gebhart/patrepeval huggingface dataset:
Machine learning in automated text categorization (2002)

The automated categorization (or classification) of texts into predefined categories has witnessed a booming interest in the last 10 years, due to the increased availability of documents in digital form and the ensuing need to organize them. In the research community the dominant approach to this problem is based on machine learning techniques: a general inductive process automatically builds a classifier by learning, from a set of preclassified documents, the characteristics of the categories. The advantages of this approach over the knowledge engineering approach (consisting in the manual definition of a classifier by domain experts) are a very good effectiveness, considerable savings in terms of expert labor power, and straightforward portability to different domains. This survey discusses the main approaches to text categorization that fall within the machine learning paradigm. We will discuss in detail issues pertaining to three different problems, namely, document representation, classifier construction, and classifier evaluation.
Human B Lymphocyte Malignancies: Exploitation of BLyS and APRIL and Their Receptors (2004)

B lymphocyte stimulator (BLyS), also referred to as B cell activating factor of the TNF family, is a recently identified tumor necrosis factor (TNF) family member shown to be critical for maintenance of normal B cell development and homeostasis and it shares significant homology with another TNF superfamily member, a proliferation inducing ligand (APRIL). Currently, three receptors have been identified that transmit signals upon BLyS and APRIL binding and these include B cell maturation antigen, B cell activating factor receptor, and transmembrane activator and CAML interactor. The striking effects of BLyS on normal B cell maintenance and survival and the largely B lineage-restricted pattern of receptor expression, raises the possibility that these TNF family ligands and receptors may be involved not only in B cell autoimmunity, but also in the pathogenesis and maintenance of mature B lineage hematological malignancies. In this article, we will review the spectrum of human B lineage malignancies and discuss current evidence supporting a role for BLyS and APRIL in fueling the growth and survival of specific B cell malignancies.
CD200 Is a Ligand for All Members of the CD200R Family of Immunoregulatory Molecules (2004)

CD200Fc, a chimeric molecule including the extracellular domain of CD200 and a murine IgG2a Fc region, regulates immune responses following engagement of a cell surface receptor, CD200R, expressed on cells of the myeloid and T cell lineage. A recent report focused attention on a family of CD200Rs, but concluded that only one member used CD200 as its ligand. We have also cloned and sequenced a family of CD200Rs, but identify an amino terminus to two of the three isoforms not recognized by previous researchers. We show by FACS, using FITC-labeled CD200Fc, that COS7 cells transfected with all CD200R isoforms bind CD200 as ligand, although the functional consequences of this binding likely differs between the different isoforms. mAbs directed against the CD200 R1/R4 isoforms altered IL-2/IL-4 cytokine production and suppressed CTL responses in a fashion comparable to CD200Fc, with a significantly lesser effect seen following addition of anti-CD200 R2/R3.
Thermodynamic comparison of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature (1999)

The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the binding constants range from 1.8 x 10(6)M(-1)for PNA(TT)/DNA to 4.15 x 10(7)M(-1)for PNA(GA)/DNA and the binding enthalpies range from -194 kJ mol(-1)for PNA(CG)/DNA to -77 kJ mol(-1)for PNA(GT)/DNA. For the corresponding DNA/DNA binding reactions, the binding constants range from 2.9 x 10(5)M(-1)for DNA(GT)/DNA to 1.9 x 10(7)M(-1)for DNA(CC)/DNA and the binding enthalpies range from -223 kJ mol(-1)for DNA(CG)/DNA to -124 kJ mol(-1)for DNA(TT)/DNA. Most of the PNA sequences exhibited tighter binding affinities than their corresponding DNA sequences resulting from smaller entropy changes in the PNA/DNA hybridization reactions. van't Hoff enthalpies and extrapolated Delta G values determined from UV melting studies on the duplexes exhibited closer agreement with the ITC binding enthalpies and Delta G values for the DNA/DNA duplexes than for the PNA/DNA duplexes.
Miniature Sodium-Selective Ion-Exchange Optode with Fluorescent pH Chromoionophores and Tunable Dynamic Range (1996)

An extension into the fluorescence mode of ion-exchange optodes is described, allowing miniaturization and its concomitant benefits. A micrometer-size, fluorescent fiber-optic sodium sensor is described, based on a highly sodium-selective, crown ether-capped calix[4]arene ionophore, capable of ratiometric operation. Three sensor configurations are given, employing different lipophilic, fluorescent pH chromoionophores (Nile Blue derivatives), demonstrating the ability to improve the detection limit and tune the dynamic range to the desired region of interest. Two of the sensors are of special interest in that their working ranges lie within those desired for measuring intracellular cytosolic or blood levels of sodium at the respective physiological pH. These optodes have excellent sodium selectivity, with other physiologically relevant cations (e.g., potassium, calcium, and magnesium) being highly discriminated. Three simple mathematical relationships are given for the three experimentally used fluorescent signal mechanisms (intensity, intensity ratios, and inner-filter or energy transfer effects), permitting visualization on a single graph and enabling direct comparison of the different sensors' optical responses on a common platform. Finally, these optodes measure the sample's sodium activity, rather than the concentration, provided that the sample's pH is measured simultaneously by another sensor, such as a glass electrode.
The rapid generation of mutation data matrices from protein sequences (1992)

An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.
Inactivating mutations of the human base excision repair gene NEIL1 in gastric cancer (2004)

Oxidized DNA base lesions, such as thymine glycol (Tg) and 8-hydroxyguanine, are often toxic and mutagenic and have been implicated in carcinogenesis. To clarify whether NEIL1 protein, which exhibits excision repair activity towards such base lesions, is involved in gastric carcinogenesis, we examined 71 primary gastric cancers from Japanese patients and four gastric cancer cell lines for mutations and genetic polymorphisms of the NEIL1 gene. We also examined 20 blood samples from Chinese patients for NEIL1 genetic polymorphisms. Three mutations (c.82_84delGAG:p.Glu28del, c.936G > A and c.1000A > G:p.Arg334Gly) and two genetic polymorphisms were identified. When the excision repair activity towards double-stranded oligonucleotide containing a Tg:A base pair was compared among six types of recombinant NEIL1 proteins, p.Glu28del-type NEIL1, found in a primary case, was found to exhibit an extremely low activity level. Moreover, c.936G > A, located in the last nucleotide of exon 10 and detected in the KATO-III cell line, was shown to be associated with a splicing abnormality using an in vivo splicing assay. An immunofluorescence analysis showed that the wild-type NEIL1 protein, but not the truncated protein encoded by the abnormal transcript arising from the c.936G > A mutation, was localized in the nucleus, suggesting that the truncated protein is unlikely to be capable of repairing nuclear DNA. An expression analysis revealed that NEIL1 mRNA expression was reduced in six of 13 (46%) primary gastric cancer specimens that were examined. These results suggest that low NEIL1 activities arising from mutations and reduced expression may be involved in the pathogenesis in a subset of gastric cancers.
Yttrium Iron Garnet Thin Films with Very Low Damping Obtained by Recrystallization of Amorphous Material (2016)

We have investigated recrystallization of amorphous Yttrium Iron Garnet (YIG) by annealing in oxygen atmosphere. Our findings show that well below the melting temperature the material transforms into a fully epitaxial layer with exceptional quality, both structural and magnetic. In ferromagnetic resonance (FMR) ultra low damping and extremely narrow linewidth can be observed. For a 56 nm thick layer a damping constant of α = (6.15 ± 1.50) · 10(-5) is found and the linewidth at 9.6 GHz is as small as 1.30 ± 0.05 Oe which are the lowest values for PLD grown thin films reported so far. Even for a 20 nm thick layer a damping constant of α = (7.35 ± 1.40) · 10(-5) is found which is the lowest value for ultrathin films published so far. The FMR linewidth in this case is 3.49 ± 0.10 Oe at 9.6 GHz. Our results not only present a method of depositing thin film YIG of unprecedented quality but also open up new options for the fabrication of thin film complex oxides or even other crystalline materials.
Multiplexed detection and applications for separations on parallel microchips (2008)

Much work has been performed since the development of the lab-on-a-chip concept that has brought microfabricated systems to the forefront of bioanalytical research. The success of using these microchips for performing complicated biological assays faster and cheaper than conventional methods has facilitated their emerging popularity among researchers. A recently exploited advantage of microfabricated technology has led to the creation of single wafers with multiple channel manifolds for high-throughput experiments. Efforts toward parallel microchip development have yielded fascinating new devices for chemical separations showing the potential for replacing conventional multiplexing techniques. This review will focus on recent work toward multiplexed separations on microdevices and complementary detection instrumentation.
Long-term Transgene Expression from Plasmid DNA Gene Therapy Vectors Is Negatively Affected by CpG Dinucleotides (2004)

CpG-reduced, CMV-based plasmid DNA constructs encoding human alpha-galactosidase A and factor IX were injected into C57Bl/6, BALB/c, and CD1 mice using hydrodynamics-based delivery of plasmid DNA (pDNA), and gene expression was monitored for 6 months. Linearized and supercoiled pDNAs were compared for their abilities to support long-term expression and to generate immune responses to the transgene product. In all mouse strains supercoiled CpG-reduced pDNA encoding alpha-galactosidase A and factor IX generated higher and more sustained levels of circulating gene product than their supercoiled CpG-replete analogs. Linearizing supercoiled CpG-reduced pDNA did not significantly increase levels of circulating gene product beyond levels supercoiled CpG-reduced pDNA could achieve. Linearizing supercoiled CpG-replete pDNA vectors significantly increased expression compared to their supercoiled CpG-replete analogs, but the increase was short-lived or subtherapeutic. Regardless of vector, liver depot expression did not elicit significant antibody responses to human alpha-galactosidase A or factor IX. Taken together, these data suggest that a clinically acceptable hydrodynamics-based approach targeting the liver combined with CpG-reduced pDNA vectors may represent a viable option for individuals with hemophilia, a lysosomal storage disease, or other disease in which prolonged depot expression of a therapeutic protein from the liver is desirable.
Recombinant human acid α-glucosidase (2006)

Recombinant human acid alpha-glucosidase is safe and effective for treatment of infantile-onset Pompe disease. Eleven patients experienced adverse events related to treatment, but none discontinued. The young age at which these patients initiated therapy may have contributed to their improved response compared to previous trials with recombinant human acid alpha-glucosidase in which patients were older.
Antibacterial Efficacy of Gentamicin Encapsulated in pH-Sensitive Liposomes against an In Vivo Salmonella enterica Serovar Typhimurium Intracellular Infection Model (2000)

Encapsulation of gentamicin in liposomes can be used to achieve intracellular delivery and broaden the clinical utility of this drug. We have previously described a novel, rationally designed, pH-sensitive liposomal carrier for gentamicin that has superior in vitro efficacy against intracellular infections compared to the efficacies of both free gentamicin and non-pH-sensitive liposomal controls. This liposomal carrier demonstrated pH-sensitive fusion that was dependent on the presence of unsaturated phosphatidylethanolamine (PE) and the pH-sensitive lipid N-succinyldioleoyl-PE. The pharmacokinetics and biodistribution of the free and liposomal gentamicin were examined in mice bearing a systemic Salmonella enterica serovar Typhimurium infection. Encapsulation of gentamicin in pH-sensitive liposomes significantly increased the concentrations of the drug in plasma compared to those of free gentamicin. Furthermore, the levels of accumulation of drug in the infected liver and spleen were increased by 153- and 437-fold, respectively, as a result of liposomal encapsulation. The increased accumulation of gentamicin in the liver and spleen effected by liposomal delivery was associated with 10(4)-fold greater antibacterial activity than that associated with free gentamicin in a murine salmonellosis model. These pH-sensitive liposomal antibiotic carriers with enhanced in vitro activity could be used to improve both in vivo intracellular drug delivery and biological activity.
Anti-IL5 therapy for asthma and beyond (2014)

Airway inflammation is considered to be the primary component contributing to the heterogeneity and severity of airway disorders. Therapeutic efficacies of diverse novel biologics targeting the inflammatory pathways are under investigation. One such target is IL-5, a type-1 cytokine that is central to the initiation and sustenance of eosinophilic airway inflammation. Over the past decade, anti-IL5 molecules have been documented to have mixed therapeutic benefits in asthmatics. Post hoc analyses of the trials reiterate the importance of identifying the IL-5-responsive patient endotypes. In fact, the currently available anti-IL5 treatments are being considered beyond asthma management; especially in clinical complications with an underlying eosinophilic pathobiology such as hypereosinophilic syndrome (HES) and eosinophilic granulomatosis and polyangitis (EGPA). In addition, closer analyses of the available data indicate alternative mechanisms of tissue eosinophilia that remain uncurbed with the current dosage and delivery platform of the anti-IL5 molecules.
STK33 promotes hepatocellular carcinoma through binding to c-Myc (2014)

STK33 plays an essential role in hepatocellular proliferation and liver tumorigenesis. The C-terminus of STK33 could be a potential therapeutic target in the treatment of patients with STK33-overexpressed HCC.
Development and Improvement of Optical Tracking Methods towards Registering the Deformations of 3D Non- Rigid Bodies in Real Time for Augmented Reality Applications (2015)

Augmented Reality (AR) is a technology that aims to embed virtual objects in the real world, showing to the user the set of objects (virtual and real) as a single world. For that purpose, it is necessary to offer a perfect alignment between virtual and real objects, which increases the effectiveness of AR. The solution to this problem is known as tracking. The object tracking consists in determining at any time the position and orientation of the camera relative to the scene. Optical sensors are most commonly used to overcome the tracking problem due to their low cost implementation. However, it is often difficult to provide robustness, accuracy and low computational cost at the same time. This thesis tackles the improvement and development of the main optical tracking techniques, primarily focused on detecting the deformations of the bodies. First, it has been achieved the tracking of rigid and non-rigid planar surfaces through a monocular camera, and then, the object deformation estimation with a more complex device as a RGB-D camera has been developed. Surface tracking systems such as those based on markers have the problem of not being able to handle occlusions. Thus, this thesis raises a new marker design that offers robustness against occlusions. Furthermore, in order to handle the deformations of surfaces, a solution that recovers the camera pose and the non-rigid surface simultaneously is proposed. Continuing with the deformation handling, it has also developed a robust tracking system for reconstructing the 3D shape of deformable objects using two different physical formulations. One offers a correct physical behaviour with a low computational cost, whereas the other achieves higher levels of accuracy at the expense of higher processing time. In addition, all the presented solutions have the common factor that all are executed in real time, which is a key property for a fluently visual feedback of an AR application
Periacetabular Osteotomy in the Treatment of Severe Acetabular Dysplasia (2006)

The periacetabular osteotomy is an effective technique for surgical correction of a severely dysplastic acetabulum in adolescents and young adults. In this series, the early clinical results were very good at an average of 4.2 years postoperatively; the two major complications did not compromise the good clinical results.
Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. (1994)

In the preceding paper [Choo, Y. & Klug, A. (1994) Proc. Natl. Acad. Sci. USA 91, 11163-11167], we showed how selections from a library of zinc fingers displayed on phage yielded fingers able to bind to a number of DNA triplets. Here, we describe a technique to deal efficiently with the converse problem--namely, the selection of a DNA binding site for a given zinc finger. This is done by screening against libraries of DNA triplet binding sites randomized in two positions but having one base fixed in the third position. The technique is applied here to determine the specificity of fingers previously selected by phage display. We find that some of these fingers are able to specify a unique base in each position of the cognate triplet. This is further illustrated by examples of fingers which can discriminate between closely related triplets as measured by their respective equilibrium dissociation constants. Comparing the amino acid sequences of fingers which specify a particular base in a triplet, we infer that in most instances, sequence-specific binding of zinc fingers to DNA can be achieved by using a small set of amino acid-nucleotide base contacts amenable to a code.
Targeted Large-Scale Deletion of Bacterial Genomes Using CRISPR-Nickases (2015)

Programmable CRISPR-Cas systems have augmented our ability to produce precise genome manipulations. Here we demonstrate and characterize the ability of CRISPR-Cas derived nickases to direct targeted recombination of both small and large genomic regions flanked by repetitive elements in Escherichia coli. While CRISPR directed double-stranded DNA breaks are highly lethal in many bacteria, we show that CRISPR-guided nickase systems can be programmed to make precise, nonlethal, single-stranded incisions in targeted genomic regions. This induces recombination events and leads to targeted deletion. We demonstrate that dual-targeted nicking enables deletion of 36 and 97 Kb of the genome. Furthermore, multiplex targeting enables deletion of 133 Kb, accounting for approximately 3% of the entire E. coli genome. This technology provides a framework for methods to manipulate bacterial genomes using CRISPR-nickase systems. We envision this system working synergistically with preexisting bacterial genome engineering methods.
Neurite Sprouting and Synapse Deterioration in the Aging Caenorhabditis elegans Nervous System (2012)

Caenorhabditis elegans is a powerful model for analysis of the conserved mechanisms that modulate healthy aging. In the aging nematode nervous system, neuronal death and/or detectable loss of processes are not readily apparent, but because dendrite restructuring and loss of synaptic integrity are hypothesized to contribute to human brain decline and dysfunction, we combined fluorescence microscopy and electron microscopy (EM) to screen at high resolution for nervous system changes. We report two major components of morphological change in the aging C. elegans nervous system: (1) accumulation of novel outgrowths from specific neurons, and (2) physical decline in synaptic integrity. Novel outgrowth phenotypes, including branching from the main dendrite or new growth from somata, appear at a high frequency in some aging neurons, but not all. Mitochondria are often associated with age-associated branch sites. Lowered insulin signaling confers some maintenance of ALM and PLM neuron structural integrity into old age, and both DAF-16/FOXO and heat shock factor transcription factor HSF-1 exert neuroprotective functions. hsf-1 can act cell autonomously in this capacity. EM evaluation in synapse-rich regions reveals a striking decline in synaptic vesicle numbers and a diminution of presynaptic density size. Interestingly, old animals that maintain locomotory prowess exhibit less synaptic decline than same-age decrepit animals, suggesting that synaptic integrity correlates with locomotory healthspan. Our data reveal similarities between the aging C. elegans nervous system and mammalian brain, suggesting conserved neuronal responses to age. Dissection of neuronal aging mechanisms in C. elegans may thus influence the development of brain healthspan-extending therapies.
Expression of osteopontin in human glioma. Its correlation with the malignancy. (1995)

These findings indicate that OPN mRNA and proteins are expressed in human glioma cells, and that the extent of OPN expression may correlate with the malignancy grade of gliomas.
Can grafted cardiomyocytes colonize peri-infarct myocardial areas? (1996)

These initial results suggest the feasibility of transplanting allogeneic cardiomyocytes into the border zone of MI areas, a prerequisite for this approach to successfully improve the function of ischemically damaged hearts.