gebhart/patrepeval huggingface dataset:
Reconstitution of an efficient thymidine salvage pathway in Saccharomyces cerevisiae (2003)

The budding yeast Saccharomyces cerevisiae is unable to incorporate exogenous nucleosides into DNA. We have made a number of improvements to existing strategies to reconstitute an efficient thymidine salvage pathway in yeast. We have constructed strains that express both a nucleoside kinase as well as an equilibrative nucleoside transporter. By also deleting the gene encoding thymidylate synthase (CDC21) we have constructed strains that are entirely dependent upon exogenous thymidine for viability and that can grow with normal kinetics at low thymidine concentrations. Using this novel approach, we show that depletion of a single deoxyribonucleoside causes reversible arrest of cells in S phase with concomitant phosphorylation and activation of the S phase checkpoint kinase, Rad53. We show that this strain also efficiently incorporates the thymidine analogue, BrdU, into DNA and can be used for pulse-chase labelling.
The Design of Filters Using Helical Resonators in the VHF Band (1976)

The design of filters using helical resonators for these bands has been given alongwith the constructional details.
Linearly-solvable Markov decision problems (2007)

We introduce a class of MPDs which greatly simplify Reinforcement Learning. They have discrete state spaces and continuous control spaces. The controls have the effect of rescaling the transition probabilities of an underlying Markov chain. A control cost penalizing KL divergence between controlled and uncontrolled transition probabilities makes the minimization problem convex, and allows analytical computation of the optimal controls given the optimal value function. An exponential transformation of the optimal value function makes the minimized Bellman equation linear. Apart from their theoretical significance, the new MDPs enable efficient approximations to traditional MDPs. Shortest path problems are approximated to arbitrary precision with largest eigenvalue problems, yielding an O (n) algorithm. Accurate approximations to generic MDPs are obtained via continuous embedding reminiscent of LP relaxation in integer programming. Off-policy learning of the optimal value function is possible without need for state-action values; the new algorithm (Z-learning) outperforms Q-learning.
Multi-Label Classification of Patient Notes a Case Study on ICD Code Assignment (2017)

In the context of the Electronic Health Record, automated diagnosis coding of patient notes is a useful task, but a challenging one due to the large number of codes and the length of patient notes. We investigate four models for assigning multiple ICD codes to discharge summaries taken from both MIMIC II and III. We present Hierarchical Attention-GRU (HA-GRU), a hierarchical approach to tag a document by identifying the sentences relevant for each label. HA-GRU achieves state-of-the art results. Furthermore, the learned sentence-level attention layer highlights the model decision process, allows easier error analysis, and suggests future directions for improvement.
Treatment of phalangeal osteomyelitis caused by a cat bite (2021)

In the case of a cat bite patient, even if the external wound is small, prophylactic antibiotics should be used early and a closed observation is needed. If symptoms persist, deep infection should be considered.
Neurometabolic Disorders: Potentially Treatable Abnormalities in Patients With Treatment-Refractory Depression and Suicidal Behavior (2016)

Examination of metabolic disorders in treatment-refractory depression identified an unexpectedly large proportion of patients with potentially treatable abnormalities. The etiology of these abnormalities remains to be determined.
A New Missense Mutation in the Leptin Gene Causes Mild Obesity and Hypogonadism without Affecting T Cell Responsiveness (2010)

These findings shed a new light on the clinical consequences of leptin deficiency. Congenital leptin deficiency should be considered possible in pediatric patients with mild obesity even if parents are lean and unrelated.
Notch Sensitivity of Titanium Alloy, Commercially Pure Titanium, and Stainless Steel Spinal Implants (2001)

Caution is recommended when bending TI or CP rods, or placing a connector and removing it when using CP rods in situations in which fatigue failure is a concern.
Noun Phrases As Surrogates for Measuring Early Phases of the Mechanical Design Process (1997)

Abstract This paper reports on the use of design histories for the purpose of process evaluation. The technique involved exploring different representations of project documentation analogous to “X-ray photographs” of the human body. The study was conducted in the context of a graduate level design class that uses industry sponsored projects. It was found that the project grades in the class were strongly associated (gamma &gt; 0.7) with the number of distinct noun phrases in the project documents while they were weakly associated with other variables like readability and number of words. These initial results show that noun phrases could serve as important surrogates for measuring the mechanical design process.
<i>Digital Signal Processing</i>—<i>Efficient Convolution and Fourier</i> <i>Transform Techniques</i> (1992)

First Page
Rapid differentiation of the closely related<i>Kluyveromyces lactis</i>var.<i>lactis</i>and<i>K. marxianus</i>strains isolated from dairy products using selective media and PCR/RFLP of the rDNA non transcribed spacer 2 (2000)

PCR/RFLP of the NTS2 (IGS2) of rDNA was applied to differentiate two closely related yeast species, Kluyveromyces lactis var. lactis (referred to as K. lactis) and K. marxianus. Using specific primers, the NTS2 region was amplified from DNA of both K. lactis and K. marxianus type and collection strains. AluI restriction of amplified fragments generated patterns characteristic for each species. The NTS2 region from K. lactis var. drosophilarum and related species K. aestuarii, K. africanus, K. dobzhanskii, and K. wickerhamii could also be amplified with the same primers, but AluI patterns generated were clearly different. PCR/RFLP of the NTS2 appears thus to be a convenient method for rapid identification of K. lactis and K. marxianus, frequently found in dairy products. This test was validated therefore on K. lactis and K. marxianus from natural habitats. We showed that all yeast strains collected from whey samples and scoring blue on X-gal glucose plates were either K. lactis or K. marxianus. For application purposes, we propose here an approach for quickly screening for K. lactis/marxianus and Saccharomyces cerevisiae in dairy products using X-gal coloured and lysine growth media.
Communication-Free Streaming Mesh Refinement (2005)

This article presents a technique for the adaptive refinement of tetrahedral meshes. What makes this method new is that no neighbor information is required for the refined mesh to be compatible everywhere. Refinement consists of inserting new vertices at edge midpoints until some tolerance (geometric or otherwise) is met. For a tetrahedron, the six edges present 26=64 possible subdivision combinations. The challenge is to triangulate the new vertices (i.e., the original vertices plus some subset of the edge midpoints) in a way that neighboring tetrahedra always generate the same triangles on their shared boundary. A geometric solution based on edge lengths was developed previously, but did not account for geometric degeneracies (edges of equal length). This article provides a solution that works in all cases, while remaining entirely communication-free.
DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy (2003)

Xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD) are genetic disorders with very different clinical features, but all associated with defects in nucleotide excision repair. Defects in the XPA or XPC genes confer sensitivity to UV carcinogenesis in both humans and mice, but only XPA(-/-) mice have increased acute responses to UV exposure, whereas XPC(-/-) mice are normal in this respect. Both XPE and XPF proteins have functions separate from their role in NER, but the exact nature of these functions has not yet been established. The CSA and CSB genes responsible for CS are both components of complexes associated with RNA polymerase II and their role is thought to be in assisting polII in dealing with transcription blocks. XPB and XPD proteins are components of transcription factor TFIIH, which is involved in both basal and activated transcription. XPB is part of the core of TFIIH and has a central role in transcription, whereas XPD connects the core to the CAK subcomplex, and can tolerate many different mutations. Subtle differences in the effects of these different mutations on the many activities of TFIIH and on its stability determine the clinical outcomes, which can be XP, TTD, XP with CS, XP with TTD or COFS. Features of single and double mutant mice indicate that the neurological and ageing features associated with these disorders result from the defects in NER in association with the transcriptional deficiencies. Skin tumours in XP patients have mutations characteristic of UV-induction in the ras, p53 and ptch genes, showing that sunlight-induced mutations in these genes are important in carcinogenesis in XP patients.
Fast hierarchical multi-level fault simulation of sequential circuits with switch-level accuracy (1993)

This paper presents FEHSIM, a new hierarchical multi-level fault simulator with switch-level fault models and swttch-level accuracy.
Targeted Therapies to Improve Tumor Immunotherapy (2008)

Durable tumor regression and potential cures of metastatic solid cancers can be achieved by a variety of cellular immunotherapy strategies, including cytokine therapy, dendritic cell-based vaccines, and immune-activating antibodies, when used in so-called immune-sensitive cancers such as melanoma and renal cell carcinoma. However, these immunotherapy strategies have very low tumor response rates, usually in the order of 5% to 10% of treated patients. We propose that the antitumor activity of adequately stimulated tumor antigen-specific T cells is limited by local factors within the tumor milieu and that pharmacologic modulation of this milieu may overcome tumor resistance to immunotherapy. By understanding the mechanisms of cancer cell immune escape, it may be possible to design rational combinatorial approaches of novel therapies able to target immunosuppressive or antiapoptotic molecules in an attempt to reverse resistance to immune system control. We term this mode of treatment "immunosensitization." Ideal candidates for immunosensitizing drugs would be targeted drugs that block key oncogenic mechanisms in cancer cells resulting in a proapoptotic cancer cell milieu and at the same time do not negatively interfere with critical lymphocyte functions.
Tensor Low Rank Modeling and Its Applications in Signal Processing (2019)

Modeling of multidimensional signal using tensor is more convincing than representing it as a collection of matrices. The tensor based approaches can explore the abundant spatial and temporal structures of the mutlidimensional signal. The backbone of this modeling is the mathematical foundations of tensor algebra. The linear transform based tensor algebra furnishes low complex and high performance algebraic structures suitable for the introspection of the multidimensional signal. A comprehensive introduction of the linear transform based tensor algebra is provided from the signal processing viewpoint. The rank of a multidimensional signal is a precious property which gives an insight into the structural aspects of it. All natural multidimensional signals can be approximated to a low rank signal without losing significant information. The low rank approximation is beneficial in many signal processing applications such as denoising, missing sample estimation, resolution enhancement, classification, background estimation, object detection, deweathering, clustering and much more applications. Detailed case study of the ways and means of the low rank modeling in the above said signal processing applications are also presented.
RGS-r, a retinal specific RGS protein, binds an intermediate conformation of transducin and enhances recycling (1996)

G proteins regulate intracellular signaling by coupling a cycle of guanine nucleotide binding and hydrolysis to transient changes of cellular functions. The mechanisms that control the recycling of transducin, the "pacesetting" G protein that regulates mammalian phototransduction, are unclear. We show that a novel retinal specific RGS-motif protein specifically binds to an intermediate conformation involved in GTP hydrolysis by transducin and accelerates phosphate release and the recycling of transducin. This specific interaction further rationalizes the kinetics of the phototransduction cascade and provides a general hypothesis to explain the mechanism of interaction of RGS proteins with other G proteins.
Single electron–photon logic device using coupled quantum dots: Computation with the Fock ground state (1996)

We propose a novel logic device using coupled quantum dots (CQDs) in which single-electron tunneling is influenced by electron–electron interaction. If occupation/unoccupation by a single electron in a quantum dot is viewed as a bit 1/0, we can say that the device can perform (N)AND and (N)OR operations simultaneously. Data input/output is performed by irradiation/absorption of photons. The (N)AND and (N)OR operations are performed by the relaxation of the electronic system to the (Fock) ground state which depends on the number of electrons in CQDs. When the device is constructed of semiconductor nanostructures, phonon emission from an electron is the main contributor to the energy dissipation process. We also present results of a theoretical analysis of the device performance. These results show that (i) the error probability at the final state depends on only the dissipation energy and becomes smaller as the dissipation energy becomes larger, and (ii) the speed of operation depends on the dissipation energy and dissipative interactions and becomes slower as the dissipation energy becomes larger if LA-phonon emission is taken into account. If the size of the dot is 10 nm, the speed of operation and the error probability are estimated to be about 10 ps and about 0.2 at 77 K, respectively. The basic idea of the device is applicable to two-dimensional (2D) pattern processing if the devices are arranged in a 2D array.
Reliability of high-NA UV non-solarizing optical fibers (2004)

A number of spectroscopic techniques make use of UV absorbance and luminescence measurements e.g. to characterize materials, for use in medical/pharmaceutical applications, for forensic and sensor applications, etc. Remote detection or monitoring, especially for hazardous environments, benefit from the use of optical fibers. Furthermore many high power applications in medicine and industry are looking to use UV wavelengths. All silica compositions are better able to provide transmission of uv wavelengths, however there have been limitations on their use. Numerical aperture and solarization of the fibers are main concerns. Fibers have been recently developed which can be used for extended periods of time at wavelengths from 193 to 400 nm without serious degradation of their transmission properties (non-solarizing) and with significant broader numerical apertures,[NA] of 0.26-0.30 allowing sampling of larger areas and greater collection of transmitted or reflected beams from materials under test. Mechanical and spectral properties for these new fibers will be presented and compared with the standard all silica fibers. This will include reliability test results at selected UV wavelengths. Possible application areas which would particularly benefit from these high NA, UV non-solarizing optical fibers will be suggested.
Presence of cartilage-derived morphogenetic proteins in articular cartilage and enhancement of matrix replacement in vitro (1998)

This study shows the presence of CDMP-1 and CDMP-2 in adult bovine and human articular cartilage. In addition, our in vitro data indicate that CDMPs 1 and 2 stimulate the metabolic activity of articular chondrocytes. Therefore, these signaling molecules may be contributing to the maintenance of the integrity of the joint surface.
High Frequency of Matrix Attachment Regions and Cut-Like Protein x/CCAAT-Displacement Protein and B Cell Regulator of IgH Transcription Binding Sites Flanking Ig V Region Genes (2002)

A major component in controlling V(D)J recombination is differential accessibility through localized changes in chromatin structure. Attachment of DNA to the nuclear matrix via matrix attachment region (MAR) sequences, and interaction with MAR-binding proteins have been shown to alter chromatin conformation, promote histone acetylation, and influence gene transcription. In this study, the flanking regions of several human and mouse Ig V(H) and Ig Vkappa genes were analyzed extensively for the presence of MARs by in vitro matrix-binding assay, and for interaction with the MAR-binding proteins cut-like protein x/CCAAT-displacement protein (Cux/CDP), B cell regulator of IgH transcription (Bright), and special AT-rich sequence-binding protein (SATB1) by EMSA. Cux/CDP and SATB1 are associated with repression, while Bright is an activator of Ig transcription. Binding sites were identified in the vicinity of all analyzed Ig V genes, and were also found flanking TCR Vbeta genes. We also show that the binding sites of the different factors do not always occur at MAR sequences. MAR sequences were also found within the Ig V loci at a much higher frequency than throughout the rest of the genome. Overall, the frequency and location of binding sites relative to the coding regions, and the strength of DNA-protein interaction showed much heterogeneity. Thus, variations in factor binding and MAR activity could potentially influence the extent of localized accessibility to V(D)J recombination and thus could play a role in unequal rearrangement of individual V genes. These sites could also contribute to effective transcription of Ig genes in mature and/or activated B cells, bringing both the promoter as well as the enhancer regions into close proximity at the nuclear matrix.
High density power for low voltage pulsed loads (2002)

Several circuit topologies have the characteristic that a capacitor at high voltage is directly transformer coupled to the low voltage output giving a capacitor multiplying effect. The use of these converters for supplying low voltage pulsed loads is investigated. The need for ultralow leakage inductance transformers is shown, and the development of these transformers is described. The effect of packaging and an equivalent circuit model is described. Experimental results from a 350 W peak, 10 V output converter with energy storage at 100 volts are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Learning Visual Predictive Models of Physics for Playing Billiards (2015)

The ability to plan and execute goal specific actions in varied, unexpected settings is a central requirement of intelligent agents. In this paper, we explore how an agent can be equipped with an internal model of the dynamics of the external world, and how it can use this model to plan novel actions by running multiple internal simulations ("visual imagination"). Our models directly process raw visual input, and use a novel object-centric prediction formulation based on visual glimpses centered on objects (fixations) to enforce translational invariance of the learned physical laws. The agent gathers training data through random interaction with a collection of different environments, and the resulting model can then be used to plan goal-directed actions in novel environments that the agent has not seen before. We demonstrate that our agent can accurately plan actions for playing a simulated billiards game, which requires pushing a ball into a target position or into collision with another ball.
Pre-equalization for MIMO wireless channels with delay spread (2002)

We consider a downlink finite impulse response (FIR) multi-input multi-output (MIMO) wireless channel with L taps. A is shown that such a channel can be pre-equalized with an FIR MIMO transmit filter with only L taps, if the angle spread due to the different multipaths is sufficiently large at the transmitter. The filter taps are derived for the cases where the transmitter has perfect and partial channel knowledge, respectively. Finally, we present a pre-filter structure which converts the available frequency diversity into spatial diversity. The resulting spatial diversity can then be exploited using conventional receivers designed for frequency-flat fading channels.
MiniCrypt (2017)

We propose MiniCrypt, the first key-value store that reconciles encryption and compression without compromising performance. At the core of MiniCrypt is an observation on data compressibility trends in key-value stores, which enables grouping key-value pairs into small key packs, together with a set of distributed systems techniques for retrieving, updating, merging and splitting encrypted packs. Our evaluation shows that MiniCrypt compresses data by as much as 4 times with respect to the vanilla key-value store, and can increase the server's throughput by up to two orders of magnitude by fitting more data in main memory.
Subtle changes in prey foraging behavior have cascading effects in a shallow estuary (2011)

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 427:51-58 (2011) - DOI: https://doi.org/10.3354/meps09041 Subtle changes in prey foraging behavior have ­cascading effects in a shallow estuary Nathan R. Geraldi1,2,3,*, Sean P. Powers1,2 1Department of Marine Science, University of South Alabama, Mobile, Alabama 36688, USA 2Dauphin Island Sea Lab, Dauphin Island, Alabama 36528, USA 3Present address: University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, North Carolina 28557, USA *Email: geraldi@email.unc.edu ABSTRACT: Direct consumption of prey and the effect of predator intimidation on prey behavior are recognized determinants of food web structure, but our understanding of the mechanisms that cause behavioral cascades (trait-mediated indirect effects, TMIE) are lacking, especially for larger, mobile species. Mechanisms of TMIE were measured by both continuous in situ monitoring (via telemetry) of predator (red drum Sciaenops ocellatus) and prey (blue crab Callinectes sapidus) behavior and resource (hard clam Mercenaria mercenaria) mortality with and without structure (artificial seagrass). The presence of a predator significantly reduced the mortality of the resource (TMIE), but the TMIE was not affected by the presence of seagrass. The behavioral results indicated that the red drum did not significantly reduce the blue crab's overall movement or habitat domain but did reduce the prey's ability to optimally forage on clam patches. The mechanisms of TMIE were disruptions of short time periods of high prey activity. Our findings highlight subtle mechanisms of TMIE that could be overlooked if qualitative and not quantitative behavioral measurements are conducted. These qualitative results have implications for interpretations of previous TMIE studies as well as risk ­taking models. KEY WORDS: Indirect effects · Non-consumptive effects · Structure · Predator–prey interactions · Prey behavior · Red drum · Blue crab · Movement · Telemetry Full text in pdf format PreviousNextCite this article as: Geraldi NR, Powers SP (2011) Subtle changes in prey foraging behavior have ­cascading effects in a shallow estuary. Mar Ecol Prog Ser 427:51-58. https://doi.org/10.3354/meps09041 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 427. Online publication date: April 12, 2011 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2011 Inter-Research.