gebhart/patrepeval huggingface dataset:
A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability (2022)

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus <i>Neomonachus.</i> The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.
Unlocking the secrets of the invisible world: incredible deep optical imaging through in-silico clearing (2023)

In-silico clearing enables deep optical imaging of biological samples by correcting image blur caused by scattering and aberration. This breakthrough method offers researchers unprecedented insights into three-dimensional biological systems, with enormous potential for advancing biology and medicine to better understand living organisms and human health.
Segment Routing: a Comprehensive Survey of Research Activities, Standardization Efforts and Implementation Results (2021)

Fixed and mobile telecom operators, enterprise network operators and cloud providers strive to face the challenging demands coming from the evolution of IP networks (e.g. huge bandwidth requirements, integration of billions of devices and millions of services in the cloud). Proposed in the early 2010s, Segment Routing (SR) architecture helps face these challenging demands, and it is currently being adopted and deployed. SR architecture is based on the concept of source routing and has interesting scalability properties, as it dramatically reduces the amount of state information to be configured in the core nodes to support complex services. SR architecture was first implemented with the MPLS dataplane and then, quite recently, with the IPv6 dataplane (SRv6). IPv6 SR architecture (SRv6) has been extended from the simple steering of packets across nodes to a general network programming approach, making it very suitable for use cases such as Service Function Chaining and Network Function Virtualization. In this paper we present a tutorial and a comprehensive survey on SR technology, analyzing standardization efforts, patents, research activities and implementation results. We start with an introduction on the motivations for Segment Routing and an overview of its evolution and standardization. Then, we provide a tutorial on Segment Routing technology, with a focus on the novel SRv6 solution. We discuss the standardization efforts and the patents providing details on the most important documents and mentioning other ongoing activities. We then thoroughly analyze research activities according to a taxonomy. We have identified main categories during our analysis of the current state of play: Monitoring, Traffic Engineering, Failure Recovery, Centrally Controlled Architectures, Path Encoding, Network Programming, Performance Evaluation and Miscellaneous. We report the current status of SR deployments in production networks and of SR implementations (including several open source projects). Finally, we report our experience from this survey work and we identify a set of future research directions related to Segment Routing.
Hy-Fi: Aggregation of LiFi and WiFi using MIMO in IEEE 802.11 (2021)

We present Hy-Fi, a system which combines light fidelity (LiFi) and radio based on the WiFi physical layer waveform by using the MIMO features available in IEEE 802.11-compliant commodity chip sets. Hy-Fi is based on two key ideas. First, we use inexpensive COTS hardware to facilitate direct transmission of WiFi waveforms over the optical wireless channel, as this is proposed in the IEEE P802.11bb task group. Second, we use the MIMO signal processing to aggregate LiFi and radio signals at the physical layer. The system was implemented as a prototype and evaluated in a small testbed. Experimental results show that our approach offers robustness against signal blockage (Shadowing) and external interference in both, the optical and RF channels. Moreover, the two media (LiFi and WiFi) can be aggregated to double the capacity in the best case.
<title>Intraplane to interplane optical interconnects using LiNbO3-based electro-optically modulated switch array for high-density holographic memory</title> (1997)

A ne optical interconnect architecture for a 3D switch array using multiple LiNbO<SUB>3</SUB>-based electro-optically modulated gratings in conjunction with substrate guided waves is reported. First the operating mechanism of the system is studied in detail, and the momentum mismatch in the operating process of the system is also demonstrated. Then, a new method for calculating coupling efficiency is derived by introducing a compensation for the mismatch. With the new calculation method and by introducing a substrate guided wave with 45 degree bouncing angle and 100-V applied voltage, an optimized coupling efficiency is obtained even though it is under the case of momentum-mismatch. Finally, the experimental result of coupling efficiency of the electro-optically modulated grating is provided, and agreements between the experimental results and the theoretical prediction are obtained.
Metabolic signatures of amyotrophic lateral sclerosis reveal insights into disease pathogenesis (2013)

Metabolic dysfunction is an important modulator of disease course in amyotrophic lateral sclerosis (ALS). We report here that a familial mouse model (transgenic mice over-expressing the G93A mutation of the Cu/Zn superoxide dismutase 1 gene) of ALS enters a progressive state of acidosis that is associated with several metabolic (hormonal) alternations that favor lipolysis. Extensive investigation of the major determinants of H(+) concentration (i.e., the strong ion difference and the strong ion gap) suggests that acidosis is also due in part to the presence of an unknown anion. Consistent with a compensatory response to avert pathological acidosis, ALS mice harbor increased accumulation of glycogen in CNS and visceral tissues. The altered glycogen is associated with fluctuations in lysosomal and neutral α-glucosidase activities. Disease-related changes in glycogen, glucose, and α-glucosidase activity are also found in spinal cord tissue samples of autopsied patients with ALS. Collectively, these data provide insights into the pathogenesis of ALS as well as potential targets for drug development.
Development of Dielectrophoresis-Based Microfluidic Separation and Detection Systems Final Report CRADA No. TC-1408-97 (2001)

The goals of this project were to: 1. Introduce a revolutionary technology for the detection, characterization and fractionation of particles by microfluidics 2. Demonstrate (using this new technology) a new paradigm for the detection of pathogenic bacteria and chemical agents using surface-activated microbeads 3. Use this new technology to perform a human differential blood cell counts for diagnosis of unknown diseases 4. Demonstrate detection of toxicants by using the technology to detect change in living cells 5. Make and demonstrate prototype in miniaturized form for stand-alone automated operation. The revolutionary techniques will enable the production of small, portable and robust, automatic devices capable of: Detecting and characterizing viral, bacterial and chemical agents including those relevant to warfare; Diagnosing humans in remote environments; Detecting environmental and agricultural toxicants.
Scanning tunneling microscopy investigation of single electron tunneling in Co–Al–O and Cu–Al–O granular films (2000)

We have investigated single electron tunneling in Co–Al–O and Cu–Al–O granular films using scanning tunneling microscopy (STM). Topographic images show well-defined granular structures where nanometer-sized metal granules are embedded in insulating matrix. The Coulomb staircases in the current–voltage (I–V) curves are clearly observed even at room temperature in both films. For the Co–Al–O film, furthermore, negative differential conductance appears in the Coulomb staircase.
Detection of Methicillin-Resistant Staphylococcus aureus by a Duplex Droplet Digital PCR Assay (2013)

Health care-associated infections with methicillin-resistant Staphylococcus aureus (MRSA) contribute to significant hospitalization costs. We report here a droplet digital PCR (ddPCR) assay, which is a next-generation emulsion-based endpoint PCR assay for high-precision MRSA analysis. Reference cultures of MRSA, methicillin-susceptible S. aureus (MSSA), and confounders were included as controls. Copan swabs were used to sample cultures and collect specimens for analysis from patients at a large teaching hospital. Swab extraction and cell lysis were accomplished using magnetic-driven agitation of silica beads. Quantitative PCR (qPCR) (Roche Light Cycler 480) and ddPCR (Bio-Rad QX100 droplet digital PCR system) assays were used to detect genes for the staphylococcal protein SA0140 (SA) and the methicillin resistance (mecA) gene employing standard TaqMan chemistries. Both qPCR and ddPCR assays correctly identified culture controls for MRSA (76), MSSA (12), and confounder organisms (36) with 100% sensitivity and specificity. Analysis of the clinical samples (211 negative and 186 positive) collected during a study of MRSA nasal carriage allowed direct comparison of the qPCR and ddPCR assays to the Cepheid MRSA GeneXpert assay. A total of 397 clinical samples were examined in this study. Cepheid MRSA GeneXpert values were used to define negative and positive samples. Both the qPCR and ddPCR assays were in good agreement with the reference assay. The sensitivities for the qPCR and ddPCR assays were 96.8% (95% confidence interval [CI], 93.1 to 98.5%) and 96.8% (95% CI, 93.1 to 98.5%), respectively. Both the qPCR and ddPCR assays had specificities of 91.9% (95% CI, 87.5 to 94.9%) for qPCR and 91.0% (95% CI, 86.4 to 94.2%) for ddPCR technology.
A Systematic Review and Meta-Analysis of Functional Outcomes and Complications Following the Photoselective Vaporization of the Prostate and Monopolar Transurethral Resection of the Prostate (2016)

Based on our findings, we believe that PVP should be considered as an alternative surgical procedure for treating male lower urinary tract symptoms secondary to benign prostatic hyperplasia.
Fault tolerant system design using adaptive estimation and control (2000)

Stimulated by the growing demand for improving system performance and reliability, fault tolerant system design has been receiving significant attention. This dissertation investigates the development of fault tolerant control methodologies using adaptive estimation and control approaches based on the on-line learning capabilities of neural networks or fuzzy systems. The objective is to detect the changes of system conditions and the occurrence of faults, and to “reconfigure” (adjust) a controller so as to retain satisfactory system performance in the presence of a variety of system uncertainties such as disturbances, faults, and time-varying dynamics. 
To achieve the above goal a hierarchical learning structure is first developed with neural/fuzzy and immunity-based hybrid learning methods for structure and parameter adjustment. These nonlinear system modeling methods serve as a foundation for fault tolerant system design by characterizing the dynamics of the target nonlinear system. Next, on-line approximation based stable adaptive neural/fuzzy control is studied for a class of input-output feedback linearizable time-varying nonlinear systems. This class of systems is large enough so that it is not only of theoretical interest but also of practical applicability. Both indirect and direct adaptive control schemes have been studied and the results have also been extended to a class of interpolated nonlinear systems so as to deal with fast time-varying dynamics by exploiting the inherent system structure. Although the adaptive controller developed with these approaches is capable of serving as a fault tolerant controller, its performance can be further improved by exploiting information estimated from a fault diagnosis unit. This model-based fault estimation system is designed by interfacing multiple models with an expert supervisory scheme and then incorporating this into an adaptive controller to achieve integrated fault tolerant control. 
The effectiveness of the proposed integrated fault tolerant control methodologies has been demonstrated by applying the approaches to the component level model simulation of the General Electric XTE46 jet engine. Furthermore, theoretical analysis has been given to study system performance including robustness, fault sensitivity, stability, and convergence.
Nondestructive Measurement of Nonlinear Conduction of Nanoscale Materials, Nanoscale SiO2, and K0.3MoO3 by Pulse Photoconductivity Method (2011)

We propose a pulse photoconductivity method (PPCM) for the nondestructive measurement of nanoscale materials with abrupt transitions into higher conduction states from insulated states. The nonlinear conductivity of the highly insulating SiO 2 and the charge density wave (CDW) are observed and demonstrated in a short time even for long-time-constant circuits. One can determine the instantaneity of the PPCM in the case of applying an in-line evaluation technique to the LSI industry.
Modeling Accommodation Control of the Human Eye: Chromatic Aberration and Color Opponency (2017)

Accommodation is the process by which the eye lens changes optical power to maintain a clear retinal image as the distance to the fixated object varies. Although luminance blur has long been considered the driving feature for accommodation, it is by definition unsigned (i.e., there is no difference between the defocus of an object closer or farther than the focus distance). Nonetheless, the visual system initially accommodates in the correct direction, implying that it exploits a cue with sign information. Here, we present a model of accommodation control based on such a cue: Longitudinal Chromatic Aberration (LCA). The model relies on color-opponent units, much like those observed among retinal ganglion cells, to make the computation required to use LCA to drive accommodation.
First measurement of time-dependent CP violation in $ B_s^0\to {K^{+}}{K^{-}} $ decays (2013)

A bstract Direct and mixing-induced CP -violating asymmetries in $ B_s^0\to {K^{+}}{K^{-}} $ decays are measured for the first time using a data sample of pp collisions, corresponding to an integrated luminosity of 1.0 fb −1 , collected with the LHCb detector at a centre-of-mass energy of 7 TeV. The results are C KK = 0 . 14 ± 0 . 11 ± 0 . 03 and S KK = 0 . 30 ± 0 . 12 ± 0 . 04, where the first uncertainties are statistical and the second systematic. The corresponding quantities are also determined for B 0 → π + π − decays to be C ππ = −0 . 38 ± 0 . 15 ± 0 . 02 and S ππ = −0 . 71 ± 0 . 13 ± 0 . 02, in good agreement with existing measurements.
ChemInform Abstract: Nocardicyclins A and B: New Anthracycline Antibiotics Produced by Nocardia pseudobrasiliensis. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Day 1 wound fluid and PDGF-BB elicit similar fibroblast behavior in vitro (2003)

We utilized a novel in vitro assay to investigate factors that modulate the behavioral phenotype of fibroblasts during wound healing. Using the Isometric Cell Traction Assay (ICTA), we quantified simultaneously the migration and traction of rat dermal fibroblasts entrapped in a collagen gel immersed in cell culture medium. We found that the addition of 10% day 1 wound fluid to culture medium inhibited fibroblast-mediated gel compaction when compared to medium with 10% rat serum or 10% day 5 rat wound fluid. Similar results were obtained after addition of 5-50 ng/ml platelet-derived growth factor-BB (PDGF-BB)+10% serum. These results suggest that PDGF-BB, a growth factor released by platelets and in abundance in early wound fluid, is an important species in stimulating phenotype transition to a migrating (early) wound fibroblast versus a tissue contracting (late) wound fibroblast.
∑++p scattering experiment at KEK (1995)

The new low energy hyperon‐nucleon scattering data have been long waited since the low statistics data were obtained in 1960s from the bubble chamber experiments. At KEK, an experiment to measure ∑++p elastic scattering has been performed utilizing the novel scintillating fiber technology. In this report we present the status of the analysis on this experiment and the preliminary total cross section data of ∑++p scattering.
Environmentally friendly processing of photoresists in scCO 2 and decamethyltetrasiloxane (2010)

The chemical waste generated in today's microelectronic fabrication processes has driven the need to develop a more environmentally benign process. Supercritical CO<sub>2</sub> (scCO<sub>2</sub>) has been evaluated as an environmentally friendly solvent for photoresist development. It is nontoxic, nonflammable, and inert under most conditions. It also possesses advantages such as liquid-like densities, gas-like diffusivity, and zero surface tension. Although scCO<sub>2</sub> is a poor solvent for most polymers, certain fluorine-and silicon-containing polymers have shown solubility in scCO<sub>2</sub>. Previously, negative-tone patterns of 100nm have also been developed in scCO<sub>2</sub> using conventional photoresists such as ESCAP and PBOCST with the aid of fluorinated quaternary ammonium salts (QAS). However, the incorporation of fluorine degrades plasma etch resistance, and because of their persistence in nature, fluorinated compounds are coming under increased scrutiny. In order to make the process more environmentally benign, the elimination of fluorine is desirable. Some molecular glass photoresists without the incorporation of fluorine and silicon have thus been designed and synthesized to be processed in scCO<sub>2</sub>. In addition to scCO<sub>2</sub>, another environmentally friendly, low VOC solvent, decamethyltetrasiloxane has also been investigated to develop conventional photoresists. In this paper, we demonstrate the patterning of photoresists in both scCO<sub>2</sub> and decamethyltetrasiloxane.
The MANTA 1-year results: the anti-VEGF debate continues: Table 1 (2012)

Antivascular endothelial growth factor (VEGF) agents have revolutionised our treatment paradigms and therapeutic approach to numerous retinal diseases. Intravitreal anti-VEGF therapies are now at the forefront of our armamentarium for the treatment of neovascular age-related macular degeneration (AMD). Three anti-VEGF drugs are now available for use: bevacizumab (Avastin), ranibizumab (Lucentis), aflibercept (Eylea). Two of these drugs are FDA-approved in the USA for the treatment of neovascular AMD: aflibercept and ranibizumab.1–3 On the other hand, bevacizumab, although approved for systemic treatment of various malignancies, is used off-label for ophthalmic applications.4

The comparative efficacy and safety of these drugs in numerous ophthalmic diseases, including neovascular AMD, continues to be actively debated as new data accumulates. The use of bevacizumab, in particular, remains among the most hotly contested topics. Questions about functional and anatomic efficacy, treatment regimens, systemic safety, and compounding safety fuel the energy within the debate.5–8 With those issues in mind, relative cost difference and cost burden maintains this discussion among clinicians, payers and governments. The cost difference in the USA is nearly 35–40-fold less for bevacizumab (∼US$50) compared with ranibizumab (∼US$2000), aflibercept (∼US$1800).9 ,10 For perspective, gold (as of now) is trading at ∼US$1800 an ounce which, as one recent article has mentioned, places the equivalent volume of liquid gold at approximately 5–6 times less than ranibizumab or aflibercept.11 What we want as a medical community is the best investment for our patients’ future vision and health; and to that end, our search continues for answers related to the relative efficacy, safety and value of these drugs so that we can help guide our patients towards the best therapeutic decision for them.

In this issue of British Journal of Ophthalmology , Krebs and colleagues add to the growing body of evidence of comparative medicine …
Stateless 4Via6 Address Sharing (2011)

This document presents an overview of the characteristics of stateless
4V6 solutions, alongside a assessment of the issues attributes. The
impact of translated or mapped tunnel transport modes is also
presented in the broader context of other industry standard reference
architectures and existing deployments.
Audio Beat Tracking Algorithm for MIREX 2006 (2006)

This paper describes an audio beat tracking algorithm submitted to the MIREX 2006 contest. The algorithm has been described in detail in the article “Analysis of the Meter of Acoustic Musical Signals ” published in IEEE Trans. Audio, Speech and Language Processing, 14(1), 2006. In summary, the method analyses musical meter jointly at three time scales, of which only the beat (tactus) level is used in this MIREX task.
Electro-Optic Computing Architectures: Volume II. Components and System Design and Analysis (1998)

Abstract : The objective of the Electro-Optic Computing Architecture (EOCA) program was to develop multi-function electro-optic interfaces and optical interconnect units to enhance the performance of parallel processor systems and form the building blocks for future electro-optic computing architectures. Specifically, three multi-function interface modules were targeted for development - an Electro-Optic Interface (EOI), an Optical Interconnection Unit (OIU), and a Space-Time Compander (STC). Electro-optic 3-D interconnection module stacks were assembled, allowing for system global communication and fast efficient data routing and sorting. The achieved goal of the system study, to identify and analyze all the architectural implications due to the addition of optical based free-space interconnects in locally connected processor arrays, is leading to new highly optimized 3-D electro-optic computer processing networks.