gebhart/patrepeval huggingface dataset:
Review of Packaging of Optoelectronic, Photonic, and MEMS Components (2011)

Packaging is a core technology to leverage the functions and the performances of micro- and nano-structures in a system. In order to bring them to application, the gap between component and environment has to be bridged by providing reliable interfaces. This paper reviews the packaging of optoelectronic, photonic, and microelectromechanical systems (MEMS) components. State-of-the-art requirements, standard technologies, and approaches are considered. Recent trends and research results in the packaging of advanced photonic, MEMS, Si-photonic components, and in 3-D, heterogeneous integration, and SiP are discussed.
Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization (2019)

Pooled-library CRISPR screening provides a powerful means to discover genetic factors involved in cellular processes in a high-throughput manner. However, the phenotypes accessible to pooled-library screening are limited. Complex phenotypes, such as cellular morphology and subcellular molecular organization, as well as their dynamics, require imaging-based readout and are currently beyond the reach of pooled-library CRISPR screening. Here we report an all imaging-based pooled-library CRISPR screening approach that combines high-content phenotype imaging with high-throughput single guide RNA (sgRNA) identification in individual cells. In this approach, sgRNAs are codelivered to cells with corresponding barcodes placed at the 3' untranslated region of a reporter gene using a lentiviral delivery system with reduced recombination-induced sgRNA-barcode mispairing. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is used to read out the barcodes and hence identify the sgRNAs with high accuracy. We used this approach to screen 162 sgRNAs targeting 54 RNA-binding proteins for their effects on RNA localization to nuclear compartments and uncovered previously unknown regulatory factors for nuclear RNA localization. Notably, our screen revealed both positive and negative regulators for the nuclear speckle localization of a long noncoding RNA, MALAT1, suggesting a dynamic regulation of lncRNA localization in subcellular compartments.
eyeSelfie (2015)

Eye alignment to the optical system is very critical in many modern devices, such as for biometrics, gaze tracking, head mounted displays, and health. We show alignment in the context of the most difficult challenge: retinal imaging. Alignment in retinal imaging, even conducted by a physician, is very challenging due to precise alignment requirements and lack of direct user eye gaze control. Self-imaging of the retina is nearly impossible. We frame this problem as a user-interface (UI) challenge. We can create a better UI by controlling the eye box of a projected cue. Our key concept is to exploit the reciprocity, "If you see me, I see you", to develop near eye alignment displays. Two technical aspects are critical: a) tightness of the eye box and (b) the eye box discovery comfort. We demonstrate that previous pupil forming display architectures are not adequate to address alignment in depth. We then analyze two ray-based designs to determine efficacious fixation patterns. These ray based displays and a sequence of user steps allow lateral (x, y) and depth (z) wise alignment to deal with image centering and focus. We show a highly portable prototype and demonstrate the effectiveness through a user study.
Pollen from Glycine species survive cryogenic exposure. (2003)

Pollen of 12 genotypes of the annual soybean and its wild perennial relatives were stored without pre-desiccation at low temperatures (-20 C and -196 C) and tested for their viability in vitro. The influence of cryopreserved pollen on pod set and seed production was also investigated. Cryopreserved pollen of all the genotypes showed germination in vitro. Pollen of annual soybean stored at -20 C retained their viability for 4 months, however, pollen of its wild perennial relatives at same storage conditions failed to germinate in vitro. Flowers pollinated with cryopreserved pollen had similar pod set and number of seeds/pod as those pollinated with fresh pollen. Results of this study suggest that cryopreservation of pollen can be used successfully for soybean breeding, and also offers the possibility of conserving the haploid gene pool of soybean and wild perennial species in a cryobank facility.
Structural variants: changing the landscape of chromosomes and design of disease studies (2006)

The near completeness of human chromosome sequences is facilitating accurate characterization and assessment of all classes of genomic variation. Particularly, using the DNA reference sequence as a guide, genome scanning technologies, such as microarray-based comparative genomic hybridization (array CGH) and genome-wide single nucleotide polymorphism (SNP) platforms, have now enabled the detection of a previously unrecognized degree of larger-sized (non-SNP) variability in all genomes. This heterogeneity can include copy number variations (CNVs), inversions, insertions, deletions and other complex rearrangements, most of which are not detected by standard cytogenetics or DNA sequencing. Although these genomic alterations (collectively termed structural variants or polymorphisms) have been described previously, mainly through locus-specific studies, they are now known to be more global in occurrence. Moreover, as just one example, CNVs can contain entire genes and their number can correlate with the level of gene expression. It is also plausible that structural variants may commonly influence nearby genes through chromosomal positional or domain effects. Here, we discuss what is known of the prevalence of structural variants in the human genome and how they might influence phenotype, including the continuum of etiologic events underlying monogenic to complex diseases. Particularly, we highlight the newest studies and some classic examples of how structural variants might have adverse genetic consequences. We also discuss why analysis of structural variants should become a vital step in any genetic study going forward. All these progresses have set the stage for a golden era of combined microscopic and sub-microscopic (cytogenomic)-based research of chromosomes leading to a more complete understanding of the human genome.
Design of a Scalable Event Notification Service: Interface and Architecture (1998)

Event-based distributed systems are programmed to operate in response to events. An event notication service is an application-independent infrastructure that supports the construction of event-based systems. While numerous technologies have been developed for supporting event-based interactions over local-area networks, these technologies do not scale well to wide-area networks such as the Internet. Wide-area networks pose new challenges that have to be attacked with solutions that specically address issues of scalability. This paper presents Siena, a scalable event notication service that is based on a distributed architecture of event servers. We rst present a formally dened interface that is based on an extension to the publish/subscribe protocol. We then describe and compare several different server topologies and routing algorithms. We conclude by briey discussing related work, our experience with an initial implementation of Siena, and a framework for evaluating the scalability of event notication services such as Siena.
Studies on heparin (1936)

demonstrated that dog liver contained a substance, heparin, that retards the coagulation of blood in vitro, much work has been done to devise methods for isolating very active preparations of this material. Chemical analyses of such products, however, have differed greatly, owing to the fact that the substance has not yet been isolated in pure form. Howell [1928] obtained a product which was N-and P-free and concluded that heparin was a derivative of glycuronic acid. Schmitz & Fischer [1933] believed heparin to be a trisaccharide C18H320.7 containing one carboxylic group. The product isolated by Scott & Charles [1933] gave a positive o-naphthol reaction but the test for glycuronic acids with naphthoresorcinol was negative. Their preparation con- tained approximately 2 % N and was readily inactivated by nitrous acid. These
Repeated sequences and open reading frames in the 3' flanking region of the gene for the RNA subunit of Escherichia coli ribonuclease P. (1983)

We have determined the identity of about 700 nucleotides in the 3' flanking region of the gene for M1 RNA, the RNA component of RNase P (EC 3.1.26.5). This region begins with a 113-base-pair segment of DNA, which is repeated approximately 3.5 times. The first repeating unit originates within the gene sequence for the 3' end of mature M1 RNA. The repeating units are highly conserved but diverge considerably after the partial fourth repeat. Segments of sequence homologous to the repeats have been identified both upstream in the M1 RNA transcription unit and downstream from the repeating units. Several overlapping open reading frames, with the potential to encode small basic proteins, have been identified in the repeated sequences. The structure of the M1 RNA gene 3' flanking region is very similar to the corresponding region at the Tyr T locus. In vitro and in vivo, transcription of the M1 RNA gene appears to terminate about 40 nucleotides downstream from the 3' terminus of mature M1 RNA. Therefore, an RNA processing event is involved in the biosynthesis of M1 RNA.
Nanning and Guangxi: China's gateway to the south-west (2000)

Extract: Nanning is a surprise. An ancient city in China's remote southwest, Nanning turns out to be a vibrant mix of traditional and modern in a region which is now poising itself to become the transport hub of southern China and Indochina as combined road, rail, air, river and port improvements reach fruition in the project called 'the Large Channel to the Sea'. A region which has known conflict and controversy, Guangxi is now striving to make the best of its geographical and cultural diversity, and to form part of a wider economic community embracing nearby Chinese provinces as well as the adjacent nations of Southeast Asia.
3D fully convolutional network for vehicle detection in point cloud (2017)

2D fully convolutional network has been recently successfully applied to the object detection problem on images. In this paper, we extend the fully convolutional network based detection techniques to 3D and apply it to point cloud data. The proposed approach is verified on the task of vehicle detection from lidar point cloud for autonomous driving. Experiments on the KITTI dataset shows significant performance improvement over the previous point cloud based detection approaches.
Neutralizing recombinant human antibodies to a conformational V2- and CD4-binding site-sensitive epitope of HIV-1 gp120 isolated by using an epitope-masking procedure. (1995)

As part of the goal of assembling a mixture of neutralizing human mAbs for possible prophylaxis and therapy of HIV-1 disease, we describe a strategy by which neutralizing human Abs to a weakly immunogenic epitope can be accessed. From a phage display library derived from an asymptomatic HIV-1 seropositive donor, a panel of recombinant Fabs against the CD4 binding site (CD4bs) of gp120 was retrieved by affinity selection using recombinant gp120 (strain LAI). Two Fabs corresponding to the dominant clones were used to mask the CD4bs epitope(s) before repeating the selection procedure. Four Fabs were then retrieved that had novel heavy chain sequences. Three recognized a novel epitope distinct from that recognized by conventional CD4bs Abs and were defined by the following criteria: 1) second V region (V2 region) dependence indicated by sensitivity to amino acid changes in the V2 loop and by competition with murine anti-V2 mAbs; 2) CD4bs dependence indicated by sensitivity to amino acid changes usually associated with CD4 binding and by inhibition of Fab binding to gp120 by soluble CD4; this dependence seemed to arise via conformational changes rather than by direct binding, as CD4bs Abs enhanced binding of two of the novel Fabs and, in a reversal of the competition format, the novel Fabs did not inhibit soluble CD4 binding to gp120; and 3) equivalent binding to glycosylated and deglycosylated gp120 and significant, although much reduced, binding to denatured gp120 in contrast with CD4bs Abs, which do not bind to deglycosylated or denatured gp120. One of the novel Fabs efficiently neutralized the MN and LAI strains of HIV-1. These results indicate the presence of a novel neutralizing conformational epitope on gp120 sensitive to the V2 loop and the CD4bs and further highlight the conformational flexibility of gp120. The strategy of masking highly immunogenic epitopes with Abs to rescue a broader range of specific Abs from combinatorial libraries should be widely applicable.
Screening of a Potent, Raw Naked Barley Saccharifying Enzyme Producer and Its Application on the Uncooked Alcohol Fermentation (1987)

Microorganisms capable of degrading the raw naked barley were isolated from soil, and the amylase productivity of each strain was examined on plate contained 2％ raw naked barley. Of the fungi and actinomycetes tested, 71 strains were subjected to subsequent testing for amylase production, and 4 strains were selected as potent amylase producers. Among them, Strain No. 281 produced the most potent raw naked barley saccharifying enzyme, and was identified as genus Rhizopus from morphological and physiological studies. The ratio of raw starch saccharifying activity (RDA) of the crude enzyme derived from the Rhizopus sp. No. 281 was showed 2-3 fold higher than that of commercial enzyme when the raw naked barley was used as the substrate. In the case of uncooked alcohol fermentation using Rhizopus sp. No. 281 glucoamylase preparation, the alcohol yield of the broth was 2％ higher than that of the commercial enzyme.
Bcl-2 family interactome analysis using bacterial surface display (2011)

Journal Article Bcl-2 family interactome analysis using bacterial surface display Get access Siyan Zhang, Siyan Zhang Department of Chemical and Biological Engineering, A207 Engineering Quadrangle, Princeton University, Princeton, NJ 08544. Fax: (609) 258-0211; Tel: (609) 258-7191 Search for other works by this author on: Oxford Academic Google Scholar A. James Link A. James Link Department of Chemical and Biological Engineering, A207 Engineering Quadrangle, Princeton University, Princeton, NJ 08544. Fax: (609) 258-0211; Tel: (609) 258-7191Department of Molecular Biology, Princeton University, Princeton, NJ 08544 E-mail: ajlink@princeton.edu Search for other works by this author on: Oxford Academic Google Scholar Integrative Biology, Volume 3, Issue 8, August 2011, Pages 823–831, https://doi.org/10.1039/c1ib00023c Published: 29 June 2011 Article history Received: 11 March 2011 Accepted: 02 June 2011 Published: 29 June 2011
Characterization of 73 kDa Thiol Protease from Serratia marcescens and Its Effect on Plasma Proteins1 (1988)

The 73-kDa protease (73K protease) was purified from a clinical isolate of Serratia marcescens kums 3958. The purified protease appeared homogeneous by sodium dodecyl sulfate polyacrylamide gel electrophoresis in the presence or absence of 2-mercaptoethanol. The protease is active in a broad pH range with maximum activity at pH 7.5-8.0. The protease appeared to be a thiol protease, since it was inhibited by sulfhydryl reactive compounds such as p-chloromercuribenzoic acid, fluorescein mercuric acetate (FMA), iodoacetamide, and N-ethylmaleimide, and the protease activity was enhanced by various reducing agents such as cysteine, glutathione, 2-mercaptoethanol, and dithiothreitol. The protease contained 2 mol of free sulfhydryl residues per mol of protease. When the protease was reacted with FMA, a maximum of 2 mol of FMA per mol of enzyme was found reacted, based on fluorescence quenching in which the enzyme inactivation was paralleled linearly with the loss of both SH groups. This indicates possible equal involvement of the two thiol groups for the enzyme activity. The inactivation of the protease by FMA was partially restored by a dialysis in the presence of cysteine or dithiothreitol. The protease was not inhibited by high molecular weight kininogen but was inhibited by alpha 2-macroglobulin. The protease bound stoichiometrically to alpha 2-macroglobulin with 1:1 molar ratio and 25% activity remained constant even after the addition of 4 molar excess of alpha 2-macroglobulin. The protease extensively degraded IgG, IgA, fibronectin, fibrinogen, and alpha 1-protease inhibitor.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of Adenovirus Protein IX (1979)

Protein IX from adenovirus type 2 was purified by two methods, one from groups of nine hexons obtained by disrupting purified virus by heating in the presence of deoxycholate, and the other by a previously published method. The purified protein was used to obtain a monospecific antiserum. Protein IX was found to possess both sub-group- and type-specific antigenic determinants which were apparently accessible within the groups of nine hexons. Approximately 15 molecules of IX were found per group of nine hexons and from considerations of symmetry it seemed possible that IX was located at the 'corner to edge' contacts between hexons in the icosahedron. The protein in infected cells was found to possess approximately neutral charge as determined by immunoelectrophoresis. This was consistent with the amino acid composition, which showed it to be rich in serine, alanine and leucine with approximately half of its glutamic and aspartic acid residues amidified, and the isoelectric point of 6.0, as determined by two dimensional gel analysis. No free N-terminal amino acid was detectable. It is suggested that a unique tryptophan residue is located at around position 70 from the blocked N-terminus, on the basis of chemical cleavage by BNPS-skatole. Based on one tryptophan residue a total of 107 amino acids and a mol. wt. of 11200 was deduced. Analysis of 35S-methionine-labelled infected cell extracts in a two-dimensional gel system showed that the synthesis of polypeptide IX could be detected early in infection, i.e. in the presence of an inhibitor of DNA synthesis.
MVA and NYVAC as Vaccines against Emergent Infectious Diseases and Cancer (2011)

Recombinants based on poxviruses have been used extensively as gene delivery systems to study many biological functions of foreign genes and as vaccines against many pathogens, particularly in the veterinary field. Based on safety record, efficient expression and ability to trigger specific immune responses, two of the most promising poxvirus vectors for human use are the attenuated modified vaccinia virus Ankara (MVA) and the Copenhagen derived NYVAC strains. Because of the scientific and clinical interest in these two vectors, here we review their biological characteristics, with emphasis on virus-host cell interactions, viral immunomodulators, gene expression profiling, virus distribution in animals, and application as vaccines against different pathogens and tumors.
Orphan GPCR research (2007)

Orphan G protein-coupled receptors (GPCRs) are receptors lacking endogenous ligands. Found by molecular biological analyses, they became the roots of reverse pharmacology, in which receptors are attempted to be matched to potential transmitters. Later, when high-throughput screening technology was applied to reverse pharmacology, dozens of orphan GPCRs became deorphanized. Furthermore, novel neuropeptides were discovered. This review retraces the history of the orphan GPCRs and of the discoveries of their endogenous ligands, it also discusses the difficulties that the search for new ligands is presently encountering.
Temperature-Dependent Detectivity of Near-Infrared Organic Bulk Heterojunction Photodiodes (2016)

Bulk heterojunction photodiodes are fabricated using a new donor-acceptor polymer with a near-infrared absorption edge at 1.2 μm, achieving a detectivity up to 10<sup>12</sup> Jones at a wavelength of 1 μm and an excellent linear dynamic range of 86 dB. The photodiode detectivity is maximized by operating at zero bias to suppress dark current, while a thin 175 nm active layer is used to facilitate charge collection without reverse bias. Analysis of the temperature dependence of the dark current and spectral response demonstrates a 2.8-fold increase in detectivity as the temperature was lowered from 44 to -12 °C, a relatively small change when compared to that of inorganic-based devices. The near-infrared photodiode shows a switching speed reaching up to 120 μs without an external bias. An application using our NIR photodiode to detect arterial pulses of a fingertip is demonstrated.
An enzyme caught in action: Direct imaging of hydrolytic function and domain formation of phospholipase A2 in phosphatidylcholine monolayers (1989)

Phospholipase A 2 , a ubiquitous lipolytic enzyme that actively catalyses hydrolysis of phospholipids, has been studied as a model for enzyme‐substrate reactions, as a membrane structural probe, and as a model for lipid‐protein interactions. Its mechanism of action remains largely controversial. We report here for the first time direct microscopic observation of the lipolytic action of fluorescently marked phospholipase A 2 ( Naja naja naja ) against phosphatidylcholine monolayers in the lipid phase transition region. Under these conditions, phospholipase A 2 is shown to target and hydrolyse solid‐phase lipid domains of L‐α‐dipalmitoylphosphatidylcholine. In addition, after a critical extent of monolayer hydrolysis, the enzyme itself aggregates into regular, visible proteinaceous domains within the lipid monolayer. Solid‐phase lipid hydrolysis indicates a preferential hydrolytic environment for phospholipase A 2 while enzyme domain formation points to a possible allosteric inhibition mechanism by hydrolysis products.
The Mitochondrial Genotype Can Influence Nuclear Gene Expression in Yeast (1987)

Isochromosomal, respiratory-deficient yeast strains, such as a mit-, a hypersuppressive petite, and a petite lacking mitochondrial DNA, are phenotypically identical in spite of differences in their mitochondrial genomes. Subtractive hybridizations of complementary DNA's to polyadenylated RNA isolated from derepressed cultures of these strains reveal the presence of nuclear-encoded transcripts whose abundance varies not only between them and their respiratory-competent parent, but among the respiratory-deficient strains themselves. Transcripts of some nuclear-encoded mitochondrial proteins, like cytochrome c and the alpha and beta subunits of the mitochondrial adenosine triphosphatase, whose abundance is affected by glucose or heme, do not vary. In the absence of major metabolic variables, yeast cells seem to respond to the quality and quantity of mitochondrial DNA and modulate the levels of nuclear-encoded RNA's, perhaps as a means of intergenomic regulation.
MANAGEMENT OF HORMONE REFRACTORY PROSTATE CANCER: CURRENT STANDARDS AND FUTURE PROSPECTS (1998)

Recent advances suggest that available therapies for hormone refractory prostate cancer can have a meaningful impact on the disease. Improving treatment of hormone refractory prostate cancer remains an area of active investigation.