gebhart/patrepeval huggingface dataset:
Next-Generation Sequencing and Emerging Technologies (2019)

Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
Materials from Mussel-Inspired Chemistry for Cell and Tissue Engineering Applications (2015)

Current advances in biomaterial fabrication techniques have broadened their application in different realms of biomedical engineering, spanning from drug delivery to tissue engineering. The success of biomaterials depends highly on the ability to modulate cell and tissue responses, including cell adhesion, as well as induction of repair and immune processes. Thus, most recent approaches in the field have concentrated on functionalizing biomaterials with different biomolecules intended to evoke cell- and tissue-specific reactions. Marine mussels produce mussel adhesive proteins (MAPs), which help them strongly attach to different surfaces, even under wet conditions in the ocean. Inspired by mussel adhesiveness, scientists discovered that dopamine undergoes self-polymerization at alkaline conditions. This reaction provides a universal coating for metals, polymers, and ceramics, regardless of their chemical and physical properties. Furthermore, this polymerized layer is enriched with catechol groups that enable immobilization of primary amine or thiol-based biomolecules via a simple dipping process. Herein, this review explores the versatile surface modification techniques that have recently been exploited in tissue engineering and summarizes polydopamine polymerization mechanisms, coating process parameters, and effects on substrate properties. A brief discussion of polydopamine-based reactions in the context of engineering various tissue types, including bone, blood vessels, cartilage, nerves, and muscle, is also provided.
Antenatal exposure of maternal secondhand smoke (SHS) increases fetal lung expression of RAGE and induces RAGE-mediated pulmonary inflammation (2014)

RAGE augmentation in developing pups exposed to maternal SHS weakens matrix deposition and influences lung inflammation.
Acceleration of Flowering of Statice (Limonium sinuatum Mill.) by Seed Vernalization (1983)

Statice (Limonium sinuatumi Mill. =Statice sinuata L.) is one of perennials, and has a low temperature requirement for bolting and flowering. It is generally stated that in perennials and biennials the low temperature requirement is satisfied when growing plants are chilled in winter, but not when germinating seeds are chilled. In this study, the effect of chilling of germinating seeds on bolting and flowering of statice was investigated. Three cultivars, ‘Early Blue’ (early flowering), ‘Midnight Blue’ (medium flowering), and ‘Super Blue’ (late flowering) were used.1. The statice plants sown in autumn developed flower stalks and formed flower buds in the following spring only when they experienced a certain amount of low temperature in winter.2. The plants from seeds vernalized by chilling at 2-3°C for 30 days flowered earlier with a smaller number of foliage leaves than those from non-vernalized seeds. The vernalized plants produced a greater number of cut flowers in early crop season, that is, until the following March. Although L. sinuatum is perennial, it proves to be a plant of seed vernalization type.3. The most effective temperature for seed vernalization was 2°C. The temperature of 5°C had less effect. Early and medium flowering cultivars were vernalized sufficiently by 2°C for 20 days, while late flowering cultivar for 40 days.4. When the vernalized seedlings were transferred directly to high temperature conditions (constant temperature of 30°C), and grown there for 5 days or more, the vernalization effect was nullified completely. Under field conditions, daily mean temperatures higher than 25°C caused the devernalization.
Secure multidimensional range queries in sensor networks (2009)

Most future large-scale sensor networks are expected to follow a two-tier architecture which consists of resource-rich master nodes at the upper tier and resource-poor sensor nodes at the lower tier. Sensor nodes submit data to nearby master nodes which then answer the queries from the network owner on behalf of sensor nodes. Relying on master nodes for data storage and query processing raises severe concerns about data confidentiality and query-result correctness when the sensor network is deployed in hostile environments. In particular, a compromised master node may leak hosted sensitive data to the adversary; it may also return juggled or incomplete query results to the network owner. This paper, for the first time in the literature, presents a suite of novel schemes to secure multidimensional range queries in tiered sensor networks. The proposed schemes can ensure data confidentiality against master nodes and also enable the network owner to verify with very high probability the authenticity and completeness of any query result by inspecting the spatial and temporal relationships among the returned data. Detailed performance evaluations confirm the high efficacy and efficiency of the proposed schemes.
Toward the mobile Internet (2002)

The promise of ubiquitous computing is a future in which highly specialized, embedded computing devices operate seamlessly within the everyday environment and are transparent to users. Realizing this vision will require next-generation networks to support mobile multimedia devices with capabilities well beyond those of today's handsets. These networks will exploit wideband radio access technologies and IP-based protocols to provide IP transparency-all network elements support IP; mobility management for a globally networked environment; unique addressing for every user; personalization of information; positioning to enable location-dependent services; and end-to-end security. Such functionality requires more than providing wireless Internet access and e-mail.
Steric requirements at position B12 for high biological activity in insulin (1993)

The alpha-helix formed by the amino acid residues 9-19 of the B-chain of insulin is involved in the stabilization of its three-dimensional structure. We have shown that modification at positions B9, B10, B12, and B16 results in analogues possessing biological activities ranging from ca. 0.2% to ca. 500% relative to that of natural insulin. The lowest potency was displayed by [B12 Asn]insulin, in which the hydrophobic B12 Val residue was replaced by the hydrophilic Asn residue. We now report the synthesis of four insulin analogues in which hydrophobicity is retained, and only the spatial arrangement of atoms in the B12 region is altered. Substitution of B12 Val with alpha-aminoisobutyric acid (Aib), D-Ala, and Phe led to analogues possessing biological activities, in lipogenesis assays, of 8.5%, 2%, and 0.2%, respectively, relative to that of natural insulin. Inversion of the B11-B12 sequence, -Leu-Val-, led to an analogue displaying 3.3% activity. A synthetic B-chain in which the B11 Leu-B12 Val sequence was replaced by B11 Ala-B12 Ile was incapable of combining with the natural A-chain. We conclude that the Val residue in the B12 position in insulin fulfills special side-chain packing requirements involved in the stability of the structure of insulin. Even slight steric alteration at position B12 results in a distortion of the overall conformation of the B-chain which affects its ability to combine with the natural A-chain. This distortion is retained in the corresponding analogue, which is reflected in diminished biological potency.
Selection of Component Carriers Using Centralized Baseband Pooling for LTE-Advanced Heterogeneous Networks (2013)

Bandwidth expansion in Long Term Evolution (LTE)-Advanced is supported via carrier aggregation (CA), which aggregates multiple component carriers (CCs) to accomplish very high data rate communications. Heterogeneous networks (HetNets), which set pico-base stations in macrocells are also a key feature of LTE-Advanced to achieve substantial gains in coverage and capacity compared to macro-only cells. When CA is applied in HetNets, transmission on all CCs may not always be the best solution due to the extremely high levels of inter-cell interference experienced by HetNets. Activated CCs that are used for transmission should be selected depending on inter-cell interference conditions and the traffic offered in the cells. This paper presents a scheme to select CCs through centralized control assuming a centralized baseband unit (C-BBU) configuration. A C-BBU involves pooling tens or hundreds of baseband resources where one baseband resource can be connected to any CC installed in remote radio heads (RRHs) via optical fibers. Fewer baseband resources can be prepared in a C-BBU than those of CCs in RRHs to reduce the cost of equipment. Our proposed scheme selects the activated CCs by considering the user equipment (UE) assigned to CCs under the criterion of maximizing the proportional fairness (PF) utility function. Convex optimization using the Karush-Kuhn-Tucker (KKT) conditions is applied to solve the resource allocation ratio that enables user throughput to be estimated. We present results from system level simulations of the downlink to demonstrate that the proposed algorithm to select CCs can outperform the conventional one that selects activated CCs based on the received signal strength. We also demonstrate that our proposed algorithm to select CCs can provide a good balance in traffic load between CCs and achieve better user throughput with fewer baseband resources.
Radiative transfer modeling of dust‐coated Pancam calibration target materials: Laboratory visible/near‐infrared spectrogoniometry (2006)

Laboratory visible/near‐infrared multispectral observations of Mars Exploration Rover Pancam calibration target materials coated with different thicknesses of Mars spectral analog dust were acquired under variable illumination geometries using the Bloomsburg University Goniometer. The data were fit with a two‐layer radiative transfer model that combines a Hapke formulation for the dust with measured values of the substrate interpolated using a He‐Torrance approach. We first determined the single‐scattering albedo, phase function, opposition effect width, and amplitude for the dust using the entire data set (six coating thicknesses, three substrates, four wavelengths, and phase angles 3°–117°). The dust exhibited single‐scattering albedo values similar to other Mars analog soils and to Mars Pathfinder dust and a dominantly forward scattering behavior whose scattering lobe became narrower at longer wavelengths. Opacity values for each dust thickness corresponded well to those predicted from the particles sizes of the Mars analog dust. We then restricted the number of substrates, dust thicknesses, and incidence angles input to the model. The results suggest that the dust properties are best characterized when using substrates whose reflectances are brighter and darker than those of the deposited dust and data that span a wide range of dust thicknesses. The model also determined the dust photometric properties relatively well despite limitations placed on the range of incidence angles. The model presented here will help determine the photometric properties of dust deposited on the MER rovers and to track the multiple episodes of dust deposition and erosion that have occurred at both landing sites.
DNA Primases (2001)

DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. These prokaryotic primases contain three distinct domains: an amino terminal domain with a zinc ribbon motif involved in binding template DNA, a middle RNA polymerase domain, and a carboxyl-terminal region that either is itself a DNA helicase or interacts with a DNA helicase. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit. The small eukaryotic primase subunit contains the active site for RNA synthesis, and its activity correlates with DNA replication during the cell cycle.
Object-oriented real-time systems using a hybrid distributed model of Ada 95's built-in DSA capability (distributed systems annex-E) and CORBA (1997)

This paper reports on the issues in design and development of Object Oriented Real-Time Distributed Systems using Ada 95. The paper is broken into the following parts: First, one of the general distributed real-time problems is introduced as it fits the domain within Boeing. Next, prototype solutions to the distributed capabilities are introduced including the new technologies present in Ada-95 through DSA (Distributed Systems Annex-E)[2] and extended with CORBA (Common Object Request Broker Architecture) capabilities[1]. Many issues are addressed with adoption and use of these technologies especially applicable as they relate to custom fine-tuned solutions used today to solve real-time constraints. As the various distributed solutions provide different strengths, a combination of the capabilities provides an attractive option. A hybrid distributed capability composed of DSA and CORBA has been developed and is discussed as it relates to the seamless introduction with the Ada language. Finally a set of research issues are raised.
Monoclonal Antibodies as Pharmacokinetic Antagonists for the Treatment of (+)-Methamphetamine Addiction (2011)

Developing specific medications to treat (+)-methamphetamine (METH) addiction is a difficult challenge because METH has multiple sites of action that are intertwined with normal neurological function. As a result, no small molecule medication for the treatment of METH addiction has made it through the FDA clinical trials process. With the invention of a new generation of proteinbased therapies, it is now possible to consider treating drug addiction by an entirely different approach. This new approach is based on the discovery of very high affinity anti-METH monoclonal antibodies (mAbs), which are non-addictive and antagonize METH effects from the blood stream without entering the brain. Due to a very long biological half-life, anti-METH mAbs would only need to be administered once every 2-4 weeks, aiding in patient compliance. As a relapse prevention medication, anti-METH mAbs could reduce or prevent the rewarding effects of a relapse to METH use and thereby improve a patient's probability of remaining in therapy and recovering from their addiction. In this review, we discuss the discovery process of anti-METH mAbs, with a focus on the preclinical development leading to high affinity anti-METH mAb antagonists.
Indirect costs associated with metastatic breast cancer. (2012)

74 Background: To estimate indirect costs (sick leave [SL]/short-term disability [STDI]) associated with metastatic breast cancer (MBC) compared to early stage breast cancer (EBC)/a general population without cancer (controls). Methods: The MarketScan Health and Productivity Management database (2005-2009) was used. Adult BC patients eligible for employee benefits of sick leave and/or STDI were identified. Difference in SL and STDI days was calculated between MBC patients and their propensity score matched EBC cohort or controls during a 12-month follow-up period. Indirect costs due to SL/ STDI were estimated by multiplying leave days with daily wages (2011 Bureau of Labor Statistics). Generalized linear model was used to examine the impact of MBC on indirect costs and potential cost drivers. Results: A total of 139 MBC/432 EBC/820 controls and 432 MBC/1,552 EBC/4,682 controls were eligible for SL and STDI respectively (not mutually exclusive), with a mean age of 49/51/50 years. After matching by age, payer type, region, index year and comorbidities, no difference was found in SL days between MBC and EBC cohorts. MBC patients had more STDI days and related cost than EBC patients and controls, with higher total indirect costs (SL + STDI). MBC patients also had more SL days/cost than controls (Table). Controlling for covariates, MBC patients incurred 47% more STDI cost vs. EBC patients (p=.009). Older patients (p=.002), non-HMO payers (p<.05), or patients not receiving chemotherapy during follow-up (p<.001) were associated with lower STDI cost. MBC patients also incurred 56% (p=.01) more SL cost and 11.6 times (p<.001) more STDI cost than controls. Conclusions: Productivity loss and associated costs in MBC patients are substantially higher than EBC patients or general population. These findings underscore the economic burden of MBC from US societal perspective. [Table: see text]
Pharmacological and therapeutic directions in ADHD: Specificity in the PFC (2008)

At a theoretical level, the advent of possible specific alpha-2A noradrenergic therapies has posed the question of the role of working memory in ADHD. Head to head comparisons of stimulant and noradrenergic alpha-2A, alpha-2B and alpha-2C agonists, utilizing vigilance and affective measures should help to clarify pharmacological and therapeutic differences.
Statistical description of monopulse parameters for tracking Rayleigh targets (2002)

Using the amplitude conditioned probability density function (PDF) for monopulse radar measurements, the Cramer-Rao lower bound (CRLB) is developed for any unbiased estimator of the direction of arrival (DOA). Maximum likelihood (ML) and method of moments (MM) estimators of the DOA are developed along with estimates of the variances associated with the monopulse ratios and DOA estimate. The case of an unknown target amplitude is addressed by using the ML estimate of the target amplitude parameter formed from the sum signal. Using simulation results, the performances of the ML and MM estimators of the DOA are compared with the standard monopulse ratio and the performance of the variance estimators is studied.
Solvent extraction of strontium nitrate by a crown ether using room-temperature ionic liquids † (1999)

The preliminary results described here show that unprecedentedly large distribution coefficient (D) values can be achieved using ionic liquids as extraction solvents for the separation of metal ions by crown ethers. This work highlights the vast opportunities in separation applications for ionic liquids with crown ethers.
SynthASR: Unlocking Synthetic Data for Speech Recognition (2021)

End-to-end (E2E) automatic speech recognition (ASR) models have recently demonstrated superior performance over the traditional hybrid ASR models. Training an E2E ASR model requires a large amount of data which is not only expensive but may also raise dependency on production data. At the same time, synthetic speech generated by the state-of-the-art text-to-speech (TTS) engines has advanced to near-human naturalness. In this work, we propose to utilize synthetic speech for ASR training (SynthASR) in applications where data is sparse or hard to get for ASR model training. In addition, we apply continual learning with a novel multi-stage training strategy to address catastrophic forgetting, achieved by a mix of weighted multi-style training, data augmentation, encoder freezing, and parameter regularization. In our experiments conducted on in-house datasets for a new application of recognizing medication names, training ASR RNN-T models with synthetic audio via the proposed multi-stage training improved the recognition performance on new application by more than 65% relative, without degradation on existing general applications. Our observations show that SynthASR holds great promise in training the state-of-the-art large-scale E2E ASR models for new applications while reducing the costs and dependency on production data.
Identification of cDNA encoding an additional alpha subunit of a human GTP-binding protein: expression of three alpha i subtypes in human tissues and cell lines. (1988)

The guanine nucleotide-binding proteins (G proteins), which mediate hormonal regulation of many membrane functions, are composed of alpha, beta, and gamma subunits. We have cloned and characterized cDNA from a human T-cell library encoding a form of alpha i that is different from the human alpha i subtypes previously reported [Didsbury, J. R., Ho, Y.-S. & Snyderman, R. (1987) FEBS Lett. 211, 160-164 and Bray, P., Carter, A., Guo, V., Puckett, C., Kamholz, J., Spiegel, A. & Nirenberg, M. (1987) Proc. Natl. Acad. Sci. USA 84, 5115-5119]. alpha i is the alpha subunit of a class of G proteins that inhibits adenylate cyclase and regulates other enzymes and ion channels. This cDNA encodes a polypeptide of 354 amino acids and is assigned to encode the alpha i-3 subtype of G proteins on the basis of its similarity to other alpha i-like cDNAs and the presence of a predicted site for ADP ribosylation by pertussis toxin. We have determined the expression of mRNA for this and two other subtypes of human alpha i (alpha i-1 and alpha i-2) in a variety of human fetal tissues and in human cell lines. All three alpha i subtypes were present in the tissues tested. However, analysis of individual cell types reveals specificity of alpha i-1 expression. mRNA for alpha i-1 is absent in T cells, B cells, and monocytes but is present in other cell lines. The finding of differential expression of alpha i-1 genes may permit characterization of distinct physiological roles for this alpha i subunit. mRNA for alpha i-2 and alpha i-3 was found in all the primary and transformed cell lines tested. Thus, some cells contain all three alpha i subtypes. This observation raises the question of how cells prevent cross talk among receptors that are coupled to effectors through such similar alpha proteins.
Expert panel consensus statement on the optimal use of pomalidomide in relapsed and refractory multiple myeloma (2014)

In this report, a panel of European myeloma experts discuss the role of pomalidomide in the treatment of relapsed and refractory multiple myeloma (RRMM). Based on the available evidence, the combination of pomalidomide and low-dose dexamethasone is a well-tolerated and effective treatment option for patients with RRMM who have exhausted treatment with lenalidomide and bortezomib. The optimal starting dose of pomalidomide is 4 mg given on days 1-21 of each 28-day cycle, whereas dexamethasone is administered at a dose of 40 mg weekly (reduced to 20 mg for patients aged >75 years). The treatment should continue until evidence of disease progression or unacceptable toxicity. Dose-modification schemes have been established for patients who develop neutropenia, thrombocytopaenia and other grade 3-4 adverse events during pomalidomide therapy. Guidance on the prevention and management of infections and venous thromboembolism is provided, based on the available clinical evidence and the experience of panel members. The use of pomalidomide in special populations, such as patients with advanced age, renal impairment or unfavourable cytogenetic features, is also discussed.