gebhart/patrepeval huggingface dataset:
Induction of Oblique Decision Trees. (1993)

This paper introduces a randomized technique for partitioning examples using oblique hyperplanes. Standard decision tree techniques, such as ID3 and its descendants, partition a set of points with axis-parallel hyperplanes. Our method, by contrast, attempts to find hyperplanes at any orientation. The purpose of this more general technique is to find smaller but equally accurate decision trees than those created by other methods. We have tested our algorithm on both real and simulated data, and found that in some cases it produces surprisingly small trees without losing predictive accuracy. Small trees allow us, in turn, to obtain simple qualitative descriptions of each problem domain. 1 Introduction Decision trees have been used successfully for many different decision making and classification tasks. A number of standard techniques have been developed in the machine learning community, most notably Quinlan&amp;apos;s ID3 (1986) and Breiman et al.&amp;apos;s CART (1984). Since the introduction of thes...
Inactivation of the srtA gene in Listeria monocytogenes inhibits anchoring of surface proteins and affects virulence (2002)

During infection of their hosts, Gram-positive bacteria express surface proteins that serve multiple biological functions. Surface proteins harbouring a C-terminal sorting signal with an LPXTG motif are covalently linked to the cell wall peptidoglycan by a transamidase named sortase. Two genes encoding putative sortases, termed srtA and srtB, were identified in the genome of the intracellular pathogenic bacterium Listeria monocytogenes. Inactivation of srtA abolishes anchoring of the invasion protein InlA to the bacterial surface. It also prevents the proper sorting of several other peptidoglycan-associated LPXTG proteins. Three were identified by a mass spectrometry approach. The DeltasrtA mutant strain is defective in entering epithelial cells, similar to a DeltainlA mutant. In contrast to a DeltainlA mutant, the DeltasrtA mutant is impaired for colonization of the liver and spleen after oral inoculation in mice. Thus, L. monocytogenes srtA is required for the cell wall anchoring of InlA and, presumably, for the anchoring of other LPXTG-containing proteins that are involved in listerial infections.
An integrated approach to extreme thermostabilization and affinity maturation of an antibody (2012)

Antibodies are important tools for a broad range of applications due to their high specificity and ability to recognize virtually any target molecule. However, in order to be practically useful, antibodies must be highly stable and bind their target antigens with high affinity. We present a combinatorial approach to generate high-affinity, highly stable antibodies through the design of stable frameworks, specificity grafting and maturation via somatic hypermutation in vitro. By collectively employing these methods, we have engineered a highly stable, high-affinity, full-length antibody with a T(m) over 90°C that retains significant activity after heating to 90°C for 1 h, and has ~95-fold improved antigen-binding affinity. The stabilized IgG framework is compatible with affinity maturation, and should provide a broadly useful scaffold for grafting a variety of complementarity-determining region loops for the development of stable antibodies with desired specificities.
Treatment of refractory ischemic skin ulcers in patients with Raynaud's phenomenon with PGE1 infusions. (1989)

Prostaglandin E1 (PGE1) is a potent vasodilator and inhibitor of platelet aggregation. We administered 20 PGE1 infusions to 12 patients with severe Raynaud's phenomenon, associated with refractory ischemic skin ulcers. There was symptomatic improvement following 17 of the 20 infusions, while 35 of the 65 ischemic ulcers healed between 2-6 weeks following treatment. The beneficial effects persisted for between 1-18 months. While the treatment was well-tolerated in most patients, the procedure is not without risks. On the basis of this retrospective study, a trial of PGE1 infusion is recommended in the treatment of patients with ischemic skin ulcers, which have been refractory to other treatment modalities.
Efficient conversion of triacylglycerols and fatty acids to biodiesel in a microwave reactor using metal triflate catalysts (2010)

We report that catalytic quantities of the Lewis acidic metal catalysts scandium triflate and bismuth triflate promote conversion of oleic, linoleic, palmitic and myristic acids and their glyceryl triesters to the corresponding methyl esters (biodiesel) in greater than 90% yield upon microwave heating. Additionally, both catalysts could be recovered and reused in esterification reactions at least six times.
Characterization of Plant Growth-Promoting Traits of Free-Living Diazotrophic Bacteria and Their Inoculation Effects on Growth and Nitrogen Uptake of Crop Plants (2009)

The search for diverse plant growth-promoting (PGP) diazotrophic bacteria is gaining momentum as efforts are made to exploit them as biofertilizers for various economically important crops. In the present study, 17 diazotrophic strains belonging to eight different genera isolated from rice paddy fields were screened for multiple PGP traits and evaluated for their inoculation effects on canola and rice plants. All of the strains tested positive for 1- aminocyclopropane-1-carboxylate (ACC) deaminase activity and production of indole 3-acetic acid (IAA) and ammonia (NH3). Additionally, four of the strains were able to solubilize phosphorus (P), five tested positive for zinc (Zn) solubilization and sulfur (S) oxidation, and eight strains produced siderophores. Based on the presence of multiple PGP traits, 10 strains were selected for inoculation studies. Treatment with Herbaspirillum sp. RFNB26 resulted in maximum root length (54.3%), seedling vigor, and dry biomass in canola, whereas Paenibacillus sp. RFNB4 exhibited the lowest activity under gnotobiotic conditions. However, under pot culture conditions, Paenibacillus sp. RFNB4 significantly increased plant height and dry biomass production by 42.3% and 29.5%, respectively. Canola plants and rhizosphere soils inoculated with Bacillus sp. RFNB6 exhibited significantly higher nitrogenase activity. In greenhouse experiments, Serratia sp. RFNB18 increased rice plant height by 35.1%, Xanthomonas sp. RFNB24 enhanced biomass production by 84.6%, and rice rhizosphere soils inoculated with Herbaspirillum sp. RFNB26 exhibited the highest nitrogenase activity. Our findings indicate that most of the selected strains possess multiple PGP properties that significantly improve the growth parameters of the two plants when tested under controlled conditions.
Holographic Diffraction Gratings Recorded in Photoresist (1974)

Good quality diffraction gratings have been produced by recording straight, parallel interference fringes in positive-working photoresist. The interference fringes are formed by overlapping two collimated beams of light from an Argon Ion laser at an angle. The photoresist is coated onto glass blanks by spinning, and after exposure is processed to give a periodic film thickness variation corresponding to the grooves of a diffraction grating. Gratings up to 6 cm diameter and with up to 3000 lines per mm have been produced in this way.
Prolonged oral treatment with low doses of allergen conjugated to cholera toxin B subunit suppresses immunoglobulin E antibody responses in sensitized mice (2000)

These results may impact on the development of therapeutic vaccines against type I allergies.
Heart Failure With Preserved Ejection Fraction What is Known and Unknown (2009)

There is an emerging interest in heart failure with preserved ejection fraction (HFPEF) because of its high prevalence in the community and several specific characteristics compared with "classic" heart failure with reduced ejection fraction. HFPEF patients are older and more often female, and lack left ventricular dilatation. A likely principal cause of HFPEF is diastolic dysfunction, particularly ventricular stiffening; however, the clinical phenotype of HFPEF is also modulated by dysfunction of other organs such as kidney, vasculature, etc. Despite its social burden, the diagnostic criteria and therapeutic strategies remain to be established. In particular, the lack of established diagnostic criteria has resulted in conceptual confusions about HFPEF in clinical practice. In this review, what is known and unknown about HFPEF is discussed, and several challenging proposals about its diagnosis and therapy are raised.
AC Temperature Calorimetry for Thin Films at Low Temperatures (1982)

An apparatus for heat-capacity measurements of thin films is devised for the temperature range 0.4–3.5 K using ac temperature calorimetry. The total heat capacity of the addenda is about 2×10 -9 J/K at 0.5 K and a heat-capacity change as small as ∼5×10 -12 J/K is detectable at this temperature. The performance of the apparatus is checked by measuring the superconducting transition of a thin Al film having a thickness of 2040 Å.
HIV-1 non-group M phenotypic susceptibility in vitro to bictegravir and cabotegravir (2021)

This study has shown encouraging results regarding the clinical use of these drugs in HIV-1/non-M-infected patients, which will need to be confirmed with clinical data.
InGaAs/InGaAlAs MQW lasers with InGaAsP guiding layers grown by gas source molecular beam epitaxy (1991)

An InGaAs/InGaAlAs multiple-quantum-well (MQW) laser was grown by gas source molecular beam epitaxy (GS-MBE). The laser has InP cladding layers and InGaAsP guiding layers, and the active layer is composed of an InGaAs/InGaAlAs MQW layer. Electrons are injected into the MQW active layer by tunneling through the barriers. The threshold current of the InGaAs/InAlAs buried-heterostructure (BH)-MQW lasers was as low as 9.6 mA. The relaxation oscillation frequency of the InGaAs/InAlAs MQW lasers was found to be larger than that of the InGaAs/InGaAsP MQW lasers with the same structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Wnt-7a maintains appropriate uterine patterning during the development of the mouse female reproductive tract (1998)

The murine female reproductive tract differentiates along the anteroposterior axis during postnatal development. This process is marked by the emergence of distinct cell types in the oviduct, uterus, cervix and vagina and is dependent upon specific mesenchymal-epithelial interactions as demonstrated by earlier heterografting experiments. Members of the Wnt family of signaling molecules have been recently identified in this system and an early functional role in reproductive tract development has been demonstrated. Mice were generated using ES-mediated homologous recombination for the Wnt-7a gene (Parr, B. A. and McMahon, A. P. (1995) Nature 374, 350-353). Since Wnt-7a is expressed in the female reproductive tract, we examined the developmental consequences of lack of Wnt-7a in the female reproductive tract. We observe that the oviduct lacks a clear demarcation from the anterior uterus, and acquires several cellular and molecular characteristics of the uterine horn. The uterus acquires cellular and molecular characteristics that represent an intermediate state between normal uterus and vagina. Normal vaginas have stratified epithelium and normal uteri have simple columnar epithelium, however, mutant uteri have stratified epithelium. Additionally, Wnt-7a mutant uteri do not form glands. The changes observed in the oviduct and uterus are accompanied by a postnatal loss of hoxa-10 and hoxa-11 expression, revealing that Wnt-7a is not required for early hoxa gene expression, but is required for maintenance of expression. These clustered hox genes have been shown to play a role in anteroposterior patterning in the female reproductive tract. In addition to this global posterior shift in the female reproductive tract, we note that the uterine smooth muscle is disorganized, indicating development along the radial axis is affected. Changes in the boundaries and levels of other Wnt genes are detectable at birth, prior to changes in morphologies. These results suggest that a mechanism whereby Wnt-7a signaling from the epithelium maintains the molecular and morphological boundaries of distinct cellular populations along the anteroposterior and radial axes of the female reproductive tract.
Structural Domains Involved in Human Cytomegalovirus Glycoprotein B-Mediated Cell-cell Fusion (1996)

A novel fusion assay was established to determine fusion activity with cocultivated human foreskin fibroblasts of stable transfectants derived from human astrocytoma cells (U373) expressing authentic or mutagenized human cytomegalovirus glycoprotein B (HCMV gB; gpUL55). Compared to transfectants expressing authentic HCMV gB, those expressing gB forms with a deletion of hydrophobic domain 1 (hd1; aa 714-747) or with deletions of specific segments in the cytoplasmic tail (aa 811-825 and 871-906) exhibited significantly reduced heterologous fusogenicity. HCMV gB-specific monoclonal antibodies (MAbs) as well as MAb against cellular annexin II prevented fusion of the transfectant expressing authentic gB. Comparable surface exposure of HCMV gB or its derivatives was demonstrated in all transfectants by FACS analysis. Our observations are compatible with the notion that indigenous fusion activity of HCMV gB depends on the extracellular hd1 domain and on the conformation of the cytoplasmic tail.
Clinical Usefulness of Serum Sialyl SSEA-1 Antigen Levels in Patients with Epithelial Ovarian Cancer (1990)

The serum levels of sialyl SSEA-1 antigen, a type 2 chain carbohydrate antigen detected using the monoclonal antibody FH-6, were elevated in 47.2% of patients with epithelial ovarian cancer, with the percent positivity increasing with the clinical stage. Of the histological type, it is interesting to note the relatively high sensitivity in patients with mucinous adenocarcinoma and clear cell carcinoma in contrast with the CA 125 antigen levels. Although the percentage of patients with ovarian cancer who had elevated sialyl SSEA-1 antigen levels is lower than that observed with elevated CA 125 antigen levels, the false-positive rate is significantly low in the sialyl SSEA-1 test. Serial sialyl SSEA-1 antigen levels obtained during follow-up were strong predictors of clinical outcome. The combined determination possible with sialyl SSEA-1 and CA 125 did not markedly increase the detection rate because of the overlap in the positivity. However, increased levels of both serum sialyl SSEA-1 antigen and CA 125 antigen indicated the presence of malignancies in pregnant women associated with ovarian tumors.
Identification of cofilin and LIM-domain-containing protein kinase 1 as novel interaction partners of 14-3-3zeta (2002)

Proteins of the 14-3-3 family have been implicated in various physiological processes, and are thought to function as adaptors in various signal transduction pathways. In addition, 14-3-3 proteins may contribute to the reorganization of the actin cytoskeleton by interacting with as yet unidentified actin-binding proteins. Here we show that the 14-3-3 zeta isoform interacts with both the actin-depolymerizing factor cofilin and its regulatory kinase, LIM (Lin-11/Isl-1/Mec-3)-domain-containing protein kinase 1 (LIMK1). In both yeast two-hybrid assays and glutathione S-transferase pull-down experiments, these proteins bound efficiently to 14-3-3 zeta. Deletion analysis revealed consensus 14-3-3 binding sites on both cofilin and LIMK1. Furthermore, the C-terminal region of 14-3-3 zeta inhibited the binding of cofilin to actin in co-sedimentation experiments. Upon co-transfection into COS-7 cells, 14-3-3 zeta-specific immunoreactivity was redistributed into characteristic LIMK1-induced actin aggregations. Our data are consistent with 14-3-3-protein-induced changes to the actin cytoskeleton resulting from interactions with cofilin and/or LIMK1.
Cathepsin L is essential for onset of autoimmune diabetes in NOD mice (2005)

Lysosomal proteases generate peptides presented by class II MHC molecules to CD4+ T cells. To determine whether specific lysosomal proteases might influence the outcome of a CD4+ T cell-dependent autoimmune response, we generated mice that lack cathepsin L (Cat L) on the autoimmune diabetes-prone NOD inbred background. The absence of Cat L affords strong protection from disease at the stage of pancreatic infiltration. The numbers of I-A(g7)-restricted CD4+ T cells are diminished in Cat L-deficient mice, although a potentially diabetogenic T cell repertoire persists. Within the CD4+ T cell compartments of Cat L-deficient mice, there is an increased proportion of regulatory T cells compared with that in Cat L-sufficient littermates. We suggest that it is this displaced balance of regulatory versus aggressive CD4+ T cells that protects Cat L-deficient mice from autoimmune disease. Our results identify Cat L as an enzyme whose activity is essential for the development of type I diabetes in the NOD mouse.
Sequence Variability of Three Alleles of the Self-Incompatibility Gene of Nicotiana alata (1989)

Marilyn A. Anderson, Geoffrey I. McFadden, Robert Bernatzky, Angela Atkinson, Timothy Orpin, Helen Dedman, Geoffrey Tregear, Ross Fernley, Adrienne E. Clarke, Sequence Variability of Three Alleles of the Self-Incompatibility Gene of Nicotiana alata, The Plant Cell, Vol. 1, No. 5 (May, 1989), pp. 483-491
Poly-dihydroacetate: A novel biodegradable bioadhesive for use in reconstructive surgery (2008)

Singh, Sunil P. BA; Zawaneh, Peter BS; Putnam, David PhD; Spector, Jason A. MD Author Information
Localization of a unique gene by direct hybridization in situ. (1981)

Previous determination of the chromosomal location of unique genes have required that the chromosomes of interest be fractionated, either by species-specific chromosome loss from interspecies hybrids, or by physical fractionation procedures. We have developed a general technique for the localization of a unique gene, which requires no prior chromosome fractionation. The technique involves the use of a labeled hybrid cDNA plasmid for direct hybridization in situ to metaphase cells from the organism under investigation. As a model system for development of this technique, we have employed a human alpha-globin cDNA plasmid (JW101) to localize the corresponding gene cluster. To obtain a sufficiently large autoradiographic signal, we have both labeled this plasmid with 125I to a high specific activity (10(9) dpm/micrograms) and taken advantage of the ability of a double-stranded probe to form networks. To obtain sufficient hybridization specificity, various experimental procedures were used, the most important of which was the choice from among a range of probe concentrations of the highest that does not yield excessive background hybridization. We have shown that, with an autoradiographic exposure time of only 12 days, use of this technique correctly localized the human alpha-globin gene cluster to chromosome 16. This technique should be generally applicable to the localization of any gene for which a corresponding cDNA hybrid plasmid is available.
Intranasal administration of peptide vaccine protects human/mouse radiation chimera from influenza infection (1999)

Influenza virus is characterized by frequent and unpredictable changes of the surface glycoproteins which enable the virus to escape the immune system. Approved vaccines which consist of the whole virus or the surface glycoproteins fail to induce broad specificity protection. We have previously reported that a peptide-based experimental recombinant vaccine which includes conserved epitopes of B and T lymphocytes was efficient in mice, leading to cross-strain, long-term protection. In the present study, this approach was adapted for the design of a human vaccine, based on epitopes recognized by the prevalent HLAs. These epitopes were expressed in Salmonella flagellin and tested for their efficacy in human/mouse radiation chimera in which human peripheral blood mononuclear cells (PBMC) are functionally engrafted. The vaccinated mice demonstrated clearance of the virus after challenge and resistance to lethal infection. The production of virus-specific human antibodies was also higher in this group. Control groups of either non-vaccinated, or vaccinated mice which had not been engrafted with the human PBMC, did not exhibit the protective immune response. FACS analysis showed that most human cells in the transplanted mice are CD8(+) and CD4(+). Hence, it may be concluded: (i) that the protection involves cellular mechanisms, but is most probably accomplished without direct lysis of influenza-infected pulmonary cells by cytotoxic T lymphocytes, but rather via a cytokine-mediated mechanism, (ii) that the human/mouse radiation chimera model may be of some value in the investigation of new vaccines, as an additional tool prior to clinical trials, and (iii) that the synthetic recombinant vaccine can induce a response in the human immune system and confers protection against influenza infection. Further investigation is needed to establish the efficacy of such a peptide vaccine in human subjects.
Strain-induced nonlinearity of filled rubbers (2005)

Dynamic strain-induced nonlinearity in the modulus of filled rubbers shows a striking similarity to what is known about the glass transition of solid materials and the jamming transition of granular materials. This analogy stems from the reality that shear strain in dynamic mechanical measurements introduces fluctuations in a filler network by forcing the system to explore different configurations. Such fluctuations can be described by an "effective temperature" that has many attributes of a true temperature, and particularly is proportional to the strain amplitude. Thus, filled rubbers with respect to strain will display many unusual phenomena that are usually observed in glass-forming materials, but now demonstrated in filled rubbers, including asymmetric kinetics, crossover effects, and glasslike kinetic transitions. The nonlinearity in the modulus of filled rubbers simply reflects a dejamming transition of fillers in rubber matrices. The agglomeration of filler in an elastomeric matrix shares a common ground of physics with the jamming process and glass formation.
Three paradoxes of ferric enterobactin uptake (2003)

Bacteria elaborate iron chelators that scavenge iron from the environment, including their human and animal hosts, and iron acquisition is a determinant of pathogenicity. One such iron chelate, the siderophore ferric enterobactin, enters Gram-negative bacteria through the FepA protein of the outer membrane. The ferric enterobactin transport process is a high-affinity, multi-specific, multi-component, energy dependent reaction, that is a paradigm of ligand-gated transport: FeEnt binding activates FepA to transport competency. On the basis of the FepA, FhuA, FecA and BtuB crystal structures, and in light of recent molecular biological, biochemical, and biophysical findings, this review considers the mechanism of ferric enterobactin uptake. The discussion focuses on three preeminent questions about the transport reaction: the function of the N-terminal globular domain that resides within the FepA channel, the mechanistic contributions of TonB to the activities of ligand-gated porins, and the energy dependence of metal transport reactions through the OM bilayer. Available data points to the idea that the N-terminal globular domains of these receptor proteins dynamically exit their pores during transport, creating a suction-force that pulls ligands through the surface loops into the periplasm. The functions of TonB and energy in these processes remain unknown.
Neuropathic Pain: New Insights, New Interventions (1998)

The past decade has seen great progress in understanding its causes and in finding new drugs that promise great benefit. An early outcome of the research has been the observation that the new drugs do not blunt normal pain sensation--a pattern beginning to find explanation through the realization that neural pain circuits rewire themselves, both anatomically and biochemically, after nerve injury.