gebhart/patrepeval huggingface dataset:
Etch rates for micromachining processing (1996)

The etch rates for 317 combinations of 16 materials (single-crystal silicon, doped, and undoped polysilicon, several types of silicon dioxide, stoichiometric and silicon-rich silicon nitride, aluminum, tungsten, titanium, Ti/W alloy, and two brands of positive photoresist) used in the fabrication of microelectromechanical systems and integrated circuits in 28 wet, plasma, and plasmaless-gas-phase etches (several HF solutions, H/sub 3/PO/sub 4/, HNO/sub 3/+H/sub 2/O+NH/sub 4/F, KOH, Type A aluminum etchant, H/sub 2/O+H/sub 2/O/sub 2/+HF, H/sub 2/O/sub 2/, piranha, acetone, HF vapor, XeF/sub 2/, and various combinations of SF/sub 6/, CF/sub 4/, CHF/sub 3/, Cl/sub 2/, O/sub 2/, N/sub 2/, and He in plasmas) were measured and are tabulated. Etch preparation, use, and chemical reactions (from the technical literature) are given. Sample preparation and MEMS applications are described for the materials.
Dynamic Channel: A Planning Framework for Crowd Navigation (2019)

Real-time navigation in dense human environments is a challenging problem in robotics. Most existing path planners fail to account for the dynamics of pedestrians because introducing time as an additional dimension in search space is computationally prohibitive. Alternatively, most local motion planners only address imminent collision avoidance and fail to offer long-term optimality. In this work, we present an approach, called Dynamic Channels, to solve this global to local quandary. Our method combines the high-level topological path planning with low-level motion planning into a complete pipeline. By formulating the path planning problem as graph searching in the triangulation space, our planner is able to explicitly reason about the obstacle dynamics and capture the environmental change efficiently. We evaluate efficiency and performance of our approach on public pedestrian datasets and compare it to a state-of-the-art planning algorithm for dynamic obstacle avoidance.
Liver Stiffness Measured by Two-Dimensional Shear-Wave Elastography: Prognostic Value after Radiofrequency Ablation for Hepatocellular Carcinoma (2018)

LS values measured by 2D-SWE was a significant predictive factor for overall survival after RFA for HCC.
Analysis of PUGNAc and NAG-thiazoline as Transition State Analogues for Human O-GlcNAcase:  Mechanistic and Structural Insights into Inhibitor Selectivity and Transition State Poise (2006)

O-GlcNAcase catalyzes the cleavage of beta-O-linked 2-acetamido-2-deoxy-beta-d-glucopyranoside (O-GlcNAc) from serine and threonine residues of post-translationally modified proteins. Two potent inhibitors of this enzyme are O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc) and 1,2-dideoxy-2'-methyl-alpha-d-glucopyranoso[2,1-d]-Delta2'-thiazoline (NAG-thiazoline). Derivatives of these inhibitors differ in their selectivity for human O-GlcNAcase over the functionally related human lysosomal beta-hexosamindases, with PUGNAc derivatives showing modest selectivities and NAG-thiazoline derivatives showing high selectivities. The molecular basis for this difference in selectivities is addressed as is how well these inhibitors mimic the O-GlcNAcase-stabilized transition state (TS). Using a series of substrates, ground state (GS) inhibitors, and transition state mimics having analogous structural variations, we describe linear free energy relationships of log(KM/kcat) versus log(KI) for PUGNAc and NAG-thiazoline. These relationships suggest that PUGNAc is a poor transition state analogue, while NAG-thiazoline is revealed as a transition state mimic. Comparative X-ray crystallographic analyses of enzyme-inhibitor complexes reveal subtle molecular differences accounting for the differences in selectivities between these two inhibitors and illustrate key molecular interactions. Computational modeling of species along the reaction coordinate, as well as PUGNAc and NAG-thiazoline, provide insight into the features of NAG-thiazoline that resemble the transition state and reveal where PUGNAc fails to capture significant binding energy. These studies also point to late transition state poise for the O-GlcNAcase catalyzed reaction with significant nucleophilic participation and little involvement of the leaving group. The potency of NAG-thiazoline, its transition state mimicry, and its lack of traditional transition state-like design features suggest that potent rationally designed glycosidase inhibitors can be developed that exploit variation in transition state poise.
Molecular Characterization of Sporadic Pediatric Thyroid Carcinoma with the DNA/RNA ThyroSeq v2 Next-Generation Sequencing Assay (2015)

The aim of this study was to test the hypothesis that our 60-gene DNA/RNA ThyroSeq v2 next-generation sequence (NGS) assay would identify additional genetic markers, including gene fusions in sporadic pediatric differentiated thyroid carcinomas (DTC) that had no known molecular alterations. Sporadic pediatric DTCs with informative molecular testing (n=18) were studied. We previously tested 15 cases by our standard 7-gene (BRAF, NRAS, HRAS, KRAS, RET/PTC1, RET/PTC3, PAX8/PPARg) mutation panel. Three cases were not tested previously. The standard 7-gene panel identified molecular alterations in 9 of 15 tumors (60%). Cases analyzed by ThyroSeq v2 NGS included the six previously negative cases by the standard 7-gene panel and three cases not previously tested. The NGS assay revealed new gene fusions in four of six previously negative cases (67%). These gene fusions included ETV6/NTRK3 (n=3) and TPR/NTRK1 (n=1). A point mutation (BRAF-V600E) was detected in one of three untested cases. While standard testing could identify only molecular alterations in 60% of cases, with the addition of the ThyroSeq v2 NGS, this increased to 87% (n=13/15). Some cases with chromosomal rearrangements, including ETV6/NTRK3, appear to be associated with an aggressive histopathologic phenotype, but had no documented history of radiation exposure. Additional work is needed to investigate if pediatric DTCs could benefit from a reclassification based on molecular subtypes, which may better reflect their underlying biologic potential. Our data support the use of broad gene panels for the molecular diagnostics of pediatric thyroid nodules to aid future classification, treatment, and clinical management recommendations.
Phosphorylation by cAMP-dependent protein kinase inhibits the degradation of tau by calpain. (1992)

The effects of cAMP-dependent protein kinase (cAMP-PK) phosphorylation on the degradation of the microtubule-associated protein tau by calpain were studied. Purified bovine brain tau that had been phosphorylated by cAMP-PK had a slower migration pattern on sodium dodecyl sulfate-polyacrylamide gels and a more acidic, less heterogeneous pattern on two-dimensional, nonequilibrium pH gradient electrophoresis (NEPHGE) gels compared with untreated tau. Phosphorylation of tau by cAMP-PK significantly inhibited its proteolysis by calpain compared with untreated tau. To our knowledge this is the first demonstration that phosphorylation of tau by a specific kinase results in increased resistance to hydrolysis by calpain. Tau dephosphorylated by alkaline phosphatase migrated more rapidly on sodium dodecyl sulfate-polyacrylamide gels and also showed an altered two-dimensional NEPHGE pattern. Dephosphorylation of tau had no effect on its susceptibility to calpain proteolysis, indicating that regulation of the susceptibility to calpain hydrolysis is due to the phosphorylation of a specific site(s). These results suggest a role for phosphorylation in regulating the degradation of tau. Abnormal phosphorylation could result in a protease-resistant tau population which may contribute to the formation of paired helical filaments in Alzheimer's disease.
Pancreatitis and the Risk of Pancreatic Cancer (1993)

The risk of pancreatic cancer is significantly elevated in subjects with chronic pancreatitis and appears to be independent of sex, country, and type of pancreatitis.
Efficient Planning for High-Speed MAV Flight in Unknown Environments Using Online Sparse Topological Graphs (2020)

Safe high-speed autonomous navigation for MAVs in unknown environments requires fast planning to enable the robot to adapt and react quickly to incoming information about obstacles within the world. Furthermore, when operating in environments not known a priori, the robot may make decisions that lead to dead ends, necessitating global replanning through a map of the environment outside of a local planning grid. This work proposes a computationally-efficient planning architecture for safe high-speed operation in unknown environments that incorporates a notion of longer-term memory into the planner enabling the robot to accurately plan to locations no longer contained within a local map. A motion primitive-based local receding horizon planner that uses a probabilistic collision avoidance methodology enables the robot to generate safe plans at fast replan rates. To provide global guidance, a memory-efficient sparse topological graph is created online from a time history of the robot's path and a geometric notion of visibility within the environment to search for alternate pathways towards the desired goal if a dead end is encountered. The safety and performance of the proposed planning system is evaluated at speeds up to 10m/s, and the approach is tested in a set of large-scale, complex simulation environments containing dead ends. These scenarios lead to failure cases for competing methods; however, the proposed approach enables the robot to safely reroute and reach the desired goal.
Carbohydrate Dramatically Influences Immune Reactivity of Antisera to Viral Glycoprotein Antigens (1984)

Analysis of the ability of heteroantisera, monoclonal antibodies, and antibodies to synthetic peptides to react with viral glycoproteins deglycosylated with endoglycosidase F revealed that the reactivities of most of the antibodies to these glycoprotein antigens were influenced by the attached carbohydrate moieties. All heteroantisera prepared in rabbits or goats to either fully glycosylated retroviruses or influenza virus were virtually unreactive toward the viral glycoproteins after carbohydrate removal. Analyses with a panel of monoclonal antibodies to purified Rauscher murine leukemia virus gp70 indicated that the reactivity of most of these antibodies improved while the reactivity of others decreased or remain unchanged after carbohydrate removal. Most of the antibodies to synthetic peptide sequences in the influenza virus hemagglutinin also improved in reactivity after carbohydrate removal. These data indicate that carbohydrate side chains on viral glycoproteins influence the immune response to these antigens, and the more native the glycoprotein immunogen, the more dramatic the carbohydrate influence. Thus the immune response to these glycoproteins is not simply a function of the immunogenicity of certain domains over others but rather is a direct measure of carbohydrate influences on the host's perception of the foreign antigen.
The Raising of a Polyclonal Antiserum to a Protein (2003)

Suitable antisera are essential for use in all immunochemical procedures. Three important properties of an antiserum are avidity, specificity, and titer. The avidity of an antiserum is a measure of the strength of the interactions of its antibodies with an antigen. The specificity of an antiserum is a measure of the ability of its antibodies to distinguish the immunogen from related antigens. The titer of an antiserum is the final (optimal) dilution at which it is employed in the procedure; it depends on the concentrations of the antibodies present and on their affinities for the antigen. The values of those parameters required for a particular antiserum very much depend on the usage to which the antiserum will be put. For example, for use in radio-immunoassay, it is best to have a monospecific antiserum of high avidity, whereas for use in immunoaffinity chromatography, the monospecific antiserum should not possess too high an avidity. Otherwise it may prove impossible to elute the desired antigen without extensive denaturation.
A Mild Preparation of Amino Acid N-Acylsulfonamides (1995)

A mild preparation of acylsulfonamide amino acids has been devised which is an improvement over existing methods. In particular, γ-substituted glutamic acid acylsulfonamide derivatives have been prepared without the competitive formation of pyroglutamates.
deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution (2016)

deconstructSigs confers the ability to define mutational processes driven by environmental exposures, DNA repair abnormalities, and mutagenic processes in individual tumors with implications for precision cancer medicine.
The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA. (1994)

Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression.
Inhibition of Caspase-3-mediated Poly(ADP-ribose) Polymerase (PARP) Apoptotic Cleavage by Human PARP Autoantibodies and Effect on Cells Undergoing Apoptosis (2000)

Autoantibodies directed to nuclear antigens are serological hallmarks of autoimmune rheumatic diseases such as systemic lupus erythematosus. Although much more is known about the molecular identity and functions of targeted self-antigens, with few exceptions, evidence that autoantibodies to these targets have a particular function and contribute directly to the pathological process is lacking. Here we show that human autoantibodies reacting with the zinc fingers of poly(ADP-ribose) polymerase involved in the recognition of damaged DNA totally prevent the cleavage of poly(ADP-ribose) polymerase by caspase-3, a process that normally occurs during early apoptosis. Furthermore, these antibodies, which are frequent in certain autoimmune rheumatic and bowel diseases, affect the characteristic features of apoptosis and increase cell survival ex vivo. This new observation is important, because failure to remove autoimmune or abnormal cells can give rise to prolonged autoimmune stimulation and tumor formation.
Substrate Specificity of Cathepsins D and E Determined by N‐Terminal and C‐terminal Sequencing of Peptide Pools (1997)

Degradation of protein antigens by cellular proteases is a crucial step in the initiation of a T-cell-mediated immune response. But still little is known about the enzymes responsible for the processing of antigens, including their specificity. In this paper, we show that the combination of automated N-terminal sequencing with a newly developed method for C-terminal sequencing of peptide pools generated by the aspartic proteases cathepsins D and E is a fast and easy method to obtain detailed information of the substrate specificity of these endopeptidases. Using a 15-residue synthetic peptide library and a native protein as substrates, we confirm and extend the knowledge about the cleavage motif of cathepsin E where positions P1 and P1' of the substrate must be occupied exclusively by hydrophobic amino acids with aromatic or aliphatic side chains. However, Val and Ile residues are not allowed at position P1. Position P2' accepts a broad range of amino acids, including charged and polar ones. Additional requirements concerning the substrate positions P3' and P4' were also defined by pool sequencing. Furthermore, pool sequencing analysis of melittin digests with the aspartic proteases cathepsin D and E provided evidence that both enzymes share the same cleavage motif, identical to the one derived from the peptide library and the native protein. Therefore, pool sequencing analysis is a valuable and fast tool to determine the substrate specificity of any endopeptidase.
Anti-tumor effect of CT-322 as an Adnectin inhibitor of vascular endothelial growth factor receptor-2 (2010)

CT-322 is a new anti-angiogenic therapeutic agent based on an engineered variant of the tenth type III domain of human fibronectin, i.e., an Adnectin™, designed to inhibit vascular endothelial growth factor receptor (VEGFR)-2. This PE Gylated Adnectin was developed using an mRNA display technology. CT-322 bound human VEGFR-2 with high affinity (K(D), 11 nM), but did not bind VEGFR-1 or VEGFR-3 at concentrations up to 100 nM, as determined by surface plasmon resonance studies. Western blot analysis showed that CT-322 blocked VEGF-induced phosphorylation of VEGFR-2 and mitogen-activated protein kinase in human umbilical vascular endothelial cells. CT-322 significantly inhibited the growth of human tumor xenograft models of colon carcinoma and glioblastoma at doses of 15-60 mg/kg administered 3 times/week. Anti-tumor effects of CT-322 were comparable to those of sorafenib or sunitinib, which inhibit multiple kinases, in a colon carcinoma xenograft model, although CT-322 caused less overt adverse effects than the kinase inhibitors. CT-322 also enhanced the anti-tumor activity of the chemotherapeutic agent temsirolimus in the colon carcinoma model. The high affinity and specificity of CT-322 binding to VEGFR-2 and its anti-tumor activities establish CT-322 as a promising anti-angiogenic therapeutic agent. Our results further suggest that Adnectins are an important new class of targeted biologics that can be developed as potential treatments for a wide variety of diseases.
Adiponectin and adiponectin receptors in insulin resistance, diabetes, and the metabolic syndrome (2006)

Adiponectin is an adipokine that is specifically and abundantly expressed in adipose tissue and directly sensitizes the body to insulin. Hypoadiponectinemia, caused by interactions of genetic factors such as SNPs in the Adiponectin gene and environmental factors causing obesity, appears to play an important causal role in insulin resistance, type 2 diabetes, and the metabolic syndrome, which are linked to obesity. The adiponectin receptors, AdipoR1 and AdipoR2, which mediate the antidiabetic metabolic actions of adiponectin, have been cloned and are downregulated in obesity-linked insulin resistance. Upregulation of adiponectin is a partial cause of the insulin-sensitizing and antidiabetic actions of thiazolidinediones. Therefore, adiponectin and adiponectin receptors represent potential versatile therapeutic targets to combat obesity-linked diseases characterized by insulin resistance. This Review describes the pathophysiology of adiponectin and adiponectin receptors in insulin resistance, diabetes, and the metabolic syndrome.
Setting the Standards: Quality Control in the Secretory Pathway (1999)

A variety of quality control mechanisms operate in the endoplasmic reticulum and in downstream compartments of the secretory pathway to ensure the fidelity and regulation of protein expression during cell life and differentiation. As a rule, only proteins that pass a stringent selection process are transported to their target organelles and compartments. If proper maturation fails, the aberrant products are degraded. Quality control improves folding efficiency by retaining proteins in the special folding environment of the endoplasmic reticulum, and it prevents harmful effects that could be caused by the deployment of incompletely folded or assembled proteins.
[MnIII4LnIII4] Calix[4]arene Clusters as Enhanced Magnetic Coolers and Molecular Magnets (2010)

The use of methylene-bridged calix[4]arenes in 3d/4f chemistry produces a family of clusters of general formula [Mn(III)(4)Ln(III)(4)(OH)(4)(C4)(4)(NO(3))(2)(DMF)(6)(H(2)O)(6)](OH)(2) (where C4 = calix[4]arene; Ln = Gd (1), Tb (2), Dy (3)). The molecular structure describes a square of Ln(III) ions housed within a square of Mn(III) ions. Magnetic studies reveal that 1 has a large number of molecular spin states that are populated even at the lowest investigated temperatures, while the ferromagnetic limit S = 22 is being approached only at the highest applied fields. This, combined with the high magnetic isotropy, makes the complex an excellent magnetic refrigerant for low-temperature applications. Replacement of the isotropic Gd(III) ions with the anisotropic Tb(III) and Dy(III) ions "switches" the magnetic properties of the cluster so that 2 and 3 behave as low-temperature molecular magnets, displaying slow relaxation of the magnetization.
Non-Catalyzed C-Alkylation of Phenols With Cyclic Secondary Alkyl Bromides (1996)

Abstract C-Alkylations of phenol with 1-chloro and 1-bromoadamantane, 2-bromoadamantane, cyclohexyl bromide and exo-2-bromonorbornane, and C-alkylations of para-substituted phenol derivatives with 2-bromoadamantane are described.
Equip tourists with knowledge mined from travelogues (2010)

With the prosperity of tourism and Web 2.0 technologies, more and more people have willingness to share their travel experiences on the Web (e.g., weblogs, forums, or Web 2.0 communities). These so-called travelogues contain rich information, particularly including location-representative knowledge such as attractions (e.g., Golden Gate Bridge), styles (e.g., beach, history), and activities (e.g., diving, surfing). The location-representative information in travelogues can greatly facilitate other tourists' trip planning, if it can be correctly extracted and summarized. However, since most travelogues are unstructured and contain much noise, it is difficult for common users to utilize such knowledge effectively. In this paper, to mine location-representative knowledge from a large collection of travelogues, we propose a probabilistic topic model, named as Location-Topic model. This model has the advantages of (1) differentiability between two kinds of topics, i.e., local topics which characterize locations and global topics which represent other common themes shared by various locations, and (2) representation of locations in the local topic space to encode both location-representative knowledge and similarities between locations. Some novel applications are developed based on the proposed model, including (1) destination recommendation for on flexible queries, (2) characteristic summarization for a given destination with representative tags and snippets, and (3) identification of informative parts of a travelogue and enriching such highlights with related images. Based on a large collection of travelogues, the proposed framework is evaluated using both objective and subjective evaluation methods and shows promising results.