gebhart/patrepeval huggingface dataset:
Hydrogel Tissue Construct-Based High-Content Compound Screening (2010)

Current pharmaceutical compound screening systems rely on cell-based assays to identify therapeutic candidates and potential toxicities. However, cells grown on 2D substrata or in suspension do not exhibit the mechanical or physiological properties of cells in vivo. To address this limitation, the authors developed an in vitro, high-throughput, 3D hydrogel tissue construct (HTC)-based assay system to quantify cell and tissue mechanical properties and multiple parameters of physiology. HTC mechanics was quantified using an automated device, and physiological status was assessed using spectroscopy-based indicators that were read on microplate readers. To demonstrate the application of this system, the authors screened 4 test compounds--rotenone (ROT), cytochalasin D (CD), 2,4-dinitrophenol (DNP), and Rho kinase inhibitor (H-1152)--for their ability to modulate HTC contractility without affecting actin integrity, mitochondrial membrane potential (MMP), or viability. All 4 compounds dose-dependently reduced HTC contractility. However, ROT was toxic, DNP dissipated MMP, and CD reduced both intracellular F-actin and viability. H-1152 was found to be the best candidate compound since it reduced HTC contractility with minimal side effects. The authors propose that their HTC-based assay system can be used to screen for compounds that modulate HTC contractility and assess the underlying physiological mechanism(s) of compound activity and toxicity.
Exploiting the DRAM Microarchitecture to Increase Memory-Level Parallelism (2018)

This paper summarizes the idea of Subarray-Level Parallelism (SALP) in DRAM, which was published in ISCA 2012, and examines the work's significance and future potential. Modern DRAMs have multiple banks to serve multiple memory requests in parallel. However, when two requests go to the same bank, they have to be served serially, exacerbating the high latency of on-chip memory. Adding more banks to the system to mitigate this problem incurs high system cost. Our goal in this work is to achieve the benefits of increasing the number of banks with a low-cost approach. To this end, we propose three new mechanisms, SALP-1, SALP-2, and MASA (Multitude of Activated Subarrays), to reduce the serialization of different requests that go to the same bank. The key observation exploited by our mechanisms is that a modern DRAM bank is implemented as a collection of subarrays that operate largely independently while sharing few global peripheral structures. Our three proposed mechanisms mitigate the negative impact of bank serialization by overlapping different components of the bank access latencies of multiple requests that go to different subarrays within the same bank. SALP-1 requires no changes to the existing DRAM structure, and needs to only reinterpret some of the existing DRAM timing parameters. SALP-2 and MASA require only modest changes (< 0.15% area overhead) to the DRAM peripheral structures, which are much less design constrained than the DRAM core. Our evaluations show that SALP-1, SALP-2 and MASA significantly improve performance for both single-core systems (7%/13%/17%) and multi-core systems (15%/16%/20%), averaged across a wide range of workloads. We also demonstrate that our mechanisms can be combined with application-aware memory request scheduling in multicore systems to further improve performance and fairness.
Haploid embryonic stem cells: an ideal tool for mammalian genetic analyses (2012)

Identification of the function of all genes in the mammalian genome is critical in understanding basic mechanisms of biology. However, the diploidy of mammalian somatic cells has greatly hindered efforts to elucidate the gene function in numerous biological processes by mutagenesis-based genetic approaches. Recently, mouse haploid embryonic stem (haES) cells have been successfully isolated from parthenogenetic and androgenetic embryos, providing an ideal tool for genetic analyses. In these studies, mouse haES cells have already shown that they could be used in cell-based forward or reverse genetic screenings and in generating gene-targeting via homologous recombination. In particular, haES cells from androgenetic embryos can be employed as novel, renewable form of fertilization agent for yielding live-born mice via injection into oocytes, thus showing the possibility that genetic analysis can be extended from cellular level to organism level.
Joint synchronization, channel length estimation, and channel estimation for the maximum likelihood sequence estimator for high speed wireless communications (2003)

The performance of channel-estimation-based maximum likelihood sequence estimator (MLSE) depends on the accuracy of the channel estimate. Conventional least-squares channel estimators preset a fixed length for the channel. For wireless communications, however, the actual length of the channel is environment-dependent and in general unknown. It is therefore desirable to modify conventional channel estimation algorithms so that the length of the channel estimator adapts to the actual channel. We propose a least-squares algorithm for joint synchronization, channel length estimation, and channel estimation. Simulation results show that the proposed scheme is robust against propagation environment and achieves the best trade-off between performance and complexity.
Natural genotypes via genetic engineering (2013)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Overexpression of a NAC‐domain protein promotes shoot branching in rice (2007)

For a better understanding of shoot branching in rice (Oryza sativa), a rice activation-tagging library was screened for mutations in tiller development. Here, an activation-tagging mutant Ostil1 (Oryza sativa tillering1) was characterized, which showed increased tillers, enlarged tiller angle and semidwarf phenotype. Flanking sequence was obtained by plasmid rescue. RNA-interfering and overexpression transgenic rice plants were produced using Agrobacterium-mediated transformation. The mutant phenotype was cosegregated with the reallocation of Ds element, and the flanking region of the reallocated Ds element was identified as part of the OsNAC2 gene. Northern analysis showed that expression of OsNAC2 was greatly induced in the mutant plants. Transgenic rice overexpressing the OsNAC2 resulted in recapture of the mutant phenotype, while downregulation of OsNAC2 in the Ostil1 mutant through RNA interfering (RNAi) complemented the mutant phenotype, confirming that the Ostil1 was caused by overexpression of OsNAC2. Overexpression of OsNAC2 regulates shoot branching in rice. Overexpression of OsNAC2 contributes tiller bud outgrowth, but does not affect tiller bud initiation. This suggests that OsNAC2 has potential utility for improving plant structure for higher light-use efficiency and higher yield potential in rice.
A first principles investigation of lithium intercalation in TiO2-B (2009)

The intercalation of lithium into the polymorph of titania, TiO2-B, has been examined using first principles methods, based on the Generalized Gradient Approximation within density functional theory. Three symmetry unique sites have been identified for the preferential location of lithium within the structure at low concentration, as well as the diffusion pathways between these sites. Lithium is found to bind most favourably at a site close to the titania octahedral layer, while the lowest activation energy for diffusion of 27 kJ mol−1 is found for diffusion along the open channel parallel to the b axis of the material. The need to activate lithium towards diffusion through the population of higher energy binding sites within the channel, along with the larger barrier for lithium to migrate through the sidewalls of nanotubular TiO2-B, provides an explanation for many of the observed experimental electrochemical properties of this potential battery material.
Epidermal growth factor receptor-reactive monoclonal antibodies: xenograft antitumor activity alone and as drug immunoconjugates. (1991)

Antibodies reactive with human epidermal growth factor receptor (EGFr), such as 225 IgG1 (Masui et al., Cancer Res., 44: 1002-1007, 1984), are effective tumor-suppressive agents in xenograft models. In the present study an additional antibody reactive with EGFr was made and compared to 225 IgG1 for antitumor activity as an unmodified antibody or as a drug immunoconjugate. This IgG1 clone, designated EGFrL11, competed with EGF and immunoprecipitated a Mr 178,000 protein identical to that immunoprecipitated with 225 IgG1. Cross-competition and immunodepletion studies indicated that the two antibodies bound to distinct epitopes on the same molecule. Immunofluorescence studies confirmed that the EGFrL11 epitope was expressed on the surface of viable human squamous cell carcinoma lines including T222. Unmodified EGFrL11 and 225 IgG1 were tested for antitumor activity in T222 xenografts. At a dose of 81 mg/kg given twice weekly for 3 weeks, tumor suppression, but not regression, occurred with EGFrL11. A similar result was obtained with 225 IgG1. To gauge the potential of these antibodies as immunoconjugates, both were tested for antitumor activity in the T222 model after conjugation to the Vinca derivative 4-desacetylvinblastine-3-carboxhydrazide. Both immunoconjugates completely regressed established tumors. These data suggest that Vinca conjugates with EGFr-reactive monoclonal antibodies warrant further investigation as possible clinical candidates.
Applying Concept Analysis to User-Session-Based Testing of Web Applications (2007)

The continuous use of the web for daily operations by businesses, consumers, and the government has created a great demand for reliable web applications. One promising approach to testing the functionality of web applications leverages user-session data collected by web servers. User-session-based testing automatically generates test cases based on real user profiles. The key contribution of this paper is the application of concept analysis for clustering user sessions and a set of heuristics for test case selection. Existing incremental concept analysis algorithms are exploited to avoid collecting and maintaining large user-session data sets and thus to provide scalability. We have completely automated the process from user session collection and test suite reduction through test case replay. Our incremental test suite update algorithm coupled with our experimental study indicate that concept analysis provides a promising means for incrementally updating reduced test suites in response to newly captured user sessions with little loss in fault detection capability and program coverage.
A hybrid method for clause splitting in unrestricted English texts (2000)

It is important to know the structure of the sentence for many NLP tasks. In this paper we propose a hybrid method for clause splitting in unrestricted English texts which requires less human work than existing approaches. The results of a machine learning algorithm, trained on an annotated corpus, are processed by a shallow rule-based module in order to improve the accuracy of the method. The evaluation of the results showed that the machine learning algorithm is useful for identification of clause&apos;s boundaries and the rule-based module improves the results. Using some very simple rules we can report precision of around 88%.
Occurrence of Multiple Subsequent Neoplasms in Long-Term Survivors of Childhood Cancer: A Report From the Childhood Cancer Survivor Study (2011)

Multiple SNs are common among aging survivors of childhood cancer. SN1 of NMSC identifies a population at high risk for invasive SMN. Survivors not exposed to radiation who develop multiple SNs represent a population of interest for studying genetic susceptibility to neoplasia.
Remote DOS disk server on a unix machine (2005)

A Remote DOS Disk Server runmng under UNIX has been designed and implemented. The service is provided by a daemon process running on the UNIX machine. The server software is built using the socket interface for network communications provided by BSD systems. In this server, each user has a login name and is authenticated by a password during login. The server can support multiple simultaneous login sessions. To access a remote disk, a user must map a remote drive number to that disk. A user may map to any dosdisk on the server provide he has the required access rights. The owner of a disk may grant access rights of different types both to individual users or to user groups. Protection is provided by having an Access Control List (ACL) for each dosdisk.
End-to-end Speech Recognition with Adaptive Computation Steps (2019)

In this paper, we present Adaptive Computation Steps (ACS) algorithm, which enables end-to-end speech recognition models to dynamically decide how many frames should be processed to predict a linguistic output. The model that applies ACS algorithm follows the encoder-decoder framework, while unlike the attention-based models, it produces alignments independently at the encoder side using the correlation between adjacent frames. Thus, predictions can be made as soon as sufficient acoustic information is received, which makes the model applicable in online cases. Besides, a small change is made to the decoding stage of the encoder-decoder framework, which allows the prediction to exploit bidirectional contexts. We verify the ACS algorithm on a Mandarin speech corpus AIShell-1, and it achieves a 31.2% CER in the online occasion, compared to the 32.4% CER of the attention-based model. To fully demonstrate the advantage of ACS algorithm, offline experiments are conducted, in which our ACS model achieves an 18.7% CER, outperforming the attention-based counterpart with the CER of 22.0%.
Dual Pressure Ratio Compressor (1989)

The dual pressure ratio centrifugal compressor was conceived and developed as part of an advanced auxiliary power unit (APU) program (Ref. 1). The objective was to provide relatively low pressure bleed flow and high pressure turbine flow from a single stage centrifugal compressor. Concept feasibility was first demonstrated by modifying and rig testing an existing centrifugal compressor. Subsequently, a second compressor (reference compressor), meeting the overall APU power section and bleed cycle pressure ratio requirements was designed and rig tested. This configuration was then scaled and tested in an APU. Test results showed that the compressor efficiency and pressure ratio were approximately as predicted for the flow split off to the turbine (referred to as the turbine flow side). The bleed flow side vaneless diffuser experienced a strong flow separation. Mechanical problems were also encountered with the flow splitter shroud. Although further development was indicated to correct the mechanical and aerodynamic problems encountered, the experiment provided a benchmark for the dual pressure ratio compressor concept.
Cornet‐Like Phosphotriazine/Diamine Polymers as Reductant and Matrix for the Synthesis of Silver Nanocomposites with Antimicrobial Activity (2010)

Abstract The synthesis of silver nanoparticles attached on the surface of a hollow cornet‐like polymer matrix which served as a reductant and host matrix is described. This hybrid organic/inorganic macromolecular matrix is exhibiting anion‐exchange properties, porous structure and hollow morphologies, and absorptions in the visible light region. Due to the anion‐exchange property and the 3D orientation of the macromolecular chains the material is defining a new functional organic/inorganic hybrid. For the synthesis of nanoparticles, no other reducing agents were used and silver nanoparticles with a mean diameter of less than 20 nm were attached on the surface of the polymer, thus inheriting the composite with high antibacterial activity tested in bacterial strains and yeasts. magnified image
Neuronal Oscillations in the Basal Ganglia and Movement Disorders: Evidence from Whole Animal and Human Recordings: Figure 1. (2004)

Neuronal oscillations underlie a number of physiological processes, such as respiration, diurnal rhythms of the sleep-wake cycle, and gait. Oscillatory activity can be observed in many different brain regions and can be synchronized across these different regions or nuclei. Oscillatory activity has
Dielectric Properties of Tumor and Normal Tissues at Radio through Microwave Frequencies (1981)

We summarize the dielectric permittivity and conductivity of various canine tumor and normal tissues, and single excised muscle fibers from the giant barnacle, at frequencies from 10 MHz to 18 GHz, with emphasis on the mechanisms thai are responsible for the dielectric properties of the tissues. We discuss the variation in the dielectric properties with tissue water content and provide simple empirical formulas to allow the estimation of the dielectric properties of other soft tissues on the basis of the net tissue water content. From these considerations, we consider the possible variation in dielectric properties of living tissue in situ, with those of the excised tissue, and of tumor vs. normal tissues.
Call admission control in an ATM network using upper bound of cell loss probability (1992)

Call admission control in ATM networks without monitoring network load is proposed. Traffic parameters specified by users are employed to obtain the upper bound of cell loss probability, thereby determining call admission. A cell loss probability standard is guaranteed to be satisfied under this control without assumptions of a cell arrival process. Implementation of this control to quickly evaluate cell loss probability after acceptance of a new call is discussed. The result is also applicable to ATM network dimensioning based on traffic parameters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The endocannabinoid 2‐arachidonoyl glycerol induces death of hepatic stellate cells <i>via</i> mitochondrial reactive oxygen species (2007)

The endocannabinoid system is an important regulator of hepatic fibrogenesis. In this study, we determined the effects of 2-arachidonoyl glycerol (2-AG) on hepatic stellate cells (HSCs), the main fibrogenic cell type in the liver. Culture-activated HSCs were highly susceptible to 2-AG-induced cell death with >50% cell death at 10 microM after 18 h of treatment. 2-AG-induced HSC death showed typical features of apoptosis such as PARP- and caspase 3-cleavage and depended on reactive oxygen species (ROS) formation. Confocal microscopy revealed mitochondria as primary site of ROS production and demonstrated mitochondrial depolarization and increased mitochondrial permeability after 2-AG treatment. 2-AG-induced cell death was independent of cannabinoid receptors but required the presence of membrane cholesterol. Primary hepatocytes were resistant to 2-AG-induced ROS induction and cell death but became susceptible after GSH depletion suggesting antioxidant defenses as a critical determinant of 2-AG sensitivity. Hepatic levels of 2-AG were significantly elevated in two models of experimental fibrogenesis and reached concentrations that are sufficient to induce death in HSCs. These findings suggest that 2-AG may act as an antifibrogenic mediator in the liver by inducing cell death in activated HSCs but not hepatocytes.
Prediction of quality of life in patients with end‐stage renal disease (2000)

Objectives. To examine the relationship between dialysis adequacy, psychological status and quality of life in patients with end‐stage renal disease (ESRD) treated with continuous ambulatory peritoneal dialysis (CAPD). Design. A single group, cross‐sectional study with correlational and multiple regression analyses. Methods. Seventy‐two patients were assessed on measures of dialysis adequacy (kinetic transfer/volume urea), self‐report depression and anxiety (Hospital Anxiety and Depression (HAD) scale), locus of control (Locus of Control of Behaviour (LCB) scale) and quality of life (Kidney Disease Quality of Life (KDQOL) instrument). Results. Using correlational and multiple regression analyses it was found that psychological factors, particularly depression, were much stronger determinants of quality of life in CAPD patients than biological indices of dialysis adequacy. A significant proportion of the patients was distressed as assessed by the HAD scale. Patients also tended to be external in locus of control orientation. Conclusions. Assessment of psychological status and psychosocial needs should be an integral part of the therapy offered to CAPD patients in order for them to achieve an optimal quality of life.
Quantum Chemical Studies on Photoinduced Cis−Trans Isomerization and Intramolecular Hydrogen Atom Transfer of 2‘-Hydroxychalcone (2003)

The reaction mechanism of the one-way isomerization of 2‘-hydroxychalcone (2HC) was studied by calculating the potential energy surfaces of the twist of the CC double bond and the intramolecular hydrogen atom transfer in the excited triplet state by the UB3LYP/6-31G** level. The calculations reveal the following. The potential energy curve of the triplet state between the keto forms (trans-2HC and cis-2HC) is similar to that of stilbene, which exhibits mutual isomerization. On the other hand, the potential energy curve between the enol forms (trans-2HC‘ and cis-2HC‘) is similar to that of styrylanthracene, which exhibits one-way isomerization from the cis to trans isomer. Although the hydrogen atom transfer has an energy barrier (<2 kcal mol-1), the relative energy of the transition state with zero-point correction is lower than that of trans-2HC. Electronic spins localize around the CC double bond in the intermediate states (p-2HC and p-2HC‘) of isomerization. During the hydrogen atom transfer, electronic spins shift from the phenyl group to the 2-hydroxyphenyl moiety. The electronic charge on hydrogen-bonded proton does not change significantly during the hydrogen atom transfer process.
Novel bacterium infecting an African snail (1977)

Nodules found in the superficial tissues of laboratory-maintained snails (Bulinus jousseaumei) contained a bacterium of two forms. This nonmotile microorganism occurred in intracellular packets as a simple gram-negative rod that appeared to undergo intrapacket transition to a cephalotrichous form. The latter is characterized by a "head" from which emerge long, thick, rigid, flagella-like, helically constituted filamentous organelles with a core and an outer component that is not an extension of the bacterial envelope. Neither form was successfully cultured, but clean snails derived from eggs removed before hatching developed nodules within 1 to 3 months of exposure to infected snails. The infectivity was specific for the host snail, and no transmission occurred to snails of 5 other genera tested. The presence of nodules did not interfere with longevity or reproduction of infected snails. Details of infectivity, transition, and taxonomic position of the bacterium remain to be explored, but it is reported because of unique morphological and ultrastructural features not previously known.