gebhart/patrepeval huggingface dataset:
Protein Kinases in Mammary Gland Development and Carcinogenesis (1998)

Elucidating the mechanisms by which hormones affect normal programs of differentiation and development in the breast is essential for understanding the complex role that hormones play in the pathogenesis of breast cancer. Studies of differentiation, development, and carcinogenesis in a variety of biological systems have emphasized the importance of protein kinases in these processes. We have identified two novel serine/threonine kinases; I43, a member of the CaM kinase family, and A32, a SNF1-related kinase. Expression analysis of I43 suggests a role late in pregnancy, possibly during differentiation since expression levels peak late in pregnancy and are also induced during NGF-treatment of PC-12 cells. Conversely, A32 levels peak early in pregnancy and decrease when PC-12 cells are treated with NGF suggesting a role early in differentiation. These kinases are also expressed in a mutually exclusive manner in mammary tumor cell lines derived from different transgenic animals. In order to determine the functional role of these kinases, we have begun to overexpress full-length clones in a variety of tissue culture systems and in transgenic mice which overexpress the kinase of interest in a mammary-specific fashion. As such, we believe these studies will contribute to our understanding of the role played by I43 and A32 in mammary gland development and carcinogenesis.
Smartphone bluetooth based social sensing (2013)

The increasing mobile technology raises a new paradigm of people-centric sensing using today's smartphones. Towards this paradigm, we present "CoSoBlue", a novel framework for Bluetooth based social sensing. In CoSoBlue, we propose novel Bluetooth semantic and statistical features, in addition to count and similarity features, and apply these discriminative features to infer context and compute sociability. We evaluate CoSoBlue on two Bluetooth datasets: (1) the longitudinal MIT friend-and-family dataset with 9+ millions records, and (2) a new 2-month dataset with ground-truth labels collected using our own developed Android app. Our primilinary experiments show CoSoBlue's efficacy on Bluetooth based social and context sensing.
Predicting Application Resource Requirements in Virtual Environments (2008)

Next Generation Data Centers (NGDC) are transforming labor-intensive, hard-coded, siloed systems into shared, virtualized, automated, and fully managed adaptive infrastructures. Virtualization technologies promise great opportunities for reducing energy and hardware costs through server consolidation. Moreover, virtualization can optimize resource sharing among applications hosted in different virtual machines to better meet their resource needs. However, to safely transition an application running natively on real hardware to a virtualized environment, one needs to estimate the additional resource requirements incurred by virtualization overheads. In this work, we design a general approach for estimating the resource requirements of applications when they are transferred to a virtual environment. Our approach has two key components: a set of microbenchmarks to profile the different types of virtualization overhead on a given platform, and a regression-based model that maps the native system usage profile into a virtualized one. This derived model can be used for estimating resource requirements of any application to be virtualized on a given platform. Our approach aims to eliminate error-prone manual processes and presents a fully automated solution. We illustrate the effectiveness of our methodology using Xen virtual machine monitor. Our evaluation shows that our automated model generation procedure effectively characterizes the different virtualization overheads of two diverse hardware platforms and that the models have median prediction error of less than 5% for both the RUBiS and TPC-W benchmarks.
Commercial latex test for Clostridium difficile toxin A does not detect toxin A (1986)

The rapid latex test recently marketed by Marion Scientific (Div. Marion Laboratories, Inc., Kansas City, Mo.) for the detection of Clostridium difficile toxin A does not react with the toxin, based on the following findings: culture filtrates from nontoxigenic strains of C. difficile gave positive reactions in the test, culture filtrate in which toxin A had been removed gave positive reactions, purified toxin A did not react in the test, and the latex reagent bound an antigen which is distinct from toxin A and which is produced in various amounts by both toxigenic and nontoxigenic strains of C. difficile.
Increased prevalence of monoclonal gammopathy, abnormal immunoglobulin levels, and recurrent infections in family members of patients with familial Waldenstrom’s macroglobulinemia (2008)

8540 Background: Waldenstrom’s macroglobulinemia (WM) is a B-cell malignancy characterized by IgM secreting lymphoplasmacytic lymphoma. Recurrent sinus infections are commonly observed in WM patients. Familial prevalence of B-cell disorders is seen in up to 20% of patients with WM (Treon et al, Ann Oncol 2006). Methods: We sought to delineate familial predilections for WM by examining a large cohort of first and second degree family members of WM patients with and without familial histories for B-cell disorders. One hundred forty five family members were enrolled, of whom 87 were in a family with a familial history. Prior medical history, complete blood counts, serum laboratories, immunoglobulin levels, serum immunofixation studies, peripheral blood and cheek cell DNA were collected as part of this IRB approved study. Results: An increased incidence of recurrent sinusitis (32.9% vs. 12.1%; p=0.004), abnormally low IgA (18.5% vs. 1.9%; p=0.003), elevated total IgM (25.9% vs. 9.4%; p=0.03), and presence of a monoclonal gammopathy (22.9% vs. 1.9%; p=0.0004) were observed among family members of WM patients with a familial B-cell disorders history. Seventeen of the 19 family members with a monoclonal gammopathy within the familial cohort had an IgM monoclonal protein, and 2 had an IgG monoclonal protein. No significant differences in complete blood counts were observed among cohorts. Conclusions: Among family members of patients with WM with a familial B-cell disorders history, a significantly higher incidence of recurrent sinus infections, abnormally low IgA and elevated IgM levels were observed, along with a ten-fold increased incidence of monoclonal gammopathies. These observations may have important implications in the pathogenesis of WM, and screening efforts for family members of WM patients. Molecular studies to elucidate the underlying genetic basis for these observations are currently underway in our laboratory. No significant financial relationships to disclose.
Electron Holography: A New View of the Microscopic (1990)

Now that coherent field-emission electron beams are available, one can exploit the wave nature of free electrons to do holography on the atomic scale.
Genetic Analysis of Biosynthesis and Roles of Anti-Herbivore Alkaloids Produced by Grass Endophytes (1999)

A characteristic of seed-borne clavicipitaceous symbionts (endophytes) that mediates their mutualisms with host grasses is production of anti-herbivore metabolites. Ergot alkaloids and indolediterpenes are potent neurotoxins in vertebrates ; saturated 1-aminopyrrolizidines (lolines) and the pyrrolopyrazine alkaloid, peramine, are active against insects. All except lolines are reported to be produced in cultures of fungal endophytes free of plant material. We identified lolines in defined-medium cultures of Neotyphodium uncinatum. We have also developed Epichloë festucae and Epichloë typhina as Mendelian genetic models to test the effects on aphids of lolines and peramine, respectively. In each case, the phenotypic difference of expression or non-expression was apparently governed by a single locus. Genotypes of E. typhina expressing peramine caused killing of greenbug aphid (Schizaphis graminum) on the host plants. Lolines were associated with killing of both greenbug and bird-cherry oat aphid (Rhopalosiphum padi). Statistically, the anti-aphid activities of the endophytes were entirely attributable to their alkaloids. Recent progress on genetic control of ergot alkaloid and indolediterpene expression holds promise for analogous tests for roles of these alkaloids in host benefits. Mendelian segregation and molecular knockouts can be used eventually to test the ecological importance of all known endophyte alkaloids in the many established endophyte effects, including increased drought tolerance, competitiveness, resistance to nematodes, and resistance to vertebrate and insect herbivores. Genetic knockouts in endophytes of genes for anti-vertebrate alkaloids will likely become an integral part of forage cultivar development.
Parallel optoelectronic data transcription with fan-out between planes of PnpN optical thyristors (1996)

Optical data transcription is implemented between differential pairs of PnpN optical thyristors. A minimum input pulse length of 500 ns is achieved, demonstrating a thyristor switching energy of 11 fJ. Parallel data transcription with fan-out over three cascaded thyristor arrays is also demonstrated, using a compact and modular optical system.
Animating oscillatory motion with overlap (2008)

Oscillatory motion is ubiquitous in computer graphics, yet existing animation techniques are ill-suited to its authoring. We introduce a new type of spline for this purpose, known as a "Wiggly Spline." The spline generalizes traditional piecewise cubics when its resonance and damping are set to zero, but creates oscillatory animation when its resonance and damping are changed. The spline provides a combination of direct manipulation and physical realism. To create overlapped and propagating motion, we generate phase shifts of the Wiggly Spline, and use these to control appropriate degrees of freedom in a model. The phase shifts can be created directly by procedural techniques or through a paint-like interface. A further option is to derive the phase shifts statistically by analyzing a time-series of a simulation. In this case, the Wiggly Spline makes it possible to canonicalize a simulation, generalize it by providing frequency and damping controls and control it through direct manipulation.
Millimeter Wave Hybrid Beamforming with DFT-MUB Aided Precoder Codebook Design (2017)

The millimeter wave (mmWave) frequency band offers substantial hitherto unused spectral resources for future wireless communication systems in order to meet the increasing capacity demand. However, mmWave frequencies suffer from high propagation losses, which may be mitigated by directional beamforming in addition to baseband precoding. This is usually referred to as hybrid beamforming. In this paper, we investigate the so-called discrete Fourier transform- mutually unbiased bases (DFT-MUB) aided codebook design conceived for limited-feedback mmWave systems, where the MUB aided codebook is applied in the baseband, while the DFT codebook is invoked for RF analog phase shifters. We demonstrate that our DFT- MUB codebook design performs similarly to the optimal digital precoding matrix, where the precoder is selected as the right singular matrix of the channel. However, our solution significantly reduces the search complexity in the baseband, while performing within 2.5 dB from the optimal digital precoder.
Directly Thiolated Modification onto the Surface of Detonation Nanodiamonds (2014)

An efficient method for modifying the surface of detonation nanodiamonds (5 and 100 nm) with thiol groups (-SH) by using an organic chemistry strategy is presented herein. Thiolated nanodiamonds were characterized by spectroscopic techniques, and the atomic percentage of sulfur was analyzed by elemental analysis and X-ray photoelectron spectroscopy. The conjugation between thiolated nanodiamonds and gold nanoparticles was elucidated by transmission electron microscopy and UV-vis spectrometry. Moreover, the material did not show significant cytotoxicity to the human lung carcinoma cell line and may prospectively be applied in bioconjugated technology. The new method that we elucidated may significantly improve the approach to surface modification of detonation nanodiamonds and build up a new platform for the application of nanodiamonds.
Flight Awareness Collaboration Tool (FACT) User Manual (2019)

The Flight Awareness Collaboration Tool (FACT) is a web-based software tool that provides important information about winter weather operations to airline dispatchers and airport personnel. This document provides instructions on how to operate FACT. It reviews FACT goals, features, functions, controls, and data displays. The manual uses text and screen shots of the screens to guide new users on how to access FACT features. This manual is required for FACT distribution to airlines and airports and is needed as part of the NASA patent process.
Rational tuning of a membrane-perforating antimicrobial peptide to selectively target membranes of different lipid composition (2020)

Abstract The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We demonstrate that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore forming peptide into a selective pore former for different lipid types. A library of 2,916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
Multi-Layer Packet Classification with Graphics Processing Units (2014)

The rapid growth of server virtualization has ignited a wide adoption of software-based virtual switches, with significant interest in speeding up their performance. In a similar trend, software-defined networking (SDN), with its strong reliance on rule-based flow classification, has also created renewed interest in multi-dimensional packet classification. However, despite these recent advances, the performance of current software-based packet classifiers is still limited, mostly by the low parallelism of general-purpose CPUs. In this paper, we explore how to accelerate packet classification using the high parallelism and latency-hiding capabilities of graphic processing units (GPUs). We implement GPU-accelerated versions for both linear and tuple search, currently deployed in virtual switches, and also introduce a novel algorithm called Bloom search. These algorithms are integrated with high-speed packet I/O to build GSwitch, a GPU-accelerated software switch. Our experimental evaluation shows that GSwitch is at least 7x faster than an equally-priced CPU classifier and is able to reach 10 Gbps with minimum-sized packets and a rule set containing 128K OpenFlow entries with 512 different wildcard patterns.
Meiotic Transmission of an In Vitro–Assembled Autonomous Maize Minichromosome (2007)

Autonomous chromosomes are generated in yeast (yeast artificial chromosomes) and human fibrosarcoma cells (human artificial chromosomes) by introducing purified DNA fragments that nucleate a kinetochore, replicate, and segregate to daughter cells. These autonomous minichromosomes are convenient for manipulating and delivering DNA segments containing multiple genes. In contrast, commercial production of transgenic crops relies on methods that integrate one or a few genes into host chromosomes; extensive screening to identify insertions with the desired expression level, copy number, structure, and genomic location; and long breeding programs to produce varieties that carry multiple transgenes. As a step toward improving transgenic crop production, we report the development of autonomous maize minichromosomes (MMCs). We constructed circular MMCs by combining DsRed and nptII marker genes with 7-190 kb of genomic maize DNA fragments containing satellites, retroelements, and/or other repeats commonly found in centromeres and using particle bombardment to deliver these constructs into embryogenic maize tissue. We selected transformed cells, regenerated plants, and propagated their progeny for multiple generations in the absence of selection. Fluorescent in situ hybridization and segregation analysis demonstrated that autonomous MMCs can be mitotically and meiotically maintained. The MMC described here showed meiotic segregation ratios approaching Mendelian inheritance: 93% transmission as a disome (100% expected), 39% transmission as a monosome crossed to wild type (50% expected), and 59% transmission in self crosses (75% expected). The fluorescent DsRed reporter gene on the MMC was expressed through four generations, and Southern blot analysis indicated the encoded genes were intact. This novel approach for plant transformation can facilitate crop biotechnology by (i) combining several trait genes on a single DNA fragment, (ii) arranging genes in a defined sequence context for more consistent gene expression, and (iii) providing an independent linkage group that can be rapidly introgressed into various germplasms.
Apolipoproteins E and CIII interact to regulate HDL metabolism and coronary heart disease risk (2018)

This work was supported by NIH grant R01HL095964 to FMS and by a grant to the Harvard Clinical and Translational Science Center (8UL1TR0001750) from the National Center for Advancing Translational Science.
A bitstream-based, scalable video-quality model for HTTP adaptive streaming: ITU-T P.1203.1 (2017)

The paper presents the scalable video quality model part of the P.1203 Recommendation series, developed in a competition within ITU-T Study Group 12 previously referred to as P.NATS. It provides integral quality predictions for 1 up to 5 min long media sessions for HTTP Adaptive Streaming (HAS) with up to HD video resolution. The model is available in four modes of operation for different levels of media-related bitstream information, reflecting different types of encryption of the media stream. The video quality model presented in this paper delivers short-term video quality estimates that serve as input to the integration component of the P.1203 model. The scalable approach consists in the usage of the same components for spatial and temporal scaling degradations across all modes. The third component of the model addresses video coding artifacts. To this aim, a single model parameter is introduced that can be derived from different types of bitstream input information. Depending on the complexity of the available input, one of four scaling-levels of the model is applied. The paper presents the different novelties of the model and scientific choices made during its development, the test design, and an analysis of the model performance across the different modes.
BK Virus-Plasmid Expression Vector That Persists Episomally in Human Cells and Shuttles into <i>Escherichia coli</i> (1984)

We describe a novel expression vector, pBK TK-1, that persists episomally in human cells that can be shuttled into bacteria. This vector includes sequences from BK virus (BKV), the thymidine kinase (TK) gene of herpes simplex virus type 1, and plasmid pML-1. TK+-transformed HeLa and 143 B cells contained predominantly full-length episomes. There were typically 20 to 40 (HeLa) and 75 to 120 143 B vector copies per cell, although some 143 B transformants contained hundreds. Low-molecular-weight DNA from TK+-transformed cells introduced into Escherichia coli were recovered as plasmids that were indistinguishable from the input vector. Removal of selective pressure had no apparent effect upon the episomal status of pBK TK-1 molecules in TK+-transformed cells. BKV T antigen may play a role in episomal replication of pBK TK-1 since this viral protein was expressed in TK+ transformants and since a plasmid that contained only the BKV origin of replication was highly amplified in BKV-transformed human cells that synthesize BKV T antigen.
Purification and Properties of a Highly Active Organophosphorus Acid Anhydrolase from <i>Alteromonas undina</i> (1993)

A highly active organophosphorus acid anhydrolase from Alteromonas undina was purified to homogeneity and found to be composed of a single polypeptide chain with a molecular weight of 53,000. With diisopropylfluorophosphate as a substrate, the purified enzyme has a specific activity of approximately 575 mumol/min/mg of protein. The enzyme has optimum activity at pH 8.0 and 55 degrees C and is stimulated by sulfhydryl reducing agents and manganese. It is capable of rapidly hydrolyzing a wide range of nerve agents and several chromogenic phosphinates.
Real-time rendering of plant leaves (2006)

This paper presents a framework for the real-time rendering of plant leaves with global illumination effects. Realistic rendering of leaves requires a sophisticated appearance model and accurate lighting computation. For leaf appearance we introduce a parametric model that describes leaves in terms of spatially-variant BRDFs and BTDFs. These BRDFs and BTDFs, incorporating analysis of subsurface scattering inside leaf tissues and rough surface scattering on leaf surfaces, can be measured from real leaves. More importantly, this description is compact and can be loaded into graphics hardware for fast run-time shading calculations, which are essential for achieving high frame rates. For lighting computation, we present an algorithm that extends the Precomputed Radiance Transfer (PRT) approach to all-frequency lighting for leaves. In particular, we handle the combined illumination effects due to lowfrequency environment light and high-frequency sunlight. This is done by decomposing the local incident radiance of sunlight into direct and indirect components. The direct component, which contains most of the high frequencies, is not pre-computed with spherical harmonics as in PRT; instead it is evaluated on-the-fly using pre-computed light-visibility convolution data. We demonstrate our framework by the rendering of a variety of leaves and assemblies thereof.