gebhart/patrepeval huggingface dataset:
Simultaneous image transformation and sparse representation recovery (2008)

Sparse representation in compressive sensing is gaining increasing attention due to its success in various applications. As we demonstrate in this paper, however, image sparse representation is sensitive to image plane transformations such that existing approaches can not reconstruct the sparse representation of a geometrically transformed image. We introduce a simple technique for obtaining transformation-invariant image sparse representation. It is rooted in two observations: 1) if the aligned model images of an object span a linear subspace, their transformed versions with respect to some group of transformations can still span a linear subspace in a higher dimension; 2) if a target (or test) image, aligned with the model images, lives in the above subspace, its pre-alignment versions would get closer to the subspace after applying estimated transformations with more and more accurate parameters. These observations motivate us to project a potentially unaligned target image to random projection manifolds defined by the model images and the transformation model. Each projection is then separated into the aligned projection target and a residue due to misalignment. The desired aligned projection target is then iteratively optimized by gradually diminishing the residue. In this framework, we can simultaneously recover the sparse representation of a target image and the image plane transformation between the target and the model images. We have applied the proposed methodology to two applications: face recognition, and dynamic texture registration. The improved performance over previous methods that we obtain demonstrates the effectiveness of the proposed approach.
Drinking Histories in Alcohol-Use-Disordered Youth: Preliminary Findings on Relationships to Platelet Serotonin Transporter Expression With Genotypes of the Serotonin Transporter (2009)

These findings provide partial support for the hypothesis that, among currently drinking adolescents with an AUD, differential expression of 5-HTT may play an important role in the onset of adolescent AUD.
Effects of N‐acetylcysteine on dense cell formation in sickle cell disease (2003)

The extent to which dense and irreversible sickle cells (ISCs) contribute to vaso-occlusive episodes in sickle cell disease remains unclear. N-Acetylcysteine (NAC) inhibits dense cell and ISC formation in sickle erythrocytes in vitro and restores glutathione levels toward normal. A phase II double-blind randomized clinical trial was completed to determine the efficacy of NAC in decreasing dense cell and ISC formation, and vaso-occlusive episodes in sickle cell disease. Twenty-one subjects with a history of at least two vaso-occlusive episodes per year and 6% dense cells were enrolled. Four treatment groups were analyzed; NAC at a dose of 2,400 mg per day decreased the percent dense cells from 20.1 +/- 2.9 to 12.6 +/- 2.1 (P < 0.05) and increased red cell glutathione levels from 292.8 +/- 74.5 to 576.7 +/- 155.1 (P < 0.05). In addition, we observed a decrease in vaso-occlusive episodes from 0.03 to 0.006 episodes per person-days and a decreased in relative risk to R = 0.39. Although NAC did not significantly decrease the number of ISCs, there was a downward trend at all doses tested. In summary, NAC inhibited dense cell formation, restored glutathione levels toward normal, and decreased vaso-occlusive episodes at a well-tolerated dose of 2,400 mg per day. To determine the long-term efficacy and safety of NAC, a multicenter phase III clinical trial is required.
ChemInform Abstract: Synthesis of Dinucleoside Pyridylphosphonates Involving Palladium(0)‐Catalyzed Phosphorus—Carbon Bond Formation as a Key Step. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The hyperfluidization of mammalian cell membranes acts as a signal to initiate the heat shock protein response (2005)

The concentrations of two structurally distinct membrane fluidizers, the local anesthetic benzyl alcohol (BA) and heptanol (HE), were used at concentrations so that their addition to K562 cells caused identical increases in the level of plasma membrane fluidity as tested by 1,6-diphenyl-1,3,5-hexatriene (DPH) anisotropy. The level of membrane fluidization induced by the chemical agents on isolated membranes at such concentrations corresponded to the membrane fluidity increase seen during a thermal shift up to 42 degrees C. The formation of isofluid membrane states in response to the administration of BA or HE resulted in almost identical downshifts in the temperature thresholds of the heat shock response, accompanied by increases in the expression of genes for stress proteins such as heat shock protein (HSP)-70 at the physiological temperature. Similarly to thermal stress, the exposure of the cells to these membrane fluidizers elicited nearly identical increases of cytosolic Ca2+ concentration in both Ca2+-containing and Ca2+-free media and also closely similar extents of increase in mitochondrial hyperpolarization. We obtained no evidence that the activation of heat shock protein expression by membrane fluidizers is induced by a protein-unfolding signal. We suggest, that the increase of fluidity in specific membrane domains, together with subsequent alterations in key cellular events are converted into signal(s) leading to activation of heat shock genes.
RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders (2014)

Repeat-associated disorders caused by expansions of short sequences have been classified as coding and noncoding and are thought to be caused by protein gain-of-function and RNA gain-of-function mechanisms, respectively. The boundary between such classifications has recently been blurred by the discovery of repeat-associated non-AUG (RAN) translation reported in spinocerebellar ataxia type 8, myotonic dystrophy type 1, fragile X tremor/ataxia syndrome and C9ORF72 amyotrophic lateral sclerosis and frontotemporal dementia. This noncanonical translation requires no AUG start codon and can initiate in multiple frames of CAG, CGG and GGGGCC repeats of the sense and antisense strands of disease-relevant transcripts. RNA structures formed by the repeats have been suggested as possible triggers; however, the precise mechanism of the translation initiation remains elusive. Templates containing expansions of microsatellites have also been shown to challenge translation elongation, as frameshifting has been recognized across CAG repeats in spinocerebellar ataxia type 3 and Huntington's disease. Determining the critical requirements for RAN translation and frameshifting is essential to decipher the mechanisms that govern these processes. The contribution of unusual translation products to pathogenesis needs to be better understood. In this review, we present current knowledge regarding RAN translation and frameshifting and discuss the proposed mechanisms of translational challenges imposed by simple repeat expansions.
GLUTATHIONE (1983)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Thrombotic Thrombocytopenic Purpura Associated with Ticlopidine: A Review of 60 Cases (1998)

Ticlopidine use may be associated with the development of thrombotic thrombocytopenic purpura, usually within 1 month of initiation of therapy. The onset of ticlopidine-associated thrombotic thrombocytopenic purpura is difficult to predict, despite close monitoring of platelet counts.
Comparison of Cation Exchange in Ganophyllite and [Na + Al]-Substituted Tobermorite: Crystal-Chemical Implications (1988)

Abstract Ganophyllite and [Na + + Al 3+ ]-substituted tobermorite exhibited similar cation exchange properties and, in particular, selective cesium exchange. [Na + + Al 3+ ]-substituted tobermorite and ganophyllite showed a selective Cs exchange of 10.77 and 8.71 meq/100 g from 0.02N NaCl and of 11.08 and 9.04 meq/100 g from 0.02N CaCl 2 , respectively. The [Na + + Al 3+ ]-substituted tobermorite is structurally similar to ganophyllite: both are roughly analogous to 2:1 layer silicates, both have cross-linking tetrahedra across the interlayer region, and both have exchangeable cations located in zeolite-like sites in the interlayer region. The similarities in cation exchange properties imply that the residual charge configuration of the analogue 2 : 1 layer must be approximately equivalent also.
Improvement of bacterial -glucanase thermostability by glycosylation (1991)

The relationship between enzyme stability and glycosylation was examined for two different Bacillus (1,3-1,4)-β-glucanases following expression of the corresponding genes in Escherichia coli and in Saccharomyces cerevisiae. Both of the (1,3-1,4)-β-glucanases secreted from yeast cells were glycosylated and a pronounced difference in the type and extent of glycosylation was observed. Thermostability analysis of the glycosylated enzymes and their unglycosylated counterparts synthesized by E. coli disclosed a substantially higher thermotolerance of the glycosylated enzymes. At 70 °C the half-life of the glycosylated form of B. macerans (1,3-1,4)-β-glucanase was 26 min, as compared to 10 min for the unglycosylated form of the enzyme. Using the same conditions, the half-life of the B. amyloliquefaciens-B. macerans hybrid (1,3-1,4)-β-glucanase was 5 min for the unglycosylated enzyme and about 100 min when the enzyme was glycosylated.
A new synthetic class A amphipathic peptide analogue protects mice from diet-induced atherosclerosis (2001)

Several synthetic class A peptide analogues have been shown to mimic many of the properties of human apo A-I in vitro. A new peptide [acetyl-(AspTrpLeuLysAlaPheTyrAspLysValPheGluLysPheLysGluPhePhe)-NH2; 5F], with increased amphipathicity, was administered by intraperitoneal injection, 20 microg/day for 16 weeks, to C57BL/6J mice fed an atherogenic diet. Mouse apo A-I (MoA-I) (50 microg/day) or phosphate-buffered saline (PBS) injections were given to other mice as controls. Total plasma cholesterol levels and lipoprotein profiles were not significantly different between the treated and control groups, except that the mice receiving 5F or MoA-I had lower high density lipoprotein (HDL) cholesterol when calculated as a percentage of total cholesterol. No toxicity or production of antibodies to the injected materials was observed. When HDL was isolated from high fat diet-administered mice injected with 5F and presented to human artery wall cells in vitro together with human low density lipoprotein (LDL), there were substantially fewer lipid hydroperoxides formed and substantially less LDL-induced monocyte chemotactic activity than with HDL from PBS-injected animals. Injection of human apo A-I produced effects similar to 5F on lipid peroxide formation and LDL-induced monocyte chemotactic activity, but injection of MoA-I was significantly less effective in reducing lipid hydroperoxide formation or lowering LDL-induced monocyte chemotactic activity. Mice receiving peptide 5F had significantly less aortic atherosclerotic lesion area compared with mice receiving PBS, whereas lesion area in mice receiving MoA-I was similar to that of the PBS-injected animals. This is the first in vivo demonstration that a model class A amphipathic helical peptide has antiatherosclerotic properties. We conclude that 5F inhibits lesion formation in high fat diet-administered mice by a mechanism that does not involve changes in the lipoprotein profile, and may have potential in the prevention and treatment of atherosclerosis.
Enhancement of phosphorus utilization in growing pigs fed phytate-rich diets by using rye bran. (1991)

Some cereal by-products, such as bran, exhibit a high phytase activity that may enhance phytate P digestibility. This was studied in growing pigs fed a phytase-rich (1,200 IU/kg) diet containing 20% rye bran. The trial involved 12 animals; six were fed a control diet and six were fed a diet containing rye bran for 2 mo. Both diets contained the same levels of energy, protein, Ca (.7%) and total P (.4%). No inorganic P was added; thus, the dietary P was mainly phytic. Pigs fed the control diet, in contrast to those fed the diet containing rye bran, developed a P deficiency, as indicated by hypophosphatemia, hypophosphaturia, hyperhydroxyprolinuria, hypercalcemia, and hypercalciuria. Phosphorus from the rye bran diet was more completely absorbed (55 vs 36%) and retained (50 vs 36%) than that from the control diet. Calcium absorption was equal for the two diets, but Ca retention was higher in pigs fed rye bran than in controls. Pigs fed the rye bran diet showed greater bone density, ash content, and bending moments than controls. In conclusion, high dietary phytase levels or phytase-rich by-products increased phytate P availability and consequently improved bone scores.
Multi-Level Surface Maps for Outdoor Terrain Mapping and Loop Closing (2006)

To operate outdoors or on non-flat surfaces, mobile robots need appropriate data structures that provide a compact representation of the environment and at the same time support important tasks such as path planning and localization. One such representation that has been frequently used in the past are elevation maps which store in each cell of a discrete grid the height of the surface in the corresponding area. Whereas elevation maps provide a compact representation, they lack the ability to represent vertical structures or even multiple levels. In this paper, we propose a new representation denoted as multi-level surface maps (MLS maps). Our approach allows to store multiple surfaces in each cell of the grid. This enables a mobile robot to model environments with structures like bridges, underpasses, buildings or mines. Additionally, they allow to represent vertical structures. Throughout this paper we present algorithms for updating these maps based on sensory input, to match maps calculated from two different scans, and to solve the loop-closing problem given such maps. Experiments carried out with a real robot in an outdoor environment demonstrate that our approach is well-suited for representing large-scale outdoor environments
Stratos: A Network-Aware Orchestration Layer for Virtual Middleboxes in Clouds (2013)

Enterprises want their in-cloud services to leverage the performance and security benefits that middleboxes offer in traditional deployments. Such virtualized deployments create new opportunities (e.g., flexible scaling) as well as new challenges (e.g., dynamics, multiplexing) for middlebox management tasks such as service composition and provisioning. Unfortunately, enterprises lack systematic tools to efficiently compose and provision in-the-cloud middleboxes and thus fall short of achieving the benefits that cloud-based deployments can offer. To this end, we present the design and implementation of Stratos, an orchestration layer for virtual middleboxes. Stratos provides efficient and correct composition in the presence of dynamic scaling via software-defined networking mechanisms. It ensures efficient and scalable provisioning by combining middlebox-specific traffic engineering, placement, and horizontal scaling strategies. We demonstrate the effectiveness of Stratos using an experimental prototype testbed and large-scale simulations.
Structure of a highly stable mutant of human fibroblast growth factor 1 (2008)

Fibroblast growth factors (FGFs) are involved in diverse cellular processes such as cell migration, angiogenesis, osteogenesis, wound healing and embryonic and foetal development. Human acidic fibroblast growth factor (FGF-1) is the only member of the FGF family that binds with high affinity to all four FGF receptors and thus is considered to be the human mitogen with the broadest specificity. However, pharmacological applications of FGF-1 are limited owing to its low stability. It has previously been reported that the introduction of single mutations can significantly improve the stability of FGF-1 and its resistance to proteolytic degradation. Here, the structure of the Q40P/S47I/H93G triple mutant of FGF-1, which exhibits much higher stability, a prolonged half-life and enhanced mitogenic activity, is presented. Compared with the wild-type structure, three localized conformational changes in the stable triple mutant were observed, which is in agreement with the perfect energetic additivity of the single mutations described in a previous study. The huge change in FGF-1 stability (the denaturation temperature increased by 21.5 K, equivalent to DeltaDeltaG(den) = 24.3 kJ mol(-1)) seems to result from the formation of a short 3(10)-helix (position 40), an improvement in the propensity of amino acids to form beta-sheets (position 47) and the rearrangement of a local hydrogen-bond network (positions 47 and 93).
The association of the glycophorin C exon 3 deletion with ovalocytosis and malaria susceptibility in the Wosera, Papua New Guinea (2001)

Erythrocyte polymorphisms, including ovalocytosis, have been associated with protection against malaria. This study in the Wosera, a malaria holoendemic region of Papua New Guinea, examined the genetic basis of ovalocytosis and its influence on susceptibility to malaria infection. Whereas previous studies showed significant associations between Southeast Asian ovalocytosis (caused by a 27- base pair deletion in the anion exchanger 1 protein gene) and protection from cerebral malaria, this mutation was observed in only 1 of 1019 individuals in the Wosera. Polymerase chain reaction strategies were developed to genotype individuals for the glycophorin C exon 3 deletion associated with Melanesian Gerbich negativity (GPCDeltaex3). This polymorphism was commonly observed in the study population (GPCDeltaex3 frequency = 0.465, n = 742). Although GPCDeltaex3 was significantly associated with increased ovalocytosis, it was not associated with differences in either Plasmodium falciparum or P vivax infection measured over the 7-month study period. Future case-control studies will determine if GPCDeltaex3 reduces susceptibility to malaria morbidity.
Transfection of mammalian cells with plasmid DNA by scrape loading and sonication loading. (1987)

Scrape loading and sonication loading are two recently described methods of introducing macromolecules into living cells. We have tested the efficacy of these methods for transfection of mammalian cells with exogenous DNA, using selection systems based either on resistance to the drug G418 (Geneticin) or on acquisition of the ability to utilize the salvage pathway of pyrimidine biosynthesis. These loading methods can be employed to generate cell lines that express the gene product of the transfected DNA molecules both transiently and stably. Optimal transfection is observed when the DNA is added to cells in physiological saline lacking divalent cations and containing K+ in place of Na+. DNA molecules 7.1 to 30 kilobases long have been introduced by the scrape loading procedure. In addition, the scrape loading procedure has been employed for cotransfection and subsequent expression of nonselectable genes encoded on DNA molecules added in a mixture with DNA molecules whose expression is selected. Cell lines expressing oncogenes or proteins that are important for regulation of cell growth and division have been obtained by this procedure. The scrape loading procedure is also useful for studies of the cellular changes that occur upon expression of an exogenous gene. As many as 80% of cells scrape loaded with the plasmid pC6, which encodes the simian virus 40 large tumor antigen, contained this protein in the nucleus between 1 and 5 days after transfection. Thus, scrape loading and sonication loading are simple, economical, and reproducible methods for introduction of DNA molecules into adherent and nonadherent cells, and these methods may be useful in the future for experimentation at both fundamental and applied levels.
Single-chip precision oscillators based on multi-frequency, high-Q aluminum nitride MEMS resonators (2009)

Aluminum nitride (AlN) contour mode resonators have been of interest because of their high quality factor, low impedance, large number of frequencies on a single chip and compatibility with CMOS processes. While AlN low insertion loss filters and oscillators have been demonstrated, CMOS integration has yet to be accomplished. This work represents the first time fully-released contour mode AlN microresonators have been integrated with CMOS circuitry to obtain completely monolithic frequency references.
Phase 1 study of low-dose prolonged exposure schedules of the hypomethylating agent 5-aza-2′-deoxycytidine (decitabine) in hematopoietic malignancies (2003)

Decitabine (5-aza-2'-deoxycytidine) inhibits DNA methylation and has dual effects on neoplastic cells, including the reactivation of silenced genes and differentiation at low doses and cytotoxicity at high doses. We evaluated, in a phase 1 study, low-dose prolonged exposure schedules of decitabine in relapsed/refractory leukemias. Patient cohorts received decitabine at 5, 10, 15, or 20 mg/m2 intravenously over one hour daily, 5 days a week for 2 consecutive weeks, doses 5- to approximately 30-fold lower than the maximum tolerated dose (MTD). There were 2 groups that also received 15 mg/m2 daily for 15 or 20 days. A total of 50 patients were treated (44 with acute myelogenous leukemia [AML]/myelodysplasia [MDS], 5 with chronic myelogenous leukemia [CML], and 1 with acute lymphocytic leukemia [ALL]), and the drug was well tolerated at all dose levels, with myelosuppression being the major side effect. Responses were seen at all dose levels. However, the dose of 15 mg/m2 for 10 days appeared to induce the most responses (11 of 17 or 65%), with fewer responses seen when the dose was escalated or prolonged (2 of 19 or 11%). There was no correlation between P15 methylation at baseline or after therapy and response to decitabine. We conclude that decitabine is effective in myeloid malignancies, and low doses are as or more effective than higher doses.
Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences (2012)

With sampling from various parts of a stool, both devices provided good reproducibility on overall microbial diversity and classification for the major phyla, but not for minor phyla. Implementation of these methods should provide insights into how broad microbial parameters, but not necessarily rare microbes, affect risk of various conditions.
Muscarinic Receptor Function and Acetylcholinesterase Activity after Chronic Administration of Tacrine to Mice at Therapeutic Drug Concentrations (1992)

We administered 9-amino-1,2,3,4-tetrahydroacridine (THA, Tacrine) to mice in doses (0.3-3 mg/kg) which have been shown to enhance cognition. Animals were sacrificed at various time points and several markers of cholinergic function were measured. Following 3 mg/kg THA, drug levels in brain were sufficient to inhibit 78-80% of brain acetylcholinesterase activity, regardless of treatment duration. However, repeated administration of THA did not alter the number of muscarinic receptors or the phosphoinositide response to muscarinic receptor agonists. Thus, at therapeutically relevant doses, THA inhibits the activity of brain acetylcholinesterase substantially, but does not affect the density of muscarinic receptors on their ability to activate second messenger systems. These results are in contrast to those obtained by other investigators who found significant decreases in muscarinic receptor number following chronic administration of higher doses of THA.
UVB induction of p53 protein expression in cultured normal human melanocytes (1993)

Experimental Dermatology Unit, London Hospital Keratinocyte Laboratory, 44 Lincolns Inn Fields, London, UK