gebhart/patrepeval huggingface dataset:
Contribution to "AIAA Aerospace Year in Review" article (2012)

The NASA Marshall Space Flight Center Microgravity Science Program is dedicated to promoting our understanding of materials processing by conducting relevant experiments in the microgravity environment and supporting related modeling efforts with the intent of improving ground-based practices. Currently funded investigations include research on dopant distribution and defect formation in semiconductors, microstructural development and transitions in dendritic casting alloys, coarsening phenomena, competition between thermal and kinetic phase formation, and the formation of glassy vs. crystalline material. NASA Microgravity Materials Science Principle Investigators are selected for funding either through a proposal in response to a NASA Research Announcement or by collaborating on a team that has successfully proposed to a foreign space agency research announcement. In the latter case, a US investigator can then apply to NASA for funding through an unsolicited proposal. The International Space Station (ISS) facilities used for the experimental investigations are provided primarily by partnering with foreign agencies and often US investigators are working as a part of a larger team studying a specific area of materials science. Facilities for conducting experiments aboard the ISS include the European Space Agency (ESA) Low Gradient Facility (LGF) and the Solidification and Quench (SQF) modular inserts to the Materials Research Rack/Materials Science Laboratory and are primarily used for controlled solidification studies. The French Space Agency (CNES) provided DECLIC facility allows direct observation of morphological development in transparent materials that solidify analogously to metals. The ESA provided Electro ]Magnetic Levitator (EML) is designed to levitate, melt and then cool samples in order to determine material properties, study nucleation behavior, and document phase transitions. Finally, the Microgravity Science Glovebox (MSG) serves as a onboard facility for supporting the hardware required to conduct a number of smaller, short-term investigations.
A Hybrid Spatio-Temporal Data Indexing Method for Trajectory Databases (2014)

In recent years, there has been tremendous growth in the field of indoor and outdoor positioning sensors continuously producing huge volumes of trajectory data that has been used in many fields such as location-based services or location intelligence. Trajectory data is massively increased and semantically complicated, which poses a great challenge on spatio-temporal data indexing. This paper proposes a spatio-temporal data indexing method, named HBSTR-tree, which is a hybrid index structure comprising spatio-temporal R-tree, B*-tree and Hash table. To improve the index generation efficiency, rather than directly inserting trajectory points, we group consecutive trajectory points as nodes according to their spatio-temporal semantics and then insert them into spatio-temporal R-tree as leaf nodes. Hash table is used to manage the latest leaf nodes to reduce the frequency of insertion. A new spatio-temporal interval criterion and a new node-choosing sub-algorithm are also proposed to optimize spatio-temporal R-tree structures. In addition, a B*-tree sub-index of leaf nodes is built to query the trajectories of targeted objects efficiently. Furthermore, a database storage scheme based on a NoSQL-type DBMS is also proposed for the purpose of cloud storage. Experimental results prove that HBSTR-tree outperforms TB*-tree in some aspects such as generation efficiency, query performance and query type.
Chordin forms a self-organizing morphogen gradient in the extracellular space between ectoderm and mesoderm in the Xenopus embryo (2013)

The vertebrate body plan follows stereotypical dorsal-ventral (D-V) tissue differentiation controlled by bone morphogenetic proteins (BMPs) and secreted BMP antagonists, such as Chordin. The three germ layers--ectoderm, mesoderm, and endoderm--are affected coordinately by the Chordin-BMP morphogen system. However, extracellular morphogen gradients of endogenous proteins have not been directly visualized in vertebrate embryos to date. In this study, we improved immunolocalization methods in Xenopus embryos and analyzed the distribution of endogenous Chordin using a specific antibody. Chordin protein secreted by the dorsal Spemann organizer was found to diffuse along a narrow region that separates the ectoderm from the anterior endoderm and mesoderm. This Fibronectin-rich extracellular matrix is called "Brachet's cleft" in the Xenopus gastrula and is present in all vertebrate embryos. Chordin protein formed a smooth gradient that encircled the embryo, reaching the ventral-most Brachet cleft. Depletion with morpholino oligos showed that this extracellular gradient was regulated by the Chordin protease Tolloid and its inhibitor Sizzled. The Chordin gradient, as well as the BMP signaling gradient, was self-regulating and, importantly, was able to rescale in dorsal half-embryos. Transplantation of Spemann organizer tissue showed that Chordin diffused over long distances along this signaling highway between the ectoderm and mesoderm. Chordin protein must reach very high concentrations in this narrow region. We suggest that as ectoderm and mesoderm undergo morphogenetic movements during gastrulation, cells in both germ layers read their positional information coordinately from a single morphogen gradient located in Brachet's cleft.
Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation (2020)

Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)<sub>2</sub>, (αβ)<sub>3</sub>, and (αβ)<sub>4</sub>] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.
Automatic layout based verification of electrostatic discharge paths (2001)

This work describes an ESD path verification methodology based on layout parasitic extraction. This approach was implemented in Cadence DFII. It provides information about the preferred ESD path between two pads and estimates the peak pad to pad voltage. The path can also be overlaid on the layout view. The methodology was applied to a 0.5 um BiCMOS design to improve its ESD robustness. In that case, weak ESD paths overlooked during conventional design reviews were identified and corrected. The ESD robustness improved from 1.0 kV to 2.5 kV and 100 V to 250 V for HBM and MM respectively.
Association Between Success Rate and Citation Count of Studies of Radiofrequency Catheter Ablation for Atrial Fibrillation (2014)

Among studies of radiofrequency catheter ablation of atrial fibrillation, high success rate was independently associated with citation count, which may indicate citation bias. To readers of the literature, radiofrequency catheter ablation of atrial fibrillation could be perceived to be more effective than the data supports. These findings may have implications for a wide variety of novel cardiovascular therapies.
3-D Object Map Building Using Dense Object Models with SIFT-based Recognition Features (2006)

This paper presents a method of object map building using object models created from image sequences captured by a single camera. Object map is a highly structured map, which is built by placing 3-D object models on the floor plane according to object recognition results. To increase the efficiency of object map building, we propose a framework to integrate dense shape and recognition features into an object model. Experimental results show that an object map of a room was built successfully using the proposed object models
Cerebral Structure on Magnetic Resonance Imaging in Language- and Learning-Impaired Children (1991)

Using magnetic resonance imaging 20 language- and learning-impaired children were compared with 12 normal control subjects. Gross brain structure was remarkably normal in the language- and learning-impaired group. Semiautomated morphometry was used to measure hemispheric volumes and cerebral asymmetries in six cerebral regions. The volume of the left posterior perisylvian region was significantly reduced in language- and learning-impaired children. Asymmetries in inferoanterior and superoposterior cerebral regions were also significantly different in this group. Results of descriptive group comparisons of estimated volumes of other cerebral gray-matter structures raise the possibility that some language- and learning-impaired children may have additional volume reductions in cortical and subcortical structures. The results suggest that hemispheric specialization of function may be anomalous in this population.
Large bandwidth aperture-coupled microstrip antenna (1990)

The feasibility of printed antennas which meet all the criteria for satellite communications antennas is considered. These criteria are a bandwidth greater than 20% for a VSWR of less than 1.5, crosspolar level lower than −30 dB over 20° solid angle, and gain better than 8 dB throughout the bandwidth.
Microbial Proline 4-Hydroxylase Screening and Gene Cloning (1999)

Microbial proline 4-hydroxylases, which hydroxylate free L-proline to trans-4-hydroxy-L-proline, were screened in order to establish an industrial system for biotransformation of L-proline to trans-4-hydroxy-L-proline. Enzyme activities were detected in eight strains, including strains of Dactylosporangium spp. and Amycolatopsis spp. The Dactylosporangium sp. strain RH1 enzyme was partially purified 3,300-fold and was estimated to be a monomer polypeptide with an apparent molecular mass of 31 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Degenerate primers based on the N-terminal amino acid sequence of the 31-kDa polypeptide were synthesized in order to amplify the corresponding 71-bp DNA fragment. A 5.5-kbp DNA fragment was isolated by using the 71-bp fragment labeled with digoxigenin as a probe for a genomic library of Dactylosporangium sp. strain RH1 constructed in Escherichia coli. One of the open reading frames found in the cloned DNA, which encoded a 272-amino-acid polypeptide (molecular mass, 29, 715 daltons), was thought to be a proline 4-hydroxylase gene. The gene was expressed in E. coli as a fused protein with the N-terminal 34 amino acids of the beta-galactosidase alpha-fragment. The E. coli recombinant exhibited proline 4-hydroxylase activity that was 13. 6-fold higher than the activity in the original strain, Dactylosporangium sp. strain RH1. No homology was detected with other 2-oxoglutarate-dependent dioxygenases when databases were searched; however, the histidine motif conserved in 2-oxoglutarate-dependent dioxygenases was found in the gene.
Comprehensive Life-Cycle Cost Analysis for Selection of Stabilization Alternatives for Better Performance of Low-Volume Roads (2011)

Low-volume roads (LVRs), such as rural, farm-to-market, and less-used local and city roads, are an important part of the world's transportation infrastructure. LVRs have been credited as a direct cause of the socioeconomic development of rural communities. It has been estimated that 60% of the road network in the United States is made up of low-volume roads. The construction, maintenance, and rehabilitation of these roads are major tasks that result in about 54% of the total annual expenditure of transportation agencies in the United States. Better design and construction methods will lead to lower maintenance and rehabilitation costs of LVRs. Stabilization of weak subgrade soils to support LVRs is a widely accepted method of improving their performance. However, the selection of a stabilization alternative on the basis of cost–benefit analysis is a crucial task for a transportation agency and one that has not been addressed in a systematic manner. In this paper, a new conceptual engineering economics tool–based life-cycle cost analysis (LCCA) is developed to optimize and to select the best stabilizer and the stabilization technique for a given subgrade soil and given traffic conditions. In this analysis, agency, user, and externality costs are addressed. Two case studies are analyzed for European and U.S. road conditions to validate the LCCA model. Results demonstrate that, under specific boundary conditions, soil stabilization can play an important role, merging the environmental and mechanical effectiveness of low-volume roads.
Persistent SARS-CoV-2 infection and increasing viral variants in children and young adults with impaired humoral immunity (2021)

The work was partially funded by The Saban Research Institute at Children's Hospital Los Angeles intramural support for COVID-19 Directed Research (X.G. and J.D.B.), the Johns Hopkins Center of Excellence in Influenza Research and Surveillance HHSN272201400007C (A.P.), NIH/NIAID R01AI127877 (S.D.B.), NIH/NIAID R01AI130398 (S.D.B.), NIH 1U54CA260517 (S.D.B.), an endowment to S.D.B. from the Crown Family Foundation, an Early Postdoc.Mobility Fellowship Stipend to O.F.W. from the Swiss National Science Foundation (SNSF), and a Coulter COVID-19 Rapid Response Award to S.D.B. L.G. is a SHARE Research Fellow in Pediatric Hematology-Oncology.
Optical Rotation Study on Solvent Dependence of Diastereomeric Salt Discrimination Properties (2006)

Abstract The optical rotation properties have been studied for two diastereomeric salts of four kinds of amine–carboxylic acid salt systems, and the results have been compared among them and their chiral salts. The diastereomeric salts of 2-(4-methylphenyl)-1-phenylethylamine/mandelic acid (1-phenyl-2-(4-methylphenyl)ethylamine; PTE/MA) and α-amino-ε-caprolactam/N-tosylphenylalanine (ACL/TPA) exhibited relatively large differences in optical rotation values and solvent dependency. In contrast, the diastereomeric salts of α-methylbenzylamine/MA and piperazine-2-carboxylic acid t-butylamide/TPA possessed similar optical rotation behavior; the values and solvent dependency were almost identical. These results were discussed in relation to the dielectrically controlled resolution phenomenon for the formers, PTE/MA and ACL/TPA, and were also compared with the crystal structures.
Evaluating Behavioral Biometrics for Continuous Authentication (2017)

In recent years, behavioral biometrics have become a popular approach to support continuous authentication systems. Most generally, a continuous authentication system can make two types of errors: false rejects and false accepts. Based on this, the most commonly reported metrics to evaluate systems are the False Reject Rate (FRR) and False Accept Rate (FAR). However, most papers only report the mean of these measures with little attention paid to their distribution. This is problematic as systematic errors allow attackers to perpetually escape detection while random errors are less severe. Using 16 biometric datasets we show that these systematic errors are very common in the wild. We show that some biometrics (such as eye movements) are particularly prone to systematic errors, while others (such as touchscreen inputs) show more even error distributions. Our results also show that the inclusion of some distinctive features lowers average error rates but significantly increases the prevalence of systematic errors. As such, blind optimization of the mean EER (through feature engineering or selection) can sometimes lead to lower security. Following this result we propose the Gini Coefficient (GC) as an additional metric to accurately capture different error distributions. We demonstrate the usefulness of this measure both to compare different systems and to guide researchers during feature selection. In addition to the selection of features and classifiers, some non- functional machine learning methodologies also affect error rates. The most notable examples of this are the selection of training data and the attacker model used to develop the negative class. 13 out of the 25 papers we analyzed either include imposter data in the negative class or randomly sample training data from the entire dataset, with a further 6 not giving any information on the methodology used. Using real-world data we show that both of these decisions lead to significant underestimation of error rates by 63% and 81%, respectively. This is an alarming result, as it suggests that researchers are either unaware of the magnitude of these effects or might even be purposefully attempting to over-optimize their EER without actually improving the system.
PAX7 expression in embryonal rhabdomyosarcoma suggests an origin in muscle satellite cells (2003)

Rhabdomyosarcoma (RMS) is a common paediatric soft tissue sarcoma that resembles developing foetal skeletal muscle. Tumours of the alveolar subtype frequently harbour one of two characteristic translocations that juxtapose PAX3 or PAX7, and the forkhead-related gene FKHR (FOXO1A). The embryonal subtype of RMS is not generally associated with these fusion genes. Here, we have quantified the relative levels of chimaeric and wild-type PAX transcripts in various subtypes of RMS (n=34) in order to assess the relevance of wild-type PAX3 and PAX7 gene expression in these tumours. We found that upregulation of wild-type PAX3 is independent of the presence of either fusion gene and is unlikely to contribute to tumorigenesis. Most strikingly, upregulated PAX7 expression is almost entirely restricted to cases without PAX3-FKHR or PAX7-FKHR fusion genes and may contribute to tumorigenesis in the absence of chimaeric PAX transcription factors. Furthermore, as myogenic satellite cells are known to express PAX7, this pattern of PAX7 expression suggests this cell type as the origin of these tumours. This is corroborated by the detection of MET (c-met) expression, a marker for the myogenic satellite cell lineage, in all RMS samples expressing wild-type PAX7.
A family with an abnormal protein C and a thrombotic tendency. (1993)

An Italian family with a dysfunctional protein C (type II deficiency) tentatively designated Protein C Padua has been investigated. Five family members had this defect. Thrombotic manifestations occurred in the propositus, his sister, and his 87-year-old mother, who suffered from a transitory ischemic attack (TIA). All other deficient patients were asymptomatic. The abnormality was consistent with normal protein C (PC) antigen level but reduced both anticoagulant and amidolytic activities after PC activation by Protac. When thrombin was used as activator, PC activity level was also reduced. The abnormal PC molecule seemed to have a defect involving the activation region or the active site mechanism (reduced activity level regardless of the PC activators and the methods used in the functional assays). The electrophoretic mobility of the dysfunctional protein, assayed by crossed-immunoelectrophoresis (CIE), was normal in presence of both Na citrate and calcium lactate. The kinetics of antigen-antibody complex formation between the abnormal PC and anti-PC polyclonal antibody was investigated by means of a laser nephelometer and a peculiar pattern was found in the affected patients suggesting a possible anomalous interaction between the antibody and the abnormal protein.
An Automated Method for Determining Glycosylation and Site Diversity in Glycoproteins (2008)

The determination of glycosylation sites and oligosaccharide heterogeneity is key toward understanding the biological roles of glycoproteins. There are no previous methods that can reliably detetermine the site of glycosylation and the glycan heterogeneity at specific sites. We have developed a procedure for the determination of glycosylation sites and oligosaccharide heterogeneity in glycoproteins. The method is based on a combination of nonspecific proteolysis, deglycosylation, and high mass accuracy mass spectrometry analysis. The glycoprotein was proteolytically degraded using a nonspecific protease into glycopeptide fragments. The exact peptide mass was calculated by subtracting the glycan mass from the observed glycopeptide mass. The amino acid sequence of a matched peptide mass was identified from the protein database. A computer program, GlycoX, was developed in MATLAB to aid in the determination of the glycosylation sites and oligosaccharide heterogeneity in glycoproteins.
Arx1 Is a Nuclear Export Receptor for the 60S Ribosomal Subunit in Yeast (2007)

We previously showed that nuclear export of the large (60S) ribosomal subunit relies on Nmd3 in a Crm1-dependent manner. Recently the general mRNA export factor, the Mtr2/Mex67 heterodimer, was shown to act as an export receptor in parallel with Crm1. These observations raise the possibility that nuclear export of the 60S subunit in Saccharomyces cerevisiae requires multiple export receptors. Here, we show that the previously characterized 60S subunit biogenesis factor, Arx1, also acts as an export receptor for the 60S subunit. We found that deletion of ARX1 was synthetic lethal with nmd3 and mtr2 mutants and was synthetic sick with several nucleoporin mutants. Deletion of ARX1 led to accumulation of pre-60S particles in the nucleus that were enriched for Nmd3, Crm1, Mex67, and Mtr2, suggesting that in the absence of Arx1, 60S export is impaired even though the subunit is loaded with export receptors. Finally, Arx1 interacted with several nucleoporins in yeast two-hybrid as well as in vitro assays. These results show that Arx1 can directly bridge the interaction between the pre-60S particle and the NPC and thus is a third export receptor for the 60S subunit in yeast.