gebhart/patrepeval huggingface dataset:
Resistance mutation conserved between insects and mites unravels the benzoylurea insecticide mode of action on chitin biosynthesis (2016)

Despite the major role of chitin biosynthesis inhibitors such as benzoylureas (BPUs) in the control of pests in agricultural and public health for almost four decades, their molecular mode of action (MoA) has in most cases remained elusive. BPUs interfere with chitin biosynthesis and were thought to interact with sulfonylurea receptors that mediate chitin vesicle transport. Here, we uncover a mutation (I1042M) in the chitin synthase 1 (CHS1) gene of BPU-resistant Plutella xylostella at the same position as the I1017F mutation reported in spider mites that confers etoxazole resistance. Using a genome-editing CRISPR/Cas9 approach coupled with homology-directed repair (HDR) in Drosophila melanogaster, we introduced both substitutions (I1056M/F) in the corresponding fly CHS1 gene (kkv). Homozygous lines bearing either of these mutations were highly resistant to etoxazole and all tested BPUs, as well as buprofezin-an important hemipteran chitin biosynthesis inhibitor. This provides compelling evidence that BPUs, etoxazole, and buprofezin share in fact the same molecular MoA and directly interact with CHS. This finding has immediate effects on resistance management strategies of major agricultural pests but also on mosquito vectors of serious human diseases such as Dengue and Zika, as diflubenzuron, the standard BPU, is one of the few effective larvicides in use. The study elaborates on how genome editing can directly, rapidly, and convincingly elucidate the MoA of bioactive molecules, especially when target sites are complex and hard to reconstitute in vitro.
713. NFkB Decoy Oligodeoxynucleotides Inhibit Osteoclast Differentiation and Activation In Vitro and Improve Osteoporosis of Ovariectomized and Vitamin C Difficient Rat Models (2006)

In this study, we focused on NFkB decoy oligodeoxynucleotides (NFkB decoy) as a new therapeutic strategy to attenuate osteoporosis. Tartrate resistant acid phosphatase (TRAP) positive multinucleated cells (osteoclasts) formed from neonatal rabbit bone marrow culture by 1,25-vitamin D3 stimulation were decreased by NFkB decoy treatment in dose dependent manner and pits formed on dentine slices by mature osteoclasts were reduced. In M-CSF and RANKL stimulated osteoclast culture system, NFkB decoy also inhibited the diffentiation and activation of osteoclast as well. In rat ovariectomized model of estrogen deficiency, continuous administration of NFkB decoy using osmotic pump attenuated the increase of TRAP activity, accompanied by a singificant increase in calcium concentration in femur and tibia and decreased in urinary deoxypyridinoline. In additional osteoporosis model of vitamin C deficient rat, inhibiton of NFkB by decoy dramatically improved the bone length, weight and mineral density as assessed by dual-energy X-ray absorptiometry. Overall, inhibition of NFkB by decoy strategy prevented osteoporosis through the inhibition of bone resorption. Targetting of NFkB might be potential therapy in various bone metabolic diseases.
Balanced alternating steady‐state elastography (2006)

A conventional balanced steady-state free precession (b-SSFP) sequence scheme was modified such that the dynamic equilibrium becomes very sensitive to small cyclic displacements, generating two distinct and alternating steady states. This novel technique is proposed for the visualization of propagating transverse acoustic shear waves, as used in MR elastography (MRE) to determine the mechanical properties of materials or in vivo soft tissue. Experiments with tissue-like agarose gel phantoms and simulations demonstrate that the novel sequence offers an increase in phase sensitivity by about one order in magnitude compared to standard motion-encoding methods. In addition, the new method benefits from the very short acquisition times achieved by b-SSFP protocols.
Trade-off between optical modulation amplitude and modulation bandwidth of silicon micro-ring modulators (2014)

An analytic model is developed to study the dynamic response of carrier-depletion silicon ring modulators. Its validity is confirmed by a detailed comparison between the modeled and the measured small signal frequency response of a practical device. The model is used to investigate how to maximize the optical modulation amplitude (OMA) and how the OMA could be traded for the bandwidth by tuning the coupling strength and the operation wavelength. Our calculation shows that for a ring modulator with equal RC time constant and photon lifetime, if its operation wavelength shifts from the position of the maximum OMA towards the direction that is away from the resonance, the 3dB modulation bandwidth increases ~2.1 times with a penalty of 3 dB to the OMA.
Incorporating User Feedback into Sequence to Sequence Model Training (2020)

As the largest professional network, LinkedIn hosts millions of user profiles and job postings. Users effectively find what they need by entering search queries. However, finding what they are looking for can be a challenge, especially if they are unfamiliar with specific keywords from their industry. Query Suggestion is a popular feature where a search engine can suggest alternate, related queries. At LinkedIn, we have productionized a deep learning Seq2Seq model to transform an input query into several alternatives. This model is trained by examining search history directly typed by users. Once online, we can determine whether or not users clicked on suggested queries. This new feedback data indicates which suggestions caught the user's attention. In this work, we propose training a model with both the search history and user feedback datasets. We examine several ways to incorporate feedback without any architectural change, including adding a novel pairwise ranking loss term during training. The proposed new training technique produces the best combined score out of several alternatives in offline metrics. Deployed in the LinkedIn search engine, it significantly outperforms the control model with respect to key business metrics.
Capacity Maximization with Polarization-Agile Antennas in the MIMO Communication System (2014)

Polarization diversity is an important candidate for improving the channel capacity in multiple-input multiple-output (MIMO) communication systems. The use of polarization-agile antennas enables to reap important benefits of polarization diversity without the need for additional up/down-conversion chains and their associated cost and energy consumption. In this paper we propose a novel scheme of polarization pre-post coding based on the theoretical (approximate) closed-form derivation of optimal transmit/receive polarization vectors to maximize channel capacity when polarization agility is available only at one link end. We use those as basis for an iterative joint polarization pre-post coding for polarization agility at both link ends. Simulations validate that the obtained capacity is in a close agreement with that obtained by exhaustive numerical search for optimal transmit/receive polarization orientation. Utilizing our scheme of joint polarization pre-post coding improves system performance by 3 dB to 5 dB in terms of the SNR.
Solving the bottleneck problem at automated highway exits (1996)

Automated Highway Systems (AHS) offer a potential solution that could triple current freeway capacity. A three-fold increase in freeway capacity would translate into a significant increase in peak freeway traffic flow. The corresponding increase of flow on urban roads due to exiting AHS vehicles could quickly overwhelm the capacity of urban streets and lead to critical bottlenecking of AHS flow. If exiting AHS vehicles can not sufficiently clear AHS exits because the local streets are jammed, traffic will spill onto the AHS mainline and reduce AHS capacity. The loss of AHS capacity due to congestion in urban destinations and the resulting back spill of traffic onto the AHS will greatly detract from the AHS system. The following Non-Intermodal Interface (NII) and Intermodal Interface (II) strategies are proposed as solutions to this critical bottleneck problem: 1) the dispersion of flow through AHS networks; 2) the dispersion of flow at commuter destinations; and 3) the consolidation of flow at central locations. Specifically, smart street signals and prioritized street design; intermodal terminals; and automated garages are identified as potential solutions. This paper discusses the advantages and disadvantages of each of the three general strategies. Specifically, it discusses the advantages and disadvantages of each of the four specific solutions through simulated scenarios which account for varying ramp volumes, trip attraction patterns, and urban structures. Our investigation shows that creative combinations of these methods can be useful to integrate future AHS with local road networks.
Supplementary Tables from Selective Androgen Receptor Modulator RAD140 Inhibits the Growth of Androgen/Estrogen Receptor–Positive Breast Cancer Models with a Distinct Mechanism of Action (2023)

&lt;p&gt;Supplementary Table S1. List of targets in the spectrum screen Supplementary Table S2. Characteristics of the breast cancer PDX models Supplementary Table S3. List of genes upregulated by more than 2-fold in RAD140-treated HBCx-22 xenografts&lt;/p&gt;
Speciation of Mercury in Selected Areas of the Petroleum Value Chain (2017)

Petroleum, natural gas, and natural gas condensate can contain low levels of mercury (Hg). The speciation of Hg can affect its behavior during processing, transport, and storage so efficient and safe management of Hg requires an understanding of its chemical form in oil, gas and byproducts. Here, X-ray absorption spectroscopy was used to determine the Hg speciation in samples of solid residues collected throughout the petroleum value chain including stabilized crude oil residues, sediments from separation tanks and condensate glycol dehydrators, distillation column pipe scale, and biosludge from wastewater treatment. In all samples except glycol dehydrators, metacinnabar (β-HgS) was the primary form of Hg. Electron microscopy on particles from a crude sediment showed nanosized (<100 nm) particles forming larger aggregates, and confirmed the colocalization of Hg and sulfur. In sediments from glycol dehydrators, organic Hg(SR)<sub>2</sub> accounted for ∼60% of the Hg, with ∼20% present as β-HgS and/or Hg(SR)<sub>4</sub> species. β-HgS was the predominant Hg species in refinery biosludge and pipe scale samples. However, the balance of Hg species present in these samples depended on the nature of the crude oil being processed, i.e. sweet (low sulfur crudes) vs sour (higher sulfur crudes). This information on Hg speciation in the petroleum value chain will inform development of better engineering controls and management practices for Hg.
Impact of chemotactic factors and receptors on the cancer immune infiltrate: a bioinformatics study revealing homogeneity and heterogeneity among patient cohorts (2018)

Multiple soluble factors including proteins (in particular chemokines), non-proteinaceous factors released by dead cells, as well as receptors for such factors (in particular chemokine receptors, formyl peptide receptors and purinergic receptors), influence the recruitment of distinct cell subsets into the tumor microenvironment. We performed an extensive bioinformatic analysis on tumor specimens from 5953 cancer patients to correlate the mRNA expression levels of chemotactic factors/receptors with the density of immune cell types infiltrating the malignant lesions. This meta-analysis, which included specimens from breast, colorectal, lung, ovary and head and neck carcinomas as well as melanomas, revealed that a subset of chemotactic factors/receptors exhibited a positive and reproducible correlation with several infiltrating cell types across various solid cancers, revealing a universal pattern of association. Hence, this meta-analysis distinguishes between homogeneous associations that occur across different cancer types and heterogeneous correlations, that are specific of one organ. Importantly, in four out of five breast cancer cohorts for which clinical data were available, the levels of expression of chemotactic factors/receptors that exhibited universal (rather than organ-specific) positive correlations with the immune infiltrate had a positive impact on the response to neoadjuvant chemotherapy. These results support the notion that general (rather than organ-specific) rules governing the recruitment of immune cells into the tumor bed are particularly important in determining local immunosurveillance and response to therapy.
Cancer Nanotechnology (2017)

Overview The advances in state‐of‐the‐art nanotechnologies have offered exciting opportunities to overcome many obstacles that contribute to the high mortality and recurrence of cancer, such as suboptimal pharmacokinetics and therapeutic efficacy of anticancer drugs, severe adverse effects, development of drug resistance, and cancer metastases. Here, we highlight the clinical stage nanoparticle technologies applied in conventional cancer therapies and for the development of novel classes of anticancer therapeutics. We also discuss recent cutting‐edge research efforts in this exciting field, which could lead to more effective therapeutic nanoparticles for cancer treatment.
Control Process Gain of Erbium Doped Fiber Amplifiers with Wavelength Division Multiplexed Signals (2006)

The pump-to-output-power control process gain is measured for a gain-flattened erbium doped fiber amplifier as a function of wavelength division multiplexed signal channel configuration and compared with wavelength independent measures.
CheckFence (2007)

Concurrency libraries can facilitate the development of multi-threaded programs by providing concurrent implementations of familiar data types such as queues or sets. There exist many optimized algorithms that can achieve superior performance on multiprocessors by allowing concurrent data accesses without using locks. Unfortunately, such algorithms can harbor subtle concurrency bugs. Moreover, they requirememory ordering fences to function correctly on relaxed memory models.
DRAG-REDUCING POLYMERS PREVENT LETHALITY AND IMPROVE BLOOD CHEMISTRY PARAMETERS IN ANIMALS EXPOSED TO ACUTE HYPOBARIC HYPOXIA (2002)

We tested the hypothesis that the presence in blood of particular blood-soluble, drag-reducing polymers (DRPs) can reduce mortality and better maintain homeostasis in animals subjected to significantly limited access to oxygen. A DRP solution was injected in rats (n=23) to yield a concentration in blood of about 2–5 ppm. Control animals (n = 23) were injected with the same volume of saline. About 45 minutes after injection, animals were placed in a hypobaric chamber where they were exposed for 5 min to oxygen concentrations corresponding to an altitude of over 25,000 it. In control animals, this acute hypoxia produced 40% mortality. In the experimental (DRP) group, all animals survived. Compared to the control animals, the animals receiving DRPs demonstrated higher pH and p02 and lower lactate levels in blood samples obtained after exposure to hypobaric hypoxia (all p < 0.001). Mechanisms underlying the obtained results are currently being elucidated. Previously, we have shown that DRPs significantly increase microcirculatory flow following a single intravenous injection in animals. We hypothesize that this salutary effect of DRPs on the microcirculation leads to an increase in oxygen delivery to tissues and organs, even at extremely low ambient oxygen concentrations. Our results suggest that DRPs warrant further investigation as a potential bioengineering-based therapy for respiratory distress/failure.
Ligand-dependent Transcription Switches and Their Potential for Gene Therapy (2000)

The potential advantage offered by gene therapy over conventional medicine for the treatment of several diseases is unquestionable. It is nonetheless also clear that efficacy, and more importantly safety, remain the main issues to be solved before this technology can be adopted routinely as a standard therapeutic practice (1,2). At the time of writing this article, beginning in 2003, clinical efficacy of gene transfer has been convincingly demonstrated only for Severe Combined Immune Deficiency (SCID). In contrast, safety concerns have been raised as a consequence of adverse side effects in several clinical trials (3-8). Therefore, the major challenge still remains the development of vectors characterized by maximum transduction efficiency combined with minimal toxicity (9,10). In current years the continuous application of ‘‘good basic science’’ to the gene therapy field has been directed at fulfilling these two main goals. With the decline of the initial concept of a ‘‘universal vector’’ for all diseases, the emerging scenario is to generate a large repertoire of safe vectors, each suited to target a given tissue or cell type, or tailored to treat a specific clinical condition. (11-13). Based on these premises, any work directed at developing systems, which allow to control and finely tune the expression of therapeutic gene(s), must be taken into serious consideration.
Reduction of Aggressiveness and Impulsiveness during Clozapine Treatment in Chronic Neuroleptic-Resistant Schizophrenic Patients (1997)

Aggressive and impulsive behavior is frequently observed in schizophrenic patients. Previous studies suggest that impulsive aggression may be the most common behavioral correlate of central serotonergic system dysfunction. This study was aimed to determine if clozapine, an atypical antipsychotic agent with potent serotonergic antagonistic properties, can reduce impulsiveness and aggression in neuroleptic-resistant chronic schizophrenic patients. Fourteen neuroleptic-resistant chronic schizophrenic patients were treated with clozapine and prospectively evaluated for aggressiveness and impulsiveness for 18 weeks. Clozapine treatment induced a marked decrease in impulsiveness (32% on the Impulsivity Scale; p < 0.0001) and aggressiveness (98% on the Overt Aggression Scale; p < 0.0001). We conclude that clozapine treatment may be effective in reducing psychotic symptoms as well as in controlling aggressive and impulsive behavior in neuroleptic-resistant chronic schizophrenic patients.
Hybrid S- to L-band fiber amplifier module with coupled structure (2005)

Erbium-doped fiber amplifiers ~EDFAs! with wide bandwidth are considerably interesting for high-capacity transmission in dense wavelength division multiplexing ~DWDM! systems. However, the transmission capacities in DWDM systems are limited by the gain bandwidth of C-band EDFAs ~1530 to 1560 nm!. Furthermore, L-band ~1560 to 1610 nm! fiber amplifier techniques have been achieved, such as EDFAs using a longer erbium-doped fiber ~EDF! than that of C-band EDFAs, fiber Raman amplifiers, or hybrid amplifiers. In addition, a wide-band EDFA from Cto L-band using a coupled structure has also been studied. In other words, two types of wide-band amplifiers with gain bandwidths of around 100 nm have been reported. The first is a coupled-structure amplifier multiplexing the gain bands, namely, the S-band thulium-doped fluoride fiber amplifier ~TDFA! or fiber Raman amplifier and the C-band and L-band erbium-doped fiber amplifiers. The other is a silica-based fiber Raman amplifier ~S-FRA! featuring a multiwavelength pump technique. Recently, a new S-band ~1450 to 1530 nm! amplification technique, which utilizes erbium-doped silica fiber with a depressed cladding design and a 980-nm pump laser to generate EDF gain extension effects, has been
Generalized Systematic Approach Applied to Design a Novel Three-Port Power Converter (2020)

There has been growing interest in multi-port power converters especially three-port converters (TPCs) over the past several years. The main reason is their growing use in applications like solar and traction applications to combine different blends of energy sources/storage. Even though there is a large body of work that exists in literature and a large number of topologies proposed as well as a few review papers, there is no generalized systematic approach explaining how to develop/design a TPC based on the involved inputs and outputs. This paper presents this generalized systematic approach. The proposed approach will be applied to two cases and the topologies that evolve out of this process will be discussed. The paper will also cover in a more comprehensive way the various modes of operation of a TPC. Also, the proposed approach has been used to develop a novel three-port power converter and the simulation results will be presented.
Polycondensation of Butenediol: Synthesis of Telechelic 2-Butene-1,4-diol Oligomers (2011)

The catalytic condensation of cis-2-butene-1,4-diol with CpRu(MQA)(C(3)H(5)) (Cp = cyclopentadienyl, MQA = 4-methoxyquinoline-2-carboxylate) generates poly(2-butenediol), an unsaturated telechelic polyether diol with molecular weights between 400 and 4600 g/mol. This Ru(IV) allyl catalyst enchains 2-butene-1,4-diol primarily as the linear trans-2-butenyl ether (92%) along with vinyl branches (8%). These telechelic oligomers are useful chain extenders and macromonomers, as demonstrated by their use in the synthesis of poly(lactide)-b-poly(butenediol)-b-poly(lactide) triblock copolymers. Model studies support a proposed mechanism involving the formation of Ru(IV) allyl intermediates from allylic alcohols and chain growth by selective nucleophilic displacement at the terminus of the Ru(IV) allyl to generate trans-2-butenyl ether linkages.
Signal Processing Strategies for Cochlear Implants Using Current Steering (2009)

In contemporary cochlear implant systems, the audio signal is decomposed into different frequency bands, each assigned to one electrode. Thus, pitch perception is limited by the number of physical electrodes implanted into the cochlea and by the wide bandwidth assigned to each electrode. The Harmony HiResolution bionic ear (Advanced Bionics LLC, Valencia, CA, USA) has the capability of creating virtual spectral channels through simultaneous delivery of current to pairs of adjacent electrodes. By steering the locus of stimulation to sites between the electrodes, additional pitch percepts can be generated. Two new sound processing strategies based on current steering have been designed, SpecRes and SineEx. In a chronic trial, speech intelligibility, pitch perception, and subjective appreciation of sound were compared between the two current steering strategies and standard HiRes strategy in 9 adult Harmony users. There was considerable variability in benefit, and the mean results show similar performance with all three strategies.
Efficient encoding of QC-LDPC codes related to cyclic MDS codes (2008)

In this paper, we present an efficient systematic encoding algorithm for quasi-cyclic (QC) low-density parity-check (LDPC) codes which are related to cyclic maximum-distance separable (MDS) codes. The algorithm has linear time complexity, and it can be easily implemented by using polynomial multiplication and division circuits. We show that the division polynomials can be completely characterized by its zeros and that the sum of the numbers of the zeros is equal to the parity-length of the codes.
Video Decoding Energy Reduction Using Temporal-Domain Filtering (2023)

In this paper, we study decoding energy reduction opportunities using temporal-domain filtering and subsampling methods. In particular, we study spatiotemporal filtering using a contrast sensitivity function and temporal downscaling, i.e., frame rate reduction. We apply these concepts as a pre-filtering to the video before compression and evaluate the bitrate, the decoding energy, and the visual quality with a dedicated metric targeting temporally down-scaled sequences. We find that decoding energy savings yield 35% when halving the frame rate and that spatiotemporal filtering can lead to up to 5% of additional savings, depending on the content.