gebhart/patrepeval huggingface dataset:
Improving Language Model Fine-tuning with Information Gain Filtration (2022)

Language model fine-tuning is essential for modern natural language processing. The effectiveness of fine-tuning is limited by the inclusion of training examples that negatively affect performance. Here we present Information Gain Filtration, a general fine-tuning method, for improving the overall final performance of a fine-tuned model. We define Information Gain of an example as the improvement on a validation metric after training on that example. A secondary learner is then trained to approximate this quantity. During fine-tuning, this learner filters informative examples from uninformative ones. We show that our method is robust and has consistent improvement across datasets, fine-tuning tasks, and language model architectures.
First International Sdn-Based Network Orchestration Of Variable-Capacity Ops Over Programmable Flexi-Grid Eon (2014)

The first experimental demonstrator of 46-108Gbps discrete-multi-tone (DMT) fixed-length variable capacity OPS over programmable, flexi-grid elastic optical path network (EON), orchestrated via multiple OpenFlow controllers in the framework of SDN is presented.
Serine protease mechanism: structure of an inhibitory complex of .alpha.-lytic protease and a tightly bound peptide boronic acid (1987)

The structure of the complex formed between alpha-lytic protease, a serine protease secreted by Lysobacter enzymogenes, and N-tert-butyloxycarbonylalanylprolylvaline boronic acid (Ki = 0.35 nM) has been studied by X-ray crystallography to a resolution of 2.0 A. The active-site serine forms a covalent, nearly tetrahedral adduct with the boronic acid moiety of the inhibitor. The complex is stabilized by seven hydrogen bonds between the enzyme and inhibitor with additional stabilization arising from van der Waals interactions between enzyme and inhibitor side chains and the burying of 330 A2 of hydrophobic surface area. Hydrogen bonding between Asp-102 and His-57 remains intact in the enzyme-inhibitor complex, and His N epsilon 2 is well positioned to donate its hydrogen to the leaving group. Little change in the positions of protease residues was observed on complex formation (root mean square main chain deviation = 0.13 A), suggesting that in its native state the enzyme is complementary to tetrahedral reaction intermediates or to the nearly tetrahedral transition state for the reaction.
The oncoprotein NPM-ALK of anaplastic large-cell lymphoma induces JUNB transcription via ERK1/2 and JunB translation via mTOR signaling (2007)

Anaplastic large cell lymphomas (ALCLs) are highly proliferating tumors that commonly express the AP-1 transcription factor JunB. ALK fusions occur in approximately 50% of ALCLs, and among these, 80% have the t(2;5) translocation with NPM-ALK expression. We report greater activity of JunB in NPM-ALK-positive than in NPM-ALK-negative ALCLs. Specific knockdown of JUNB mRNA using small interfering RNA and small hairpin RNA in NPM-ALK-expressing cells decreases cellular proliferation as evidenced by a reduced cell count in the G2/M phase of the cell cycle. Expression of NPM-ALK results in ERK1/2 activation and transcriptional up-regulation of JUNB. Both NPM-ALK-positive and -negative ALCL tumors demonstrate active ERK1/2 signaling. In contrast to NPM-ALK-negative ALCL, the mTOR pathway is active in NPM-ALK-positive lymphomas. Pharmacological inhibition of mTOR in NPM-ALK-positive cells down-regulates JunB protein levels by shifting JUNB mRNA translation from large polysomes to monosomes and ribonucleic particles (RNPs), and decreases cellular proliferation. Thus, JunB is a critical target of mTOR and is translationally regulated in NPM-ALK-positive lymphomas. This is the first study demonstrating translational control of AP-1 transcription factors in human neoplasia. In conjunction with NPM-ALK, JunB enhances cell cycle progression and may therefore represent a therapeutic target.
Sparsity and Sentence Structure in Encoder-Decoder Attention of\n Summarization Systems (2021)

Transformer models have achieved state-of-the-art results in a wide range of\nNLP tasks including summarization. Training and inference using large\ntransformer models can be computationally expensive. Previous work has focused\non one important bottleneck, the quadratic self-attention mechanism in the\nencoder. Modified encoder architectures such as LED or LoBART use local\nattention patterns to address this problem for summarization. In contrast, this\nwork focuses on the transformer's encoder-decoder attention mechanism. The cost\nof this attention becomes more significant in inference or training approaches\nthat require model-generated histories. First, we examine the complexity of the\nencoder-decoder attention. We demonstrate empirically that there is a sparse\nsentence structure in document summarization that can be exploited by\nconstraining the attention mechanism to a subset of input sentences, whilst\nmaintaining system performance. Second, we propose a modified architecture that\nselects the subset of sentences to constrain the encoder-decoder attention.\nExperiments are carried out on abstractive summarization tasks, including\nCNN/DailyMail, XSum, Spotify Podcast, and arXiv.\n
Supplementary Figure S24 from Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition (2023)

&lt;p&gt;Supplementary Figure S24 shows that amplification of the enhancer region 640 kb upstream of the androgen receptor (AR) is common.&lt;/p&gt;
Effects of short-term hyperoxemia on cerebral autoregulation and tissue oxygenation in acute brain injured patients (2023)

<b>Introduction:</b> Potential detrimental effects of hyperoxemia on outcomes have been reported in critically ill patients. Little evidence exists on the effects of hyperoxygenation and hyperoxemia on cerebral physiology. The primary aim of this study is to assess the effect of hyperoxygenation and hyperoxemia on cerebral autoregulation in acute brain injured patients. We further evaluated potential links between hyperoxemia, cerebral oxygenation and intracranial pressure (ICP). <b>Methods:</b> This is a single center, observational, prospective study. Acute brain injured patients [traumatic brain injury (TBI), subarachnoid hemorrhage (SAH), intracranial hemorrhage (ICH)] undergoing multimodal brain monitoring through a software platform (ICM+) were included. Multimodal monitoring consisted of invasive ICP, arterial blood pressure (ABP) and near infrared spectrometry (NIRS). Derived parameters of ICP and ABP monitoring included the pressure reactivity index (PRx) to assess cerebral autoregulation. ICP, PRx, and NIRS-derived parameters (cerebral regional saturation of oxygen, changes in concentration of regional oxy- and deoxy-hemoglobin), were evaluated at baseline and after 10 min of hyperoxygenation with a fraction of inspired oxygen (FiO<sub>2</sub>) of 100% using repeated measures <i>t</i>-test or paired Wilcoxon signed-rank test. Continuous variables are reported as median (interquartile range). <b>Results:</b> Twenty-five patients were included. The median age was 64.7 years (45.9-73.2), and 60% were male. Thirteen patients (52%) were admitted for TBI, 7 (28%) for SAH, and 5 (20%) patients for ICH. The median value of systemic oxygenation (partial pressure of oxygen-PaO<sub>2</sub>) significantly increased after FiO<sub>2</sub> test, from 97 (90-101) mm Hg to 197 (189-202) mm Hg, <i>p</i> < 0.0001. After FiO<sub>2</sub> test, no changes were observed in PRx values (from 0.21 (0.10-0.43) to 0.22 (0.15-0.36), <i>p</i> = 0.68), nor in ICP values (from 13.42 (9.12-17.34) mm Hg to 13.34 (8.85-17.56) mm Hg, <i>p</i> = 0.90). All NIRS-derived parameters reacted positively to hyperoxygenation as expected. Changes in systemic oxygenation and the arterial component of cerebral oxygenation were significantly correlated (respectively ΔPaO<sub>2</sub> and ΔO<sub>2</sub>Hbi; r = 0.49 (95% CI = 0.17-0.80). <b>Conclusion:</b> Short-term hyperoxygenation does not seem to critically affect cerebral autoregulation.
Behavioral anomaly detection using Bayesian modelization based on a global vision of the system (2007)

National audience
Molecular engineering of NLO-phores for new NLO microscopies (2002)

Novel microscopies based on nonlinear optical (NLO) phenomena such as two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) have gained overwhelming popularity in the biology community owing to the many advantages they provide in biological imaging. Examples of molecular engineering approaches toward NLO-probes specifically designed for SHG and/or TPEF imaging of lipid membranes and biological cells are given here, providing an illustration of their intriguing potential in the area of real-time, non-damaging imaging of biological structures. Optimized NLO-markers open new routes for improved monitoring and better understanding of fundamental dynamic processes.
New technique for EUV mask defect mitigation: "Reversal Technology" (2005)

International audience
Impact of optimal MAC layer attacks on the network layer (2006)

Node misbehavior in wireless ad hoc networks leads to sudden unpredictable changes in network topology, resulting in fluctuation of traffic load and capacity for already existing links. In this work we consider node misbehavior in the Medium Access Control (MAC) layer and its effects on the performance of the network layer. In order to capture uncertainty of the attacker's strategy as well as the unpredictable nature of the wireless medium, we quantify the optimal attack strategy by using the principle of minimum cross-entropy. Following that, we apply the obtained results for analysis of the IEEE 802.11 DCF MAC protocol and investigate the effects of such optimal attacks on the network layer. Finally, we evaluate the robustness of two different routing protocols against the worst-case MAC layer attacks and justify the need for the MAC layer-based Intrusion Detection Sytems (IDS).
Sulfur polymer composites as controlled-release fertilisers (2018)

Sulfur polymer composites were prepared by the reaction of canola oil and elemental sulfur in the presence of the NPK fertiliser components ammonium sulfate, calcium hydrogen phosphate, and potassium chloride. These composites released nutrients in a controlled fashion, resulting in less wasted fertiliser and better health for potted tomato plants when compared to free NPK.
Communication and distributional complexity of joint probability mass functions (2004)

The problem of truly-lossless (P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> =0) distributed source coding requires knowledge of the joint statistics of the sources. In particular the locations of the zeroes of the probability mass functions (pmfs) are crucial for encoding at rates below (H(X),H(Y)). We consider the distributed computation of the empirical joint pmf P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> of a sequence of random variable pairs observed at physically separated nodes of a network. We consider both worst-case and average measures of information exchange and treat both exact calculation of P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> and a notion of approximation. We find that in all cases the communication cost grows linearly with the size of the input. Further, we consider the problem of determining whether the empirical pmf has a zero in a particular location and show that in most cases considered this also requires a communication cost that is linear in the input size
Investigating the dependency of an induction machine's main inductance on the supply frequency (2008)

According to several papers, an induction machine's main flux path's saturation state is not only conditioned by the magnetizing current. In the paper at hand the dependency of the magnetization curve on the supply frequency is investigated. Measurements show that the flux linkage decreases with rising supply frequency. This should be considered when incorporating control algorithms based on the main inductance. The magnetization curves calculated from the data retrieved are presented and compared to FEM calculations for validation of the effect under investigation.
Near Net Shape Manufacturing of New, Low Cost Titanium Powders for Industry (2013)

to fabricate finished parts. Given the increasing role of titanium in commercial aircraft, new titanium technologies are needed to create a more sustainable manufacturing strategy that consumes less energy, requires less material, and significantly reduces material and fabrication costs. A number of emerging processes are under development which could lead to a breakthrough in extraction technology. Several of these processes produce titanium alloy powder as a product. The availability of low-cost titanium powders may in turn enable a more efficient approach to the manufacture of titanium components using powder metallurgical processing. The objective of this project was to define energy-efficient strategies for manufacturing large-scale titanium structures using these low-cost powders as the starting material. Strategies include approaches to powder consolidation to achieve fully dense mill products, and joining technologies such as friction and laser welding to combine those mill products into near net shape (NNS) preforms for machining. The near net shape approach reduces material and machining requirements providing for improved affordability of titanium structures. Energy and cost modeling was used to define those approaches that offer the largest energy savings together with the economic benefits needed to drive implementation. Technical feasibility studies were performed to identify the most viable approaches to NNS preform fabrication using basic powder metallurgy mill product forms as the building blocks and advanced joining techniques including fusion and solid state joining to assemble these building blocks into efficient machining performs.
The Use of Presence Data in Modelling Demand for Transportation (2018)

We consider the applicability of the data from operators of cellular systems to modelling demand for transportation. While individual-level data may contain precise paths of movement, stringent privacy rules prohibit their use without consent. Presence data aggregate the individual-level data to information on the numbers of transactions at each base transceiver station (BTS) per each time period. Our work is aimed at demonstrating value of such aggregate data for mobility management while maintaining privacy of users. In particular, given mobile subscriber activity aggregated to short time intervals for a zone, a convex optimisation problem estimates most likely transitions between zones. We demonstrate the method on presence data from Warsaw, Poland, and compare with official demand estimates obtained with classical econometric methods.
Use of Photolithography to Encode Cell Adhesive Domains into Protein Microarrays (2008)

Protein microarrays are rapidly emerging as valuable tools in creating combinatorial cell culture systems where inducers of cellular differentiation can be identified in a rapid and multiplexed fashion. In the present study, protein microarraying was combined with photoresist lithography to enable printing of extracellular matrix (ECM) protein arrays while precisely controlling "on-the-spot" cell-cell interactions. In this surface engineering approach, the micropatterned photoresist layer formed on a glass substrate served as a temporary stencil during the microarray printing, defining the micrometer-scale dimensions and the geometry of the cell-adhesion domains within the printed protein spots. After removal of the photoresist, the glass substrates contained micrometer-scale cell-adhesive regions that were encoded within 300 or 500 microm diameter protein domains. Fluorescence microscopy and atomic force microscopy (AFM) were employed to characterize protein micropatterns. When incubated with micropatterned surfaces, hepatic (HepG2) cells attached on 300 or 500 mum diameter protein spots; however, the extent of cell-cell contacts within each spot varied in accordance with dimensions of the photoresist stencil, from single cells attaching on 30 microm diameter features to multicell clusters residing on 100 or 200 microm diameter regions. Importantly, the photoresist removal process was shown to have no detrimental effects on the ability of several ECM proteins (collagens I, II, and IV and laminin) to support functional hepatic cultures. The micropatterning approach described here allows for a small cell population seeded onto a single cell culture substrate to be exposed to multiple scenarios of cell-cell and cell-surface interactions in parallel. This technology will be particularly useful for high-throughput screening of biological stimuli required for tissue specification of stem cells or for maintenance of differentiated phenotype in scarce primary cells.
The nature of the defects generated from plasma exposure in pristine and ultraviolet-cured low-k organosilicate glass (2011)

Defects in low-k organosilicate glass produced during air and nitrogen plasma exposure were investigated. The defects, through the measurements of electron-spin resonance and Fourier-transform infrared spectroscopy, were found to be silicon-dangling bonds. Air-plasma exposure increases the defect concentrations by breaking silicon–hydrogen bonds. Nitrogen-plasma exposure as well as free-radical exposure has only a small influence on the bond breaking. It was also shown that ultraviolet curing improves the chemical-damage resistance of the dielectric.
Seventy Years of Radar and Communications: The Road from Separation to Integration (2022)

Radar and communications (R&amp;C) as key utilities of electromagnetic (EM) waves have fundamentally shaped human society and triggered the modern information age. Although R&amp;C have been historically progressing separately, in recent decades they have been converging towards integration, forming integrated sensing and communication (ISAC) systems, giving rise to new, highly desirable capabilities in next-generation wireless networks and future radars. To better understand the essence of ISAC, this paper provides a systematic overview on the historical development of R&amp;C from a signal processing (SP) perspective. We first interpret the duality between R&amp;C as signals and systems, followed by an introduction of their fundamental principles. We then elaborate on the two main trends in their technological evolution, namely, the increase of frequencies and bandwidths, and the expansion of antenna arrays. We then show how the intertwined narratives of R&amp;C evolved into ISAC, and discuss the resultant SP framework. Finally, we overview future research directions in this field.
Levetiracetam attenuates hippocampal expression of synaptic plasticity-related immediate early and late response genes in amygdala-kindled rats (2010)

The present study provides mRNA expression data that suggest that levetiracetam attenuates expression of genes known to regulate synaptic remodelling. In the kindled rat, levetiracetam does so by shortening the AD duration thereby reducing the seizure-induced changes in mRNA expression in the hippocampus.
Recursive least-squares backpropagation algorithm for stop-and-go decision-directed blind equalization (2002)

Stop-and-go decision-directed (S-and-G-DD) equalization is the most primitive blind equalization (BE) method for the cancelling of intersymbol-interference in data communication systems. Recently, this scheme has been applied to complex-valued multilayer feedforward neural network, giving robust results with a lower mean-square error at the expense of slow convergence. To overcome this problem, in this work, a fast converging recursive least squares (RLS)-based complex-valued backpropagation learning algorithm is derived for S-and-G-DD blind equalization. Simulation results show the effectiveness of the proposed algorithm in terms of initial convergence.
Lipophilic G-Quadruplexes Are Self-Assembled Ion Pair Receptors, and the Bound Anion Modulates the Kinetic Stability of These Complexes (2003)

With an eye toward the eventual selective modification of noncovalent structures, we used ESI-MS, X-ray crystallography, and NMR spectroscopy to study the anion's influence on the structure and dynamics of self-assembled ion pair receptors formed from guanosine G 1. We compared five complexes of formula (G 1)(16).2Ba(2+).4A(-) containing different organic anions: 2,4,6-trinitrophenolate (2), 2,6-dinitrophenolate (3), 4-methyl-2,6-dinitrophenolate (4), 4-methoxy-2,6-dinitrophenolate (5), and 2,5-dinitrophenolate (6). Crystallography reveals that anion-nucleobase hydrogen bond geometry is sensitive to both phenolate basicity and structure. For the 2,6-substituted anions 2-5, progressive shortening of anion-nucleobase hydrogen bonds is correlated with increased phenolate basicity. Lipophilic G-quadruplexes with different anions also have much different kinetic stabilities in CD(2)Cl(2) solution. Proton NMR shows that free 6 exchanges faster with G-quadruplex-bound anion than do the 2,6-dinitrophenolates 2-5. The increased lability of 6 is probably because, unlike the 2,6-dinitrophenolates, this anion cannot effectively chelate separate G(8).M(2+) octamers via anion-nucleobase hydrogen bonds. In addition to these structural effects, the anion's basicity modulates the anion exchange rate between its free and bound states. 2D EXSY NMR shows that 3 and 5 exchange about 7 times slower than the less basic picrate (2). The use of 3, a relatively basic dinitrophenolate that hydrogen bonds with the amino groups of the two "inner" G(4)-quartets, resulted in extraordinary kinetic stabilization of the G-quadruplex in CD(2)Cl(2). Thus, no isomerization product (G 1)(8).Ba(2+).(G 1)(8).Sr(2+).4(3) was observed even 2 months after the separate G-quadruplexes (G 1)(16).2Ba(2+).4(3) and (G 1)(16).2Sr(2+).4(3) were combined in CD(2)Cl(2). In sharp contrast, G-quadruplexes containing the isomeric 6 anion have isomerization half-lives of approximately t(1/2) = 30 min under identical conditions. All the evidence indicates that the structure and electronics of the organic anions, bound to the assembly's periphery, are crucial for controlling the kinetic stability of these cation-filled G-quadruplexes.
Critical Amino Acids in the Active Site of Meprin Metalloproteinases for Substrate and Peptide Bond Specificity (2003)

The protease domains of the evolutionarily related alpha and beta subunits of meprin metalloproteases are approximately 55% identical at the amino acid level; however, their substrate and peptide bond specificities differ markedly. The meprin beta subunit favors acidic residues proximal to the scissile bond, while the alpha subunit prefers small or aromatic amino acids flanking the scissile bond. Thus gastrin, a peptide that contains a string of five Glu residues, is an excellent substrate for meprin beta, while it is not hydrolyzed by meprin alpha. Work herein aimed to identify critical amino acids in the meprin active sites that determine the substrate specificity differences. Sequence alignments and homology models, based on the crystal structure of the crayfish astacin, showed electrostatic differences within the meprin active sites. Site-directed mutagenesis of active site residues demonstrated that replacement of a hydrophobic residue by a basic amino acid enabled the meprin alpha protease to cleave gastrin. The meprin alphaY199K mutant was most effective; the corresponding mutation of meprin betaK185Y resulted in decreased activity toward gastrin. Peptide cleavage site determinations and kinetic analyses using a variety of peptides extended evidence that meprin alphaTyr-199/betaLys-185 are substrate specificity determinants in meprin active sites. These studies shed light on the molecular basis for the substrate specificity differences of astacin metalloproteinases.