gebhart/patrepeval huggingface dataset:
A colorimetric gold nanoparticle biosensor: effect of particle size on sensitivity (2003)

We have previously developed a label-free optical method to study biomolecular interactions in real time at the surface of an optically transparent substrate. The method relies on the change in the absorbance spectrum of a self-assembled monolayer of gold nanoparticles on glass as a function of biomolecular binding at the surface of the immobilized nanoparticles. Here, we report upon optimization of this sensor by examining the effect of particle size on the analytical sensitivity of the sensor. Increasing the diameter of the gold nanoparticles from 13 nm to 47 nm is shown to increase the sensitivity of the sensor by a factor of three for the model streptavidin-biotin receptor-ligand pair.
Marrow transplantation for chronic myelocytic leukemia: a controlled trial of cyclosporine versus methotrexate for prophylaxis of graft- versus-host disease (1985)

Forty-eight patients with chronic myelocytic leukemia, aged 11 to 47, were treated with high-dose cyclophosphamide and fractionated total body irradiation, followed by infusion of marrow from HLA-identical siblings. They were randomized to receive either methotrexate (MTX) (n = 23) or cyclosporine (CSP) (n = 25) as postgrafting prophylaxis for graft-v-host disease (GVHD). All patients had evidence of sustained hematopoietic engraftment. Seventeen of the 25 patients receiving CSP and 17 of the 23 patients receiving MTX are alive between one and almost four (median, 1.7) years, with an actuarial survival rate at three years of 62% and 66%, respectively (P = .60). Also, with respect to most other parameters studied, the two drugs were identical. The probability of acute GVHD was .42 and .46, respectively (P = .70), that of chronic GVHD, .50 and .63 (P = .44), and that of death from transplant-related causes, .30 and .24 (P = .51). There were no differences in the speed of granulocyte and platelet engraftment (P = .82 and .94, respectively), and the duration of hospitalization was comparable (P = .58). Patients receiving MTX required red cell transfusions for a shorter period of time (P = .02), but had a slightly increased morbidity from early oral mucositis. The leukemia recurrence rates were comparable (P = .60). With the regimens used in this study, we conclude that CSP failed to reduce the incidence of GVHD and improve the survival of patients with chronic myelocytic leukemia when compared to results with standard MTX.
Nanoparticles and cancer therapy: a concise review with emphasis on dendrimers. (2009)

The emergence of nanotechnology has had a profound effect on many areas of healthcare and scientific research. Having grown exponentially, the focus of nanotechnology has been on engineering diversified novel applications that even go beyond therapeutic activity; nanotechnology also offers the ability to detect diseases, such as cancer, much earlier than ever imaginable. Often, patients diagnosed with breast, lung, colon, prostate, and ovarian cancer have hidden or overt metastatic colonies. With the advent of diagnostic nanotechnology, these numbers are expected to greatly diminish. This review provides a brief description of nanoparticle (liposome, quantum dot, and dendrimer)-mediated cancer therapy in the last decade with an emphasis on the development and use of dendrimers in cancer therapeutics.
Woman Battering and Welfare Reform: The View from a Welfare-To-Work Program (1999)

This research compares employment training program staff estimates (N = 118) and enrollee reports (N = 122) of woman battering, that is, the physical violence and other abuse men deploy against their wives and girlfriends. The vast majority of staff estimate that woman battering obstructs the transition from welfare to work for at least some of their clients. Overall, staff respondents' relative sense of the frequency of battering quite accurately reflects enrollee reports. However, staff are especially reluctant to give estimates of physical violence and injury. Moreover, many give very low estimates for those items that are obvious markers of battering, which enrollees report at nontrivial levels. Such discrepancies are particularly disturbing because successful welfare reform implementation depends in part on staff understandings of woman battering as an obstacle to welfareto- work transition
TGF-β1attenuates myocardial ischemia-reperfusion injury via inhibition of upregulation of MMP-1 (2003)

Ischemia-reperfusion (I/R) is thought to upregulate the expression and activity of matrix metalloproteinases (MMPs), which regulate myocardial and vascular remodeling. Previous studies have shown that transforming growth factor-beta(1) (TGF-beta(1)) can attenuate myocardial injury induced by I/R. TGF-beta(1) is also reported to suppress the release of MMPs. To study the modulation of MMP-1 by TGF-beta(1) in I/R myocardium, Sprague-Dawley rats were given saline and subjected to 1 h of myocardial ischemia [total left coronary artery (LCA) ligation] followed by 1 h of reperfusion (n = 9). Parallel groups of rats were pretreated with recombinant TGF-beta(1) (rTGF-beta(1), 1 mg/rat, n = 9) before reperfusion or exposure to sham I/R (control group). I/R caused myocardial necrosis and dysfunction, indicated by decreased first derivative of left ventricular pressure, mean arterial blood pressure, and heart rate (all P < 0.01 vs. sham-operated control group). Simultaneously, I/R upregulated MMP-1 (P < 0.01). Treatment of rats with rTGF-beta(1) reduced the extent of myocardial necrosis and dysfunction despite I/R (all P < 0.01). rTGF-beta(1) treatment also inhibited the upregulation of MMP-1 in the I/R myocardium (P < 0.05). To determine the direct effect of MMP-1 on the myocardium, isolated adult rat myocytes were treated with active MMP-1, which caused injury and death of cultured myocytes, measured as lactate dehydrogenase release and trypan blue staining, in a dose- and time-dependent manner (P < 0.05). Pretreatment with PD-166793, a specific MMP inhibitor, attenuated myocardial injury and death induced by active MMP-1. The present study for the first time shows that MMP-1 can directly cause myocyte injury or death and that attenuation of myocardial I/R injury by TGF-beta(1) may, at least partly, be mediated by the inhibition of upregulation of MMP-1.
Form and Function in Multilayer Assembly: New Applications at the Nanoscale (2004)

Abstract New frontiers in materials and polymer science include the development of assembly processes that are flexible, allow the access and implementation of nanoscale structure and order, can provide access to a broad range of materials systems, and yet can be implemented at relatively low cost. The ability to fine tune the composition of nanostructured thin films on the nanometer length scale, when combined with inexpensive patterning and templating routes, provides a powerful tool for nano‐ and microscale assembly of devices and novel new material systems. The layer‐by‐layer electrostatic assembly technique is a rich, versatile, and significantly inexpensive approach to the formation of thin films via alternating adsorption of positively and negatively charged species from aqueous solutions; this method has also been extended to include the alternation of polymers with hydrogen‐bond donor and acceptor groups. Polymer organic and organic/inorganic thin films formed using this technique may contain a number of different functional groups, including electro‐optic, electroluminescent, conducting, and dielectric layers, and functional organic and inorganic nanoparticles. Newly developed materials systems based on alternating layer methods will be addressed, as well as a number of frontier areas and future areas for the use of these systems, ranging from nanomechanical composites to electrochemical devices and templated deposition of functional microspheres. Both new functionalities incorporated within these materials and new means of patterning and templating these structures in two and three dimensions will be addressed in this review.
Evaluation of a Triplex PCR Assay To DiscriminateStaphylococcus aureusfrom Coagulase-Negative Staphylococci and Determine Methicillin Resistance from Blood Cultures (2002)

A triplex PCR targeting the 16S rRNA, mecA, and nuc genes was developed for identification of staphylococci and detection of methicillin resistance. After validation of the assay with a collection of strains of staphylococci and enterococci (n = 169), the assay was evaluated with cultures of blood with gram-positive cocci from 40 patients. Accurate results were obtained for 59 (98%) of 61 cultures within 6 h of growth detection.
Direct Arylation as a Synthetic Tool for the Synthesis of Thiophene-Based Organic Electronic Materials (2011)

The efficient synthesis of thiophene based organic electronic materials can be carried out in high yields using simple starting materials by employing palladium-catalyzed direct arylation. The direct arylation method was applied to the (formal) synthesis of ten molecules that have exhibited promise for applications as optoelectronic materials. The syntheses feature the following advantages over traditional cross-coupling techniques: (1) higher yields, (2) fewer synthetic operations, (3) lower catalyst loadings, and (4) does not employ organometallic intermediates. The advantages of direct arylation make it an ideal strategy for the synthesis of thiophene containing organic electronic materials.
Dual reactivity of a photochemically-generated cyclic enyne–allene (2009)

A reactive ten-membered ring enyne-allene (tau(25 degrees C) = 5-6 min) is efficiently generated (Phi(300 nm) = 0.57) by UV irradiation of a thermally stable precursor in which a triple bond is masked as a cyclopropenone moiety.
Association of the 72-kDa protein-tyrosine kinase PTK72 with the B cell antigen receptor. (1992)

The antigen receptors on B lymphocytes are cell-surface immunoglobulins. Antibodies against surface IgM (sIgM) coimmunoprecipitate several sIgM-associated proteins. Incubation of anti-IgM complexes with [gamma-32P]ATP leads to the phosphorylation on tyrosine of IgM-associated proteins including MB-1 and a protein of 72 kDa. Peptide mapping and reimmunoprecipitation experiments indicate that the 72-kDa phosphoprotein is PTK72, a protein-tyrosine kinase that is expressed at highest levels in B lymphocytes. MB-1 is also phosphorylated in immune complexes prepared with antibodies to PTK72, indicating that components of the IgM complex are associated with PTK72. In addition, PTK72 is associated with sIgD complexes isolated from spleen B lymphocytes. The cross-linking of sIgM antigen receptors on B lymphocytes leads to the rapid phosphorylation of PTK72 on tyrosine and to the activation of PTK72 as measured by autophosphorylation and by the phosphorylation of an exogenous substrate in anti-PTK72 immune complexes. These results suggest that the signaling cascade initiated by engagement of the B cell antigen receptor involves the increased enzymatic activity of PTK72, which is already present in a preformed antigen receptor complex.
Mapping, cloning, expression, and sequencing of the rhaT gene, which encodes a novel L-rhamnose-H+ transport protein in Salmonella typhimurium and Escherichia coli. (1992)

A L-rhamnose transport-negative strain of Escherichia coli was generated by Mu d(ApR,lac)I mutagenesis. This strain was used to isolate a clone of Salmonella typhimurium DNA that encoded L-rhamnose-H+ transport activity, the gene for which, rhaT, was sequenced. The rhaT gene was mapped on the E. coli chromosome between rhaR and sodA at 87.9 min, initially by Southern blot analysis and then by the isolation, expression, and sequencing of the rhaT gene. Both rhaT genes encoded a hydrophobic protein of 344 amino acids (91% identical) that contained 10 putative transmembrane regions. The RhaT protein represents a novel class of sugar transport protein.
Mammalian α-mannosidases—multiple forms but a common purpose? (1994)

Previously, alpha-mannosidases were classified as enzymes that process newly formed N-glycans or degrade mature glycoproteins. In this review, we suggest that two endoplasmic reticulum (ER) alpha-mannosidases, previously assigned processing roles, have important catabolic activities. Based on new evidence, we propose that the ER/cytosolic mannosidase is involved in the degradation of dolichol intermediates that are not needed for protein glycosylation, whereas the soluble form of Man9-mannosidase is responsible for the degradation of glycans on defective or malfolded proteins that are specifically retained and broken down in the ER. The degradation of oligosaccharides derived from dolichol intermediates by ER/cytosolic mannosidase now explains why cats and cattle with alpha-mannosidosis store and excrete some unexpected oligosaccharides containing only one GlcNAc residue. Similarly, the action of ER/cytosolic mannosidase, followed by the action of the recently described human lysosomal alpha(1 --> 6)-mannosidase, together explain why alpha-mannosidosis patients store and excrete large amounts of oligosaccharides that resemble biosynthetic intermediates, rather than partially degraded glycans. The relative contributions of the lysosomal and extra-lysosomal catabolic pathways can be derived by comparing the ratio of trisaccharide Man beta (1 --> 4)GlcNAc beta (1 --> 4)GlcNAc to disaccharide Man beta (1 --> 4)GlcNAc accumulated in tissues from goats with beta-mannosidosis. A similar determination in human beta-mannosidosis patients is not possible because the same intermediate, Man beta (1 --> 4)-GlcNAc is a product of both pathways. Based on inhibitor studies with pyranose and furanose analogues, alpha-mannosidases may be divided into two groups. Those in Class 1 are (1 --> 2)-specific enzymes like Golgi mannosidase I, whereas those in Class 2, like lysosomal alpha-mannosidase, can hydrolyse (1 --> 2), (1 --> 3) and (1 --> 6) linkages. A similar classification has recently been derived by others from protein sequence homologies. Based on this new classification of the alpha-mannosidases, it is possible to speculate about their probable evolution from two primordial genes. The first would have been a Class 1 ER enzyme involved in the degradation of glycans on incompletely assembled or malfolded glycoproteins. The second would have been a Class 2 lysosomal enzyme responsible for turnover. Later, other alpha-mannosidases, with new processing or catabolic functions, would have developed from these, by loss or gain of critical insertion or retention sequences, to yield the full complement of alpha-mannosidases known today.
<title>Optimal sensor layout for shape estimation from strain sensors</title> (1995)

A procedure is developed for mapping strain sensor readings into displacements. Optimal sensor layouts are determined by examining predicted mode shapes from synthesized strain data. The singular values of the transformation matrix bound the error in the inferred displacements. Issues of spatial aliasing as well as sensor spacing are also addressed. The methodology was validated by comparing both static and dynamic shape estimations with experiments.
Tailoring New Gene Delivery Designs for Specific Targets (2000)

Advancing biotechnology spurs the development of new pharmaceutically engineered gene delivery vehicles with the capability to target specific cell types. The low density lipoprotein (LDL) element of the terplex gene carrier is shown to be efficient in delivery to smooth muscle cells as well as inducing minimal toxicity to A7R5 cells in culture. The terplex system condensed plasmid DNA into polyplex sizes ranging from 100 to 400 nm. Terplex demonstrated higher transfection efficacy than Lipofectin. Lactose was conjugated through a poly(ethyl glycol) (PEG) spacer to poly(L-lysine) (PLL) to tailor a gene carrier capable of condensing plasmid DNA. This cationic polymer targeted Hep G2 cells preferentially in culture. The inclusion of a lactose targeting moiety greatly increased the efficacy of the gene carrier over PEG-PLL and Lipofectin. A biodegradable nanoparticle gene carrier, polysaccharide-graft-PLL and poly(D,L-lactic acid), was synthesized and characterized. The nanoparticle size was controllable by changing the copolymer concentration, where the particles could be as small as 60 nm. When polysaccharide was used in the copolymer, the nanoparticle became more DNA adsorbent. The JLI mAb was linked to PLL. This gene carrier targets the antigen confined to stage II immature cortical thymocytes for leukemia therapy. A 20,000 mw PLL backbone was sufficient for compaction of DNA. Folic acid linked to PLL through a PEG spacer is currently being studied for DNA condensation and delivery to membrane associated folate binding protein positive endothelial cancer cells.
Characterization of the biosynthesis, processing, and sorting of human HBP/CAP37/azurocidin (1999)

Azurocidin is a multifunctional endotoxin-binding serine protease homolog synthesized during the promyelocytic stage of neutrophil development. To characterize the biosynthesis and processing of azurocidin, cDNA encoding human preproazurocidin was stably transfected to the rat basophilic leukemia cell line RBL-1 and the murine myeloblast-like cell line 32D cl3; cell lines previously utilized to study the related proteins cathepsin G and proteinase 3. After 30 min of pulse radiolabeling, two forms of newly synthesized proazurocidin (34.5 and 37 kDa), differing in carbohydrate content but with protein cores of identical sizes, were recognized. With time, the 34.5-kDa form disappeared, while the 37-kDa form was further processed proteolytically, as judged by digestion with N-glycosidase F. Conversion of high-mannose oligosaccharides into complex forms was shown by acquisition of complete resistance to endoglycosidase H. Radiosequence analysis demonstrated that the amino-terminal seven amino acid propeptide of proazurocidin was removed in a stepwise manner during processing; initial removal of five amino acids was followed by cleavage of a dipeptide. Presence of the protease inhibitors Gly-Phe-diazomethyl ketone, bestatin, or leupeptin inhibited only the cleavage of the dipeptide, thus indicating the involvement of at least two amino-terminal processing enzymes. Translocation of azurocidin to granules was shown by subcellular fractionation. Similar results, with efficient biosynthesis, processing, and targeting to granules in both cell lines, were obtained with a mutant form of human preproazurocidin lacking the amino-terminal heptapropeptide. In conclusion, this investigation is an important addition to our previous studies on related azurophil granule proteins, and provides novel information concerning the biosynthesis and distinctive amino-terminal processing of human azurocidin.
A Successful and Simplified Filgrastim Primed Single Apheresis Method Without Large Volume Apheresis for Peripheral Blood Stem Cell Collection (2000)

Adequate numbers of peripheral stem cells were harvested by G-CSF in a single apheresis without large volume apheresis even in heavily pretreated patients. Rapid and complete engraftment occurred in all patients and it was faster in single than multiple apheresis.
Comparison of the efficacy of gentamicin for 5 days plus doxycycline for 8 weeks versus streptomycin for 2 weeks plus doxycycline for 45 days in the treatment of human brucellosis: a randomized clinical trial (2010)

The results show that the efficacy of gentamicin for 5 days plus doxycycline for 8 weeks is not superior to that of streptomycin for 2 weeks plus doxycycline for 45 days.
The pathogenesis of emphysema: the elastase:antielastase hypothesis 30 years later. (1995)

Thirty years ago the concept of the elastase:antielastase hypothesis was introduced. Neutrophil elastase:A1PI balance was found to be critical, predisposing patients deficient in A1PI to panacinar emphysema; however, the causative elastases in common cigarette-induced pulmonary emphysema are unclear. Several members of the serine, cysteine, and metalloproteinase families have been identified in inflammatory and resident lung cells. We propose to use gene-targeted mice, deficient in individual elastases to determine the relative contribution of candidate elastases to cigarette-smoking-related emphysema. This does not guarantee that humans will respond to cigarette smoke with the same array of elastases as mice. However, these studies may guide labor intensive therapeutic trials with specific proteinase inhibitors and ultimately lead to rational therapy.
Least-commitment action selection (1996)

The principle of least commitment was embraced early in planning research. Hierarchical task networks (HTNs) reason about high-level tasks without commit-ting to specific low-level steps. Partial-order planning arose from a complementary desire to avoid unnec-essary ordering commitments. But most of today’s partial-order planning algorithms commit to a single producing step when supporting an open condition--even when multiple alternatives exist. Each possibility results in a different child plan, and therefore a branch in the search tree. If the various choices have com-mon features, computation may be duplicated unnec-essarily on the various branches. The FABIAN planner attempts to avoid such waste. FABIAN separates the decision to add a step from the choice of which step to add. FABIAN supports an open condition by adding an abstract action to the plan representing the disjunc-tion of possible new supporting steps; only later does it refine this choice to a particular concrete action. We show that this abstraction can lead to exponential sav-ings, and argue that in the worst case FABIAN never explores more than a slightly larger space of plans than does a traditional planner such as SNLP.
m RNA Untranslated Regions ( UTRs ) (2011)

Abstract Eukaryotic messenger ribonucleic acids (mRNAs) possess a tripartite structure that comprises a 5′ untranslated region, a coding region made up of the amino acid coding triplet codons and a 3′ untranslated region. During nuclear maturation of primary transcripts, both ends of mRNA are post‐transcriptionally modified through the addition of a 7‐methyl‐guanosine cap structure at the 5′ end and a polyadenosine tail at the 3′ end. Untranslated regions are involved in the post‐transcriptional regulation of gene expression by modulating mRNA stability, nucleo‐cytoplasm transport, subcellular localisation and translation efficiency thus allowing a fine control of the protein product. This regulatory activity is mediated by cis ‐acting oligonucleotide elements that interact with binding proteins and noncoding RNAs through a combination of primary and secondary structures. Key Concepts: UTRs are involved in the post‐transcriptional regulation of gene expression. UTRs regulate mRNA stability, nucleo‐cytoplasm transport, subcellular localisation and translation efficiency. Alternative splicing can result in mRNAs encoding the same protein under the control of different UTRs.
Image Orientation Estimation with Convolutional Networks (2015)

Rectifying the orientation of scanned documents has been an important problem that was solved long ago. In this paper, we focus on the harder case of estimating and correcting the exact orientation of general images, for instance, of holiday snapshots. Especially when the horizon or other horizontal and vertical lines in the image are missing, it is hard to find features that yield the canonical orientation of the image. We demonstrate that a convolutional network can learn subtle features to predict the canonical orientation of images. In contrast to prior works that just distinguish between portrait and landscape orientation, the network regresses the exact orientation angle. The approach runs in real-time and, thus, can be applied also to live video streams.