gebhart/patrepeval huggingface dataset:
RECONSTRUCTION OF BUILDINGS FROM AIRBORNE LASER SCANNING DATA (2006)

For mapping applications the reconstruction of buildings from the point cloud offers promising prospects for rapid generation of large scale 3D models, e.g., for city modeling. Reconstruction requires, however, knowledge on a variety of parameters that refer both to the point cloud and to the modeled building. For the point cloud the separation of the laser points describing the buildings from the rest of the data is one concern; the other is ensuring that this subset reflects indeed a building and not another object, e.g., vegetation. The generation of a building model from this subset requires then to learn the roof parts from the data, and then convert these elements into an actual building model that complies with topological and geometrical rules. The complexity of this task has led many researchers to use external information, mostly in the form of detailed ground plans to identify the subset of the point cloud and to provide first approximation of the building shape. This information is however not available everywhere and generally cannot be taken for granted. In this paper we present a reconstruction model that automatically detects buildings within the point cloud and reconstruct their shape. For the detection we develop safeguards that reduce the chance of misclassification of a building to a minimum. The reconstruction involves the aggregation of the point set into individual faces, and learning the building shape from these aggregates. We show the effect of imposing geometric constrains on the reconstruction to generate realistic models of the buildings.
Nuclear Reprogramming in Nuclear Transplant Rabbit Embryos (1988)

The first six genetically verified nuclear transplant rabbits have been produced in this study. Individual eight-cell stage embryo blastomeres were transferred and fused with enucleated mature oocytes of which six full-term offspring were produced out of 164 manipulated eggs. The following efficiency rates were determined for the nuclear transplantation procedure: chromosomal removal from oocytes, 92%; fusion rate, 84%; activation rate, 46%; embryo transfer rate, 27%. Additional reasons for the low efficiency rate of nuclear transplant embryos may include limited development due to aging in recipient oocytes and asynchronous transfers of manipulated embryos to recipient females. The successful development to term may have been due to the ability of the mature oocyte to reprogram the eight-cell stage nuclei. The number of cells in blastocysts derived from isolated eight-cell blastomeres (18 +/- .08) was lower than that of nonmanipulated pronuclear (106 +/- 5.1) and nuclear transplant embryos derived from eight-cell stage nuclei (91 +/- 10.2) (p less than 0.001). This evidence along with the significant amount of nuclear swelling in nuclear transplant embryos and a delay in the time of blastocyst formation indicate that nuclear reprogramming had taken place in these embryos. Successful nuclear reprogramming indicates that serial transfers could result in the expanded multiplication of mammalian embryos.
Approximating the average stretch factor of geometric graphs (2012)

Let G be a geometric graph whose vertex set S is a set of n points in ℝd. The stretch factor of two distinct points p and q in S is the ratio of their shortest-path distance in G and their Euclidean distance. We consider the problem of approximating the average of the n choose 2 stretch factors determined by all pairs of points in S. We show that for paths, cycles, and trees, this average can be approximated, within a factor of 1+ε, in O(n polylog(n)) time. For plane graphs in ℝ2, we present a (2+ε)-approximation algorithm with running time O(n5/3polylog(n)), and a (4+ε)-approximation algorithm with running time O(n3/2polylog(n)). Finally, we show that, for any tree in ℝ2, the exact average of the squares of the n choose 2 stretch factors can be computed in O(n11/6) time.
1.25 /spl mu/m low threshold current density dots-in-a-well (DWELL) lasers (1999)

It has been predicted that the threshold current density of quantum dot lasers should be lower than that of quantum well lasers due to the reduction of the density of states. In particular, efforts have been made in the past few years to reduce the threshold current density of quantum dot lasers on GaAs substrates. A recently developed approach is to put the InAs dots in a strained In/sub 0.2/Ga/sub 0.8/As quantum well. This "dots in a well" (DWELL) design not only improves carrier capture by the dots, but also increases the density of quantum dots over growth on GaAs directly. Consequently, ground state lasing from a single layer of dots is possible at reasonable cavity lengths. While competition with radiative quantum well transitions was suggested as a concern, quantum well transitions were not observed in previous work or in this study. Further improvements have been made by putting a single layer of InAs quantum dots into a strained In/sub 0.15/Ga/sub 0.85/As quantum well. An extremely low threshold current density of 26 Acm/sup -2/ has been achieved for a 7.8 mm cavity length, cleaved facet laser.
Determination of thimerosal in ophthalmic solutions by radial compression separation HPLC. (1982)

A new technology in high pressure liquid chromatography has been validated for the determination of the preservative thimerosal. This technology, Radial Compression Separation, has been found to be an extremely fast and reliable method for the stability analysis of thimerosal in aqueous pharmaceutical preparations. The application of this method has eliminated sample preparation and extraction required by other HPLC methods.
Domain III substitution in Bacillus thuringiensis delta-endotoxin CryIA(b) results in superior toxicity for Spodoptera exigua and altered membrane protein recognition (1996)

To test our hypothesis that substitution of domain III of Bacillus thuringiensis delta-endotoxin (Cry) proteins might improve toxicity to pest insects, e.g., Spodoptera exigua, in vivo recombination was used to produce a number of cryIA(b)-cryIC hybrid genes. A rapid screening assay was subsequently exploited to select hybrid genes encoding soluble protoxins. Screening of 120 recombinants yielded two different hybrid genes encoding soluble proteins with domains I and II of CryIA(b) and domain III of CryIC. These proteins differed by only one amino acid residue. Both hybrid protoxins gave a protease-resistant toxin upon in vitro activation by trypsin. Bioassays showed that one of these CryIA(b)-CryIC hybrid proteins (H04) was highly toxic to S. exigua compared with the parental CryIA(b) protein and significantly more toxic than CryIC. In semiquantitative binding studies with biotin-labelled toxins and intact brush border membrane vesicles of S. exigua, this domain III substitution appeared not to affect binding-site specificity. However, binding to a 200-kDa protein by CryIA(b) in preparations of solubilized and blotted brush border membrane vesicle proteins was completely abolished by the domain III substitution. A reciprocal hybrid containing domains I and II of CryIC and domain III of CryIA(b) did bind to the 200-kDa protein, confirming that domain III of CryIA(b) was essential for this reaction. These results show that domain III of CryIC protein plays an important role in the level of toxicity to S. exigua, that substitution of domain III may be a powerful tool to increase the repertoire of available active toxins for pest insects, and that domain III is involved in binding to gut epithelium membrane proteins of S. exigua.
Topographical and Temporal Diversity of the Human Skin Microbiome (2009)

Human skin is a large, heterogeneous organ that protects the body from pathogens while sustaining microorganisms that influence human health and disease. Our analysis of 16S ribosomal RNA gene sequences obtained from 20 distinct skin sites of healthy humans revealed that physiologically comparable sites harbor similar bacterial communities. The complexity and stability of the microbial community are dependent on the specific characteristics of the skin site. This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin.
Synthetic riboswitches for the conditional control of gene expression in Streptomyces coelicolor (2013)

We have demonstrated the portability of theophylline-dependent synthetic riboswitches for the conditional control of gene expression in Streptomyces coelicolor. The riboswitches mediate dose-dependent, up to 260-fold activation of reporter gene expression. Riboswitch regulation is a simple method requiring a sequence of only ~85 nt to be inserted between a transcriptional start site and the start codon; no additional auxiliary factors are necessary. The promoters galP2, ermEp1 and SF14 worked well in concert with the riboswitches. They allowed theophylline-dependent expression of not only the heterologous β-glucuronidase reporter gene but also dagA, an endogenous agarase gene. The successful combination of all tested promoters with the riboswitches underlines the orthogonality of riboswitch regulation. We anticipate that any additional natural or synthetic promoters can be combined with the riboswitch.
Camera calibration with a near-parallel imaging system based on geometric moments (2011)

This paper presents a novel approach of camera calibration under the near-parallel condition based on geometric moments. The near-parallel condition means that the calibration board is near parallel (or parallel) to the imaging plane. A camera calibration model for the near-parallel condition and a calibration board with arranged rectangular features are suggested. Before calibration, feature regions on the image of calibration board are extracted, and centroid and rotation of each feature are detected using geometric moments. These centroids are used for feature points, and meanwhile mean value of rotations is used for the rotation around axis Z. Then, the closed-form solutions to the translations, other two angles and effective focal length are provided by combining Gauss lens model with camera model. Subsequently, principal point is received by radial alignment constraint (RAC), and distortion coefficients are calculated. Finally, all camera parameters are refined by a nonlinear minimization procedure according to the distortion coefficients. Simulations and experiments are performed to verify the proposed camera calibration algorithm. The precision of detecting feature points and calibrating camera parameters are analyzed. The precision of camera calibration results is also evaluated.
Cardioprotective c-kit+ cells are from the bone marrow and regulate the myocardial balance of angiogenic cytokines (2006)

Clinical trials of bone marrow stem/progenitor cell therapy after myocardial infarction (MI) have shown promising results, but the mechanism of benefit is unclear. We examined the nature of endogenous myocardial repair that is dependent on the function of the c-kit receptor, which is expressed on bone marrow stem/progenitor cells and on recently identified cardiac stem cells. MI increased the number of c-kit+ cells in the heart. These cells were traced back to a bone marrow origin, using genetic tagging in bone marrow chimeric mice. The recruited c-kit+ cells established a proangiogenic milieu in the infarct border zone by increasing VEGF and by reversing the cardiac ratio of angiopoietin-1 to angiopoietin-2. These oscillations potentiated endothelial mitogenesis and were associated with the establishment of an extensive myofibroblast-rich repair tissue. Mutations in the c-kit receptor interfered with the mobilization of the cells to the heart, prevented angiogenesis, diminished myofibroblast-rich repair tissue formation, and led to precipitous cardiac failure and death. Replacement of the mutant bone marrow with wild-type cells rescued the cardiomyopathic phenotype. We conclude that, consistent with their documented role in tumorigenesis, bone marrow c-kit+ cells act as key regulators of the angiogenic switch in infarcted myocardium, thereby driving efficient cardiac repair.
Surface modification of PLGA microspheres (2003)

Microspheres made of poly(lactic-co-glycolic acid) (PLGA) are biocompatible and biodegradable, rendering them a promising tool in the context of drug delivery. However, nonspecific adsorption of plasma proteins on PLGA micro- and nanospheres is a main limitation of drug targeting. Poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG), physisorbed on flat metal oxide surfaces, has previously been shown to suppress protein adsorption drastically. The goal of our work was to characterize the efficiency of the protein repellent character of PLL-g-PEG on PLGA microspheres and to show the feasibility of introducing functional groups on the PLGA microspheres via functionalized PLL-g-PEG. To quantify the adsorbed amount of protein, a semiquantitative method that uses confocal laser scanning microscopy (CLSM) was applied. The first part of the experiment confirms the feasibility of introducing specific functional groups on PLL-g-PEG-coated PLGA microspheres. In the second part of the experiment, PLL-g-PEG-coated PLGA microspheres show a drastic decrease of adsorbed proteins by two orders of magnitude in comparison to uncoated PLGA microspheres. Low protein-binding, functionalizable microspheres provide a fundamental basis for the design of drug delivery and biosensor systems.
An O ( n log n ) Algorithm for Rectilinear Minimal Spanning Trees (1979)

article Free Access Share on An O(n log n) Algorithm for Rectilinear Minimal Spanning Trees Author: F. K. Hwang Bell Laboratories, 600 Mountain Avenue, Murray Hill, NJ Bell Laboratories, 600 Mountain Avenue, Murray Hill, NJView Profile Authors Info & Claims Journal of the ACMVolume 26Issue 2April 1979 pp 177–182https://doi.org/10.1145/322123.322124Online:01 April 1979Publication History 104citation911DownloadsMetricsTotal Citations104Total Downloads911Last 12 Months34Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
AP-1 and NF-kB Regulation in Rheumatoid Arthritis and Murine Collagen-Induced Arthritis (1998)

The DNA binding activity of AP-1 and NF-kappaB are markedly increased in both CIA and RA. In CIA, activation of AP-1 and NF-kappaB precede both clinical arthritis and metalloproteinase gene expression. NF-kappaB expression correlated better than AP-1 with metalloproteinase expression.
Development of Thin-Film Composite forward Osmosis Hollow Fiber Membranes Using Direct Sulfonated Polyphenylenesulfone (sPPSU) as Membrane Substrates (2013)

This study investigates a new approach to fabricate thin-film composite (TFC) hollow fiber membranes via interfacial polymerization for forward osmosis (FO) applications. Different degrees of sulfonation of polyphenylenesulfone (PPSU) were adopted as membrane substrates to investigate their impact on water flux. It has been established that the degree of sulfonation plays a role in both creating a macrovoid-free structure and inducing hydrophilicity to bring about higher water fluxes. The fabricated membranes exhibit extremely high water fluxes of 30.6 and 82.0 LMH against a pure water feed using 2.0 M NaCl as the draw solution tested under FO and pressure retarded osmosis (PRO) modes, respectively, while maintaining low salt reverse fluxes below 12.7 gMH. The structural parameter (S) displays remarkable decreases of up to 4.5 times as the membrane substrate is switched from a nonsulfonated to sulfonated one. In addition, the newly developed TFC-FO membranes containing 1.5 mol % sPPSU in the substrate achieves a water flux of 22 LMH in seawater desalination using a 3.5 wt % NaCl model solution and 2.0 M NaCl as the draw solution under the PRO mode. To the best of our knowledge, this value is the highest ever reported for seawater desalination using flat and hollow fiber FO membranes. The use of sulfonated materials in the FO process opens up a frontier for sustainable and efficient production of potable water.
Design optimization methods for genomic DNA tiling arrays (2005)

A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central issue in designing tiling arrays is that of arriving at a single-copy tile path, as significant sequence cross-hybridization can result from the presence of non-unique probes on the array. Due to the fragmentation of genomic DNA caused by the widespread distribution of repetitive elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequence tiles that are to be included in the design. This becomes increasingly problematic when considering complex eukaryotic genomes that contain many thousands of interspersed repeats. The general problem of sequence tiling can be framed as finding an optimal partitioning of non-repetitive subsequences over a prescribed range of tile sizes, on a DNA sequence comprising repetitive and non-repetitive regions. Exact solutions to the tiling problem become computationally infeasible when applied to large genomes, but successive optimizations are developed that allow their practical implementation. These include an efficient method for determining the degree of similarity of many oligonucleotide sequences over large genomes, and two algorithms for finding an optimal tile path composed of longer sequence tiles. The first algorithm, a dynamic programming approach, finds an optimal tiling in linear time and space; the second applies a heuristic search to reduce the space complexity to a constant requirement. A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences.
Mesothelin as a Potential Therapeutic Target in Human Cholangiocarcinoma (2010)

Mesothelin is overexpressed in one-third of CCA tissues. SS1P targeting mesothelin reveals a remarkable single agent activity against CCA in vitro. These findings indicate a potential for SS1P in the immunotherapeutic treatment of CCA.
FGF21 Analogs of Sustained Action Enabled by Orthogonal Biosynthesis Demonstrate Enhanced Antidiabetic Pharmacology in Rodents (2011)

Fibroblast growth factor 21 (FGF21) mitigates many of the pathogenic features of type 2 diabetes, despite a short circulating half-life. PEGylation is a proven approach to prolonging the duration of action while enhancing biophysical solubility and stability. However, in the absence of a specific protein PEGylation site, chemical conjugation is inherently heterogeneous and commonly leads to dramatic loss in bioactivity. This work illustrates a novel means of specific PEGylation, producing FGF21 analogs with high specific activity and salutary biological activities. Using homology modeling and structure-based design, specific sites were chosen in human FGF21 for site-specific PEGylation to ensure that receptor binding regions were preserved. The in vitro activity of the PEGylated FGF21 ana-logs corresponded with the site of PEG placement within the binding model. Site-specific PEGylated analogs demonstrated dramatically increased circulating half-life and enhanced efficacy in db/db mice. Twice-weekly dosing of an optimal FGF21 analog reduced blood glucose, plasma lipids, liver triglycerides, and plasma glucagon and enhanced pancreatic insulin content, islet number, and glucose-dependent insulin secretion. Restoration of insulin sensitivity was demonstrated by the enhanced ability of insulin to induce Akt/protein kinase B phosphorylation in liver, muscle, and adipose tissues. PEGylation of human FGF21 at a specific and preferred site confers superior metabolic pharmacology.
Juvenile Delinquency: A Judge's View of Our Past, Present, and Future (1993)

Juvenile crime is quickly becoming a national epidemic.In the last decade alone violent juvenile crime rose 27%.2The statistics in Oklahoma are far worse.From 1983 to 1992, violent crimes committed by Oklahoma's juveniles skyrocketed 262%.'These crimes committed by juveniles are becoming increasingly brutal and sophisticated, with incidents of rape, robbery, and murder frequently reported 4 Oklahoma's juvenile laws are ill-equipped to deter this increase in juvenile crime.A recent murder at a local schoolhouse illustrates this point.A fourteen-year-old student approached a fellow student, drew a gun, and shot him point blank in the heads Because of Oklahoma's Juvenile Code, this teenager need not fear criminal prosecution or punishment.Even though the juvenile admitted committing the murder, he cannot be convicted of any crime nor suffer any punishment.'Oklahoma's Juvenile Code, at best, allows the judge to assign the juvenile to the Department of Human Services (DHS).Once assigned, Oklahoma's Juvenile Code forbids DHS from even punishing him.Moreover, the judge has no authority to order DHS to incarcerate the juvenile.Instead, the Juvenile Code authorizes his release at
The role of plant hormones during grafting (2017)

For millennia, people have cut and joined different plant tissues together through a process known as grafting. By creating a chimeric organism, desirable properties from two plants combine to enhance disease resistance, abiotic stress tolerance, vigour or facilitate the asexual propagation of plants. In addition, grafting has been extremely informative in science for studying and identifying the long-distance movement of molecules. Despite its increasing use in horticulture and science, how plants undertake the process of grafting remains elusive. Here, we discuss specifically the role of eight major plant hormones during the wound healing and vascular formation process, two phenomena involved in grafting. We furthermore present the roles of these hormones during graft formation and highlight knowledge gaps and future areas of interest for the field of grafting biology.
Structure of the RNA-dependent RNA polymerase from COVID-19 virus (2020)

A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase [(RdRp), also named nsp12] is the central component of coronaviral replication and transcription machinery, and it appears to be a primary target for the antiviral drug remdesivir. We report the cryo-electron microscopy structure of COVID-19 virus full-length nsp12 in complex with cofactors nsp7 and nsp8 at 2.9-angstrom resolution. In addition to the conserved architecture of the polymerase core of the viral polymerase family, nsp12 possesses a newly identified β-hairpin domain at its N terminus. A comparative analysis model shows how remdesivir binds to this polymerase. The structure provides a basis for the design of new antiviral therapeutics that target viral RdRp.