riverside, CA, in 1987. Twelve of these cowpea accessions were studied under similar conditions in 1988. Gas exchange measurements were made of A and leaf conductance to water vapor ( g h ), and leaves were sampled for Δ. Significant drought‐induced reduction in Δ of 1.6 × 10 −3 was observed and an increase in A/g of 42% which is similar to the value (36%) predicted based upon the change in Δ. The drought‐induced increase in A/g was due to substantial decreases in g h , which more than compensated for a 59% reduction in A . Genotypic differences in Δ of up to 2 × 10 −3 were observed which were predicted to be associated with 43% higher A/g ; however, genotypic differences in A/g were small, and genotypic means of A/g and Δ were not associated as expected based on theory. Genotypic differences in Δ were more consistent than differences in A/g , A , or g h , and should be easier to select in breeding, but the physiological basis for the genotypic differences in Δ has not been elucidated for cowpea.
Active appearance motion model segmentation (2002)

An adaptive method for temporal sequence segmentation was developed and its performance assessed in the segmentation of cardiac motion image sequences. The primary contribution of this paper is the development of a novel, 2D+time active appearance motion model (AAMM) that represents the dynamics of the cardiac cycle in combination with the shape and image appearance of the heart. Cootes' 2D active appearance model (AAM) framework was extended by considering a complete image sequence as a single shape/intensity sample. This way, the proven strength of AAMs, like robustness and ability to capture observer preference, are augmented with temporal consistency over an image sequence.
LEVELS OF EVIDENCE (2009)

Evidence-Based Ophthalmology 10(4):p 179-180, October 2009. | DOI: 10.1097/01.IEB.0000361664.37801.41
Internalization of nerve growth factor by PC12 cells. A description of cellular pools. (1988)

Binding and internalization of nerve growth factor (NGF) by responsive cells is a complex process. We have incubated rat pheochromocytoma cells (PC12) with 125I-NGF at 37 degrees C and measured the association of ligand after removal of subsets of bound ligand by different methods. Chase with unlabeled NGF at either 4 or 37 degrees C, acid stripping, nonionic detergent stability, and combinations of these protocols were utilized. These variations of the binding assay were able to distinguish ligand bound to fast versus slow cell surface receptors, NGF bound to slow receptors at the cell surface versus cell interior, and soluble ligand versus cytoskeletally attached NGF. Quantitative and temporal relations among five cellular pools were defined. Experiments with the inhibitors chloroquine, cytochalasin B, and colchicine defined pools of NGF in terms of the route through the cell from the plasma membrane to the lysosome. Chloroquine caused accumulation of NGF only in the pool that was not associated with the cytoskeleton, implicating the involvement of this pool in supplying ligand to the lysosome. Results with cytochalasin B and colchicine suggest that both microfilaments and microtubules are involved in pathways leading to NGF degradation. A semiquantitative model for the movement of NGF through the cell is presented based on these observations.
Cleaning and storage of rigid contact lenses prior to dispensing. (1992)

Most care regimens used with rigid contact lenses are composed of three solutions: 1) a "cleaning" solution; 2) a "combination" solution intended for storage, disinfection, and wetting prior to placement of rigid lenses on the eye; and 3) an in-eye "rewetting" or "lubricating" solution. While solutions (1) and (3) have only single functions, solution (2) must fulfill three fairly disparate functions. A "2-solution" care regimen is offered by Sherman Pharmaceuticals and consists of (a) a solution for cleaning, storage, and disinfection; and (b) a "wetting" solution that doubles as an in-eye lubricant. Through a more compatible and efficient matching of multiple functions within solutions, Sherman Pharmaceuticals claims to more adequately clean and prepare rigid gas-permeable (RGP) lens surfaces for wear. We investigated this strategy in terms of in-eye wettability of initially "ill-prepared" RGP lens surfaces, as measured with the in vivo contact angle technique. For this study, lenses were intentionally not cleaned of residues or solvents by the manufacturer at the end of production so as to create the well-known "first-day non-wetting syndrome." The ability of the 2-solution care regimen to even then provide wettable surfaces was compared to that of a saline control "regimen" and the most popular competing "3-solution" care system. We concluded that use of both care regimens dramatically enhanced in-eye wettability and, therefore, reduced the incidence of the "first-day non-wetting syndrome". However, the 2-solution care regimen provided significantly better wettability overall, lower incidence of functionally non-wetting surfaces, and more consistently wettable RGP lenses.
Computer Algorithms C (1996)

Using the popular object-oriented language C++, this book incorporates the latest research and state-of-the-art applications while focusing on design techniques rather than on individual algorithms.
Initial Anatomical Changes Associated with Tuber Formation on Single-node Potato (Solanum tuberosum L.) Cuttings: A Re-evaluation (1999)

Cell division and cell expansion during early stages of tuber development were studied using developing axillary buds on single-leaf cuttings from potato (Solanum tuberosum L.). Cuttings taken from plants induced to form tubers, by short day (SD) treatment, were compared with cuttings from non-induced (long day, LD) plants. In the apical zone of the buds, cell division occurred from the first day after cutting, in both LD and SD cuttings. The planes of these divisions were transverse, associated with elongation of the buds. At day 5, a new orientation of cell division was observed in the subapical zone of SD cuttings only. These divisions were longitudinal, associated with radial growth. Cell expansion occurred in both SD and LD cuttings, and was not uniquely related to the onset of tuber formation.
Study of the shrinkage caused by holographic grating formation in acrylamide based photopolymer film (2011)

We study the shrinkage in acrylamide based photopolymer by measuring the Bragg detuning of transmission diffraction gratings recorded at different slant angles and at different intensities for a range of spatial frequencies. Transmission diffraction gratings of spatial frequencies 500, 1000, 1500 and 2000 lines/mm were recorded in an acrylamide based photopolymer film having 60 ± 5 μm thickness. The grating thickness and the final slant angles were obtained from the angular Bragg selectivity curve and hence the shrinkage caused by holographic recording was calculated. The shrinkage of the material was evaluated for three different recording intensities 1, 5 and 10 mW/cm2 over a range of slant angles, while the total exposure energy was kept constant at 80 mJ/cm2. From the experimental results it can be seen that the shrinkage of the material is lower for recording with higher intensities and at lower spatial frequencies.
Asymmetric Synthesis of New β‐Lactam Lipopeptides as Bacterial Signal Peptidase I Inhibitors (2011)

Abstract The transmembrane bacterial enzyme, signal peptidase I, is recognized as being a promising target for reducing the emergence of drug resistance. The asymmetric synthesis and the biological evaluation of original β‐lactam lipopeptides have been performed to discover potent signal peptidase inhibitors. The importance of the azetidinone motif of these lipopeptides has been demonstrated and can serve as a starting point to exploit and improve the reactivity of the β‐lactam in peptidomimetics.
Adaptive display luminance for viewing smartphones under low illuminance (2015)

The study investigates the optimal display luminance for viewing smartphones in conditions of low illuminance. This proposes a model of adaptive display in that display luminance changes gradually with the passage of watching time. It starts at a fairly low display luminance of 10 cd/m2, and after 10 seconds, the luminance increases slowly until it reaches 40 cd/m2 for 20 seconds and maintains the luminance. For the development of the model, an experiment was conducted to identify the optimal luminance for initial viewing and that for continuous viewing, as well as the change speed of display luminance. In order to validate the model, users' subjective judgments and activation of alpha rhythm were observed, and the result confirmed the superiority of the adaptive display luminance compared to the current display luminance in terms of physiological comfort and psychological satisfaction. It is expected that this study contributes to the pleasing use of displays at night under low illuminance by applying to diverse types of display devices.
A high data rate, low power all-digital correlation circuit design (2005)

Correlation techniques are widely used in analog and digital signal processing; e.g. in optiman receiver design. In this paper, a new digital output correlator circuit design is proposed. The correlation results are presented as a binary count of the number of bits in agreement between 31-bit reference and input sequences. Correlation results could be presented at data rates up to about 50MHz. The proposed new circuit could be implemented in a high speed bipolar transistor technology as a monolithic large-scale-integrated circuit with a power dissipation of about .5 watts. A novel pipelined 31-bit digital summing circuit will be presented that employs new multivalued, multithresholded latching and counting circuits in the formation of its binary-coded output. Comparisons with an all-binary digital correlator circuit are made.
Serum Angiotensin-I-Converting Enzyme andCarboxypeptidase N in Crohn’s Disease and Ulcerative Colitis (1986)

Angiotensin-I-converting enzyme (ACE) and carboxypeptidase N1 and N2 (CPN1, CPN2) inactivate kinins and might therefore play a role in the development of inflammatory reactions via an influence on the release of prostaglandins and inactivation of anaphylatoxic peptides of the complement system. In the present study, the serum activity of these enzymes was determined in 60 patients with Crohn's disease, 18 patients with ulcerative colitis and 70 healthy control subjects. ACE was significantly lowered in active Crohn's disease (CDAI greater than 150) and in ulcerative colitis (p less than 0.01), as long as the ileum or cecum was affected. Since ACE was detected in high concentrations in the human intestinal mucosa, decreased values may be explained by damage to the site of its production. CPN1 and CPN2 were raised in both diseases (p less than 0.005), irrespective of their activity and location. These alterations in the activity of the kininases investigated may play a role in the pathogenesis of inflammatory bowel diseases.
Developmental expression of rat insulin-like growth factor-II/mannose 6-phosphate receptor messenger ribonucleic acid. (1992)

We have examined the developmental pattern of the insulin-like growth factor-II (IGF-II)/mannose 6-phosphate (M6P) receptor mRNA in various rat tissues from 20-day gestation fetuses and 20-day postnatal animals by Northern blotting and solution hybridization/RNase protection assays. The major mRNA species in all fetal and postnatal tissues was 9.0 kilobases. The rank order of receptor mRNA concentrations among the fetal tissues was heart greater than limb/muscle, lung, intestine, kidney, liver greater than brain, which agrees with the previously reported rank order of the tissue concentrations of receptor protein. The concentration of IGF-II/M6P receptor mRNA was significantly lower in postnatal tissues, again reflecting the relative levels of receptor protein in fetal and postnatal tissues. We measured IGF-II/M6P receptor mRNA copy number in fetal heart, the tissue with the highest concentration of receptor protein and mRNA, by including in the solution hybridization/RNase protection assay known amounts of a sense strand transcript of the receptor cDNA. This sense strand standard was quantitated by incorporating a tracer amount of [32P]UTP into the transcript and measuring the radioactivity in the product purified by gel electrophoresis. The receptor mRNA copy number in fetal heart was 74 molecules/cell. We conclude that the IGF-II/M6P receptor mRNA concentration is an important determinant of the level of receptor protein in most tissues.
Key factors for a high-quality VR experience (2017)

For many years, Virtual Reality has been presented as a promising technology that could deliver a truly new experience to users. The media and entertainment industry is now investigating the possibility to offer a video-based VR 360 experience. Nevertheless, there is a substantial risk that VR 360 could have the same fate as 3DTV if it cannot offer more than just being the next fad. The present paper aims at presenting the various quality factors required for a high-quality VR experience. More specifically, this paper will focus on the main three VR quality pillars: visual, audio and immersion.
Dendritic Cells as Arbiters of Peritoneal Immune Responses (2006)

During the past few years, there has been a substantial increase in the understanding of innate immunity. Dendritic cells are emerging as key players in the orchestration of this early phase of immune responses, with a role that will translate into the subsequent type of adaptive immune response against infection. Here we provide an overview of dendritic cell differentiation and function, with particular emphasis on those features unique to the immune defense of the peritoneal cavity and in the context of peritoneal dialysis-associated immune responses. The reader is referred to the primary references included in the accompanying list for specific details in this fascinating field.
TGF-β inhibition enhances chemotherapy action against triple-negative breast cancer (2013)

After an initial response to chemotherapy, many patients with triple-negative breast cancer (TNBC) have recurrence of drug-resistant metastatic disease. Studies with TNBC cells suggest that chemotherapy-resistant populations of cancer stem-like cells (CSCs) with self-renewing and tumor-initiating capacities are responsible for these relapses. TGF-β has been shown to increase stem-like properties in human breast cancer cells. We analyzed RNA expression in matched pairs of primary breast cancer biopsies before and after chemotherapy. Biopsies after chemotherapy displayed increased RNA transcripts of genes associated with CSCs and TGF-β signaling. In TNBC cell lines and mouse xenografts, the chemotherapeutic drug paclitaxel increased autocrine TGF-β signaling and IL-8 expression and enriched for CSCs, as indicated by mammosphere formation and CSC markers. The TGF-β type I receptor kinase inhibitor LY2157299, a neutralizing TGF-β type II receptor antibody, and SMAD4 siRNA all blocked paclitaxel-induced IL8 transcription and CSC expansion. Moreover, treatment of TNBC xenografts with LY2157299 prevented reestablishment of tumors after paclitaxel treatment. These data suggest that chemotherapy-induced TGF-β signaling enhances tumor recurrence through IL-8-dependent expansion of CSCs and that TGF-β pathway inhibitors prevent the development of drug-resistant CSCs. These findings support testing a combination of TGF-β inhibitors and anticancer chemotherapy in patients with TNBC.
Studies in the Apocynaceae. I. A Critical Study of the Apocynoideae (With Special Reference to the FGenus Apocynum) (1930)

Robert E. Woodson, Jr., Studies in the Apocynaceae. I. A Critical Study of the Apocynoideae (With Special Reference to the FGenus Apocynum), Annals of the Missouri Botanical Garden, Vol. 17, No. 1/2 (Feb. - Apr., 1930), pp. 1-172+174-212
On the complexity of global scheduling constraints under structural restrictions (2013)

We investigate the computational complexity of two global constraints, CUMULATIVE and INTERDISTANCE. These are key constraints in modeling and solving scheduling problems. Enforcing domain consistency on both is NP-hard. However, restricted versions of these constraints are often sufficient in practice. Some examples include scheduling problems with a large number of similar tasks, or tasks sparsely distributed over time. Another example is runway sequencing problems in air-traffic control, where landing periods have a regular pattern. Such cases can be characterized in terms of structural restrictions on the constraints. We identify a number of such structural restrictions and investigate how they impact the computational complexity of propagating these global constraints. In particular, we prove that such restrictions often make propagation tractable. 1