gebhart/patrepeval huggingface dataset:
Memory model sensitive analysis of concurrent data types (2007)

Concurrency libraries can facilitate the development of multi-threaded programs by providing concurrent implementations of familiar data types such as queues and sets. Many optimized algorithms that use lock-free synchronization have been proposed for multiprocessors. Unfortunately, such algorithms are notoriously difficult to design and verify and may contain subtle concurrency bugs. Moreover, it is often difficult to place memory ordering fences in the implementation code. Such fences are required for correct function on relaxed memory models, which are common on contemporary multiprocessors. 
To address these difficulties, we describe an automated verification procedure based on bounded model checking that can exhaustively check all concurrent executions of a given test program on a relaxed memory model and can either (1) verify that the data type is sequentially consistent, or (2) construct a counterexample. 
Given C implementation code, a bounded test program, and an axiomatic memory model specification, our CheckFence prototype verifies operation-level sequential consistency by encoding the existence of inconsistent executions as solutions to a propositional formula and using a standard SAT solver to decide satisfiability. 
We applied CheckFence to five previously published algorithms and found several bugs (some not previously known). Furthermore, we determined where to place memory ordering fences in the implementations and verified their sufficiency on our test suite.
Automated assignment of SCOP and CATH protein structure classifications from FSSP scores (2002)

We present an automated procedure to assign CATH and SCOP classifications to proteins whose FSSP score is available. CATH classification is assigned down to the topology level, and SCOP classification is assigned to the fold level. Because the FSSP database is updated weekly, this method makes it possible to update also CATH and SCOP with the same frequency. Our predictions have a nearly perfect success rate when ambiguous cases are discarded. These ambiguous cases are intrinsic in any protein structure classification that relies on structural information alone. Hence, we introduce the "twilight zone for structure classification." We further suggest that to resolve these ambiguous cases, other criteria of classification, based also on information about sequence and function, must be used.
Guidelines for Human-AI Interaction (2019)

Advances in artificial intelligence (AI) frame opportunities and challenges for user interface design. Principles for human-AI interaction have been discussed in the human-computer interaction community for over two decades, but more study and innovation are needed in light of advances in AI and the growing uses of AI technologies in human-facing applications. We propose 18 generally applicable design guidelines for human-AI interaction. These guidelines are validated through multiple rounds of evaluation including a user study with 49 design practitioners who tested the guidelines against 20 popular AI-infused products. The results verify the relevance of the guidelines over a spectrum of interaction scenarios and reveal gaps in our knowledge, highlighting opportunities for further research. Based on the evaluations, we believe the set of design guidelines can serve as a resource to practitioners working on the design of applications and features that harness AI technologies, and to researchers interested in the further development of human-AI interaction design principles.
Automation of Regional Data Validation (1990)

A computerized system has been developed to assist in U.S. Environmental Protection Agency data validation studies of organic analytical data collected for hazardous waste site assessments. The Regional Automated Data Auditing System (RADAS) is a data evaluation and management computer program that provides data entry, file maintenance, data qualifying, and report generation for results from gas chromatography and gas chromatography/mass spectrometry analyses. The RADAS system determines the validity of individual analyte concentrations reported by the laboratory. This determination is based on instrument calibration, sample holding time, blank contamination, and contract required detection limit. Delivery-ready reports are produced, including data tables, sample and calibration listings, and a documented summary of data validation. The system developed has been found to perform appropriately and its use represents a significant improvement in terms of turn-around time, completeness, and consistency of data validation studies.
iCoding: Countermeasure Against Interference and Eavesdropping in Wireless Communications (2021)

With the rapid development of wireless communication technologies, interference management (IM) and security/privacy in data transmission have become critically important. On one hand, due to the broadcast nature of wireless medium, the interference superimposed on the desired signal can destroy the integrity of data transmission. On the other hand, malicious receivers (Rxs) may eavesdrop a legitimate user's transmission and thus breach the confidentiality of communication. To counter these threats, we propose a novel encoding method, called immunizing coding (iCoding), which handles both IM and physical-layer security simultaneously. By exploiting both channel state information (CSI) and data carried in the interference, an iCoded signal is generated and sent by the legitimate transmitter (Tx). The iCoded signal interacts with the interference at the desired/legitimate Rx, so that the intended data can be recovered without the influence of disturbance, i.e., immunity to interference is achieved. In addition, since the data carried in the iCoded signal which is obtained via encoding the desired data and interference cooperatively, is different from the original desired data, the eavesdropper cannot access legitimate information by wiretapping the desired signal. Therefore, immunity to eavesdropping is achieved. Our theoretical analysis and in-depth simulation have shown iCoding to effectively manage interference while preventing potential eavesdropping, hence enhancing the legitimate user's data transmission and secrecy thereof.
Gigapixel holography (2011)

Relatively low cost focal plane arrays and the availability of high performance digital memory and processing enable computational holographic imaging on unprecedented scale. Recent progress in registration and optimization enables coherent imaging over relatively large sensor arrays based on scanning. This talk describes work on large pixel count holographic imaging in our group and discusses multi-sensor array image fusion in computational holographic imagers.
A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses (2021)

The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses <i>in vitro</i> and confirmed that K378T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
Expectation for Neutron Scattering from a Materials Scientist (2010)

We have experienced essential importance of neutron scattering in our recent materials research, i.e. iron pnictide superconductor and RT stable electride C12A7:e-. The neuron scattering provided more direct and unique information that cannot be obtained by other method. I describe two events experienced associated with neutron scattering and requests viewed from a materials scientist.
Experimental and Computational Study of the ZnnSn and ZnnSn+ Clusters (2005)

Zinc sulfide clusters produced by direct laser ablation and analyzed in a time-of-flight mass-spectrometer, showed evidence that clusters composed of 3, 6, and 13 monomer units were ultrastable. The geometry and energies of neutral and positively charged Zn(n)S(n) clusters, up to n = 16, were obtained computationally at the B3LYP/6-311+G level of theory with the assistance of an algorithm to generate all possible structures having predefined constraints. Small neutral and positive clusters were found to have planar geometries, neutral three-dimensional clusters have the geometry of closed-cage polyhedra, and cationic three-dimensional clusters have structures with a pair of two-coordinated atoms. Physical properties of the clusters as a function of size are reported. The relative stability of the positive stoichiometric clusters provides a thermodynamic rationale for the experimental results.
Nanoaggregates of Diverse Asphaltenes by Mass Spectrometry and Molecular Dynamics (2017)

Asphaltene nanoaggregates from three diverse source materials—coal-derived asphaltenes dominated by aromatic carbon, petroleum asphaltenes with comparable abundances of aromatic and aliphatic carbon, and immature source-rock asphaltenes dominated by aliphatic carbon—are examined by means of surface-assisted laser desorption ionization mass spectrometry (SALDI-MS) coupled with laser desorption laser ionization mass spectrometry (L2MS). All three types of asphaltenes form nanoaggregates with aggregation numbers close to 7. Molecular dynamics calculations for proposed island molecular structures show the important roles that π-stacking and alkane steric hindrance play in nanoaggregate formation and structure. These results are discussed in terms of entropy and enthalpy changes. All results are consistent with the Yen-Mullins model, which bodes well for its expanded use in oilfield reservoir evaluations.
Chiroptical properties and absolute configuration of pyrroloisoquinoline antidepressants (1998)

Circular dichroism (CD) spectra were determined for the bioactive (+)-enantiomers of 1 · HCl, 3 · HCl, and 4 · HBr to characterize the chiroptical properties of these pyrroloisoquinoline antidepressants. The compounds showed a low-intensity negative CD band with much fine structure between 252 and 272 nm, a medium negative CD band with fine structure between 215 and 225 nm, and a high-intensity negative CD maximum between 198 and 203 nm. Except for amplitude variation, the three CD spectra were essentially superimposable in sign and position of the bands. The CD curves for the (−)-enantiomers of 1 · HCl and 4 · HBr were opposite in sign and comparable within 5% to the (+)-enantiomers. The results are consistent with the previously assigned (Maryanoff et al. J. Med. Chem. 30:1433–1454, 1987) absolute configurations of (6S, 10bR) for 1 and 3, and (6R, 10bR) for 4. Chirality 10:169–172, 1998. © 1998 Wiley-Liss, Inc.
Host cell phospholipids are trafficked to and then modified by Chlamydia trachomatis (1997)

There is little information on the trafficking of eukaryotic lipids from a host cell to either the cytoplasmic membrane of or the vacuolar membrane surrounding intracellular pathogens. Purified Chlamydia trachomatis, an obligate intracellular bacterial parasite, contains several eukaryotic glycerophospholipids, yet attempts to demonstrate transfer of these lipids to the chlamydial cell membrane have not been successful. In this report, we demonstrate that eukaryotic glycerophospholipids are trafficked from the host cell to C. trachomatis. Phospholipid trafficking was assessed by monitoring the incorporation of radiolabelled isoleucine, a precursor of C. trachomatis specific branched-chain fatty acids, into host-derived glycerophospholipids and by monitoring the transfer of host phosphatidylserine to chlamydiae and its subsequent decarboxylation to form phosphatidylethanolamine. Phospholipid trafficking to chlamydiae was unaffected by brefeldin A, an inhibitor of Golgi function. Furthermore, no changes in trafficking were observed when C. trachomatis was grown in a mutant cell line with a nonfunctional, nonspecific phospholipid transfer protein. Host glycerophospholipids are modified by C. trachomatis, such that a host-synthesized straight-chain fatty acid is replaced with a chlamydia-synthesized branched-chain fatty acid. We also demonstrate that despite the acquisition of host-derived phospholipids, C. trachomatis is capable of de novo synthesis of phospholipids typically synthesized by prokaryotic cells. Our results provide novel information on chlamydial phospholipid metabolism and eukaryotic cell lipid trafficking, and they increase our understanding of the evolutionary steps leading to the establishment of an intimate metabolic association between an obligate intracellular bacterial parasite and a eukaryotic host cell.
Cup-to-Disc Ratio From Heidelberg Retina Tomograph 3 and High-Definition Optical Coherence Tomography Agrees Poorly With Clinical Assessment (2015)

In general, there is poor correlation and a lack of agreement of VCDR measured using HRT-3, HD-OCT, and clinical grading. HD-OCT has somewhat better agreement with clinical measurements of VCDR. Compared with clinical grading, HD-OCT tended to overestimate VCDR, whereas HRT-3 tended to underestimate it.
Eine DNA‐Doppelhelix mit größerem Durchmesser (2004)

Ach du dicke DNA! Kürzlich wurde der Aufbau einer artifiziellen xDNA-Doppelhelix mit vergrößertem Durchmesser beschrieben. Das Paarungssystem basiert auf Nucleobasenanaloga, die die natürlichen Watson-Crick-Bindungsstellen erhalten, kombiniert mit größeren aromatischen Oberflächen. Das Bild zeigt eine Aufsicht auf DNA und xDNA.
Matrix metalloproteinase activation by free neutrophil elastase contributes to bronchiectasis progression in early cystic fibrosis (2015)

Neutrophil elastase is the most significant predictor of bronchiectasis in early-life cystic fibrosis; however, the causal link between neutrophil elastase and airway damage is not well understood. Matrix metalloproteinases (MMPs) play a crucial role in extracellular matrix modelling and are activated by neutrophil elastase. The aim of this study was to assess if MMP activation positively correlates with neutrophil elastase activity, disease severity and bronchiectasis in young children with cystic fibrosis.Total MMP-1, MMP-2, MMP-7, MMP-9, tissue inhibitor of metalloproteinase (TIMP)-2 and TIMP-1 levels were measured in bronchoalveolar lavage fluid collected from young children with cystic fibrosis during annual clinical assessment. Active/pro-enzyme ratio of MMP-9 was determined by gelatin zymography. Annual chest computed tomography imaging was scored for bronchiectasis.A higher MMP-9/TIMP-1 ratio was associated with free neutrophil elastase activity. In contrast, MMP-2/TIMP-2 ratio decreased and MMP-1 and MMP-7 were not detected in the majority of samples. Ratio of active/pro-enzyme MMP-9 was also higher in the presence of free neutrophil elastase activity, but not infection. Across the study cohort, both MMP-9/TIMP-1 and active MMP-9 were associated with progression of bronchiectasis.Both MMP-9/TIMP-1 and active MMP-9 increased with free neutrophil elastase and were associated with bronchiectasis, further demonstrating that free neutrophil elastase activity should be considered an important precursor to cystic fibrosis structural disease.
Lateral velocity estimation for automotive radar applications (2007)

Automotive radar sensors are applied to measure the target range, azimuth angle and radial velocity simultaneously even in multiple target situations. But it is also possible to calculate the lateral velocity by a single radar measurement. Based on some analytical and experimental results it is shown in this paper that the lateral velocity of a radar target can also be measured precisely even in a single observation situation. This additional information of lateral speed is of much interest in all target tracking procedures, especially for typical city traffic situations and for advanced driver assistance systems (ADAS). (4 pages)
Connecting insect brain imaging to data mining tools - a neuroimage extension for the KNIME platform. (2009)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
Hierarchical Nanostructures: Hierarchical Nanostructures: Design for Sustainable Water Splitting (Adv. Energy Mater. 23/2017) (2017)

In article number 1700559, Johnny C. Ho and co-workers present an overview of recent research advances in the development of hierarchical nanostructures and give valuable guidelines for the rational design of these materials for their applications in electrocatalytic and photoelectrochemical water splitting systems, with special emphasis on demonstrating the mechanisms for the structured-related performance improvement.
Statistical Analysis and Optimal Design for Efficient Mobile Satellite Broadcast With Diversity (2008)

The design of mobile satellite broadcast architectures requires complex tradeoffs involving technical, economical, and regulatory aspects. A satisfactory quality of service in terms of the number of receivers successfully receiving the broadcasted services can be ensured using space, terrestrial, and time diversity techniques. The amount of applied diversity affects the system's spectral efficiency and performance. In addition, dedicated satellite and terrestrial networks represent significant investments, and regulatory limitations on terrestrial deployment may further complicate the system design. Herein, we provide insights into the technical aspects of the aforementioned tradeoffs by deriving an efficient method to estimate what system resources in terms of spectrum and delay are required to provide a satisfactory number of end users with mobile broadcast services using space, terrestrial, and time diversity techniques. The presented results are based on statistical models of the mobile satellite channel for which efficient analytical design and error rate estimation methods are derived. To provide a coded space and time diversity, a generalized approach is taken that includes most transmission schemes in use, or considered for use, for mobile satellite broadcast as special cases. As a side result, it is shown that for optimal error rate performance, the provided time diversity should be designed by taking into account channel statistics. An efficient yet simple method of enumerating time-varying Markov chains is also included. The proposed techniques and results are illustrated with numerical examples using temporal Ku-band channel statistics. The examples include a wide range of possible transmission schemes in system configurations with and without space and terrestrial diversity and, thus, demonstrate how different transmission schemes and infrastructure configurations can be compared.
Direct Evidence for Neutrino Flavor Transformation from Neutral-Current Interactions in SNO (2002)

The Sudbury Neutrino Observatory (SNO) is a 1,000 tonne heavy water Cerenkov‐based neutrino detector situated 2,000 meters underground in INCO’s Creighton Mine near Sudbury, Ontario, Canada. For the neutrinos from 8B decay in the Sun SNO observes the Charged Current neutrino reaction sensitive only to electron neutrinos and others (Neutral Current and Elastic Scattering) sensitive to all active neutrino types and thereby can search for direct evidence of neutrino flavor change. Using these reactions and assuming the standard 8B shape, the ve component of the 8B solar flux is φe = 1.76−0.05+0.05(stat.)−0.09+0.09 (syst.) × 106 cm−2s−1 for a kinetic energy threshold of 5 MeV. The non‐ve component is φμτ = 3.41−0.45+0.45(stat.)−0.45+0.48 (syst.) × 106 cm−2s−1, 5.3σ greater than zero, providing strong evidence for solar ve flavor transformation. The total flux measured with the NC reaction is φNC = 5.09−0.43+0.44(stat.)−0.43+0.46 (syst.) × 106 cm−2s−1, consistent with solar models. For charged current events, assuming an undistorted 8B spectrum, the night minus day rate is 14.0% ± 6.3%−1.4+1.5% of the average rate. If the total flux of active neutrinos is additionally constrained to have no asymmetry, the ve asymmetry is found to be 7.0% ± 4.9%−1.2+1.3%. A global solar neutrino analysis in terms of matter‐enhanced oscillations of two active flavors strongly favors the Large Mixing Angle (LMA) solution.
Abstract B33: The oligoclonal antibody MM-151 overcomes acquired resistance to cetuximab and panitumumab in colorectal cancer cells harboring EGFR extracellular domain mutations (2016)

Abstract The anti-EGFR antibodies cetuximab and panitumumab are used to treat ‘RAS’ wild type colorectal cancers (CRCs), but their efficacy is limited by development of drug resistance. At relapse, approximately 20% of tumors carry EGFR extracellular domain (ECD) mutations (S492R, R451C, S464L, G465R, G465E, K467T, I491M) that impair antibody binding. We find that these EGFR genetic variants are effectively targeted by the oligoclonal anti-EGFR antibody MM-151. Both EGFR mediated signaling and proliferation of colorectal cancer (CRC) cells carrying EGFR ECD mutations are impaired by MM-151. Notably, EGFR extracellular domain mutations, which are found in circulating free tumor DNA (ctDNA) of CRC patients who relapsed upon anti-EGFR antibodies treatment, decline during MM-151 therapy. In conclusion, MM-151 based therapy may be valuable for the treatment of secondary resistance to cetuximab and panitumumab driven by EGFR ECD mutations. Further prospective clinical evaluation is warranted. Citation Format: Sabrina Arena, Giulia Siravegna, Benedetta Mussolin, Jeffrey D. Kearns, Beni B. Wolf, Sandra Misale, Luca Lazzari, Andrea Bertotti, Livio Trusolino, Alex Adjei, Clara Montagut, Federica Di Nicolantonio, Rachel Nering, Alberto Bardelli. The oligoclonal antibody MM-151 overcomes acquired resistance to cetuximab and panitumumab in colorectal cancer cells harboring EGFR extracellular domain mutations. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B33.
Robust Knowledge Distillation from RNN-T Models with Noisy Training Labels Using Full-Sum Loss (2023)

This work studies knowledge distillation (KD) and addresses its constraints for recurrent neural network transducer (RNN-T) models. In hard distillation, a teacher model transcribes large amounts of unlabelled speech to train a student model. Soft distillation is another popular KD method that distills the output logits of the teacher model. Due to the nature of RNN-T alignments, applying soft distillation between RNNT architectures having different posterior distributions is challenging. In addition, bad teachers having high word-error-rate (WER) reduce the efficacy of KD. We investigate how to effectively distill knowledge from variable quality ASR teachers, which has not been studied before to the best of our knowledge. We show that a sequence-level KD, full-sum distillation, outperforms other distillation methods for RNN-T models, especially for bad teachers. We also propose a variant of full-sum distillation that distills the sequence discriminative knowledge of the teacher leading to further improvement in WER. We conduct experiments on public datasets namely SpeechStew and LibriSpeech, and on in-house production data.