gebhart/patrepeval huggingface dataset:
Switching Human Telomerase On and Off with hPOT1 Protein in Vitro (2005)

POT1 (protection of telomeres 1) protein binds the G-rich single-stranded telomeric DNA at the ends of chromosomes. In human cells hPOT1 is involved in telomere length regulation, but the mechanism of this regulation remains unknown. Examination of the high-resolution crystal structure of the hPOT1-TTAGGGTTAG complex suggested that it would not be extended by telomerase, a hypothesis that we confirm by in vitro assays with recombinant telomerase. On the other hand, when hPOT1 is bound at a position one telomeric repeat before the 3'-end, leaving an 8-nucleotide 3'-tail, the complex is extended with improved activity and processivity. Thus, depending on its location relative to the DNA 3'-end, hPOT1 can either inhibit telomerase action or form a preferred substrate for telomerase. We propose that another factor catalyzes the interconversion of these states in vivo.
SDF-1α/OPF/BP Composites Enhance the Migrating and Osteogenic Abilities of Mesenchymal Stem Cells (2021)

<i>In situ</i> cell recruitment is a promising regenerative medicine strategy with the purpose of tissue regeneration without stem cell transplantation. This chemotaxis-based strategy is aimed at ensuring a restorative environment through the release of chemokines that promote site-specific migration of healing cell populations. Stromal cell-derived factor-1<i>α</i> (SDF-1<i>α</i>) is a critical chemokine that can regulate the migration of mesenchymal stem cells (MSCs). Accordingly, here, SDF-1<i>α</i>-loaded microporous oligo[poly(ethylene glycol) fumarate]/bis[2-(methacryloyloxy)ethyl] phosphate composites (SDF-1<i>α</i>/OPF/BP) were engineered and probed. SDF-1<i>α</i>/OPF/BP composites were loaded with escalating SDF-1<i>α</i> concentrations, namely, 0 ng/ml, 50 ng/ml, 100 ng/ml, and 200 ng/ml, and were cocultured with MSC. Scratching assay, Transwell assay, and three-dimensional migration model were utilized to assess the migration response of MSCs. Immunofluorescence staining of Runx2 and osteopontin (OPN), ELISA assay of osteocalcin (OCN) and alkaline phosphatase (ALP), and Alizarin Red S staining were conducted to assess the osteogenesis of MSCs. All SDF-1<i>α</i>/OPF/BP composites engendered a release of SDF-1<i>α</i> (>80%) during the first four days. SDF-1<i>α</i> released from the composites significantly promoted migration and osteogenic differentiation of MSCs documented by upregulated expression of osteogenic-related proteins, ALP, Runx2, OCN, and OPN. SDF-1<i>α</i> at 100 ng/ml was optimal for enhanced migration and osteogenic proficiency. Thus, designed SDF-1<i>α</i>/OPF/BP composites were competent in promoting the homing and osteogenesis of MSCs and thus offer a promising bioactive scaffold candidate for on-demand bone tissue regeneration.
A new moment-tensor decomposition for seismic events in anisotropic media (2011)

Investigating the mechanisms of small seismic sources usually consists of three steps: determining the moment tensor of the source; decomposing the moment tensor into parameters that can be interpreted in terms of physical mechanisms and displaying those parameters. This paper concerns the second and third steps. Two existing methods-the Riedesel-Jordan and Hudson-Pearce-Rogers parameters and displays-are reviewed, compared and contrasted, and advantages and disadvantages of the two methods are discussed. One disadvantage is that neither method takes into consideration the effect of anisotropy on the interpretation. In microseisms, anisotropy can be important. A new procedure based on the biaxial decomposition of the potency tensor is introduced which explicitly allows for anisotropy and interprets the moment tensor in terms of an isotropic pressure change and a displacement discontinuity on a fault. It is shown that this interpretation is always possible for any moment tensor whatever the anisotropy. To compare the pressure change with the displacement discontinuity, it is useful to be able to determine the volume change from the pressure source in any medium. This depends on the embedded bulk modulus, which differs from the normal bulk modulus. The embedded modulus in isotropic media is well known and the equivalent anisotropic result is derived in this paper. Interpreting a seismic source in terms of the volume change due to a pressure change and a displacement discontinuity on a fault allows a simple 3-D graphical glyph to be used to display the interpretation.
Optimal training sequences for low complexity ML multi-channel estimation in multi-user MIMO OFDM-based communications (2004)

The goal of this paper is to propose new binary training sequences that allow for optimal joint estimation of multiple channels by relying explicitly on the cyclo-stationary structure of the signals in the OFDM-based communication systems. The new estimator is perfectly suited for multiple-user MIMO types of communication systems where multiple channels have to he estimated simultaneously at each receive antenna. It is shown that the resulting estimator is not only optimal in the sense that it minimizes the channel estimation error variance, but also requires a very low complexity computational effort. Considering two different types of systems, it is shown that the proposed estimator allows for significant SNR gain in comparison to existing methods.
5G Uniform Linear Arrays With Beamforming and Spatial Multiplexing at 28, 37, 64, and 71 GHz for Outdoor Urban Communication: A Two-Level Approach (2017)

Multiple-input multiple-output (MIMO) spatial multiplexing and beamforming are regarded as key technology enablers for the fifth-generation (5G) millimeter wave (mmWave) mobile radio services. Spatial multiplexing requires sufficiently separated and incoherent antenna array elements, while in the case of beamforming, the antenna array elements need to be coherent and closely spaced. Extensive 28-, 60-, and 73-GHz ultrawideband propagation measurements in cities of New York City and Austin have indicated formation of two or more spatial lobes for the angles-of-departure and angles-of-arrival even for line-of-sight (LOS) transmission, which is an advantageous feature of mmWave channels, indicating that the transmitting and receiving array antenna elements can be co-located, thus enabling a single architecture for both spatial multiplexing and beamforming. In this paper, a two-level beamforming architecture for uniform linear arrays is proposed that leverages the formation of these spatial lobes. The antenna array is composed of sub-arrays, and the impact of sub-array spacing on the spectral efficiency is investigated through simulations using a channel simulator named NYUSIM developed based on extensive measured data at mmWave frequencies. Simulation results indicate spectral efficiencies of 18.5-28.1 bits/s/Hz with a sub-array spacing of 16 wavelengths for an outdoor mmWave urban LOS channel. The spectral efficiencies obtained are for single-user (SU) MIMO transmission at the recently allocated 5G carrier frequencies in July 2016. The method and results in this paper are useful for designing antenna array architectures for 5G wireless systems.
GT-SAGA: A fast incremental gradient method for decentralized finite-sum minimization (2020)

In this paper, we study decentralized solutions for finite-sum minimization problems when the underlying training data is distributed over a network of nodes. In particular, we describe the GT-SAGA algorithm that combines variance reduction and gradient tracking to achieve both robust performance and fast convergence. Variance reduction is implemented locally to asymptotically estimate each local batch gradient at each node, while gradient tracking fuses the local estimated gradients across the nodes. Combining variance reduction and gradient tracking thus enables linear convergence to the optimal solution of strongly-convex problems while keeping a low periteration computation complexity at each node. We cast the convergence and behavior of GT-SAGA and related methods in the context of certain practical tradeoffs and further compare their performance over a logistic regression problem with strongly convex regularization.
Actin-Dependent Propulsion of Endosomes and Lysosomes by Recruitment of N-Wasp✪ (2000)

We examined the spatial and temporal control of actin assembly in living Xenopus eggs. Within minutes of egg activation, dynamic actin-rich comet tails appeared on a subset of cytoplasmic vesicles that were enriched in protein kinase C (PKC), causing the vesicles to move through the cytoplasm. Actin comet tail formation in vivo was stimulated by the PKC activator phorbol myristate acetate (PMA), and this process could be reconstituted in a cell-free system. We used this system to define the characteristics that distinguish vesicles associated with actin comet tails from other vesicles in the extract. We found that the protein, N-WASP, was recruited to the surface of every vesicle associated with an actin comet tail, suggesting that vesicle movement results from actin assembly nucleated by the Arp2/3 complex, the immediate downstream target of N-WASP. The motile vesicles accumulated the dye acridine orange, a marker for endosomes and lysosomes. Furthermore, vesicles associated with actin comet tails had the morphological features of multivesicular endosomes as revealed by electron microscopy. Endosomes and lysosomes from mammalian cells preferentially nucleated actin assembly and moved in the Xenopus egg extract system. These results define endosomes and lysosomes as recruitment sites for the actin nucleation machinery and demonstrate that actin assembly contributes to organelle movement. Conversely, by nucleating actin assembly, intracellular membranes may contribute to the dynamic organization of the actin cytoskeleton.
Autocalibrated signal reconstruction from linear measurements using adaptive GAMP (2013)

In this paper, we reconstruct signals from underdetermined linear measurements where the componentwise gains of the measurement system are unknown a priori. The reconstruction is performed through an adaptation of the messagepassing algorithm called adaptive GAMP that enables joint gain calibration and signal estimation. To evaluate our approach, we apply it to the problem of sparse recovery and compare it against an ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -based approach. We numerically show that adaptive GAMP yields excellent results even for a moderate amount of data. It approaches the performance of oracle GAMP where the gains are perfectly known asymptotically.
True color scanning laser ophthalmoscopy and optical coherence tomography handheld probe (2014)

Scanning laser ophthalmoscopes (SLOs) are able to achieve superior contrast and axial sectioning capability compared to fundus photography. However, SLOs typically use monochromatic illumination and are thus unable to extract color information of the retina. Previous color SLO imaging techniques utilized multiple lasers or narrow band sources for illumination, which allowed for multiple color but not "true color" imaging as done in fundus photography. We describe the first "true color" SLO, handheld color SLO, and combined color SLO integrated with a spectral domain optical coherence tomography (OCT) system. To achieve accurate color imaging, the SLO was calibrated with a color test target and utilized an achromatizing lens when imaging the retina to correct for the eye's longitudinal chromatic aberration. Color SLO and OCT images from volunteers were then acquired simultaneously with a combined power under the ANSI limit. Images from this system were then compared with those from commercially available SLOs featuring multiple narrow-band color imaging.
ORBIT: Ordering Based Information Transfer Across Space and Time for\n Global Surface Water Monitoring (2017)

Many earth science applications require data at both high spatial and\ntemporal resolution for effective monitoring of various ecosystem resources.\nDue to practical limitations in sensor design, there is often a trade-off in\ndifferent resolutions of spatio-temporal datasets and hence a single sensor\nalone cannot provide the required information. Various data fusion methods have\nbeen proposed in the literature that mainly rely on individual timesteps when\nboth datasets are available to learn a mapping between features values at\ndifferent resolutions using local relationships between pixels. Earth\nobservation data is often plagued with spatially and temporally correlated\nnoise, outliers and missing data due to atmospheric disturbances which pose a\nchallenge in learning the mapping from a local neighborhood at individual\ntimesteps. In this paper, we aim to exploit time-independent global\nrelationships between pixels for robust transfer of information across\ndifferent scales. Specifically, we propose a new framework, ORBIT (Ordering\nBased Information Transfer) that uses relative ordering constraint among pixels\nto transfer information across both time and scales. The effectiveness of the\nframework is demonstrated for global surface water monitoring using both\nsynthetic and real-world datasets.\n
Identification of Nevirapine‐Resistant HIV‐1 in the Latent Reservoir after Single‐Dose Nevirapine to Prevent Mother‐to‐Child Transmission of HIV‐1 (2009)

A single dose of nevirapine can establish antiretroviral resistance within the latent reservoir. This results in a potentially lifelong risk of reemergence of nevirapine-resistant virus and highlights the need for strategies to prevent transmission that do not compromise successful future treatment.
DoS and DDoS in Named Data Networking (2013)

With the growing realization that current Internet protocols are reaching the limits of their senescence, several on-going research efforts aim to design potential next-generation Internet architectures. Although they vary in maturity and scope, in order to avoid past pitfalls, these efforts seek to treat security and privacy as fundamental requirements. Resilience to Denial-of-Service (DoS) attacks that plague today's Internet is a major issue for any new architecture and deserves full attention. In this paper, we focus on DoS in Named Data Networking (NDN) -- a specific candidate for next-generation Internet architecture designs. By naming data instead of its locations, NDN transforms data into a first-class entity and makes itself an attractive and viable approach to meet the needs for many current and emerging applications. It also incorporates some basic security features that mitigate classes of attacks that are commonly seen today. However, NDN's resilience to DoS attacks has not been analyzed to-date. This paper represents a first step towards assessment and possible mitigation of DoS in NDN. After identifying and analyzing several new types of attacks, it investigates their variations, effects and counter-measures. This paper also sheds some light on the debate about relative virtues of self-certifying, as opposed to human-readable, names in the context of content-centric networking.
Requirements for Abstraction and Control of Transport Networks (2015)

This draft provides a set of requirements for abstraction and control
of transport networks.
Observation of a New Type of Electron Bubble in Superfluid Helium (2005)

We report on the observation of a new type of electron bubble in superfluid helium-4. This object appears to be larger than the normal electron bubble and is associated with the presence of quantized vortices in the liquid.
Analysis of Active Site Residues in Escherichia coli Chorismate Mutase by Site-Directed Mutagenesis (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAnalysis of Active Site Residues in Escherichia coli Chorismate Mutase by Site-Directed MutagenesisDavid R. Liu, Sharon T. Cload, Richard M. Pastor, and Peter G. SchultzView Author Information Howard Hughes Medical Institute, Department of Chemistry University of California, Berkeley, California 94720Cite this: J. Am. Chem. Soc. 1996, 118, 7, 1789–1790Publication Date (Web):February 21, 1996Publication History Received13 September 1995Published online21 February 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja953151ohttps://doi.org/10.1021/ja953151orapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views672Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Genetics,Monomers,Noncovalent interactions,Peptides and proteins,Transition states Get e-Alerts
Leveraging Molecular Properties to Tailor Mixed-Dimensional Heterostructures beyond Energy Level Alignment (2021)

The surface sensitivity and lack of dielectric screening in two-dimensional (2D) materials provide numerous intriguing opportunities to tailor their properties using adsorbed π-electron organic molecules. These organic-2D mixed-dimensional heterojunctions are often considered solely in terms of their energy level alignment, i.e., the relative energies of the frontier molecular orbitals versus the 2D material conduction and valence band edges. While this simple model is frequently adequate to describe doping and photoinduced charge transfer, the tools of molecular chemistry enable additional manipulation of properties in organic-2D heterojunctions that are not accessible in other solid-state systems. Fully exploiting these possibilities requires consideration of the details of the organic adlayer beyond its energy level alignment, including hybridization and electrostatics, molecular orientation and thin-film morphology, nonfrontier orbitals and defects, excitonic states, spin, and chirality. This Perspective explores how these relatively overlooked molecular properties offer unique opportunities for tuning optical and electronic characteristics, thereby guiding the rational design of organic-2D mixed-dimensional heterojunctions with emergent properties.
Chronic Aichi Virus Infection As a Cause of Long-Lasting Multiorgan Involvement in Patients With Primary Immune Deficiencies (2023)

The similarity of the clinical presentation, the detection of AiV in a subgroup of patients suffering from immunodysregulation, the absence of AiV in asymptomatic patients, the detection of viral genome in infected organs by ISH, and the reversibility of symptoms after treatment argue for AiV causality.
Neer Modification of Open Bankart Procedure: What are the Rates of Recurrent Instability, Functional Outcome, and Arthritis? (2012)

The open Bankart procedure modified by Neer provided high function scores but a relatively low rate of return to sport and high rate of recurrent instability. Our rate of recurrent instability, similar to that obtained with arthroscopic Bankart procedures, has prompted us to abandon the open procedure.
Management of Ischemic Stroke (2000)

This comprehensive text provides practical management guidelines for those managing the patient with stroke. The first part of the book reviews emergency management of the stroke patient, subacute management in the ICU, stroke rehabilitation, management in the first two months post-stroke including discussion of risk management, and chronic stroke problems including post-stroke brain, depression, aphasia, sexual relationships, and physical activities. The second part of the book addresses the specific causes of stroke and the underlying pathophysiology. Common and uncommon causes are reviewed.
Neugier und Wissenschaft (2018)

Neugier als Starthilfe für die achtsame Beobachtung der Natur und der Gesellschaft zu benutzen, ist keine einfache Fertigkeit, aber ein Ausgangspunkt für neue intellektuelle Bestrebungen und Abenteuer. Sie trägt einen essentiellen Teil zur Kreativität in der Wissenschaft bei und ist ein Anfang, um neue Ideen in die unflexible Strenggläubigkeit der Berufsstände zu drängen.
Acute intermittent porphyria and mental illness – a family study (1994)

All cases of acute intermittent porphyria (AIP) are believed to be caused by a mutation in the gene encoding for porphobilinogen deaminase, a rate-limiting enzyme in the haem synthetic pathway. This gene has been mapped to the long arm of chromosome 11, a region of the genome that has recently attracted considerable attention as a possible location for genes implicated in major mental disorder. This study was designed to show whether major mental illness co-segregated with acute intermittent porphyria in families where the two conditions are found. The study also investigated the relation between clinical mental symptoms and biochemical parameters of acute intermittent porphyria. The case records of 344 consecutive patients admitted to the Porphyrias Research Group in the Western Infirmary in Glasgow between 1950 and 1988 with acute intermittent porphyria were examined for evidence of psychiatric contact. Of 16 individuals identified, 12 were available for the study. Forty relatives of these 12 probands, including 9 who were asymptomatic carriers of AIP, were interviewed for lifetime history of mental illness and current symptoms. Comparisons were made between 4 groups of patients based on urinary porphyrin levels and erythrocyte enzyme activity; 1) manifest acute intermittent porphyria, 2) latent acute intermittent porphyria, 3) normal relatives and 4) total acute intermittent porphyria (latent and manifest combined). No association was found between AIP and schizophrenia or manic-depressive illness. Only one patient with schizophrenia was found in the sample of 344 case notes, and in 2 families bipolar illness was found but did not segregate with acute intermittent porphyria. The commonest psychiatric diagnosis in patients was generalized anxiety.(ABSTRACT TRUNCATED AT 250 WORDS)
Leptin signalling reduces the severity of cardiac dysfunction and remodelling after chronic ischaemic injury (2007)

These data demonstrate that HF increases ObR signalling in cardiomyocytes and that activation of ObR signalling improves functional outcomes in chronic ischaemic injury leading to HF.