gebhart/patrepeval huggingface dataset:
Optimized Nuclear Pellet Method for Extracting Next-Generation Sequencing Quality Genomic DNA from Fresh Leaf Tissue (2019)

Next-generation sequencing (NGS) is a revolutionary advancement allowing large-scale discovery of functional molecular markers that has many applications, including plant breeding. High-quality genomic DNA (gDNA) is a prerequisite for successful NGS library preparation and sequencing; however, few reliable protocols to obtain such plant gDNA exist. A previously reported nuclear pellet (NP) method enables extraction of high-yielding gDNA from fresh leaf tissue of maize (<i>Zea mays</i> L.), but the quality does not meet the stringent requirements of NGS. In this study, we optimized the NP method for whole-genome sequencing of rice (<i>Oryza sativa</i> L.) through the integration of simple purification steps. The optimized NP method relied on initial nucleus enrichment, cell lysis, extraction, and subsequent gDNA purification buffers. The purification steps used proteinase K, RNase A, phenol/chloroform/isoamyl alcohol (25:24:1), and chloroform/isoamyl alcohol (24:1) treatments for protein digestion and RNA, protein, and phenol removal, respectively. Our data suggest that this optimized NP method allowed extraction of consistently high-yielding and high-quality undegraded gDNA without contamination by protein and RNA. Moreover, the extracted gDNA fulfilled the quality metrics of NGS library preparation for the Illumina HiSeq X Ten platform by the TruSeq DNA PCR-Free Library Prep Kit (Illumina). We provide a reliable step-by-step guide to the extraction of high-quality gDNA from fresh leaf tissues of rice for molecular biologists with limited resources.
Characterization of On-Chip Multiport Inductors for Small-Area RF Circuits (2008)

This paper proposes a novel calculation method to derive self and mutual components of each segment in multiport inductors. In the proposed method, a set of S-parameters of the multiport inductor is mathematically decomposed into several matrices, which express self and mutual effects of each segment in the inductor. Due to this mathematics-based method, the multiport inductor can be characterized without numerical extractions. In this paper, a small-area distributed amplifier (DA) utilizing five-port inductors is also demonstrated as an application of the proposed analysis method. In the experimental results using a 0.18-mum CMOS process, the three-stage DA utilizing two five-port inductors to replace eight two-port inductors shows that the multiport inductor can successfully reduce layout area.
Discovery of complex behaviors through contact-invariant optimization (2012)

We present a motion synthesis framework capable of producing a wide variety of important human behaviors that have rarely been studied, including getting up from the ground, crawling, climbing, moving heavy objects, acrobatics (hand-stands in particular), and various cooperative actions involving two characters and their manipulation of the environment. Our framework is not specific to humans, but applies to characters of arbitrary morphology and limb configuration. The approach is fully automatic and does not require domain knowledge specific to each behavior. It also does not require pre-existing examples or motion capture data. At the core of our framework is the contact-invariant optimization (CIO) method we introduce here. It enables simultaneous optimization of contact and behavior. This is done by augmenting the search space with scalar variables that indicate whether a potential contact should be active in a given phase of the movement. These auxiliary variables affect not only the cost function but also the dynamics (by enabling and disabling contact forces), and are optimized together with the movement trajectory. Additional innovations include a continuation scheme allowing helper forces at the potential contacts rather than the torso, as well as a feature-based model of physics which is particularly well-suited to the CIO framework. We expect that CIO can also be used with a full physics model, but leave that extension for future work.
The direct agglutination test for diagnosis of visceral leishmaniasis under field conditions in Sudan: comparison of aqueous and freeze-dried antigens (1997)

The performance of the direct agglutination test (DAT) was evaluated under field conditions in an endemic area of visceral leishmaniasis in eastern Sudan, using aqueous (Aq) antigen which has to be kept refrigerated and a newly developed freeze-dried (FD) antigen which is stable at ambient temperature. Both antigens compared well, with 92-98% of readings being identical or only with one dilution difference in titre. FD antigen gave titres that were identical with Aq antigen in 73% of samples, higher in 19%, and lower in 8%. Owing to high ambient temperatures and low humidity, microtitre plate wells dried out during the standard procedures for elution and incubation. However, shortening the elution time from 12 to 4 h proved possible for both antigens; incubation could be reduced from 24 to 10 h for Aq antigen, after which the plates could still be read. Incubation with FD antigen required 18 h and the plates needed to be kept cool because of evaporation. Despite the longer procedure with the FD antigen, the DAT can be completed in 24 h and the use of this stable antigen, that does not require refrigeration, is a major improvement in performing the DAT under unfavourable field conditions.
Potent Inhibition of CD4/TCR-Mediated T Cell Apoptosis by a CD4-Binding Glycoprotein Secreted from Breast Tumor and Seminal Vesicle Cells (1999)

We previously isolated a CD4 ligand glycoprotein, gp17, from human seminal plasma; this glycoprotein is identical with gross cystic disease fluid protein-15 (GCDFP-15), a factor specifically secreted from primary and secondary breast tumors. The function of gp17/GCDFP-15 in physiological as well as in pathological conditions has remained elusive thus far. As a follow up to our previous findings that gp17 binds to CD4 with high affinity and interferes with both HIV-1 gp120 binding to CD4 and syncytium formation, we investigated whether gp17 could affect the T lymphocyte apoptosis induced by a separate ligation of CD4 and TCR. We show here that gp17/GCDFP-15 is in fact a strong and specific inhibitor of the T lymphocyte programmed cell death induced by CD4 cross-linking and subsequent TCR activation. The antiapoptotic effect observed in the presence of gp17 correlates with a moderate up-regulation of Bcl-2 expression in treated cells. The presence of gp17 also prevents the down-modulation of Bcl-2 expression in Bcl-2bright CD4+ T cells that is caused by the triggering of apoptosis. Our results suggest that gp17 may represent a new immunomodulatory CD4 binding factor playing a role in host defense against infections and tumors.
Anti-Programmed Cell Death 1 Antibody Reduces CD4+PD-1+ T Cells and Relieves the Lupus-Like Nephritis of NZB/W F1 Mice (2010)

Programmed cell death 1 (PD-1) is an immunosuppressive receptor that transduces an inhibitory signal into activated T cells. Although a single nucleotide polymorphism in the gene for PD-1 is associated with susceptibility to systemic lupus erythematosus, the role of PD-1 in systemic lupus erythematosus is still not well understood. In this study, we used NZB/W F1 mice, a model of lupus-like nephritis, to examine the function of PD-1 and its ligands. PD-1 was predominantly expressed on CD4(+) T cells that infiltrated the kidney, and CD4(+)PD-1(high) T cells produced higher levels of IFN-gamma than CD4(+)PD-1(low) or CD4(+)PD-1(-) T cells. Stimulation with PMA/ionomycin caused splenic CD4(+)PD-1(+) T cells to secrete high levels of IFN-gamma, IL-10, low levels of TNF-alpha, faint levels of IL-2, IL-21, and no IL-4, IL-17. In vivo anti-PD-1 mAb treatment reduced the number of CD4(+)PD-1(+) T cells in the kidney of NZB/W F1 mice and significantly reduced their mortality rate (p = 0.03). Conversely, blocking PD-L1 using an anti-PD-L1 mAb increased the number of CD4(+)PD-1(+) T cells in the kidney, enhanced serum IFN-gamma, IL-10, and IgG2a ds-DNA-Ab levels, accelerated the nephritis, and increased the mortality rate. We conclude that CD4(+)PD-1(high) T cells are dysregulated IFN-gamma-producing, proinflammatory cells in NZB/W F1 mice.
Pentacene organic thin-film transistors-molecular ordering and mobility (1997)

Pentacene-based organic thin-film transistors (TFT's) with field-effect mobility as large as 0.7 cm/sup 2//V/spl middot/s and on/off current ratio larger than 10/sup 8/ have been fabricated. Pentacene films deposited by evaporation at elevated temperature at low-to-moderate deposition rates have a high degree of molecular ordering with micrometer-sized and larger dendritic grains. Such films yield TFT's with large mobility. Films deposited at low temperature or by flash evaporation have small grains and poor molecular ordering and yield TFT's with low mobility.
Atomic arrangement at the AlN/Si (111) interface (2003)

High-quality GaN epilayers have been grown on Si (111) substrates by metalorganic vapor phase epitaxy using a low-temperature AlN nucleation layer. The atomic arrangement at the epilayer/substrate interface has been investigated by high-resolution electron microscopy. A crystallographically abrupt interface is observed along most of the epilayer, indicating that the AlN/Si interface is thermodynamically stable and of high crystalline quality. Lattice images at the interface show a periodic array of misfit dislocations. The lattice images have been analyzed in detail in order to obtain information about the atomic arrangement, and interface bonding models are proposed.
Proxy means test for targeting welfare benefits in Sri Lanka (2005)

Section I of this paper will briefly discuss the rationale and methodology for proxy means tests, placing them in the context of some of the relevant economic literature on the topic. Section II will describe the data and methodology for developing the targeting formula for the Sri Lankan case. Section III will present results and identify the models considerable best suited for the purpose. Section IV will analyze the targeting outcomes derived from simulations with the models and relate these to possible choices for eligibility thresholds. Section V will compare the selected models with some alternative methods for estimating the model. Section VI will derive and compare welfare gains for a few examples of payment schedules used to distribute benefits to the eligible groups identified by the formulas, and Section VII will conclude by summarizing some of the important conclusions from the exercise.
The CQL Continuous Query Language : Semantic Foundations and Query Execution (2003)

CQL, a Continuous Query Language, is supported by the STREAM prototype Data Stream Management System at Stanford. CQL is an expressive SQL-based declarative language for registering continuous queries against streams and updatable relations. We begin by presenting an abstract semantics that relies only on &amp;quot;black box&amp;quot; mappings among streams and relations.
Acceleration of cartilage repair by genetically modified chondrocytes over expressing bone morphogenetic protein‐7 (2003)

Rehabilitation after cell-based cartilage repair can be prolonged, leading to decreased patient productivity and quality of life. This study shows the feasibility of using genetically modified chondrocytes to accelerate cartilage healing.
Identification of N-(5-tert-Butyl-isoxazol-3-yl)-N′-{4-[7-(2-morpholin-4-yl-ethoxy)imidazo[2,1-b][1,3]benzothiazol-2-yl]phenyl}urea Dihydrochloride (AC220), a Uniquely Potent, Selective, and Efficacious FMS-Like Tyrosine Kinase-3 (FLT3) Inhibitor (2009)

Treatment of AML patients with small molecule inhibitors of FLT3 kinase has been explored as a viable therapy. However, these agents are found to be less than optimal for the treatment of AML because of lack of sufficient potency or suboptimal oral pharmacokinetics (PK) or lack of adequate tolerability at efficacious doses. We have developed a series of extremely potent and highly selective FLT3 inhibitors with good oral PK properties. The first series of compounds represented by 1 (AB530) was found to be a potent and selective FLT3 kinase inhibitor with good PK properties. The aqueous solubility and oral PK properties at higher doses in rodents were found to be less than optimal for clinical development. A novel series of compounds were designed lacking the carboxamide group of 1 with an added water solubilizing group. Compound 7 (AC220) was identified from this series to be the most potent and selective FLT3 inhibitor with good pharmaceutical properties, excellent PK profile, and superior efficacy and tolerability in tumor xenograft models. Compound 7 has demonstrated a desirable safety and PK profile in humans and is currently in phase II clinical trials.
NK T Cell-Induced Protection Against Diabetes in Vα14-Jα281 Transgenic Nonobese Diabetic Mice Is Associated with a Th2 Shift Circumscribed Regionally to the Islets and Functionally to Islet Autoantigen (2001)

The onset of autoimmune diabetes is related to defective immune regulation. Recent studies have shown that NK T cells are deficient in number and function in both diabetic patients and nonobese diabetic (NOD) mice. NK T cells, which are CD1d restricted, express a TCR with an invariant V alpha 14-J alpha 281 chain and rapidly produce large amounts of cytokines. V alpha 14-J alpha 281 transgenic NOD mice have increased numbers of NK T cells and are protected against diabetes onset. In this study we analyzed where and how NK T cells interfere with the development of the anti-islet autoimmune response. NK T cells, which are usually rare in lymph nodes, are abundant in pancreatic lymph nodes and are also present in islets. IL-4 mRNA levels are increased and IFN-gamma mRNA levels decreased in islets from diabetes-free V alpha 14-J alpha 281 transgenic NOD mice; the IgG1/IgG2c ratio of autoantibodies against glutamic acid decarboxylase is also increased in these mice. Treatment with IL-12 (a pro-Th1 cytokine) or anti-IL-4 Ab abolishes the diabetes protection in V alpha 14-J alpha 281 NOD mice. The protection from diabetes conferred by NK T cells is thus associated with a Th2 shift within islets directed against autoantigen such as glutamic acid decarboxylase. Our findings also demonstrate the key role of IL-4.
High-density plasma chemical vapor deposition of silicon-based dielectric films for integrated circuits (1999)

In this paper, we present and review recent developments in the high-density plasma chemical vapor deposition (HDP CVD) of silicon-based dielectric films, and of films of recent interest in the development of lower-dielectric-constant alternatives. Aspects relevant to the HDP CVD process and using the process to achieve interlevel insulation, gap filling, and planarization are discussed. Results obtained thus far suggest that the process may play an important role in the future fabrication of integrated circuits, provided several metal-contamination and process-integration concerns can be effectively addressed.
Amphiphilic poly(ethylene glycol)-poly(ε-caprolactone) AB2 miktoarm copolymers for self-assembled nanocarrier systems: synthesis, characterization, and effects of morphology on antitumor activity (2014)

Miktoarm-structured PEG-PCL<sub>2</sub> copolymers with morphological versatility for drug delivery.
Blockers of the Kv1.5 channel for the treatment of atrial arrhythmias (2002)

AbstractAtrial arrhythmias are a common problem in cardiological practice. Despite the availability of several antiarrhythmic drugs there is a medical need for safer and more efficient treatments. The voltage-gated potassium channel Kv1.5 is regarded as a promising target for the development of new atrial selective drugs with fewer side effects. This review summarises patents claiming such compounds. The chemistry and biological data disclosed in these patents are discussed in light of recent work demonstrating the antiarrhythmic effects of Kv1.5 blockers in vivo.Keywordsarrhythmiaatrial fibrillationIKurKv1.5potassium channel blockers
Identification of a Soluble Form of B7-H1 That Retains Immunosuppressive Activity and Is Associated with Aggressive Renal Cell Carcinoma (2011)

Our observations suggest that sB7-H1 may be detected in the sera of ccRCC patients and that sB7-H1 may systemically impair host immunity, thereby fostering cancer progression and subsequent poor clinical outcome.
N,N-DiethylO-Carbamate: Directed Metalation Group and Orthogonal Suzuki−Miyaura Cross-Coupling Partner (2009)

The first Suzuki-Miyaura cross-coupling of an aryl O-carbamate, a versatile and powerful directed metalation group (DMG) in directed ortho metalation (DoM) chemistry, is described using the inexpensive, bench-stable catalyst NiCl(2)(PCy(3))(2). Broad synthetic scope and good efficiency are demonstrated for aryl and heteroaryl O-carbamates. The role of water and hydrolysis equilibrium between free boronic acid and boroxine was established to be a crucial parameter for this transformation. When combined with DoM and traditional Pd-catalyzed Suzuki-Miyaura strategies, the methodology offers concise routes to uniquely substituted molecules, avoiding the need for protection/deprotection of the phenol and the use of strongly nucleophilic cross-coupling partners.
Identification of HLA-A*0201-Presented T Cell Epitopes Derived from the Oncofetal Antigen-Immature Laminin Receptor Protein in Patients with Hematological Malignancies (2006)

The oncofetal Ag immature laminin receptor (OFA-iLR) is a potential target molecule for immunotherapeutic studies in several tumor entities, including hematological malignancies. In the present study, we characterize two HLA-A*0201-presented epitopes eliciting strong OFA-iLR peptide-specific human cytotoxic T cell (CTLs) responses in vitro. Both allogeneic HLA-A*0201-matched and autologous CTLs recognized and killed endogenously OFA-iLR-expressing tumor cell lines and primary malignant cells from patients with hemopoietic malignancies in an MHC-restricted fashion but spared nonmalignant hemopoietic cells. Spontaneous OFA-iLR peptide-specific T cell reactivity was detectable in a significant proportion of leukemia patients. Interestingly, in patients with chronic lymphocytic leukemia and multiple myeloma but not in those with acute myeloid leukemia, significant frequencies of OFA peptide-specific CTLs could be detected in an early stage of disease but disappeared in patients with progressive disease. The identification of OFA-iLR-derived peptide epitopes provides a basis for tumor immunological studies and therapeutic vaccination strategies in patients with OFA-iLR-expressing malignancies.
An integrated biotechnology platform for developing sustainable chemical processes (2014)

Genomatica has established an integrated computational/experimental metabolic engineering platform to design, create, and optimize novel high performance organisms and bioprocesses. Here we present our platform and its use to develop E. coli strains for production of the industrial chemical 1,4-butanediol (BDO) from sugars. A series of examples are given to demonstrate how a rational approach to strain engineering, including carefully designed diagnostic experiments, provided critical insights about pathway bottlenecks, byproducts, expression balancing, and commercial robustness, leading to a superior BDO production strain and process.
The Image Processing Handbook (2011)

Whether obtained by microscopes, space probes, or the human eye, the same basic tools can be applied to acquire, process, and analyze the data contained in images. Ideal for self study, The Image Processing Handbook, Sixth Edition, first published in 1992, raises the bar once again as the gold-standard reference on this subject. Using extensive new
Past, Present, and Possible Future Human Infection with Influenza Virus A Subtype H7 (2009)

Influenza A subtype H7 viruses have resulted in >100 cases of human infection since 2002 in the Netherlands, Italy, Canada, the United States, and the United Kingdom. Clinical illness from subtype H7 infection ranges from conjunctivitis to mild upper respiratory illness to pneumonia. Although subtype H7 infections have resulted in a smaller proportion of hospitalizations and deaths in humans than those caused by subtype H5N1, some subtype H7 strains appear more adapted for human infection on the basis of their virus-binding properties and illness rates among exposed persons. Moreover, increased isolation of subtype H7 influenza viruses from poultry and the ability of this subtype to cause severe human disease underscore the need for continued surveillance and characterization of these viruses. We review the history of human infection caused by subtype H7. In addition, we discuss recently identified molecular correlates of subtype H7 virus pathogenesis and assess current measures to prevent future subtype H7 virus infection.
In vitro selection identifies key determinants for loop–loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1 (1999)

We selected RNA aptamers specific for the trans-activation responsive (TAR) RNA, a stem-loop structure crucial for the transcription of the integrated genome of the human immunodeficiency virus. Most of the selected sequences could be folded as imperfect hairpins and displayed a 5'-GUCCCAGA-3' consensus motif constituting the apical loop. The six central bases of this consensus sequence are complementary to the entire TAR loop, leading to the formation of TAR RNA-aptamer "kissing" complexes. The consensus G and A residues closing the aptamer loop contributed to the high affinity (Kd = 30 nM at 23 degrees C) of the aptamers for the TAR RNA. This G A pair was shown to be crucial for binding to TAR at a low magnesium concentration. The selection also identified 5'-PuPy and 5'-PyPu base pairs at alpha and beta positions of the stem, next to the loop, respectively. This strategy offered a way to identify key determinants of loop-loop interactions and to generate high affinity ligands of TAR RNA structure.
Automatic metadata generation using associative networks (2009)

In spite of its tremendous value, metadata is generally sparse and incomplete, thereby hampering the effectiveness of digital information services. Many of the existing mechanisms for the automated creation of metadata rely primarily on content analysis which can be costly and inefficient. The automatic metadata generation system proposed in this article leverages resource relationships generated from existing metadata as a medium for propagation from metadata-rich to metadata-poor resources. Because of its independence from content analysis, it can be applied to a wide variety of resource media types and is shown to be computationally inexpensive. The proposed method operates through two distinct phases. Occurrence and cooccurrence algorithms first generate an associative network of repository resources leveraging existing repository metadata. Second, using the associative network as a substrate, metadata associated with metadata-rich resources is propagated to metadata-poor resources by means of a discrete-form spreading activation algorithm. This article discusses the general framework for building associative networks, an algorithm for disseminating metadata through such networks, and the results of an experiment and validation of the proposed method using a standard bibliographic dataset.