gebhart/patrepeval huggingface dataset:
Evading Defenses to Transferable Adversarial Examples by Translation-Invariant Attacks (2019)

Deep neural networks are vulnerable to adversarial examples, which can mislead classifiers by adding imperceptible perturbations. An intriguing property of adversarial examples is their good transferability, making black-box attacks feasible in real-world applications. Due to the threat of adversarial attacks, many methods have been proposed to improve the robustness. Several state-of-the-art defenses are shown to be robust against transferable adversarial examples. In this paper, we propose a translation-invariant attack method to generate more transferable adversarial examples against the defense models. By optimizing a perturbation over an ensemble of translated images, the generated adversarial example is less sensitive to the white-box model being attacked and has better transferability. To improve the efficiency of attacks, we further show that our method can be implemented by convolving the gradient at the untranslated image with a pre-defined kernel. Our method is generally applicable to any gradient-based attack method. Extensive experiments on the ImageNet dataset validate the effectiveness of the proposed method. Our best attack fools eight state-of-the-art defenses at an 82% success rate on average based only on the transferability, demonstrating the insecurity of the current defense techniques.
Genomic insights into neonicotinoid sensitivity in the solitary bee Osmia bicornis (2019)

The impact of pesticides on the health of bee pollinators is determined in part by the capacity of bee detoxification systems to convert these compounds to less toxic forms. For example, recent work has shown that cytochrome P450s of the CYP9Q subfamily are critically important in defining the sensitivity of honey bees and bumblebees to pesticides, including neonicotinoid insecticides. However, it is currently unclear if solitary bees have functional equivalents of these enzymes with potentially serious implications in relation to their capacity to metabolise certain insecticides. To address this question, we sequenced the genome of the red mason bee, Osmia bicornis, the most abundant and economically important solitary bee species in Central Europe. We show that O. bicornis lacks the CYP9Q subfamily of P450s but, despite this, exhibits low acute toxicity to the N-cyanoamidine neonicotinoid thiacloprid. Functional studies revealed that variation in the sensitivity of O. bicornis to N-cyanoamidine and N-nitroguanidine neonicotinoids does not reside in differences in their affinity for the nicotinic acetylcholine receptor or speed of cuticular penetration. Rather, a P450 within the CYP9BU subfamily, with recent shared ancestry to the Apidae CYP9Q subfamily, metabolises thiacloprid in vitro and confers tolerance in vivo. Our data reveal conserved detoxification pathways in model solitary and eusocial bees despite key differences in the evolution of specific pesticide-metabolising enzymes in the two species groups. The discovery that P450 enzymes of solitary bees can act as metabolic defence systems against certain pesticides can be leveraged to avoid negative pesticide impacts on these important pollinators.
High efficiency Agrobacterium‐mediated site‐specific gene integration in maize utilizing the FLP‐FRT recombination system (2019)

An efficient Agrobacterium-mediated site-specific integration (SSI) technology using the flipase/flipase recognition target (FLP/FRT) system in elite maize inbred lines is described. The system allows precise integration of a single copy of a donor DNA flanked by heterologous FRT sites into a predefined recombinant target line (RTL) containing the corresponding heterologous FRT sites. A promoter-trap system consisting of a pre-integrated promoter followed by an FRT site enables efficient selection of events. The efficiency of this system is dependent on several factors including Agrobacterium tumefaciens strain, expression of morphogenic genes Babyboom (Bbm) and Wuschel2 (Wus2) and choice of heterologous FRT pairs. Of the Agrobacterium strains tested, strain AGL1 resulted in higher transformation frequency than strain LBA4404 THY- (0.27% vs. 0.05%; per cent of infected embryos producing events). The addition of morphogenic genes increased transformation frequency (2.65% in AGL1; 0.65% in LBA4404 THY-). Following further optimization, including the choice of FRT pairs, a method was developed that achieved 19%-22.5% transformation frequency. Importantly, >50% of T0 transformants contain the desired full-length site-specific insertion. The frequencies reported here establish a new benchmark for generating targeted quality events compatible with commercial product development.
Deficiency of Fibroblast Growth Factor-Inducible 14 (Fn14) Preserves the Filtration Barrier and Ameliorates Lupus Nephritis (2014)

TNF ligand superfamily member 12, also known as TNF-related weak inducer of apoptosis (TWEAK), acts through its receptor, fibroblast growth factor-inducible 14 (Fn14), to mediate several key pathologic processes involved in tissue injury relating to lupus nephritis. To explore the potential for renal protection in lupus nephritis by targeting this pathway, we introduced the Fn14 null allele into the MRL-lpr/lpr lupus mouse strain. At 26-38 weeks of age, female Fn14-knockout MRL-lpr/lpr mice had significantly lower levels of proteinuria compared with female wild-type MRL-lpr/lpr mice. Furthermore, Fn14-knockout mice had significantly improved renal histopathology accompanied by attenuated glomerular and tubulointerstitial inflammation. There was a significant reduction in glomerular Ig deposition in Fn14-knockout mice, despite no detectable differences in either serum levels of antibodies or splenic immune cell subsets. Notably, we found that the Fn14-knockout mice displayed substantial preservation of podocytes in glomeruli and that TWEAK signaling directly damaged barrier function and increased filtration through podocyte and glomerular endothelial cell monolayers. Our results show that deficiency of the Fn14 receptor significantly improves renal disease in a spontaneous lupus nephritis model through prevention of the direct injurious effects of TWEAK on the filtration barrier and/or modulation of cytokine production by resident kidney cells. Thus, blocking the TWEAK/Fn14 axis may be a novel therapeutic intervention in immune-mediated proliferative GN.
Survival of neuroblastoma patients treated by long-term infusion of anti-GD2 antibody ch14.18/CHO and killer-cell Ig-like receptor (KIR) genotypes and Fcγ-receptor polymorphisms. (2017)

111 Background: Receptors expressed on natural killer (NK) cells and their ligands on target cells involved in antibody-dependent cell-mediated cytotoxicity (ADCC) may influence outcome in patients (pts) with high-risk relapsed/refractory neuroblastoma (NB) treated by long-term infusion (LTI) of anti-GD 2 antibody ch14.18/CHO Methods: 53 pts received 6x10 6 IU/m 2 sc IL-2 (d1-5; 8-12), LTI of 100 mg/m 2 ch14.18/CHO (d8-17) and 160 mg/m 2 oral 13-cis-RA (d19-32) in a closed single center program (53 pts) (APN311-303). Polymorphisms in Fcγ-receptor genes 2A (H131R), -3A (V158F) and -3B (NA1/NA2), and KIR- as well as KIR ligand expression (HLA-C1; HLA-C2; HLA-Bw4+) were determined by real-time PCR. Results: The survival update of the APN311-303 cohort revealed a 5-y OS of 56.4±7.1% (mean OS 4.35y [0.3-6.2y]) and a 5-y PFS of 29.1±6.3% (mean PFS 2.4y [0.1 - 5.9y]). Median TTP/PFS was 1.35 y (95% CI: 0.21-2.48 y). This result is clearly superior to historical controls not treated with ch14.18/CHO with a 5-y OS of 14.8±6.8% (p &lt; 0.005), indicating clinical efficacy of the treatment. In this cohort, we identified 26/53 pts with the NK- stimulatory KIR haplotype (2DS2+) who had superior OS- and PFS-rates compared to 18/53 pts with an inhibitory haplotype and KIR/KIR-ligand match (2DS2-, 3DL1+, Bw4+) (p &lt; 0.02). Similarly, we found 33/53 pts with low affinity FCGR alleles (FCGR2A-H131R/R and/or FCGRA3A-V158 F/F). These patients showed lower PFS rates compared to 20/53 patients with high affinity FCGR polymorphisms (p &lt; 0.01). ADCC analysis on day 15 of cycle 1 showed higher levels in the pt group with NK- stimulatory versus NK- inhibitory KIR/KIR ligand haplotypes (23±6 % vs. 6±2%, p &lt; 0.01). A similar effect was observed in pts with high affinity FCGR polymorphisms with an ADCC increase of 20±6% compared to 11±2% in the low affinity FCGR control. Conclusions: KIR-haplotypes and FCGR- polymorphisms correlated with the functional immune parameter ADCC and clinical outcome, and thus support the relevance of ADCC for clinical efficacy of ch14.18/CHO in neuroblastoma.
Pulmonary Veins to Left Atrium Cycle Length Gradient Predicts Procedural and Clinical Outcomes of Persistent Atrial Fibrillation Ablation (2014)

The PV to LA CL gradient may identify the subset of patients in whom persistent AF is likely to terminate after PV isolation or limited substrate ablation and better long-term outcomes are achieved.
Proceedings of the 30th Annual ACM Symposium on User Interface Software and Technology (2017)

Welcome to the 30th Annual ACM Symposium on User Interface Software and Technology (UIST), held from October 22nd to October 25th 2017, in Québec City, Canada. UIST is the premier forum for the presentation of research innovations in the software and technology of human-computer interfaces. Sponsored by ACM's special interest groups on computer-human interaction (SIGCHI) and computer graphics (SIGGRAPH), UIST brings together researchers and practitioners from diverse areas including graphical & web user interfaces, tangible & ubiquitous computing, virtual & augmented reality, multimedia, new input & output devices, fabrication, wearable computing and CSCW. UIST 2017 received 324 technical paper submissions. After a thorough review process, the 42-member program committee accepted 73 papers (22.5%). Each anonymous submission that entered the full review process was first reviewed by three external reviewers, and a meta-review was provided by a program committee member. If, after these four reviews, the submission was deemed to pass a rebuttal threshold, we asked the authors to submit a short rebuttal addressing the reviewers' concerns and a second member of the program committee to review the paper. The program committee met in person at Carnegie Mellon University in Pittsburgh, PA, USA on June 23rd and 24th, 2017, to select the papers to invite for the program. Submissions were accepted only after the authors provided a final revision addressing the committee's comments. Three papers (<1% of submissions) were recognized by the reviewers and the program committee as Best Papers and eight (2.5%) received Honorable Mentions. In addition to papers, our program includes 26 posters, 56 demonstrations, and 8 student presentations in the thirteenth annual Doctoral Symposium. Our program also features the ninth annual Student Innovation Contest -- teams from all over the world will compete in this year's contest, in which we explore how novel input, interaction, actuation, and output techniques can augment experiences that literally "reach out" into the world. Student teams will develop novel input and output techniques for an Arduino Braccio, a desktop-sized and fully-customizable, multi-DOF robotic arm. The opening keynote will be given by Prof. Gabriella Coleman from McGill University and the closing keynote will be given by Prof. Niki Kittur from Carnegie Mellon University. Both will highlight impactful and sometimes unexpected ways in which interactive technology can be used to shape our society. Once again: Welcome to Québec City and to UIST 2017!
Single-channel speaker diarization based on spatial features (2015)

Speaker diarization has gained much importance over the past five years in helping overcome key challenges faced by automatic meeting transcription systems. Current state-of-the-art algorithms can only utilize spatial information when multi-microphone recordings are available. In this paper, we propose the novel use of reverberation as a source of spatial information obtained from single-channel recordings to perform speaker diarization. The proposed system is shown to reduce speaker classification errors by 34% when compared with current MFCC based single-channel systems.
Evolution of the human X – a smart and sexy chromosome that controls speciation and development (2002)

In humans, as in other mammals, sex is determined by an XX female/XY male chromosome system. Most attention has focused on the small, degenerate Y chromosome, which bears the male-dominant gene SRY. The X, in contrast, has been considered a well-behaved and immaculately conserved element that has hardly changed since the pre-mammal days when it was just another autosome pair. However, the X, uniquely in the genome, is present in two copies in females and only one in males. This has had dire consequences genetically on the evolution of its activity--and now it appears, on its gene content and/or the function of its genes. Here we will discuss the origin of the human X, and the evolution of dosage compensation and gene content, in the light of recent demonstrations that particular functions in sex and reproduction and cognition have accumulated on it.
A Personalized Cyber-physical Laboratory For A Real-time Systems Interfacing Course (2021)

This paper describes an example of a successful attempt to migrate an intensive hardware-software lab into a fully personalized scheme with team interactions. Each student in the course performed each lab individually, and was expected to collaborate with another selected or assigned class team member remotely. When completed, the team demonstrated the lab results to the Teaching Assistants and the Instructor through a secure Learning Management System installed at the university. The importance of this lab scheme is that it is universal in that the specific form and method of delivery of this scheme is suitable for other secure networking environments.
Sequence of Shiga Toxin 2 Phage 933W fromEscherichia coliO157:H7: Shiga Toxin as a Phage Late-Gene Product (1999)

Lysogenic bacteriophages are major vehicles for the transfer of genetic information between bacteria, including pathogenicity and/or virulence determinants. In the enteric pathogen Escherichia coli O157:H7, which causes hemorrhagic colitis and hemolytic-uremic syndrome, Shiga toxins 1 and 2 (Stx1 and Stx2) are phage encoded. The sequence and analysis of the Stx2 phage 933W is presented here. We find evidence that the toxin genes are part of a late-phage transcript, suggesting that toxin production may be coupled with, if not dependent upon, phage release during lytic growth. Another phage gene, stk, encodes a product resembling eukaryotic serine/threonine protein kinases. Based on its position in the sequence, Stk may be produced by the prophage in the lysogenic state, and, like the YpkA protein of Yersinia species, it may interfere with the signal transduction pathway of the mammalian host. Three novel tRNA genes present in the phage genome may serve to increase the availability of rare tRNA species associated with efficient expression of pathogenicity determinants: both the Shiga toxin and serine/threonine kinase genes contain rare isoleucine and arginine codons. 933W also has homology to lom, encoding a member of a family of outer membrane proteins associated with virulence by conferring the ability to survive in macrophages, and bor, implicated in serum resistance.
Many-worlds browsing for control of multibody dynamics (2007)

Animation techniques for controlling passive simulation are commonly based on an optimization paradigm: the user provides goals a priori , and sophisticated numerical methods minimize a cost function that represents these goals. Unfortunately, for multibody systems with discontinuous contact events these optimization problems can be highly nontrivial to solve, and many-hour offline optimizations, unintuitive parameters, and convergence failures can frustrate end-users and limit usage. On the other hand, users are quite adaptable, and systems which provide interactive feedback via an intuitive interface can leverage the user's own abilities to quickly produce interesting animations. However, the online computation necessary for interactivity limits scene complexity in practice. We introduce Many-Worlds Browsing , a method which circumvents these limits by exploiting the speed of multibody simulators to compute numerous example simulations in parallel (offline and online), and allow the user to browse and modify them interactively. We demonstrate intuitive interfaces through which the user can select among the examples and interactively adjust those parts of the scene that do not match his requirements. We show that using a combination of our techniques, unusual and interesting results can be generated for moderately sized scenes with under an hour of user time. Scalability is demonstrated by sampling much larger scenes using modest offline computations.
Rapid and homogeneous electrochemical detection by fabricating a high affinity bispecific antibody-enzyme complex using two Catcher/Tag systems (2020)

Antibody-enzyme complexes (AECs) with binding ability to specific targets and catalytic activities to gain signals are known to be ideal sensing elements; however, AEC-based universal sensors applicable to point-of-care testing (POCT) have not yet been developed. Here, we achieved rapid and homogeneous electrochemical detection by fabricating a high-affinity bispecific AEC (bsAEC) using two Catcher/Tag systems. Recently, we reported a convenient and universal method to fabricate AECs using the SpyCatcher/SpyTag system. The resultant anti-epidermal growth factor receptor (anti-EGFR) AEC worked efficiently as a sensing element; however, the sensitivities did not meet the clinically required detection range of the soluble ectodomain of EGFR (sEGFR). To induce high affinity even to monomeric targets like sEGFR, we designed a convenient fabrication method for bsAEC using two Catcher/Tag systems, which did not express cross-reactivity. The anti-EGFR bsAEC was successfully prepared by constructing glucose dehydrogenase with two different catcher domains at the N- and C-terminus and by combining two corresponding Tag-fused anti-EGFR single-chain Fvs (scFvs), which recognize different epitopes on sEGFR. As expected, bsAEC showed a higher affinity than that of bivalent AEC with two identical anti-EGFR scFvs at low concentrations of sEGFR, and met the clinically required detection range of sEGFR. Further, by combining magnet beads, we established a rapid and wash-free homogeneous electrochemical detection method. This study offers new insights into the fabrication of universal POCT devices.
Dihydrofolate Reductase from a Resistant Subline of the L1210 Lymphoma (1967)

Abstract Dihydrofolate reductase has been purified 1000-fold from a methotrexate-resistant subline of the L1210 lymphoma with 49% yield and purity up to 100%. The procedure involves ammonium sulfate and acid precipitation, gel filtration on Sephadex G-100, and chromatography on hydroxylapatite. Purity has been determined by titrating enzymic activity and protein fluorescence with a stoichiometric inhibitor, methotrexate, and confirmed by electrophoresis and immunodiffusion. The isoelectric point in phosphate buffer is approximately pH 6.0, but in tris(hydroxymethyl)aminomethane buffer, the isoelectric point is above pH 8.5. The protein contains one reactive sulfhydryl group and is stabilized to heat and to urea denaturarion by each of its substrates.
The effect of p53‐RNAi and p53 knockout on human 8‐oxoguanine DNA glycosylase (hOgg1) activity (2005)

Recent evidence indicates that in vitro p53 augments base excision repair (BER) activities in mammalian cells. To understand the role of p53 in BER, we analyzed the repair activity of hOgg1 in isogenic cell lines HCT116p53+/+ and HCT116p53-/-. We found that hOgg1 activity was significantly decreased in HCT116p53-/- cells as compared with HCT116p53+/+ cells, indicating a functional role for p53 in the regulation of hOGG1. Using gel-shift assays, we showed that p53 binds to its putative cis-elements within the hOGG1 promoter. In addition we demonstrated that supplementing p53 in HCT116p53-/- cells enhanced the transcription of hOGG1. To further strengthen our findings, we used p53-RNAi to study the effects of decreased p53 levels on hOgg1 activity. We observed that p53-RNAi resulted in decreased hOGG1 expression both at the mRNA and protein levels. This decrease in hOGG1 expression was associated with reduced cell viability upon oxidative damage and reduced hOgg1 activity as evidenced by the 8-oxoG incision assay. Taken together, our results indicate that loss of p53 function can lead to decreased hOgg1 repair activity.
[Radio-cinematographic study of active elevation of the prosthetic shoulder]. (1992)

In order to verify whether it is possible to reproduce the physiologic anterior elevation of the shoulder with a non constrained Neer type prosthesis, the authors have examined the dynamic comportement of 21 total shoulder arthroplasties. Recording of anterior active elevation with video-fluoroscopy and evaluation glenohumeral motion and scapulothoracic motion allowed to distinguish 3 types of biomechanics after total shoulder replacement. A first group of prosthesis (4 cases) had normal biomechanics with conservation of a normal scapulohumeral rythm. This concerned arthroplasties performed for necrosis or osteoarthritis with no cuff tear or loose bone stock and no technical error. A second group of prosthesis (10 cases) had an abnormal biomechanics. There was a superior excursion of the humeral head prosthesis without real glenohumeral motion. A more severe pathology (cuff tear arthropathy, rheumatoid arthritis, old traumas) with bone and/or muscular destruction was sufficient to explain this elevation possible only because of the scapulothoracic motion. Finally, there was a third group of prosthesis (7 cases) which had a reversed scapulohumeral rythm: there was less motion between the prosthetic components but the scapulothoracic motion was unchanged. Three factors can be responsible for this reversed scapulohumeral rythm: 1) The initial pathology, because of the difference in the cuff trophicity. 2) The surgical technic because of the difficulties to respect the position of the joint line and the lever arms. 3) The prosthesis itself, because of the higher degree of conformity and stability between the prosthetic components.
Accidents to patients in hospital: a comparative study. (1994)

A comparative study of 50 reported accident patients (cases) and 50 non-accident patients (controls) was carried out in 10 wards in a large, acute hospital, using primary and secondary data from patients, nurses and records. Folstein's Mini-Mental State test was used to measure the mental status of patients. The mental status of the controls was significantly better than that of the cases. Nurses' responses indicated that significantly more accident patients were incontinent of urine than non-accident patients. There were also indications from patients of three additional unreported accidents. Further study was needed to estimate, more closely, the frequency of unreported patient accidents. This is the second paper in a series of three. The first appeared in Nursing Times on August 17, and the final one will be published on September 28, along with implications for practice and recommendations.