gebhart/patrepeval huggingface dataset:
Representation Learning via Semi-Supervised Autoencoder for Multi-task Learning (2015)

Multi-task learning aims at learning multiple related but different tasks. In general, there are two ways for multi-task learning. One is to exploit the small set of labeled data from all tasks to learn a shared feature space for knowledge sharing. In this way, the focus is on the labeled training samples while the large amount of unlabeled data is not sufficiently considered. Another way has a focus on how to share model parameters among multiple tasks based on the original features space. Here, the question is whether it is possible to combine the advantages of both approaches and develop a method, which can simultaneously learn a shared subspace for multiple tasks and learn the prediction models in this subspace? To this end, in this paper, we propose a feature representation learning framework, which has the ability in combining the autoencoders, an effective way to learn good representation by using large amount of unlabeled data, and model parameter regularization methods into a unified model for multi-task learning. Specifically, all the tasks share the same encoding and decoding weights to find their latent feature representations, based on which a regularized multi-task softmax regression method is used to find a distinct prediction model for each task. Also, some commonalities are considered in the prediction models according to the relatedness of multiple tasks. There are several advantages of the proposed model: 1) it can make full use of large amount of unlabeled data from all the tasks to learn satisfying representations, 2) the learning of distinct prediction models can benefit from the success of autoencoder, 3) since we incorporate the labeled information into the softmax regression method, so the learning of feature representation is indeed in a semi-supervised manner. Therefore, our model is a semi-supervised autoencoder for multi-task learning (SAML for short). Finally, extensive experiments on three real-world data sets demonstrate the effectiveness of the proposed framework. Moreover, the feature representation obtained in this model can be used by other methods to obtain improved results.
Synthesis of Corneal Keratan Sulfate Proteoglycans by Bovine Keratocytes in Vitro (1996)

Keratan sulfate proteoglycans (KSPGs) are the major proteoglycans of the cornea and are secreted by keratocytes in the corneal stroma. Previous studies have been able to show only transient secretion of KSPG in cell culture. In this study, cultures of bovine keratocytes were found to secrete the three previously characterized KSPG proteins into culture medium. Reactivity with monoclonal antibody I22 demonstrated substitution of these proteins with keratan sulfate chains. KSPG constituted 15% of the proteoglycan metabolically labeled with [35S]sulfate in keratocyte culture medium. This labeled KSPG contained keratan sulfate chains of 4700 Da compared to 21,000 Da for bovine corneal keratan sulfate. Labeled keratan sulfate from cultures contained nonsulfated, monosulfated, and disulfated disaccharides that were released by digestion with endo-beta-galactosidase or keratanase II. Nonsulfated disaccharides were relatively more abundant in keratan sulfate from culture than in corneal keratan sulfate. These results show that cultured bovine keratocytes maintain the ability to express all three of the known KSPG proteins, modified with keratan sulfate chains and sulfated on both N-acetylglucosamine and galactose moieties. KSPG made in vitro differs from that found in vivo in the length and sulfation of its keratan sulfate chains. The availability of cell cultures secreting corneal keratan sulfate proteoglycans provides an opportunity to examine biosynthesis and control of this important class of molecules.
Changes in MRS neuronal markers and T cell phenotypes observed during early HIV infection (2009)

These results verify metabolism changes occurring in the brain early during HIV infection. Lower NAA and Glx levels in the cortical gray matter suggests that HIV causes neuronal dysfunction soon after infection, which correlates to the expansion of CD8+ T cells, specifically to an activated phenotype. Utilizing magnetic resonance spectroscopy to track NAA levels may provide important information on brain metabolic health while allowing better understanding of the virus-host interactions involved in CNS functional deficits.
Nanocarriers for Nitric Oxide Delivery (2011)

Nitric oxide (NO) is a promising pharmaceutical agent that has vasodilative, antibacterial, and tumoricidal effects. To study the complex and wide-ranging roles of NO and to facilitate its therapeutic use, a great number of synthetic compounds (e.g., nitrosothiols, nitrosohydroxyamines, N-diazeniumdiolates, and nitrosyl metal complexes) have been developed to chemically stabilize and release NO in a controlled manner. Although NO is currently being exploited in many biomedical applications, its use is limited by several factors, including a short half-life, instability during storage, and potential toxicity. Additionally, efficient methods of both localized and systemic in vivo delivery and dose control are needed. One strategy for addressing these limitations and thus increasing the utility of NO donors is based on nanotechnology.
Mast cell involvement in various inflammatory processes. (1987)

Mast cells from different tissue sites may have different histochemical, chemical, and functional properties. Whatever the basis for these differences, they must be important in terms of their biologic significance. Through their mediators, mast cells are involved in many different acute and chronic inflammatory processes. They act in delayed hypersensitivity, immediate hypersensitivity, and in granulomatous reactions. They can influence phagocytosis, chemokinesis, and many aspects of immune activity in several different T and B cell pathways, to mention only a few effects. Mast cells are involved in repair processes including fibroblast function and fibrosis. Their growth may be influenced by T cell-derived factors as well as factors derived from the epithelium. They appear to be intimately involved with nerves and can form apparent communications with neurones, especially those containing Substance P, which causes all types of mast cells to degranulate. Mast cells may therefore act as central switchboards between the central nervous system and migrating and sessile cell types in inflammatory processes.
Combined heart rate and activity improve estimates of oxygen consumption and carbon dioxide production rates (1996)

Oxygen consumption (VO2) and carbon dioxide production (VCO2) rates were measured by electronically recording heart rate (HR) and physical activity (PA). Mean daily VO2 and VCO2 measurements by HR and PA were validated in adults (n = 10 women and 10 men) with room calorimeters. Thirteen linear and nonlinear functions of HR alone and HR combined with PA were tested as models of 24-h VO2 and VCO2. Mean sleep VO2 and VCO2 were similar to basal metabolic rates and were accurately estimated from HR alone [respective mean errors were -0.2 +/- 0.8 (SD) and -0.4 +/- 0.6%]. The range of prediction errors for 24-h VO2 and VCO2 was smallest for a model that used PA to assign HR for each minute to separate active and inactive curves (VO2, -3.3 +/- 3.5%; VCO2, -4.6 +/- 3%). There were no significant correlations between VO2 or VCO2 errors and subject age, weight, fat mass, ration of daily to basal energy expenditure rate, or fitness. VO2, VCO2, and energy expenditure recorded for 3 free-living days were 5.6 +/- 0.9 ml.min-1.kg-1, 4.7 +/- 0.8 ml. min-1.kg-1, and 7.8 +/- 1.6 kJ/min, respectively. Combined HR and PA measured 24-h VO2 and VCO2 with a precision similar to alternative methods.
Block Copolymer Thermodynamics: Theory and Experiment (1990)

Block copolymers are macromolecules composed of sequences, or blocks, of chemically distinct repeat units. The development of this field originated with the discovery of termination-free anionic polymerization, which made possible the sequential addition of monomers to various carbanion-ter­ minated (living) linear polymer chains. Polymerization of just two dis­ tinct monomer types (e.g. styrene and isoprene) leads to a class of materials referred to as AB block copolymers. Within this class, a variety of molec­ ular architectures is possible. For example, the simplest combination, obtained by the two-step anionic polymerization of A and B monomers, is an (A-B) dioblock copolymer. A three-step reaction provides for the preparation of (ABA) or (BAB) triblock copolymer. Alternatively, living diblock copolymers can be reacted with an n-functional coupling agent to produce (A-B)n star-block copolymers, where n = 2 constitutes a triblock copolymer. Several representative (A-B)n block copolymer architectures
Contents, Vol. 49, 1989 (1989)

Drug DosageThe authors and the
Expression of the markers BDCA‐2 and BDCA‐4 and production of interferon‐α by plasmacytoid dendritic cells in systemic lupus erythematosus (2003)

SLE patients had a reduced number of BDCA-2-expressing PDCs, also termed natural IFN alpha-producing cells, and their IFN alpha production could be inhibited by anti-BDCA-2/4 mAb. Such mAb may be a therapeutic option for inhibiting the ongoing IFN alpha production in SLE patients.
Comparison of Early Invasive and Conservative Strategies in Patients with Unstable Coronary Syndromes Treated with the Glycoprotein IIb/IIIa Inhibitor Tirofiban (2001)

In patients with unstable angina and myocardial infarction without ST-segment elevation who were treated with the glycoprotein IIb/IIIa inhibitor tirofiban, the use of an early invasive strategy significantly reduced the incidence of major cardiac events. These data support a policy involving broader use of the early inhibition of glycoprotein IIb/IIIa in combination with an early invasive strategy in such patients.
Physical Unclonable Functions and Their Applications to Vehicle System Security (2009)

In recent years, there has been a tremendous increase in the usage of IT based systems in vehicles, with predictions that in the near future, more than 90% of innovations in the automotive sector will be centered on IT software and hardware. However, innovation also means that intellectual property (IP) is created, which is valuable to third (potentially) untrusted and malicious parties. In particular, automobiles are already suffering from security issues, such as illegal copying of software IP, counterfeiting of electronic components, illegal tampering with digital data inside the electronic control units (ECUs), etc. Recently, physical unclonable functions (PUFs) attracted significant interest for numerous applications such as protection of software and hardware IP, secure key storage and component identification, to name a few. In this paper, we describe how PUFs can be used for secure key storage, component identification, IP protection in vehicle applications, and their suitability for vehicle insurance applications.
Structural relationships in the two-zinc insulin hexamer (1979)

The refinement of the crystal structure of two-Zn pig insulin using 1.5-A (1A = 0.1 nm) resolution data by Fourier and fast Fourier least-squares methods allows us to make detailed comparisons between the two independent molecules present in the two-Zn insulin dimer and to describe their interactions in the monomer, dimer, and hexamer. The main chain structures for the two molecules agree well except at the N terminus of the A chain and the C terminus of the B chain. The residues along the line of the local two-fold axes, apart from the B25 side chain, conform extremely closely to the two-fold symmetry, although the discrepancies are much more apparent away from this axis. The ability of the insulin molecule to adopt different conformations may be an important factor in the expression of its biological activity.
Rapid identification and antimicrobial susceptibility profiling of Gram-positive cocci in blood cultures with the Vitek 2 system (2009)

Rapid identification and antimicrobial susceptibility profiling of the bacteria in blood cultures can result in clinical and financial benefits. Addition of saponin to the fluid from blood culture bottles promotes the recovery of the bacteria and thus may shorten the turnaround time of the microbiological analyses. In this study we compared the identification and susceptibility profiles of saponin-treated and untreated (standard method) blood cultures monomicrobial for Gram-positive cocci using Vitek 2. We concordantly identified 49 (89%) of 55 monobacterial cultures using the results with the standard method as reference. Complete categorical agreement between the susceptibility profiles with the new and the standard method was found for 26 (53%) of 49 isolates, while discrepancies were seen for 23 (47%) cultures. E-tests indicated that the new method resulted in a correct susceptibility profile for 8 (35%) of these 23 blood cultures. Therefore, 34 (69%) of 49 cultures showed a concordant/correct susceptibility profile for all antimicrobials with an overall error rate of 2.3%. Thus, addition of saponin to the fluid from blood culture bottles of the Bactec 9240 leads to the rapid (results available >or=12 hours earlier) and reliable identification and susceptibility profiling of Gram-positive cocci in blood cultures with Vitek 2.
PCR Targeted to the 16S-23S rRNA Gene Intergenic Spacer Region of Clostridium difficile and Construction of a Library Consisting of 116 Different PCR Ribotypes (1999)

A reference library of types of Clostridium difficile has been constructed by PCR ribotyping isolates (n = 2,030) from environmental (n = 89), hospital (n = 1,386), community practitioner (n = 395), veterinary (n = 27), and reference (n = 133) sources. The library consists of 116 distinct types identified on the basis of differences in profiles generated with PCR primers designed to amplify the 16S-23S rRNA gene intergenic spacer region. Isolates from 55% of infections in hospitals in the United Kingdom belonged to one ribotype (type 1), but this type was responsible for only 7. 5% of community infections.
Selective Oral Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor ZD1839 Is Generally Well-Tolerated and Has Activity in Non–Small-Cell Lung Cancer and Other Solid Tumors: Results of a Phase I Trial (2002)

Rash and diarrhea, generally mild and tolerable at doses <or= 600 mg/d, were DLTs at 800 mg/d (maximum-tolerated dose). Antitumor activity was observed at all doses. Pharmacokinetic analyses confirmed suitability of once-daily oral dosing.
The mycobacterial binuclear iron monooxygenases require a specific chaperonin‐like protein for functional expression in a heterologous host (2012)

The mimABCD gene clusters in Mycobacterium smegmatis strain mc(2) 155 and Mycobacterium goodii strain 12523 encode binuclear iron monooxygenases that oxidize propane and phenol. In this study, we attempted to express each mimABCD gene cluster in a heterologous host. The actinomycetous strain Rhodococcus opacus B-4, which is phylogenetically close to Mycobacterium, was selected as the host. Each mimABCD gene cluster was cloned into the Rhodococcus-Escherichia coli shuttle vector, pTip-QC2, and then introduced into R. opacus cells. Although whole-cell assays were performed with phenol as a substrate, the transformed R. opacus cells did not oxidize this substrate. SDS/PAGE analysis revealed that the oxygenase large subunit MimA was expressed in the insoluble fraction of R. opacus cells. We found that a gene designated mimG, which lies downstream of mimABCD, exhibits similarity in the amino acid sequence of its product with the products of genes encoding the chaperonin GroEL. When the mimG gene was cloned and coexpressed with each mimABCD gene cluster in R. opacus strain B-4, this host successfully acquired oxidation activity towards phenol. SDS/PAGE and western blotting analyses demonstrated that MimA was clearly soluble when in the presence of MimG. These results indicated that MimG played essential roles in the productive folding of MimA, and that the resulting soluble MimA protein led to the active expression of MimABCD.
Digital rights management and watermarking of multimedia content for m-commerce applications (2000)

E-commerce has become a huge business and a driving factor in the development of the Internet. Online shopping services are well established and will, with the advent of evolved 2G and 3G mobile networks, soon be complemented by their wireless counterparts. Furthermore, online delivery of digital media, such as MP3 audio or video, is very popular today and will become an increasingly important part of e-commerce and mobile e-commerce (m-commerce). However, a major obstacle for digital media distribution and associated business is the possibility of unlimited consecutive copying in the digital domain, which threatens intellectual property rights (e.g., copyrights). Digital rights management systems are required to protect rights and business. DRM systems typically incorporate encryption, conditional access, copy control mechanisms, and media identification and tracing mechanisms. Watermarking is the technology used for copy control and media identification and tracing. Most proposed watermarking methods use a so-called spread spectrum approach: a pseudo-noise signal with small amplitude is added to the host signal, and later on detected using correlation methods. A secret key is used to ensure that the watermark can only be detected and removed by authorized parties. Thus, watermarking is an essential component of modern DRM systems. Several standardization bodies are involved in DRM standardization. Some examples, (MPEG-4, SDMI, and DVD), are discussed in this article. Watermarking as an enabling technology is especially highlighted. Furthermore, the relation between DRM and m-commerce, and the impact on business models for m-commerce are discussed. A common experience today is that Internet e-commerce applications cannot always easily be adapted for mobile telecommunications systems. We emphasize, however, that DRM and watermarking can benefit from the additional information available in mobile telecommunications systems, and can thus help to improve rights management for digital media delivery.
Purification and Structural Determination of a Phosphorylated Peptide with Anti-calcification and Chitin-binding Activities in the Exoskeleton of the Crayfish, Procambarus clarkii (2001)

Organic matrices in calcified hard tissues have been considered to control calcification. A matrix peptide, designated CAP-1, was extracted and purified by anion-exchange and reverse-phase high performance liquid chromatographies from the exoskeleton of the crayfish, Procambarus clarkii. The amino acid sequence of CAP-1 was determined by mass spectral and sequence analyses of the intact peptide and its enzymatically digested peptides. CAP-1 consisted of 78 amino acid residues, including a phosphoserine residue, and was rich in acidic amino acid residues. CAP-1 had a Rebers-Riddiford consensus sequence, which is conserved in cuticle proteins from many arthropods. CAP-1 inhibited precipitation of calcium carbonate in an in vitro anticalcification assay dose-dependently, and completely inhibited it at 3 x 10(-7) M. CAP-1 also showed chitin-binding ability, indicating that this molecule was bifunctional and played an important role in formation of the exoskeleton.
Balancing histogram optimality and practicality for query result size estimation (1995)

Many current database systems use histograms to approximate the frequency distribution of values in the attributes of relations and based on them estimate query result sizes and access plan costs. In choosing among the various histograms, one has to balance between two conflicting goals: optimality, so that generated estimates have the least error, and practicality, so that histograms can be constructed and maintained efficiently. In this paper, we present both theoretical and experimental results on several issues related to this trade-off. Our overall conclusion is that the most effective approach is to focus on the class of histograms that accurately maintain the frequencies of a few attribute values and assume the uniform distribution for the rest, and choose for each relation the histogram in that class that is optimal for a self-join query.
Dendritic cells and natural killer cells interact via multiple TNF family molecules (2004)

Dendritic cells (DC) and natural killer (NK) cells are essential components of the innate immune system, which rapidly sense and eliminate invading pathogens and transformed cells, mediate inflammation, and initiate adaptive immune responses. During the early immune events, DC and NK cells interact and regulate each other. The cellular "cross talk" and its molecular mediators are believed to be critical to the quality and magnitude of innate and adaptive immune responses. The goal of the present manuscript is to identify and initially assess major molecular mediators of DC-NK cell interaction. We have previously shown that DC and NK cells constitutively express several tumor necrosis factor family ligands (TNFfLs) and corresponding TNF family receptors (TNFfRs). Therefore, DC and NK cells might be able to interact via cognate interplays of TNFfLs and TNFfRs. Here, we provide initial experimental evidence supporting this possibility. We found that combined but not individual ligation of several TNFfRs induced substantial increases in secretion of interleukin-12 and interferon-gamma by DC and NK cells, respectively. In contrast, specific, individual disruptions of the engagements of the corresponding TNfL-TNFfR pairs greatly impaired DC and NK cell abilities to reciprocally mediate the increases in cytokine secretion. These findings indicate that multiple TNFfLs mediate DC-NK cell interaction.
Specific inhibition of mRNA translation by complementary oligonucleotides covalently linked to intercalating agents. (1986)

Synthetic oligodeoxynucleotides that are covalently linked at their 3' end to an acridine derivative and are complementary to the repeated sequence UUAAAUUAAAUUAAA adjacent to the ribosome binding site of the gene 32-encoded mRNA from phage T4 have been used to regulate the synthesis of gene 32-encoded protein in vitro. These modified, synthetic oligonucleotides specifically block the translation of gene 32-encoded mRNA with a higher efficiency than the homologous unsubstituted oligonucleotides. The inhibition produced by these short "anti-messengers" is due to the formation of specific mRNA . oligodeoxynucleotide hybrids that are stabilized by the intercalation of the acridine ring in the RNA . DNA duplex.
Biodistribution and Targeting Potential of Poly(ethylene glycol)-modified Gelatin Nanoparticles in Subcutaneous Murine Tumor Model (2004)

The results of this study show that PEGylated gelatin nanoparticles do possess long circulating properties and can preferentially distribute in the tumor mass after systemic delivery.