gebhart/patrepeval huggingface dataset:
Single sided substrates and packages based on laminate materials (2010)

Laminate based substrates have traditionally been of two or more layers of metal because thin Cu clad laminate cores (CCL) have not been available, nor was the equipment/process technology available to circuitize these CCLs. Concomitantly, the designs on both die and substrate level have always assumed the multi-layer nature of the substrate which allowed for wire crossings by using plated through holes (PTH). Thin CCLs, 60 μ or less, are now routinely available and equipment/process technology have evolved to where these thin CCLs can be processed with good yields. Several process flows have been devised to manufacture single sided substrates, termed aS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3™</sup> substrates as well as corresponding packages. The common structure for these substrates is a single layer of circuit pattern that is supported by a layer of dielectric core material. Blind vias (BV) in the dielectric are co-located over lands of the circuit pattern. These BVs are equivalent to ball pad openings (BPO) in solder mask of standard BGA substrates and serve as solder mask defined ball pads. The circuit pattern on the opposite site has wire bond fingers connecting via traces to the lands which are larger than BPOs. If necessary, the traces and lands can be protected with solder mask. Surface finishes of bond finger and ball pad can follow any option available for standard BGA substrates. Design examples will be given which demonstrate that many two-layer designed substrates can be converted to single layer substrates. To take full advantage of a larger range of packages, the die pin out should be optimized to facilitate single layer routing. The benefit of this new type of substrate is the cost savings which is derived from a simplified process flow and bill of materials. Further, in many cases, a shrink in substrate size has been demonstrated which translates into additional cost savings. Assembly and reliability of aS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> packages have been demonstrated. The assembly process can follow the usual rules of thin substrate assembly. Reliability for small packages is excellent. Drop test performance shows very high survival rates and moisture sensitivity levels of one have been demonstrated. A significant design feature for wire bond packages is that both fan-in and fan-out are allowed.
The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats (2003)

A single radish nuclear gene, Rfo, restores Ogura (ogu) cytoplasmic male sterility (CMS) in Brassica napus. A map-based cloning approach relying on synteny between radish and Arabidopsis was used to clone Rfo. A radish gene encoding a 687-amino-acid protein with a predicted mitochondrial targeting pre-sequence was found to confer male fertility upon transformation into ogu CMS B. napus. This gene, like the recently described Petunia Rf gene, codes for a pentatricopeptide repeat (PPR)-containing protein with multiple, in this case 16, PPR domains. Two similar genes that do not appear to function as Rfo flank this gene. Comparison of the Rfo region with the syntenic Arabidopsis region indicates that a PPR gene is not present at the Rfo-equivalent site in Arabidopsis, although a smaller and related PPR gene is found about 40 kb from this site. The implications of these findings for the evolution of restorer genes and other PPR encoding genes are discussed.
Evidence for a role of EGF receptor in the progression of human lung carcinoma. (1993)

Sixty-three primary lung carcinomas were examined immunohistochemically for the presence of epidermal growth factor receptors (EGF-R). Of these tumors 35 (55.5%) were positive for EGF-R. A positive correlation between overexpression of EGF-R, on the one hand, and high metastatic rate, poor tumor differentiation and high rate of tumor proliferation, on the other hand, was found. From one tumor with an extremely high amount of EGF-R a primary cell culture was established. The addition of anti-EGF-R serum to this culture decreased cell proliferation. Our results support the evidence for a positive relationship between overexpression of EGF-R and invasiveness, poor differentiation and high growth rate of tumor cells. The blockade of EGF-R with specific antibodies suppressed tumor cell proliferation, suggesting a role of EGF-R in tumor progression.
A Plan to Capture Human Diversity in 1000 Genomes (2008)

Over the next 3 years, an international team plans to create a massive new catalog containing the complete genome sequences of 1000 individuals. It will help fill out the list of new genetic markers for common diseases that came out in 2007.
Fast food recognition from videos of eating for calorie estimation (2009)

Accurate and passive acquisition of dietary data from patients is essential for a better understanding of the etiology of obesity and development of effective weight management programs. Self-reporting is currently the main method for such data acquisition. However, studies have shown that data obtained by self-reporting seriously underestimate food intake and thus do not accurately reflect the real habitual behavior of individuals. Computer food recognition programs have not yet been developed. In this paper, we present a study for recognizing foods from videos of eating, which are directly recorded in restaurants by a web camera. From recognition results, our method then estimates food calories of intake. We have evaluated our method on a database of 101 foods from 9 food restaurants in USA and obtained promising results.
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data (2013)

Supplementary data are available at Bioinformatics online.
Generation and characterization of monoclonal antibody against Advanced Glycation End Products in chronic kidney disease (2016)

Advanced Glycation End Products (AGEs) are toxins that are involved in structural and functional alterations of several organs and tissues, resulting in various pathologies. Several types of AGEs have been described but carboxymethyllysine (CML) is the major antigenic AGE compound. In this study, three different immunogenic carrier proteins (KLH, keyhole limpet hemocyanin; BSA, bovine serum albumin; and HSA, human serum albumin) were modified by glycation. The glycated molecules were used to produce epitope-specific monoclonal antibodies able to recognize the CML domain and to detect uremic toxins in the serum of patients with chronic kidney disease (CKD). A competitive ELISA was standardized in order to quantify CML in the sera of CKD patients. An increase in uremic toxins can compromise the clinical condition of these patients, thus, the detection and quantification of these toxins should contribute to a better management and understanding of this disease.
Sustained Mitogen-activated Protein Kinase (MAPK) and Cytoplasmic Phospholipase A2 Activation by Macrophage Migration Inhibitory Factor (MIF) (1999)

Macrophage migration inhibitory factor (MIF) is an important pro-inflammatory mediator with the unique ability to counter-regulate the inhibitory effects of glucocorticoids on immune cell activation. MIF is released from cells in response to glucocorticoids, certain pro-inflammatory stimuli, and mitogens and acts to regulate glucocorticoid action on the ensuing inflammatory response. To gain insight into the molecular mechanism of MIF action, we have examined the role of MIF in the proliferation and intracellular signaling events of the well characterized, NIH/3T3 fibroblast cell line. Both endogenously secreted and exogenously added MIFs stimulate the proliferation of NIH/3T3 cells, and this response is associated with the activation of the p44/p42 extracellular signal-regulated (ERK) mitogen-activated protein kinases (MAP). The MIF-induced activation of these kinases was sustained for a period of at least 24 h and was dependent upon protein kinase A activity. We further show that MIF regulates cytosolic phospholipase A2 activity via a protein kinase A and ERK dependent pathway and that the glucocorticoid suppression of cytokine-induced cytoplasmic phospholipase A2 activity and arachidonic acid release can be reversed by the addition of recombinant MIF. These studies indicate that the sustained activation of p44/p42 MAP kinase and subsequent arachidonate release by cytoplasmic phospholipase A2 are important features of the immunoregulatory and intracellular signaling events initiated by MIF and provide the first insight into the mechanisms that underlie the pro-proliferative and inflammatory properties of this mediator.
Polynucleotides. XLV1)Synthesis and properties of poly(2′-azido-2′-deoxyinosinic acid) (1977)

Poly (2'-azido-2'-deoxyinosinic acid), [poly (Iz)], was synthesized from 2'-azido-2'-deoxyinosine diphosphate by the action of polynucleotide phosphorylase. Poly (Iz) has UV absorption properties similar to poly (I) and hypochromicity of 11% at 0.15M Na+ and neutrality. In solutions of high Na+ ion concentration, poly (Iz) forms a multi-stranded complex and its Tm at 1.0M Na+ ion concentration was 43 degrees. Upon mixing with poly (C), poly (Iz) forms a 1:1 complex having a Tm lower than that of poly (I)-poly (C) complex in the same conditions. The effect of substitution at the 2'-position of the poly (I) strand was discussed in relation to the interferon-inducing activity.
Differential Usage of VH Gene Segments Is Mediated by cis Elements (1998)

Ig diversity is generated in large part by the combinatorial joining of the Ig gene segments, VH, D, and JH, that together encode the variable domain of Ig. The final Ig repertoire, however, not only reflects the diversity generated through V(D)J recombinatorial joining, but it is also the product of a number of developmental restraints and selections. To avoid such restrictions and assess the recombination potential of individual Ig gene segments, we constructed Ig heavy (H) chain microlocus plasmids, each of which contain germline coding, recombination signal, and flanking sequences of a VH, D, and JH gene segment. These plasmids allow us to assess the recombination potential of the segments in the context of their natural flanking DNA sequences, but in the absence of any higher order chromatin structure or cellular selection. We found that the frequency and extent of deletions and additions at the recombination breakpoints are similar to those observed at rearranged Ig H chain loci in intact animals. The relative frequencies of the types of rearrangements--VD-J, V-DJ, VinvD-J (invD = inverted D), and VDJ--however, differ strongly. Moreover, V81x, the most used VH gene segment in intact mice, also is overused in this plasmid assay, 15 to 30 times that of another VH segment. This result indicates that the overuse of V81x in the early B cell repertoire can be a consequence of its DNA sequence and not of cellular activities.
Interleukin‐10 inhibition of the progression of established collagen‐induced arthritis (1996)

IL-10 suppresses established CIA, probably by inhibiting proinflammatory cytokine production. Our results, taken together with previously reported findings, indicate a potential therapeutic role for IL-10 in RA.
Biosynthesis of diaminopimelate, the precursor of lysine and a component of peptidoglycan, is an essential function of Mycobacterium smegmatis (1996)

Diaminopimelate (DAP) is a unique metabolite used for both the biosynthesis of lysine in bacteria and the construction of the peptidoglycan of many species of bacteria, including mycobacteria. DAP is synthesized by bacteria as part of the aspartate amino acid family, which includes methionine, threonine, isoleucine, and lysine. Aspartokinase, the first enzyme in this pathway, is encoded by the ask gene in mycobacteria. Previous attempts to disrupt this gene in Mycobacterium smegmatis were unsuccessful, even when the cells were supplied with all the members of the aspartate family, suggesting that unlike other bacteria, mycobacteria may have an absolute requirement for this pathway even when growing in rich medium containing DAP. The purpose of this study was to determine if the ask gene and the aspartate pathway are essential to M. smegmatis. This study describes a test for gene essentiality in mycobacteria, utilizing a counterselectable marker (streptomycin resistance) in conjunction with a specially constructed merodiploid strain. We have used this system to show that the ask gene could not be disrupted in wild-type M. smegmatis, using selective rich medium supplemented with DAP unless there was an extra copy of ask provided elsewhere in the chromosome. Disruption of ask was also possible in a lysine auxotroph incapable of converting DAP to lysine. The ask mutant, mc21278 (ask1::aph), exhibits multiple auxotrophy (Met-, Thr-, DAP-, and Lys-) and is complemented by the ask gene. This is the first description of DAP auxotrophy in mycobacteria. The ask mutant lyses when deprived of DAP in culture, a characteristic which can be exploited for the reproducible preparation of protoplasts and mycobacterial extracts. The evidence presented here indicates that the aspartate pathway is essential to M. smegmatis and that DAP is the essential product of this pathway.
Glucagon administration – underevaluated and undertaught (2001)

Abstract Glucagon treatment requires a manually dexterous ‘operator’ who is composed, confident and competent in the whole procedure. Anecdotal reports from parents of teenagers describing difficulties in administering this procedure during severe hypoglycaemia led us to investigate the ‘techniques’ of 136 parents (106 parents of teenagers and 30 parents of young children). A simulated administration by parents using Novo Nordisk Glucagen ® Hypokits was timed, rated and compared with a group of diabetes health professionals. Parent's ‘real life’ experiences of education and administration were obtained with a standard questionnaire. Glucagon residues in syringes and vials were estimated in a laboratory. Sixty nine per cent had handling difficulties ranging from opening the container to drawing the correct dose into the syringe. There was no statistical difference in time taken to complete the procedure between the two parent groups. However there was a significant difference between parents and the professional group. Parents were not accurate in administering dosages as recommended. Young children weighing more than 25 kg would have received less than the required dose. All parents reported verbal instruction with demonstration of the procedure at initial education. We suggest that glucagon administration needs to be taught ‘hands on’ and the skill reassessed on an annual basis. Copyright © 2001 John Wiley &amp; Sons, Ltd.
An object-oriented approach to template guided visual inspection (2003)

The concepts and design issues that provide the basis for the I/sup 2/F (image interpretation foundations) system are described. The I/sup 2/F system combines object-oriented design for machine vision software and constraint-based geometric modeling into a flexible and effective system for automatic template-guided visual inspection. Object-oriented design for 2-D geometry-based image analysis is discussed, and results from processing experimental X-ray data are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis, antibacterial activity and mode of action of novel linoleic acid–dipeptide–spermidine conjugates (2012)

Towards therapeutically viable mimics of host defense cationic peptides (HDCPs) here we report the design and synthesis of a small library, based on a novel hydrophobic-dipeptide-spermidine template. Lipidated sequences 11, 14, 15, 16, 18 and 19 exhibited potent activity against susceptible as well as drug resistant Gram-positive and Gram-negative bacterial strains. Structure-activity relationships of the template revealed a hydrophobicity window of 50-70% with minimum +2 charges to be crucial for activity and cell selectivity. Active sequences 14, 15 and 16 exhibited different modes of action based on dipeptide composition as revealed by studies on model membranes, intact bacterial cells and DNA. Further, severe damage to surface morphology of methicillin resistant S. aureus caused by 14, 15 and 16 at 10 × MIC was observed. The present study provides us two active sequences (14 and 16) with a membrane perturbing mode of action, cell selectivity to hRBCs and keratinocytes along with potent activity against clinically relevant pathogen MRSA. The designed template thus may prove to be a suitable probe to optimize sequences for better selectivity and potential to combat a wide range of drug resistant strains in further research.
Vaccination with Aβ-Displaying Virus-Like Particles Reduces Soluble and Insoluble Cerebral Aβ and Lowers Plaque Burden in APP Transgenic Mice (2009)

In transgenic animal models, humoral immunity directed against the beta-amyloid peptide (Abeta), which is deposited in the brains of AD patients, can reduce Abeta plaques and restore memory. However, initial clinical trials using active immunization with Abeta1-42 (plus adjuvant) had to be stopped as a subset of patients developed meningoencephalitis, likely due to cytotoxic T cell reactions against Abeta. Previously, we demonstrated that retrovirus-like particles displaying on their surface repetitive arrays of self and foreign Ags can serve as potent immunogens. In this study, we generated retrovirus-like particles that display the 15 N-terminal residues of human Abeta (lacking known T cell epitopes) fused to the transmembrane domain of platelet-derived growth factor receptor (Abeta retroparticles). Western blot analysis, ELISA, and immunogold electron microscopy revealed efficient incorporation of the fusion proteins into the particle membrane. Without the use of adjuvants, single immunization of WT mice with Abeta retroparticles evoked high and long-lived Abeta-specific IgG titers of noninflammatory Th2 isotypes (IgG1 and IgG2b) and led to restimulatable B cell memory. Likewise, immunization of transgenic APP23 model mice induced comparable Ab levels. The CNS of immunized wild-type mice revealed neither infiltrating lymphocytes nor activated microglia, and no peripheral autoreactive T cells were detectable. Importantly, vaccination not only reduced Abeta plaque load to approximately 60% of controls and lowered both insoluble Abeta40 as well as Abeta42 in APP23 brain, but also significantly reduced cerebral soluble Abeta species. In summary, Abeta retroparticle vaccination may thus hold promise as a novel efficient future candidate vaccine for active immunotherapy of Alzheimer's disease.
Neural crest stem cells in melanoma development (2014)

The development of new therapies, targeting RAF-MEK-ERK pathway, provided major improvements in outcomes for patients with metastatic melanoma; however, acquired resistance followed by tumor recurrence represents a major clinical challenge. The striking parallels between embryonic NCSCs (eNCSCs) and melanoma cells might lead to the development of new targeted therapeutics selectively eliminating cell populations accountable for tumor initiation, progression and relapse.
Molecular Biology of the Androgen Receptor (2002)

Androgen receptor (AR) is a member of the steroid hormone receptor family of molecules. AR primarily is responsible for mediating the physiologic effects of androgens by binding to specific DNA sequences that influence transcription of androgen-responsive genes. The three-dimensional structure of the AR ligand-binding domain has shown it is similar to other steroid hormone receptors and that ligand binding alters the protein conformation to allow binding of coactivator molecules that amplify the hormone signal and mediate transcriptional initiation. However, AR also undergoes intramolecular interactions that regulate its interactions with coactivators and influence its activity. A large number of naturally occurring mutations of the human AR gene have provided important information about AR molecular structure and intermolecular interactions. AR is also a critical mediator of prostate cancer promotion, conferring growth signals to prostate cancer cells throughout the natural history of the disease. Late-stage prostate cancer, unresponsive to hormonal deprivation, sustains AR signaling through a diverse array of molecular strategies. Variations in the AR gene may also confer genetic predisposition to prostate cancer development and severity. Further understanding of AR action and new strategies to interfere with AR signaling hold promise for improving prostate cancer therapy.
Synthesis of Monodisperse Biotinylated p(NIPAAm)-Coated Iron Oxide Magnetic Nanoparticles and their Bioconjugation to Streptavidin (2007)

We describe here the synthesis of 10 nm, monodisperse, iron oxide nanoparticles that we have coated with temperature-sensitive, biotinylated p(NIPAAm) (b-PNIPAAm). The PNIPAAm was prepared by the reversible addition fragmentation chain transfer polymerization (RAFT), and one end was biotinylated with a PEO maleimide-activated biotin to form a stable thioether linkage. The original synthesized iron oxide particles were stabilized with oleic acid. They were dispersed in dioxane, and the oleic acid molecules were then reversibly exchanged with a mixture of PNIPAAm and b-PNIPAAm at 60 degrees C. The b-PNIPAAm-coated magnetic nanoparticles were found to have an average diameter of approximately 15 nm by dynamic light scattering and transmission electron microscopy. The ability of the biotin terminal groups on the b-PNIPAAm-coated nanoparticles to interact with streptavidin was confirmed by fluorescence and surface plasmon resonance. It was found that the b-PNIPAAm-coated iron oxide nanoparticles can still bind with high affinity to streptavidin in solution or when the streptavidin is immobilized on a surface. We have also demonstrated that the binding of the biotin ligands on the surface of the temperature-responsive magnetic nanoparticles to streptavidin can be turned on and off as a function of temperature.
Carbocationic Polymerization of Isobutylene Using Methylaluminum Bromide Coinitiators:  Synthesis of Bromoallyl Functional Polyisobutylene (2006)

The carbocationic polymerization of isobutylene (IB) was studied in conjunction with AlBr3, MeAlBr2, Me1.5AlBr1.5, and Me2AlBr coinitiators in hexanes(Hex)/methyl chloride (MeCl) 60/40 (v/v) solvent mixtures at −80 °C in the presence of a proton trap, 2,6-di-tert-butylpyridine. The observed Mns were directly proportional to monomer-to-initiator ratio with 2-chloro-2,4,4-trimethylpentane (TMPCl) as initiator and MeAlBr2, Me1.5AlBr1.5, and Me2AlBr coinitiators; however, with AlBr3 the Mns are much lower than the theoretical values. Chain extension “incremental monomer addition” (IMA) experiments resulting in bimodal distributions demonstrate that termination is operational with Me2AlBr. With MeAlBr2 the chain-extended PIBs exhibited close to theoretical Mns, but the molecular weigh distribution was broad. Using Me1.5AlBr1.5, Mn of the polymers increased in direct proportion and the molecular weight distributions remained narrow. 1H and 13C NMR spectroscopy of the polyisobutylene (PIB) obtained with Me1.5AlBr1.5 suggested virtually quantitative bromo end functionality. With MeAlBr2 and Me2AlBr the bromo functionality was lower (0.8−0), decreasing with the increase of Lewis acid concentration and polymerization time. The capping reaction of living polyisobutylene cation (PIB+) with 1,3-butadiene (BD) in Hex/MeCl 60/40 (v/v) solvent mixtures at −80 °C was also studied in conjunction with methylaluminum bromide coinitiators. Quantitative crossover reaction from living PIB chain end to BD followed by instantaneous termination and selective formation of 1,4-addition product bromoallyl functional PIB (PIB-AllylBr) was obtained only with Me1.5AlBr1.5 coinitiator.