gebhart/patrepeval huggingface dataset:
Domain Orientation and Dynamics in Multidomain Proteins from Residual Dipolar Couplings (1999)

The data most commonly available for the determination of macromolecular structures in solution are NOE based distance estimates and spin-spin coupling constant based dihedral angle estimates. This information is, unfortunately, inherently short-range in nature. Thus, for many multidomain proteins, little information is available to accurately position weakly interacting domains with respect to each other. Recent studies of proteins aligned in dilute liquid crystalline solvents have shown the utility of measuring anisotropic spin interactions, such as residual dipolar couplings, to obtain unique long-range structural information. In this work, the latter approach is taken to explore the relative domain orientation in a two-domain fragment from the protein barley lectin. An approach based on singular value decomposition as opposed to simulated annealing is used to directly determine order tensors for each domain from residual (15)N-(1)H dipolar couplings, and the limitations of the two approaches are discussed. Comparison of the order tensor principal axis frames as separately determined for each domain indicates that the two domains are not oriented as in the crystal structure of wheat germ agglutinin, a highly homologous protein ( approximately 95% sequence identical). Furthermore, differences in the order tensor values suggest that the two domains are not statically positioned but are experiencing different reorientational dynamics and, to a large degree, may be considered to reorient independently. Data are also presented that suggest that a specific association occurs between one domain and the lipid bicelles comprising the liquid crystal solvent.
Visual Tracking by Affine Kernel Fitting Using Color and Object Boundary (2007)

Kernel-based trackers aggregate image features within the support of a kernel (a mask) regardless of their spatial structure. These trackers spatially fit the kernel (usually in location and in scale) such that a function of the aggregate is optimized. We propose a kernel-based visual tracker that exploits the constancy of color and the presence of color edges along the target boundary. The tracker estimates the best affinity of a spatially aligned pair of kernels, one of which is color-related and the other of which is object boundary-related. In a sense, this work extends previous kernel-based trackers by incorporating the object boundary cue into the tracking process and by allowing the kernels to be affinely transformed instead of only translated and isotropically scaled. These two extensions make for more precise target localization. Moreover, a more accurately localized target facilitates safer updating of its reference color model, further enhancing the tracker's robustness. The improved tracking is demonstrated for several challenging image sequences.
Integration of diskless workstations in unix united (1985)

Abstract This document evaluates the feasibility of diskless UNIX systems connected to a disk‐providing machine via a local area network. The diskless UNIX systems are to be used as workstations in a UNIX United UNIX is a trademark of A. T. &amp; T. Bell Laboratories. environment. Several solutions are presented and estimated to enable booting, file system access and swapping. Implementation techniques, compatible with the UNIX United philosophy, are proposed. Specific topics covered are file servers, swap servers, disk servers, indirect drivers, system call service access from kernel coroutines of UNIX processes, and communication subsystems. It is shown that the modifications to the UNIX system can be limited to one new device driver in the diskless workstation and one in the system providing the secondary storage facility.
High Seropositivity Rate of Neutralizing Antibodies to Astrovirus VA1 in Human Populations (2021)

Astroviruses are common pathogens of the human gastrointestinal tract, but they have been recently identified from cases of fatal meningoencephalitis. Astrovirus VA1 is the most frequently detected astrovirus genotype from cases of human encephalitis, but the prevalence of neutralizing antibodies to VA1 in human sera is unknown. We developed a focus reduction neutralization assay (FRNT) for VA1 and measured the seroprevalence of neutralizing antibodies from two cohorts of adult and pediatric serum samples: (i) an age-stratified cohort from St. Louis, MO, collected from 2007 to 2008 and (ii) a cohort from the Peruvian Amazonian River Basin collected in the late 1990s. In the St. Louis cohort, the lowest seropositivity rate was in children 1 year of age (6.9%), rising to 63.3% by ages 9 to 12, and 76.3% of adults ≥20 years were positive. The Peruvian Amazon cohort showed similar seropositivity rates across all ages, with individuals under age 20 having a rate of 75%, while 78.2% of adults ≥20 years were seropositive. In addition, we also identified the presence neutralizing antibodies to VA1 from commercial lots of intravenous immunoglobulin (IVIG). Our results demonstrate that a majority of humans are exposed to VA1 by adulthood, with the majority of infections occurring between 2 and 9 years of age. In addition, our results indicate that VA1 has been circulating in two geographically and socioeconomically divergent study cohorts over the past 20 years. Nonetheless, a significant proportion of the human population lacks neutralizing immunity and remains at risk for acute infection. <b>IMPORTANCE</b> Astroviruses are human pathogens with emerging disease associations, including the recent recognition of their capacity to cause meningoencephalitis. Astrovirus VA1 is the most commonly identified astrovirus genotype from cases of human encephalitis, but it is unknown what percentage of the human population has neutralizing antibodies to VA1. We found that 76.3 to 78.2% of adult humans ≥20 years of age in two geographically and socioeconomically distinct cohorts are seropositive for VA1, with the majority of infections occurring between 2 and 9 years of age. These results demonstrate that VA1 has been circulating in human populations over the past 2 decades and that most humans develop neutralizing antibodies against this virus by adulthood. However, a subset of humans lack evidence of neutralizing antibodies and are at risk for diseases caused by VA1, including encephalitis.
First TDAE Reactivity Using Benzonitrile Derivatives as Substrates and Its Application to the Synthesis of 3-Substituted Isochroman-1-ones (2018)

The first TDAE-initiated reaction between benzonitrile derivatives as substrates and substituted benzaldehydes to form substituted hydroxyethylbenzonitrile derivatives is reported. The 2-hydroxyethyl benzonitrile derivatives thus formed were good candidates for one-pot lactonization in a mixture of hydrochloric acid and methanol at 70 °C over five hours. These reactions furnished the corresponding 3-substituted isochroman-1-one derivatives in good yields.
Synthesis of Natural (+)-Methyl Tuberonate, (-)-Jasmine Ketolactone and its Epimer. (1995)

Natural methyl tuberonate 6b, jasmine ketolactone 3 and its epimer 4 were synthesized from the intermediate 7 in almost optically pure form (over 99% e. e. ). Jasmonoids are now interesting for their various activities to the plants, so our synthetic samples must be useful for their further biological study.
<title>Development of a new high-dexterity manipulator for robot-assisted microsurgery</title> (1995)

We are developing a new robotic system applicable to micro- and minimally invasive surgeries. The goal is a dexterity-enhancing master-slave that will refine the scale of current microsurgeries, and minimize effects of involuntary tremor and jerk in surgeons' hands. As a result, new procedures of the eye, ear, brain and other critical faculties will become possible, and the positive outcome rates in conventional procedures will improve. In nominal configuration, this new robot assisted microsurgery (RAMS) system has a surgeon's hand controller immediately adjacent to the robot. The RAMS system is also potentially applicable to `telesurgery' -- surgeries to be carried out in local-remote settings and time-delayed operating theaters -- as considered important in field emergencies and displaced expertise scenarios. As of August 1994 we have developed and demonstrated a new 6 degree-of- freedom robot (slave) for the RAMS system. The robot and its associated Cartesian controls enable relative positioning of surgical tools to approximately 25 microns within a non-indexed and singularity-free work volume of approximately 20 cubic centimeters. This implies the capability to down-scale hand motion inputs by two to three times, and the consequent performance of delicate procedures in such areas as vitreo-retinal surgery, for which clinical trials of this robot are planned in 1996. Further, by virtue of an innovative drive actuation, the robot can sustain full extent loads up to three pounds, making it applicable to both fine manipulation of microsurgical tools and also the dexterous handling of larger powered devices of minimally invasive surgery. In this paper, we overview the robot mechanical design, controls implementation, and our preliminary experimentation with same. Our accompanying oral presentation includes a five minute video tape display of some engineering laboratory results achieved to date.
Three-Dimensional, Kinematic, Human Behavioral Pattern-Based Features for Multimodal Emotion Recognition (2017)

This paper presents a multimodal emotion recognition method that uses a feature-level combination of three-dimensional (3D) geometric features (coordinates, distance and angle of joints), kinematic features such as velocity and displacement of joints, and features extracted from daily behavioral patterns such as frequency of head nod, hand wave, and body gestures that represent specific emotions. Head, face, hand, body, and speech data were captured from 15 participants using an infrared sensor (Microsoft Kinect). The 3D geometric and kinematic features were developed using raw feature data from the visual channel. Human emotional behavior-based features were developed using inter-annotator agreement and commonly observed expressions, movements and postures associated to specific emotions. The features from each modality and the behavioral pattern-based features (head shake, arm retraction, body forward movement depicting anger) were combined to train the multimodal classifier for the emotion recognition system. The classifier was trained using 10-fold cross validation and support vector machine (SVM) to predict six basic emotions. The results showed improvement in emotion recognition accuracy (The precision increased by 3.28% and the recall rate by 3.17%) when the 3D geometric, kinematic, and human behavioral pattern-based features were combined for multimodal emotion recognition using supervised classification.
Apoptosis signal-regulating kinase 1 mediates striatal degeneration via the regulation of C1q (2016)

Apoptosis signal-regulating kinase-1 (ASK1), an early signaling element in the cell death pathway, has been hypothesized to participate in the pathology of neurodegenerative diseases. The systemic administration of 3-nitropropionic acid (3-NP) facilitates the development of selective striatal lesions. However, it remains unclear whether specific neurons are selectively targeted in 3-NP-infused striatal degeneration. Recently, it has been proposed that complement-mediated synapse elimination may be reactivated aberrantly in the pathology of neurodegenerative diseases. We hypothesized that ASK1 is involved in striatal astrocyte reactivation; reactive astrocyte secretes molecules detrimental to neuron; and striatal neurons are more susceptible to these factors. Our results indicate that striatal astrocyte is reactivated and ASK1 level increases after 3-NP general and chronic infusion. Reactive striatal astrocyte increases TGF-beta differentially to cortex and striatum. ASK1 may be involved in regulation of astrocyte TGF-beta and it is linked to the C1q level in spatial and temporal, and moreover in the earlier stage of progressing striatal neuronal loss. Conclusively the present study suggests that ASK1 mediates 3-NP toxicity and regulates C1q level through the astrocyte TGF-beta. And also it may suggest that C1q level may be a surrogate of prediction marker representing neurodegenerative disease progress before developing behavioral impairment.
Emotional memory impairments in a genetic rat model of depression: involvement of 5-HT/MEK/Arc signaling in restoration (2011)

Cognitive dysfunctions are common in major depressive disorder, but have been difficult to recapitulate in animal models. This study shows that Flinders sensitive line (FSL) rats, a genetic rat model of depression, display a pronounced impairment of emotional memory function in the passive avoidance (PA) task, accompanied by reduced transcription of Arc in prefrontal cortex and hippocampus. At the cellular level, FSL rats have selective reductions in levels of NMDA receptor subunits, serotonin 5-HT(1A) receptors and MEK activity. Treatment with chronic escitalopram, but not with an antidepressant regimen of nortriptyline, restored memory performance and increased Arc transcription in FSL rats. Multiple pharmacological manipulations demonstrated that procognitive effects could also be achieved by either disinhibition of 5-HT(1A)R/MEK/Arc or stimulation of 5-HT₄R/MEK/Arc signaling cascades. Taken together, studies of FSL rats in the PA task revealed reversible deficits in emotional memory processing, providing a potential model with predictive and construct validity for assessments of procognitive actions of antidepressant drug therapies.
Liver function markers predict cardiovascular and renal outcomes in the CANVAS Program (2022)

Higher γGT levels are top LFT markers of risk of HHF and death in patients with diabetes and high CV risk, while ALT are protective. Canagliflozin lowers the risk of HHF and renal damage independently of LFTs and potential confounders.
Analysis of microarray data from the macaque corpus luteum; the search for common themes in primate luteal regression (2010)

The factors and processes involved in regression of the primate corpus luteum (CL) are complex and not fully understood. Systemic identification of those genes that are differentially expressed utilizing macaque model systems of luteal regression could help clarify some of the important molecular events involved in loss of primate luteal structure and function during luteolysis. In addition, examining gene pathways involved in luteal regression may help elucidate novel approaches for overcoming infertility or designing ovary-based contraceptives. This review provides an overview of the current published microarray experiments evaluating the transcriptome of the macaque CL, and compares and contrasts the data from spontaneous, GnRH antagonist and prostaglandin F2α-induced luteal regression. In addition, further uses of these databases are discussed, as well as limitations of both array technology and the rhesus macaque genome array.
High-<inline-formula> <tex-math notation="LaTeX">$Q$ </tex-math> </inline-formula> and High-Sensitivity One-Dimensional Photonic Crystal Slot Nanobeam Cavity Sensors (2015)

We present and theoretically investigate an optical sensor based on a one-dimensional photonic crystal slot nanobeam cavity. The cavity possesses a high calculated Q-factor of 174000 and an ultra-small effective mode volume of ~0.0236 (λ/n) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> at a resonant wavelength of 1535 nm. Using a slot nanobeam structure, we can strongly confine the resonant-mode field in the air slot region, and thus, the spatial overlap and interaction of light field and detected analytes can be greatly enhanced. An estimated sensitivity as high as 851 nm/refractive index unit is achieved. Due to the high Q and high sensitivity of the cavity, the figure of merit for sensing is very high at 96465. These are the best results for optical sensors based on photonic crystal cavities featuring both a high sensitivity and a high Q-factor to the best of our knowledge. In addition, the total size for the sensing part of the sensor is only 20 × 2 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
A new methodology for polyvalent intravenous immunoglobulin solution production with a two-stage process of viral inactivation (2010)

Highly purified intravenous immunoglobulin G concentrate (IV IgG) was produced with the use of polyethylene glycol associated to a single-stage precipitation by ethanol, instead of the classic Cohn-Oncley process, which employs cold alcohol as the precipitating agent, in a three-stage process. Precipitation of crude fraction containing more than 95% of immunoglobulin G was performed by liquid chromatography with a cation exchanger, CM-Sepharose, as a stationary phase. During the process, the product was subjected to two-stage viral inactivation. The first stage was performed by the action of sodium caprylate, 30 mM at pH 5.1+/- 0.1, and the second stage was performed by the action of a solvent-detergent mixture. The finished product was formulated at 5% with 10% sucralose as the stabilizing agent. The process yields 3.3g of IgG/liter of plasma. The finished product analysis showed an anti-complementary activity lower than 1CH50. Polymer and aggregate percent levels were lower than 3% in the five batches studied. The analysis of neutralizing capacity showed the presence of antibacterial and antiviral antibodies in at least three times higher concentrations than the levels found in source plasma. The finished product fulfilled all purity requirements stated in the 4th edition of the European pharmacopeia.
The HER2 (c-erbB-2) oncogene is frequently amplified in in situ carcinomas of the breast. (1992)

Amplification and overexpression of the HER2 (c-erbB-2) oncogene was assessed in paraffin-embedded specimens from 27 in situ carcinomas of the breast and from 122 stage II breast cancers. Gene amplification detected in these archival tissues by differential polymerase chain reaction (PCR) was found in 48% of in situ carcinomas and in 21% of stage II lesions (chi 2 = 7.62, p less than or equal to 0.01). In addition, the level of gene amplification correlated with the level of HER2 oncoprotein expression as measured by immunohistochemistry for both in situ cancers (p less than or equal to 0.025) and stage II cancers (p less than or equal to 0.0005). This high incidence of HER2 gene amplification with accompanying overexpression in non-invasive breast tumors suggests that perturbations of the HER2 oncogene are among the earliest and most common genetic lesions in human breast cancer.
Using Distributed Analytics to Enable Real-Time Exploration of Discrete Event Simulations (2014)

Discrete event simulations (DES) provide a powerful means for modeling complex systems and analyzing their behavior. DES capture all possible interactions between the entities they manage, which makes them highly expressive but also compute-intensive. These computational requirements often impose limitations on the breadth and/or depth of research that can be conducted with a discrete event simulation. This work describes our approach for leveraging the vast quantity of computing and storage resources available in both private organizations and public clouds to enable real-time exploration of a discrete event simulation. Rather than considering the execution speed of a single simulation run, we autonomously generate novel scenario variants to explore an entire subset of the simulation parameter space. These workloads are orchestrated in a distributed fashion across a wide range of commodity hardware. The resulting outputs are analyzed to produce models that accurately forecast simulation outcomes in real time, providing interactive feedback and bolstering research possibilities.
Structural study of InGaAs/GaAs quantum dots grown by metalorganic chemical vapor deposition for optoelectronic applications at 1.3 μm (2001)

We have studied the influence of difference growth conditions on the two-dimensional to three-dimensional growth mode transition for a specific class of InGaAs/GaAs quantum dots (QDs) optimized for applications to optical devices operating around 1.3 μm (In content x≈0.5). The dots are grown by low-pressure metalorganic chemical vapor deposition on GaAs substrates. We demonstrate that the critical layer thickness corresponding to optimized single-QD layer structures (i.e., with reduced wetting layer thickness and high uniformity) can be controlled by kinetic effects. The optimized growth conditions allow us to grow six-layers stacked QD structures as active material for the fabrication of a light emitting devices operating around 1.3 μm at room temperature.
Use of comprehensive chromosomal screening for embryo assessment: microarrays and CGH (2008)

One of the most important factors influencing embryo viability is chromosome imbalance (aneuploidy). Embryos derived from aneuploid gametes have little potential for forming a viable pregnancy, but cannot be distinguished from normal embryos using standard morphological evaluation. For more than a decade, preimplantation genetic screening (PGS) has been used to assist in the identification of aneuploid embryos. However, current strategies, based upon cell biopsy followed by fluorescent in situhybridization, allow less than half of the chromosomes to be screened. In this review, we discuss methods that overcome the limitations of earlier PGS strategies and provide screening of the entire chromosome complement in oocytes and embryos. In recent months, there has been a rapid growth in the number of PGS cycles utilizing one such method, comparative genomic hybridization (CGH). Data from IVF cycles utilizing CGH must be considered preliminary, but appear to indicate a dramatic increase in embryo implantation following comprehensive chromosomal screening. It is expected that methods based upon microarrays will yield similar clinical results and may be sufficiently rapid to permit comprehensive screening without the need for embryo cryopreservation. Some microarray platforms also offer the advantage of embryo fingerprinting and the potential for combined aneuploidy and single gene disorder diagnosis. However, more data concerning accuracy and further reductions in the price of tests will be necessary before microarrays can be widely applied.
Software-managed energy-efficient hybrid DRAM/NVM main memory (2015)

This paper evaluates the viability of user-level software management of a hybrid DRAM/NVM main memory system. We propose an operating system (OS) and programming interface to place data from within the user application. We present a profiling tool to help programmers decide on the placement of application data in hybrid memory systems. Cycle-accurate simulation of modified applications confirms that our approach is more energy-efficient than state-of-the-art hardware or OS approaches at equivalent performance. Moreover, our results are validated on several candidate NVM technologies and a wide set of 14 benchmarks.
LightShop (2007)

Light fields can be used to represent an object's appearance with a high degree of realism. However, unlike their geometric counterparts, these image-based representations lack user control for manipulating them. We present a system that allows a user to interactively manipulate, composite and render multiple light fields. LightShop is a modular system consisting of three parts: 1) a set of functions that allow a user to model a scene containing multiple light fields, 2) a ray-shading language that describes how an image should be constructed from a set of light fields, and 3) a real-time light field rendering system in OpenGL that can plug into existing 3D engines as a GLSL shader.