gebhart/patrepeval huggingface dataset:
<emph type="ital">SQSTM1</emph> Mutations in Familial and Sporadic Amyotrophic Lateral Sclerosis (2011)

Using candidate gene identification based on prior biological knowledge and the functional prediction of rare variants, we identified several novel SQSTM1 mutations in patients with ALS. Our findings provide evidence of a direct genetic role for p62 in ALS pathogenesis and suggest that regulation of protein degradation pathways may represent an important therapeutic target in motor neuron degeneration.
Convolutional Experts Constrained Local Model for 3D Facial Landmark Detection (2017)

Constrained Local Models (CLMs) are a well-established family of methods for facial landmark detection. CE-CLM, the newest member of CLMs, brings CLMs back to state of the art performance. This is done through CE-CLMs ability to model the very complex individual landmark appearance that is affected by expression, illumination, facial hair, makeup, and accessories. A crucial component of CE-CLM is a novel local detector - Convolutional Experts Network (CEN) - that brings together the advantages of neural architectures and mixtures of experts in an end-to-end framework. In this paper we use CE-CLM to learn position of dense 84 landmark positions. To achieve best performance on the Menpo3D dense landmark detection challenge, we use two complementary networks alongside CE-CLM: a network that maps the output of CE-CLM to 84 landmarks called Adjustment Network, and a Deep Residual Network called Correction Networks that learns dataset specific corrections for CE-CLM.
W-Panning and O-Format, Tools for Object Spatialization (2002)

INTRODUCTION The primary problem in spatialization is creating and controlling the perception of sound from different directions, since then in principle any soundfield can be simulated by mixing appropriate sounds in different directions. [1, 2, 3, 8, 10] are all focused on this objective. By contrast, little has been written about the secondary problem of simulating composite structures that generate a variety of sound from different directions over an extended space. The need for doing this arises very naturally from the sound produced by composite real objects, whether solid or fluid in nature. For instance, a passing vehicle emits a variety of different sounds from different parts, projected in various directions. A swarm of bees flying past the listener even creates a soundfield that completely envelopes the listener. One approach to modelling such complex audio scenes is to break it into a set of independent point sources. The game audio technology provider Sensaura [13] does t
Single-cell analysis of senescent epithelia reveals targetable mechanisms promoting fibrosis (2022)

Progressive fibrosis and maladaptive organ repair result in significant morbidity and millions of premature deaths annually. Senescent cells accumulate with aging and after injury and are implicated in organ fibrosis, but the mechanisms by which senescence influences repair are poorly understood. Using 2 murine models of injury and repair, we show that obstructive injury generated senescent epithelia, which persisted after resolution of the original injury, promoted ongoing fibrosis, and impeded adaptive repair. Depletion of senescent cells with ABT-263 reduced fibrosis in reversed ureteric obstruction and after renal ischemia/reperfusion injury. We validated these findings in humans, showing that senescence and fibrosis persisted after relieved renal obstruction. We next characterized senescent epithelia in murine renal injury using single-cell RNA-Seq. We extended our classification to human kidney and liver disease and identified conserved profibrotic proteins, which we validated in vitro and in human disease. We demonstrated that increased levels of protein disulfide isomerase family A member 3 (PDIA3) augmented TGF-β-mediated fibroblast activation. Inhibition of PDIA3 in vivo significantly reduced kidney fibrosis during ongoing renal injury and as such represented a new potential therapeutic pathway. Analysis of the signaling pathways of senescent epithelia connected senescence to organ fibrosis, permitting rational design of antifibrotic therapies.
Impact of Design Parameters on Performance of Adaptive Network-on-Chips (2012)

International audience
Learning image query concepts via intelligent sampling (2001)

In this paper, we propose an active and inductive combined learning method to learn users’ image query concepts. We model query concepts in -CNF, which can be used to express most practical queries. To learn a user’s query concept, we propose MEGA. MEGA initializes a user’s query concept as the conjunction of all disjunctions of at most length of the predicates. It then intelligently selects unlabeled data to present to the user for gathering information to eliminate the maximum expected number of disjunctions. MEGA maximizes the usefulness of each example it generates for learning a user’s query concept and hence expedites the convergence to the target concept. Through analysis and experiments, we show that MEGA can learn a complex image query concept much faster than some traditional schemes.
Superior Activity of a Thromboxane Receptor Antagonist as Compared with Aspirin in Rat Models of Arterial and Venous Thrombosis (1993)

We determined the effects of aspirin and a novel thromboxane A2/prostaglandin endoperoxide (TP)-receptor antagonist, BMS-180291, on thrombosis and bleeding times in skin and mesenteric arteries. In anesthetized rats, occlusive thrombosis was induced in the carotid artery by topical application of ferrous chloride and in the vena cava by blood flow stasis combined with either infusion of thromboplastin or hypotonic saline. Aspirin (1, 10, and 50 mg/kg) did not reduce arterial or venous thrombus weight significantly. BMS 180,291 (150 micrograms/kg/min) decreased arterial thrombus weight and hypotonic saline-induced caval thrombus weight by 58 and 57%, respectively. BMS-180291 lacked antithrombotic activity at a lower dose (50 micrograms/kg/min) and failed to inhibit thromboplastin-induced caval thrombosis. BMS-180291 (150 micrograms/kg/min) significantly reduced arterial thrombus weight by 40% when plasma epinephrine concentration was increased to 5 ng/ml. BMS-180291 and aspirin produced increases of only < or = 30% in bleeding times. These results demonstrate that BMS-180291 has antithrombotic activity in experimental aspirin-resistant arterial and venous thrombosis. Both aspirin and BMS-180291 have only modest effects on small artery hemostasis in rats.
Isoproterenol Activates Extracellular Signal–Regulated Protein Kinases in Cardiomyocytes Through Calcineurin (2001)

Calcineurin, which is activated by marked elevation of intracellular Ca(2+) levels by the Ca(2+)-induced Ca(2+) release mechanism, regulates isoproterenol-induced activation of ERKs in cardiomyocytes.
Figures S1-S6 from Small-Molecule Inhibition of PD-1 Transcription Is an Effective Alternative to Antibody Blockade in Cancer Therapy (2023)

&lt;p&gt;GSK-3 inhibition effects on T-cells and anti-tumor responses&lt;/p&gt;
Tricarbonyliron complexes derived from dimethyl 1,3-butadiene-2,3-dicarboxylate: formation of [Fe(CO)3]2–dimethyl 1,3-butadiene-2,3-dicarboxylate (1999)

Treatment of dimethyl 1,3-butadiene-2,3-dicarboxylate with Fe 2 (CO) 9 provided the corresponding tricarbonyl(η 4 -dimethyl 1,3-butadiene-2,3-dicarboxylato-O)iron, [Fe(C 8 H 10 O 4 )(CO) 3 ], (II), as the main product and the novel μ-[(1,2-η,κO 3 :3,4-η,κO 2 )-dimethyl 1,3-butadiene-2,3-dicarboxylato]bis(tricarbonyliron), [Fe 2 (C 8 H 10 O 4 )(CO) 6 ], (III). In the crystal structure of (II), the electron-deficient butadiene complexes with one Fe(CO) 3 group, whereas in (III), the butadiene adopts an unusual conformation and forms a complex with two Fe(CO) 3 groups. In (III), each Fe atom possesses a trigonal bipyramidal geometry, with one olefinic bond and two carbonyl ligands occupying the basal positions, and the keto oxygen of the ester and the other carbonyl ligand occupying apical positions.
Single channel speech enhancement based on masking properties of the human auditory system (1999)

This paper addresses the problem of single channel speech enhancement at very low signal-to-noise ratios (SNRs) (<10 dB). The proposed approach is based on the introduction of an auditory model in a subtractive-type enhancement process. Single channel subtractive-type algorithms are characterized by a tradeoff between the amount of noise reduction, the speech distortion, and the level of musical residual noise, which can be modified by varying the subtraction parameters. Classical algorithms are usually limited to the use of fixed optimized parameters, which are difficult to choose for all speech and noise conditions. A new computationally efficient algorithm is developed based on masking properties of the human auditory system. It allows for an automatic adaptation in time and frequency of the parametric enhancement system, and finds the best tradeoff based on a criterion correlated with perception. This leads to a significant reduction of the unnatural structure of the residual noise. Objective and subjective evaluation of the proposed system is performed with several noise types form the Noisex-92 database, having different time-frequency distributions. The application of objective measures, the study of the speech spectrograms, as well as subjective listening tests, confirm that the enhanced speech is more pleasant to a human listener. Finally, the proposed enhancement algorithm is tested as a front-end processor for speech recognition in noise, resulting in improved results over classical subtractive-type algorithms.
Measuring the Wear of Milled Tooth Bits Using MWD Torque and Weight-on-Bit (1985)

ABSTRACT A bit torque relationship based on a force balance concept has been proposed by Warren1. The relationship shows that for a given bit, the torque is determined by the applied weight-on-bit and the depth of tooth penetration. This paper extends the torque model for soft formation milled tooth bits to show how the effects of tooth wear can be taken into account. The method is intended for formations like shales that are drilled by a gouging and scraping action. An interpretation technique, based on the model, is developed. It is called the Mechanical Efficiency Log (MEL)TM. It uses time averaged values of penetration rate, rotation speed, and measurements while drilling (MWD) values of torque and weight-on-bit. The result of the interpretation is real time calculations of tooth wear, drilling efficiency, and the in situ shear strength of the rock.
Doppler Radar for USA Weather Surveillance (2012)

Weather radar had its beginnings at the end of Word War II when it was noticed that storms clutter radar displays meant to reveal enemy aircraft. Thus radar meteorology was born. Until the sixties only the return power from weather tracers was measured which offered the first glimpses into precipitation structure hidden inside clouds. Possibilities opened up to recognize hail storms, regions of tornadoes (i.e., hook echoes), the melting zone in stratiform precipitation, and even determine precipitation rates at the ground, albeit with considerable uncertainty.
Properties, biosynthesis and processing of a sulfur‐rich protein in Brazil nut (Bertholletia excelsa H.B.K.) (1987)

An abundant seed protein, which is exceptionally rich in the sulfur-containing amino acids, methionine (18%) and cysteine (8%), is synthesized in Brazil nut embryos about 9 months after flowering. This sulfur-rich protein consists of two low-molecular-mass polypeptide components, a 9-kDa polypeptide and a 3-kDa polypeptide. The two-subunit polypeptides associate through disulfide linkage(s) to form a 12-kDa protein molecule. We have demonstrated through in vitro translation studies, using RNA from 9-month-old embryos, that the sulfur-rich protein is synthesized as a larger precursor polypeptide of 18 kDa. In addition, data from in vivo labelling studies of 9-month-old Brazil nuts suggest that there are two intermediate precursors of the sulfur-rich protein, one of 15 kDa and another of 12 kDa. One of these precursors, the 12-kDa polypeptide, accumulates for a 2-month period in the developing embryos. From these data we infer that at least three stepwise cleavages are involved in the maturation of the sulfur-rich protein from its 18-kDa precursor.
Quantifying the security of preference-based authentication (2008)

We describe a technique aimed at addressing longstanding problems for password reset: security and cost. In our approach, users are authenticated using their preferences. Experiments and simulations have shown that the proposed approach is secure, fast, and easy to use. In particular, the average time for a user to complete the setup is approximately two minutes, and the authentication process takes only half that time. The false negative rate of the system is essentially 0% for our selected parameter choice. For an adversary who knows the frequency distributions of answers to the questions used, the false positive rate of the system is estimated at less than half a percent, while the false positive rate is close to 0% for an adversary without this information. Both of these estimates have a significance level of 5%.
Answering Key Fuel Cycle Questions (2016)

The Advanced Fuel Cycle Initiative (AFCI) program has both “outcome” and “process” goals because it must address both waste already accumulating as well as completing the fuel cycle in connection with advanced nuclear power plant concepts. The outcome objectives are waste geological repository capacity and cost, energy security and sustainability, proliferation resistance, fuel cycle economics, and safety. The process objectives are readiness to proceed and adaptability and robustness in the face of uncertainties. A classic decision-making approach to such a multi-attribute problem would be to weight individual quantified criteria and calculate an overall figure of merit. This is inappropriate for several reasons. First, the goals are not independent. Second, the importance of different goals varies among stakeholders. Third, the importance of different goals is likely to vary with time, especially the “energy future.” Fourth, some key considerations are not easily or meaningfully quantifiable at present. Instead, at this point, we have developed 16 questions the AFCI program should answer and suggest an approach of determining for each whether relevant options improve meeting each of the program goals. We find that it is not always clear which option is best for a specific question and specific goal; this helps identify key issues for future work. In general, we suggest attempting to create as many win-win decisions (options that are attractive or neutral to most goals) as possible. Thus, to help clarify why the program is exploring the options it is, and to set the stage for future narrowing of options, we have developed 16 questions, as follows: · What are the AFCI program goals? · Which potential waste disposition approaches do we plan for? · What are the major separations, transmutation, and fuel options? · How do we address proliferation resistance? · Which potential energy futures do we plan for? · What potential external triggers do we plan for? · Should we separate uranium? · If we separate uranium, should we recycle it, store it or dispose of it? · Is it practical to plan to fabricate and handle “hot” fuel? · Which transuranic elements (TRU) should be separated and transmuted? · Of those TRU separated, which should be transmuted together? · Should we separate and/or transmute Cs and Sr isotopes that dominate near-term repository heating? · Should we separate and/or transmute very long-lived Tc and I isotopes? · Which separation technology? · What mix of transmutation technologies? · What fuel technology best supports the above decisions?
A Human Corneal Organ Culture Model of Descemet's Stripping Only with Accelerated Healing Stimulated by Engineered Fibroblast Growth Factor 1 (2022)

Fuchs Endothelial Corneal Dystrophy (FECD) results from dysfunctional corneal endothelial cells (CECs) and is currently treated by transplantation of the whole cornea or Descemet's membrane. Recent developments in ocular surgery have established Descemet's Stripping Only (DSO), a surgical technique in which a central circle of guttae-dense Descemet's membrane is removed to allow for the migration of CECs onto the smooth stroma, restoring function and vision to the cornea. While this potential treatment option is of high interest in the field of ophthalmic research, no successful ex vivo models of DSO have been established and clinical data is limited. This work presents a novel wound-healing model simulating DSO in human donor corneas. Using this approach to evaluate the efficacy of the human engineered FGF1 (NM141), we found that treatment accelerated healing via stimulation of migration and proliferation of CECs. This finding was confirmed in 11 pairs of human corneas with signs of dystrophy reported by the eye banks in order to verify that these results can be replicated in patients with Fuchs' Dystrophy, as the target population of the DSO procedure.
Abstract 5714: AXL and GAS6 Co-expression in lung adenocarcinoma as a prognostic classifier (2017)

Abstract AXL, a receptor tyrosine kinase implicated in cell survival, proliferation, and migration, is also associated with acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor therapy. However, its prognostic significance in lung adenocarcinoma (AD) remains unclear. We therefore evaluated the prognostic significance of the expression of AXL and/or its ligand, growth arrest-specific 6 (GAS6), in completely resected lung AD. We evaluated the relationship between AXL, GAS6, and vimentin expression, as determined by immunohistochemistry (IHC) analysis, with overall survival and disease-free survival in 113 patients with stages I-III lung AD. Protein expression was also assayed using western blot analysis in 10 lung AD cell lines. AXL-positive (AXL+), GAS6-positive (GAS6+), or AXL+/GAS6+ staining was significantly associated with vimentin-positive (vimentin+) expression. AXL+/GAS6+ and vimentin+ showed a negative tendency toward an association with EGFR mutation. AXL+, GAS6+, or AXL+/GAS6+ statuses significantly correlated with poor overall survival. In stage I cases, an AXL+/GAS6+ status significantly correlated with poor overall survival and disease-free survival, especially in cases with wild-type EGFR. In multivariate analysis, AXL/GAS6 classifications in stage I as well as in stages I-III lung AD were found to be independent factors for poor patient outcomes. Unlike lung AD cell lines with mutant EGFR, those with wild-type EGFR closely correlated with AXL and vimentin expression by western blotting. AXL+ and GAS6+ expression is relevant to a poor prognosis in resected lung AD patients at stage I. AXL/GAS6 might serve as crucial predictive and prognostic biomarkers and targets to identify individuals at high risk of post-operative death. Citation Format: Masahiro Seike, Ritaro Noro, Cheol-Hong Kim, Fenfei Zou, Kaoru Kubota, Akihiko Gemma. AXL and GAS6 Co-expression in lung adenocarcinoma as a prognostic classifier [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5714. doi:10.1158/1538-7445.AM2017-5714
IMPROVED MICROPOROUS BIORESORBABLE INTRAVASCULAR STENTS FOR GENE THERAPY APPLICATIONS (1996)

Ye, Y-W; Landau, C.; Meidell, R.; Willard, J.; Moskowitz, A.; Aziz, S.; Carlisle, E.; Nelson, K.; Eberhart, R. Author Information
Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1 (2021)

Cas12i is a newly identified member of the functionally diverse type V CRISPR-Cas effectors. Although Cas12i has the potential to serve as genome-editing tool, its structural and functional characteristics need to be investigated in more detail before effective application. Here we report the crystal structures of the Cas12i1 R-loop complexes before and after target DNA cleavage to elucidate the mechanisms underlying target DNA duplex unwinding, R-loop formation and cis cleavage. The structure of the R-loop complex after target DNA cleavage also provides information regarding trans cleavage. Besides, we report a crystal structure of the Cas12i1 binary complex interacting with a pseudo target oligonucleotide, which mimics target interrogation. Upon target DNA duplex binding, the Cas12i1 PAM-interacting cleft undergoes a remarkable open-to-closed adjustment. Notably, a zipper motif in the Helical-I domain facilitates unzipping of the target DNA duplex. Formation of the 19-bp crRNA-target DNA strand heteroduplex in the R-loop complexes triggers a conformational rearrangement and unleashes the DNase activity. This study provides valuable insights for developing Cas12i1 into a reliable genome-editing tool.
Thick Origami Based Foldable Patch Antenna Array (2019)

This paper presents a thick origami based foldable patch antenna array with a packing efficiency of 50%. The array is designed on low-cost FR4 substrate having a thickness of 1.5 mm and an overall dimension of 180 mm × 96 mm. The peak gain at broadside is approximately 6.3 dB. The array is capable to reconfigure to a compressed form factor making it suitable for efficient packing and deployment applications.
Autolysis of phytic acid and protein in canola meal (Brassica spp.), wheat bran (Triticum spp.) and fish silage blends (1984)

Abstract Fish silage, canola meal, and wheat bran were blended to form an acid‐stabilised, paste‐like product. Changes in protein nitrogen, non‐protein nitrogen, phytic acid, and orthophosphorus contents of the acidified blends were measured over a 5‐week period of storage at room temperature (20–22°C). During the storage period, phytic acid from the canola meal was dephosphorylated by phytase from the wheat bran. Changes in the level of non‐protein nitrogen showed that the fish proteins were partially hydrolysed and liquefied during storage, and that the fish enzymes may have partially hydrolysed the canola meal and wheat bran proteins. The resulting product could be stored at room temperature without spoiling and could be dried in conventional drying equipment. This process provides a means of improving the nutritional value of canola meal by reducing its high phytate content, and of producing a homogeneous dry feed commodity from liquid fish silage.
Rapid formation of N-nitrosamines from nitric oxide in the presence of silver(I) salts (1978)

B. C. Challis and J. R. Outram, J. Chem. Soc., Chem. Commun., 1978, 707 DOI: 10.1039/C39780000707
Improving the Operations of the Earth Observing One Mission via Automated Mission Planning (2010)

We describe the modeling and reasoning about operations constraints in an automated mission planning system for an earth observing satellite - EO-1. We first discuss the large number of elements that can be naturally represented in an expressive planning and scheduling framework. We then describe a number of constraints that challenge the current state of the art in automated planning systems and discuss how we modeled these constraints as well as discuss tradeoffs in representation versus efficiency. Finally we describe the challenges in efficiently generating operations plans for this mission. These discussions involve lessons learned from an operations model that has been in use since Fall 2004 (called R4) as well as a newer more accurate operations model operational since June 2009 (called R5). We present analysis of the R5 software documenting a significant (>50%) increase in the number of weekly observations scheduled by the EO-1 mission. We also show that the R5 mission planning system produces schedules within 15% of an upper bound on optimal schedules. This operational enhancement has created value of millions of dollars US over the projected remaining lifetime of the EO-1 mission.