gebhart/patrepeval huggingface dataset:
Fast time-of-flight camera based surface registration for radiotherapy patient positioning (2011)

The proposed solution is able to solve surface registration problems with an accuracy suitable for radiotherapy cases where external surfaces offer primary or complementary information to patient positioning. The system shows promising dynamic properties for its use in gating/tracking applications. The overall system is competitive with commonly-used surface registration technologies. Its main benefit is the usage of a cost-effective off-the-shelf technology for surface acquisition. Further strategies to improve the registration accuracy are under development.
USe of PCR primers containing a 3' terminal ribose residuce to prevent cross-contamination of amplified sequences (1993)

Cross-contamination with previously amplified products poses a serious limitation in the use of PCR for clinical testing and in certain research applications as well. In the present study we report the use of novel primers containing a 3'-terminal ribose residue to circumvent this problem. Extension of the primer by Taq DNA polymerase generates a cleavable ribonucleotide linkage within the amplified product. Cleavage of the primer by base or with a ribonuclease interferes with further replication of the product should carry over to another sample occur. Primers terminating in any of the 4 ribose residues function equally well as all DNA primers. Taq DNA polymerase is thus able to both efficiently extend and copy the single ribose residue. In translating from all DNA primers to ones containing a 3'-ribose residue no modification of the PCR protocol is required. The products formed can be used in all applications of the PCR. Since neither the original sample DNA, the primers or the extension products are modified by base or ribonuclease treatment both pre- and post-amplification sterilization can be carried out. Pre-amplification treatment with RNase A can yield as high as 10(4)-fold sterilization. Under these conditions the addition of beta-mercaptoethanol or other sulfhydryl reducing agent is necessary to inactivate the enzyme during thermocycling. Post-amplification treatment with NaOH readily yields at least 10(6)-fold sterilization. This alone is sufficient for most, if not all, applications of PCR. It is especially useful for quantitative RT-PCR, since the original target RNA sequence, which may be present in high copy numbers, is also destroyed.
Treatment Patterns and Clinical Outcomes in Patients With Metastatic Colorectal Cancer Initially Treated with FOLFOX–Bevacizumab or FOLFIRI–Bevacizumab: Results From ARIES, a Bevacizumab Observational Cohort Study (2012)

In first-line mCRC patients, the FOLFOX-bevacizumab and FOLFIRI-bevacizumab regimens were associated with similar treatment patterns and clinical outcomes.
Human platelet aggregation by murine monoclonal antiplatelet antibodies is subtype-dependent (1993)

Twenty murine monoclonal antibodies (MoAbs) generated against different human platelet antigens induced clumping of human platelets in plasma and buffer. Whereas one MoAb could agglutinate platelets, clumping for 19 MoAbs was blocked by metabolic inhibitors, indicating that these induce platelet activation. Fifteen MoAbs were of IgG1, two of IgG2a, and two of IgG2b subtype. F(ab')2 fragments of these did not evoke an aggregatory response, but specifically inhibited aggregations by and binding of their respective intact MoAbs to platelets. Single-platelet counting technology indicated that the MoAbs bind through their antigen- binding and Fc domains mainly to the surface of the same platelet, rather than cause interplatelet-binding. Despite these similarities, the mechanism of action was nevertheless subtype-dependent. Aggregation induced by all IgG1 antibodies could consistently be prevented by blocking the Fc gamma II-receptor, whereas aggregations induced by all IgG2 antibodies still occurred with blocked Fc-receptor, provided functional complement was present. We therefore conclude that platelet activation by MoAb-binding is initiated by antigen recognition followed by an Fc domain-dependent step, which involves the Fc gamma II-receptor for IgG1-type MoAbs and complement-binding for IgG2-type MoAbs. Thus, antibodies of different subtypes can aggregate platelets via different pathways.
Optimal camera placement for total coverage (2009)

In this document, we study the problem of optimally placing a mixture of directional and omnidirectional cameras. In our solution, the workspace is represented by an occupancy grid map [1]. Then, using surface-projected workspace and camera perception models, we develop a binary integer programming algorithm. The results of the algorithm are applied successfully to a variety of simulated scenarios.
Genetic Encoding of Bicyclononynes and trans-Cyclooctenes for Site-Specific Protein Labeling in Vitro and in Live Mammalian Cells via Rapid Fluorogenic Diels–Alder Reactions (2012)

Rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists. Enzyme-mediated labeling approaches may be rapid but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many "bioorthogonal" reactions for which a component can be genetically encoded are too slow to effect quantitative site-specific labeling of proteins on a time scale that is useful for studying many biological processes. We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines that is 3-7 orders of magnitude faster than many bioorthogonal reactions. Unlike the reactions of strained alkenes, including trans-cyclooctenes and norbornenes, with tetrazines, the BCN-tetrazine reaction gives a single product of defined stereochemistry. We have discovered aminoacyl-tRNA synthetase/tRNA pairs for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli , and in live mammalian cells. These approaches may be extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on labeling and imaging studies.
Proteins associated with the promyelocytic leukemia gene product (PML)-containing nuclear body move to the nucleolus upon inhibition of proteasome-dependent protein degradation (2001)

Several recent findings have indicated that the promyelocytic leukemia gene product (PML) oncogenic domains (PODs) are involved in proteasome-mediated degradation of ubiquitinated proteins. We wanted to examine the intracellular distribution of PML protein in the presence of a proteasome inhibitor. We used high-resolution microscopy to study the distribution of PML protein and other POD-associated proteins along with the proteasomes themselves under normal conditions and in cells treated with the proteasome inhibitor, MG132. Inhibition of the proteasomes in MCF-7, HeLa, and IB-4 cell lines resulted in a radical redistribution of the POD-associated proteins PML, Sp100, and SUMO-1. After 6-10 h of MG132 treatment, PML, Sp100, and SUMO-1 were no longer detectable in the PODs and accumulated mainly in the nucleolus. Moreover, MG132 treatment changed the cellular distribution of the proteasomes. Interestingly, this included the accumulation in euchromatin areas of the nucleus and within the nucleoli. Several non-POD-associated proteins did not change their cellular distribution under the same conditions. The accumulation of POD-associated proteins and proteasomes in the nucleoli of MG132-treated cells indicates that these proteins may target the nucleoli under normal conditions and that the nucleolus may have a function in the regulation of proteasomal protein degradation.
Enhanced CO2 Separation Selectivity in Oligo(ethylene glycol) Functionalized Room-Temperature Ionic Liquids (2007)

Novel imidazolium-based room-temperature ionic liquids (RTILs) with one, two, or three oligo(ethylene glycol) substituents were synthesized. Solubilities and ideal solubility selectivities of CO2, N2, and CH4 at low pressure (1 atm) in these RTILs were determined using a pressure decay technique. Comparison to corresponding alkyl analogues of these RTILs reveals similar levels of CO2 solubility but lower solubilities of N2 and CH4. As a consequence, RTILs with oligo(ethylene glycol) substituents were observed to have 30−75% higher ideal solubility selectivities for CO2/N2 and CO2/CH4.
Novel Inhibitors of Human Histone Deacetylases:  Design, Synthesis, Enzyme Inhibition, and Cancer Cell Growth Inhibition of SAHA-Based Non-hydroxamates (2005)

To find novel non-hydroxamate histone deacetylase (HDAC) inhibitors, a series of compounds modeled after suberoylanilide hydroxamic acid (SAHA) was designed and synthesized. In this series, compound 7, in which the hydroxamic acid of SAHA is replaced by a thiol, was found to be as potent as SAHA, and optimization of this series led to the identification of HDAC inhibitors more potent than SAHA. In cancer cell growth inhibition assay, S-isobutyryl derivative 51 showed strong activity, and its potency was comparable to that of SAHA. The cancer cell growth inhibitory activity was verified to be the result of histone hyperacetylation and subsequent induction of p21(WAF1/CIP1) by Western blot analysis. Kinetical enzyme assay and molecular modeling suggest the thiol formed by enzymatic hydrolysis within the cell interacts with the zinc ion in the active site of HDACs.
Chondroitinase ABC promotes axonal regeneration of Clarkeʼs neurons after spinal cord injury (2000)

We examined whether enzymatic digestion of chondroitin sulfate (CS) promoted the axonal regeneration of neurons in Clarke's nucleus (CN) into a peripheral nerve (PN) graft following injury of the spinal cord. After hemisection at T11, a segment of PN graft was implanted at the lesion site. Either vehicle, brain-derived neurotrophic factor (BDNF) or chondroitinase ABC was applied at the implantation site. The postoperative survival period was 4 weeks. Treatment with vehicle or BDNF did not promote the axonal regeneration of CN neurons into the PN graft. Application of 2.5 unit/ml chondroitinase ABC resulted in a significant increase (12.8%) in the number of regenerated CN neurons. Double labeling with Fluoro-Gold and NADPH-diaphorase histochemistry showed that the regenerated CN neurons did not express nitric oxide synthase (NOS). Our results suggest that CS is inhibitory to the regeneration of CN neurons following injury of the spinal cord.
Protein targeting and secretion (1992)

Part 1 General principles: subcellular principles targeting sequences and patches cytoplasmic synthesis of proteins the pathways that proteins take through cells ways of identifying targeting sequences evolutionary relationships in targeting the role of targeting sequences in protein folding the role of chaperone proteins. Part 2 Bacterial protein translocation: experimental approaches for determining protein localization the structure of prokaryotic signal peptides the membrane trigger hypothesis and M13 coat protein components of the export machinery translocation from the inner to the outer membrane the novel secretion of haemolysin from Escherichia coli. Part 3 Protein translocation at the rough endoplasmic reticulum: historical background the use of in vitro systems for studying protein translocation structure and function of signal peptides proteins involved in eukaryotic translocation endoplasmic reticulum of yeast. Part 4 Assembly of membrane proteins: mode of attachment of proteins to membranes topography of integral membrane proteins mechanisms of assembly hydrophobic modifications of proteins. Part 5 Protein sorting and motivation: regulated and bulk flow export form the endoplasmic reticulum glycosylation budding and fusion of transport vesicles sorting at the trans-Golgi network endocytosis sorting in polarized cells alternative pathways of secretion. Part 6 Import of proteins from the cytosol: mitochondria chloroplasts peroxisomes the nucleus.
Spontaneous Formation of Bonelike Apatite Layer on Chemically Treated Titanium Metals (1996)

Generally, artificial materials implanted into bone defects are encapsulated by a fibrous tissue isolating them from the surrounding bone. Only limited kinds of ceramics are known to bond to living bone without forming the fibrous tissue, and already they are being used clinically as important artificial bones. However, they cannot be used under highly loaded conditions, since their fracture toughnesses are not so high as that of human cortical bone. The present study shows that even pure titanium metal and its alloys can bond to living bone, if their surfaces are pre‐treated with alkali hydroxide solutions. Thus‐treated metals are believed to be useful as artificial bones even under highly loaded conditions because of their high bone‐bonding ability as well as high fracture toughness.
Large-area low-noise seven-channel dc SQUID magnetometer for brain research (1987)

The design, construction, and performance of a new high-sensitivity dc SQUID magnetometer, covering a circular area of 93-mm diameter, is described. The device, now used routinely in our brain research, comprises seven asymmetric first-order gradiometers, located on a spherical surface of 125-mm radius and with the symmetry axis tilted 30° with respect to the vertical. The pickup coil diameter is 20 mm, and the channels are separated by 36.5 mm from each other in a hexagonal array. The overall field sensitivity of the system, measured inside our magnetically shielded room, is 5 fT/(Hz)1/2, mainly limited by the thermal noise in the radiation shields of the Dewar. The optimization of the coil configuration and the measurement system is discussed in detail, and a system to determine automatically the position and orientation of the Dewar with respect to certain fixed points on the subject’s head is described. Finally, some examples of measurements carried out with the new device are given.
Conserved Structural and Sequence Elements Implicated in the Processing of Gene-encoded Circular Proteins (2004)

The cyclotides are the largest family of naturally occurring circular proteins. The mechanism by which the termini of these gene-encoded proteins are linked seamlessly with a peptide bond to form a circular backbone is unknown. Here we report cyclotide-encoding cDNA sequences from the plant Viola odorata and compare them with those from an evolutionarily distinct species, Oldenlandia affinis. Individual members of this multigene family encode one to three mature cyclotide domains. These domains are preceded by N-terminal repeat regions (NTRs) that are conserved within a plant species but not between species. We have structurally characterized peptides corresponding to these NTRs and show that, despite them having no sequence homology, they form a structurally conserved alpha-helical motif. This structural conservation suggests a vital role for the NTR in the in vivo folding, processing, or detoxification of cyclotide domains from the precursor protein.
Pedestrian detection for driving assistance systems: single-frame classification and system level performance (2004)

We describe the functional and architectural breakdown of a monocular pedestrian detection system. We describe in detail our approach for single-frame classification based on a novel scheme of breaking down the class variability by repeatedly training a set of relatively simple classifiers on clusters of the training set. Single-frame classification performance results and system level performance figures for daytime conditions are presented with a discussion about the remaining gap to meet a daytime normal weather condition production system.
Necrotic and apoptotic myocyte cell death in the aging heart of Fischer 344 rats (1996)

To determine the effects of aging on myocyte cell death, Fischer 344 rats at 3, 7, 12, 16, and 24 mo of age were injected with myosin monoclonal antibody for the localization and quantification of necrotic myocyte cell death in the left ventricle, interventricular septum, and right ventricle. Conversely, the presence of DNA strand breaks in myocyte nuclei, indicative of programmed cell death, was evaluated by the terminal deoxynucleotidyl transferase assay and confirmed by DNA laddering. Myocyte necrosis, which involved nearly 1,000 myocytes in the left ventricular free wall at 3 mo, progressively increased with aging, reaching a value of 13,600 myocytes at 24 mo. Corre- sponding values in the interventricular septum were 300 and 9,400 myocytes. In the right ventricle, there were 270 necrotic myocytes at 3 mo and 9,000 at 24 mo. Programmed myocyte cell death was restricted to the left ventricular free wall and included 140 cells at 3 mo. This form of myocyte cell death increased at the subsequent age intervals, resulting in the involvement of 874 cells at 24 mo. The combination of necrosis and apoptosis in the left ventricular free wall was associated with 1,150 cells dying at 3 mo and 14,500 at 24 mo. In conclusion, myocyte cell death, apoptotic and necrotic in nature, constitutes an important determinant of the aging process, possibly mediating the occurrence of ventricular dysfunction and failure in the old heart.
The Codebreakers: The Story of Secret Writing (1968)

CONTENTS Preface to the Revised Edition Preface A Few Words 1. One Day of Magic THE PAGENT OF CRYPTOLOGY 2. The First 3,000 Years 3. The Rise of the West 4. On the Origin of a Species 5. The Era of the Black Chambers 6. The Contribution of the Dilettantes 7. Crises of the Union 8. The Professor, the Soldier, and the Man on Devil's Island 9. Room 40 10. A War of Intercepts: I 11. A War of Intercepts: II 12. Two Americans 13. Secrecy for Sale 14. Duel in the Ether: The Axis 15. Duel in the Ether: Neutrals and Allies 16. Censors, Scramblers, and Spies 17. The Scrutable Orientals 18. Russkaya Kriptologiya (Russian Cryptology) 19. N.S.A. SIDESHOWS 20. The Anatomy of Cryptology 21. Heterogeneous Impulses 22. Rumrunners, Businessmen, and Makers of Non-secret Codes 23. Ciphers in the Past Tense 24. The Pathology of Cryptology PARACRYPTOLOGY 25. Ancestral Voices 26. Messages from Outer Space THE NEW CRYPTOLOGY 27. Cryptology Goes Public Bibliography Notes to Text Acknowledgments Notes to Illustrations Index
Transmembrane signals generated through MHC class II, CD19, CD20, CD39, and CD40 antigens induce LFA-1-dependent and independent adhesion in human B cells through a tyrosine kinase-dependent pathway (1991)

Transmembrane signals generated following mAb binding to CD19, CD20, CD39, CD40, CD43, Leu-13 Ag, and HLA-D region gene products induced rapid and strong homotypic adhesion in a panel of human B cell lines. Lower levels of adhesion were also observed after engagement of CD21, CD22, and CD23. Adhesion induced by mAb binding to these Ag was identical with respect to the kinetics of adhesion and the morphology of the resulting cellular aggregates, and was distinct from PMA-induced adhesion in both of these properties. Adhesion was not observed in response to mAb binding to MHC class I, CD24, CD38, CD44, CD45RA, or CD72. In contrast to B cell lines, homotypic adhesion was not induced in two pre-B cell lines, in spite of their high level expression of CD19 and HLA-D. Adhesion induced by suboptimal stimulation through these surface Ag or by PMA was mediated primarily through LFA-1 and ICAM-1. However, optimal stimulation through CD19, CD20, CD39, CD40, and HLA-D induced strong homotypic adhesion that was not blocked by anti-LFA-1 mAb. This alternate pathway of adhesion was also observed in LFA-1-deficient cell lines and in the presence of EDTA, suggesting that adhesion was not mediated by integrins. Adhesion in response to engagement of cell-surface Ag was unaffected by H7 or genestein, but was significantly inhibited by staurosporine, and was completely ablated by sphingosine and herbimycin. These studies indicate that engagement of multiple B cell-surface molecules initiates a signal transduction cascade that involves tyrosine kinases but not protein kinase C, and which leads to homotypic adhesion. Furthermore, adhesion was mediated by at least two distinct cell-surface adhesion receptors: LFA-1/ICAM-1 and a heretofore unknown adhesion receptor.
Reverse genetics system for generation of an influenza A virus mutant containing a deletion of the carboxyl-terminal residue of M2 protein (1995)

We established a reverse genetics system for the M gene of influenza A virus, using amantadine resistance as a selection criterion. Transfection of an artificial M ribonucleoprotein complex of A/Puerto Rico/8/34 (H1N1), a naturally occurring amantadine-resistant virus, and superinfection with amantadine-sensitive A/equine/Miami/1/63 (H3N8), followed by cultivation in the presence of the drug, led to the generation of a transfectant virus with the A/Puerto Rico/8/34 (H1N1) M gene. With this system, we attempted to generate a virus containing a deletion in an M-gene product (M2 protein). Viruses lacking the carboxyl-terminal Glu of M2, but not those lacking 5 or 10 carboxyl-terminal residues, were rescued in the presence of amantadine. These findings indicate that carboxyl-terminal residues of the M2 protein play an important role in influenza virus replication. The M-gene-based reverse genetics system will allow the study of different M-gene mutations to achieve a balance between attenuation and virus replication, thus facilitating the production of live vaccine strains.
Screen for mutations affecting development of zebrafish neural crest (1996)

The neural crest provides a useful model to learn how cell fate diversification is regulated during vertebrate development. Our approach is to isolate zebrafish mutations in which the development of neural crest derivatives is disrupted, in order to learn about the underlying genetic mechanisms. We describe a screen in which parthenogenetic diploid embryos are examined both for visible phenotypes and for cellular defects in neural crest-derived sensory neurons recognized immunohistochemically. We present preliminary results from this screen and briefly describe a few representative mutations. We also discuss the general utility of our strategy and comment on the future directions of this approach.
A Rapid Esterification by Means of Mixed Anhydride and Its Application to Large-ring Lactonization (1979)

Abstract A rapid and mild esterification method using carboxylic 2,4,6-trichlorobenzoic anhydrides in the presence of 4-dimethylaminopyridine was developed. The method was also successfully applied to the synthesis of large-ring lactones, including Dl-2,4,6-tridemethyl-3-deoxymethynolide.
Germ cell specification in mice: signaling, transcription regulation, and epigenetic consequences (2010)

Abstract The specification of germ cell fate in development initiates mechanisms essential for the perpetuation of genetic information across the generations. Recent studies in mice have shown that germ cell specification requires at least three key molecular/cellular events: repression of the somatic program, re-acquisition of potential pluripotency, and an ensuing genome-wide epigenetic reprogramming. Moreover, a signaling and transcriptional principle governing these processes has been identified, raising the possibility of inducing the germ cell fate precisely from pluripotent stem cells in culture. These advances will in turn serve as a basis to explore the mechanism of germ cell specification in other mammals, including humans. The recapitulation of germ cell development in humans in culture will provide unprecedented opportunities to understand the basis of the propagation of our genome, both under normal and diseased conditions.