gebhart/patrepeval huggingface dataset:
A critical role for peptidoglycan N-deacetylation in <i>Listeria</i> evasion from the host innate immune system (2007)

Listeria monocytogenes is a human intracellular pathogen that is able to survive in the gastrointestinal environment and replicate in macrophages, thus bypassing the early innate immune defenses. Peptidoglycan (PG) is an essential component of the bacterial cell wall readily exposed to the host and, thus, an important target for the innate immune system. Characterization of the PG from L. monocytogenes demonstrated deacetylation of N-acetylglucosamine residues. We identified a PG N-deacetylase gene, pgdA, in L. monocytogenes genome sequence. Inactivation of pgdA revealed the key role of this PG modification in bacterial virulence because the mutant was extremely sensitive to the bacteriolytic activity of lysozyme, and growth was severely impaired after oral and i.v. inoculations. Within macrophage vacuoles, the mutant was rapidly destroyed and induced a massive IFN-beta response in a TLR2 and Nod1-dependent manner. Together, these results reveal that PG N-deacetylation is a highly efficient mechanism used by Listeria to evade innate host defenses. The presence of deacetylase genes in other pathogenic bacteria indicates that PG N-deacetylation could be a general mechanism used by bacteria to evade the host innate immune system.
Improved final height in girls with Turner's syndrome treated with growth hormone and oxandrolone (1996)

The spontaneous growth process in Turner's syndrome is characterized by a progressive decline in height velocity during childhood and no pubertal growth spurt. Therefore, therapy aimed at improving height during childhood as well as increasing final height is desirable for most girls with Turner's syndrome. Forty-five girls with Turner's syndrome, 9-16 yr of age (mean age, 12.2 yr), were allocated to three study groups. Group 1 (n = 13) was initially treated with oxandrolone alone; after 1 yr of treatment, GH without (group 1a; n = 6) or with (group 1b; n = 7) ethinyl estradiol was added. Group 2 (n = 17) was treated with GH plus oxandrolone. Group 3 (n = 15) was treated with GH, oxandrolone, and ethinyl estradiol. The dosages were: GH, 0.1 IU/kg · day; oxandrolone, 0.05 mg/kg · day; and ethinyl estradiol, 100 ng/kg · day. A height of 150 cm or more was achieved in 61%, 75%, and 60% of the girls in groups 1, 2, and 3, respectively. The most impressive increase in height was seen in group 2. In this group the mean final height was 154.2 cm (SD = 6.6), which is equivalent to a mean net gain of 8.5 cm (SD = 4.6) over the projected final height. In group 3, in which ethinyl estradiol was included from the start of therapy, the initially good height velocity decelerated after 1-2 yr of treatment. Their mean final height was 151.1 (SD = 4.6) cm, equivalent to a mean net gain of 3.0 cm (SD = 3.8). A similar growth-decelerating effect of ethinyl estradiol was seen in group 1b. We conclude that in girls with Turner's syndrome who are older than 9 yr of age, treatment with GH in combination with oxandrolone results in significant growth acceleration, imitating that in normal puberty, leading to a more favorable height during childhood. This mode of treatment also results in a significantly increased final height, permitting a great number of the girls to attain a final height of more than 150 cm. However, early addition of estrogen decelerates the height velocity and reduces the gain in height.
Bone-Tissue-Engineering Material Poly(propylene fumarate):  Correlation between Molecular Weight, Chain Dimensions, and Physical Properties (2006)

Poly(propylene fumarate) (PPF) is an important biodegradable and cross-linkable polymer designed for bone-tissue-engineering applications. For the first time we report the extensive characterization of this biomaterial including molecular weight dependences of physical properties such as glass transition temperature Tg, thermal degradation temperature Td, density rho, melt viscosity eta0, hydrodynamic radius RH, and intrinsic viscosity [eta]. The temperature dependence of eta0 changes progressively with molecular weight, whereas it can be unified when the temperature is normalized to Tg. The plateau modulus and entanglement molecular weight Me have been obtained from the rheological master curves. A variety of chain microstructure parameters such as the Mark-Houwink-Sakurada constants K and alpha, characteristic ratio Cinfinity, unperturbed chain dimension r0(2)/M, packing lengthp, Kuhn length b, and tube diameter a have been deduced. Further correlation between the microstructure and macroscopic physical properties has been discussed in light of recent progress in polymer dynamics to supply a better understanding about this unsaturated polyester to advance its biomedical uses. The molecular weight dependence of Tg for six polymer species including PPF has been summarized to support that Me is irrelevant for the finite length effect on the glass transition, whereas surprisingly these polymers can be divided into two groups when their normalized Tg is plotted simply against Mw to indicate the deciding roles of inherent chain properties such as chain fragility, intermolecular cooperativity, and chain end mobility.
Transillumination and reflectance probes for<i>in vivo</i>near-IR imaging of dental caries (2014)

Previous studies have demonstrated the utility of near infrared (NIR) imaging for caries detection employing transillumination and reflectance imaging geometries. Three intra-oral NIR imaging probes were fabricated for the acquisition of <i>in vivo,</i> real time videos using a high definition InGaAs SWIR camera and near-IR broadband light sources. Two transillumination probes provide occlusal and interproximal images using 1300-nm light where water absorption is low and enamel manifests the highest transparency. A third reflectance probe utilizes cross polarization and operates at >1500-nm, where water absorption is higher which reduces the reflectivity of sound tissues, significantly increasing lesion contrast. These probes are being used in an ongoing clinical study to assess the diagnostic performance of NIR imaging for the detection of caries lesions in teeth scheduled for extraction for orthodontic reasons.
Experiments in Session Variability Modelling for Speaker Verification (2006)

Presented is an approach to modelling session variability for GMM-based text-independent speaker verification incorporating a constrained session variability component in both the training and testing procedures. The proposed technique reduces the data labelling requirements and removes discrete categorisation needed by previous techniques and provides superior performance. Experiments on Mixer conversational telephony data show improvements of as much as 46% in equal error rate over a baseline system. In this paper the algorithm used for the enrollment procedure is described in detail. Results are also presented investigating the response of the technique to short test utterances and varying session subspace dimension
Diagnostic Uses of Snake Venom (2001)

Snake venom toxins are invaluable for the assay of coagulation factors and for the study of haemostasis generally. Thrombin-like enzymes (SVTLE) are used for fibrinogen and fibrinogen breakdown product assays as well as detecting dysfibrinogenaemias. Since SVTLE are not inhibited by heparin, they can be used for assaying antithrombin III in samples containing heparin. Snake venom prothrombin activators are utilised in prothrombin assays, whilst Russell's viper venom (RVV) can be used to assay clotting factors V, VII, X and lupus anticoagulants (LA). Activators from the taipan, Australian brown snake and saw-scaled viper have also been used to assay LA. Protein C (PC) and activated PC (APC) resistance can be measured by means of RVV, Protac (from Southern copperhead snake venom) and STA-Staclot (from Crotalus viridis helleri) whilst von Willebrand factor can be studied with Botrocetin (Bothrops jararaca). Finally, snake venom C-type lectins and metalloproteinase disintegrins are being used to study platelet glycoprotein receptors and show great potential for use in the routine coagulation laboratory.
TED: a graphical technology description editor (1987)

Design verification has historically been performed on mainframes and minis. As a result of the pervasive use of character terminals, process technology specifications have always been provided in textual form. It is difficult to visualize and understand layer dependencies, design rules and material properties by looking at a textual description of what can be a large and complex network of relationships.
Peak Pain Relief Is Delayed and Duration of Relief Is Extended Following Intravenous Phentolamine Infusion:: Preliminary Report (1995)

A delay in peak pain relief was reported following 25/27 i.v.Ps. Peak pain relief occurred most often at least 24 hours after infusion completion. In these patients, duration of pain relief was at least 2 days. Placebo controlled studies are needed to verify these observations.
Signaling‐Based Optimization (2017)

Network KPIs are more and more concerned by the customer, such as RRC and E-RAB establish, retainablity, and handover success rate. Worst cells need to be monitored and treated continuously. This chapter shows how the engineers analyze signaling and explains the results to better understand and protect the LTE system from any network performance in the future. There are three important interfaces to be analyzed for the network optimization, Uu, X2, and S1. The main purpose of the S1 interface is to provide connectivity between eNB and MME through control plane protocols including NAS signaling. Signaling radio bearers are used only for the transmission of RRC and NAS messages. The chapter also discusses signaling storm and signaling troubleshooting method. Service request procedure is used when a UE in ECM-idle state attempts to send user data or wants to send uplink signaling messages, or a paging from the network was received to reestablish EPS bearers.
Spatial acquisition of wideband frequency-hopping signals using adaptive array processing (2003)

Algorithms for an adaptive antenna system are developed to estimate the direction of arrival for multiple signals to reduce spatial search. The system works in conjunction with a frequency hopping modem to minimize average acquisition time while improving the signal-to-interference-plus-noise ratio at the modem input. Simulation results indicate that an adaptive antenna can optimize acquisition time and estimate signal direction simultaneously in the presence of interference.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Self-ensembling for visual domain adaptation (2017)

This paper explores the use of self-ensembling for visual domain adaptation problems. Our technique is derived from the mean teacher variant (Tarvainen et al., 2017) of temporal ensembling (Laine et al;, 2017), a technique that achieved state of the art results in the area of semi-supervised learning. We introduce a number of modifications to their approach for challenging domain adaptation scenarios and evaluate its effectiveness. Our approach achieves state of the art results in a variety of benchmarks, including our winning entry in the VISDA-2017 visual domain adaptation challenge. In small image benchmarks, our algorithm not only outperforms prior art, but can also achieve accuracy that is close to that of a classifier trained in a supervised fashion.
Pore-size distributions of cationic polyacrylamide hydrogels of different compositions maintained at the same swelling capacity (1994)

Abstract Pore-size distributions have been measured for cationic acrylamide-based hydrogels of different compositions maintained at the same swelling capacity (27.8 ± 0.7 g swollen gel/g dry gel) by varying the ionic strength of the surrounding solution. Swelling equilibria were measured at about 6°C in pure water and aqueous sodium azide solutions ranging in concentration from to 10−3 to 10−1 M. The mixed-solute-exclusion method (introduced by Kuga) was used to obtain the experimental solute-exclusion curve, which represents the amount of imbibed liquid inside the gel inaccessible to a solute of radius r. The pore-size distribution was obtained by using Casassa's Brownian-motion model and numerically solving the Fredholm integral equation. The modes of the pore radii range from 20.4 to 47.1 Å for acrylamide-based hydrogels containing varying amounts of cationic comonomer (1.5 and 4.0 %M), crosslinker (0.3 and 1.0 %C), and initial concentration of total monomer (15 and 35 % T).
Evidence of possible dose-dependent doxorubicin plasma kinetics in man. (1983)

The published plasma clearance profiles of doxorubicin in man (with differing liver status) have been analyzed further using a kinetic model instead of a linear regression model. At high (60 mg/m2 and 45 mg/m2) and intermediate (30 mg/m2) doxorubicin dose levels, a triphasic drug clearance pattern is apparent. However, at a low dose level (15 mg/m2), a biphasic profile can adequately describe the kinetics. This association of the kinetics with drug dose has been demonstrated in several ways, the simplest of which involves graphic overlaying of juxtaposed plasma clearances, and shows the emergence of a kinetic profile for low dose levels that is markedly different from that at high dose levels. At doses greater than about 45 mg/m2, a probable saturation of response mechanisms is observed. It is not possible to interpret these results in terms of pure dose-dependent responses because of the varying health status of the individual subjects between and within experimental treatment. However, in light of our findings further investigation into the possibility of such an effect should be undertaken, particularly in view of its clinical ramifications.
Rey-Osterrieth complex figure: Psychometric characteristics in a geriatric sample (1991)

Abstract We studied the psychometric characteristics of the Rey-Osterrieth Complex Figure (ROCF) in an aged sample. One hundred and seven healthy white males and females, 50 to 79 years of age, received the ROCF and Taylor Complex Figure (TCF) as well as a screening battery of neuropsychological tests. Interrater, alternate form, test-retest, and internal consistency reliability were adequate to good for recall trials of the ROCF, with the copy trial generally lower in reliability. Validity procedures confirmed the sensitivity of the ROCF to Alzheimer's Disease, while factor analysis suggested that the ROCF loaded on a visuospatial perceptual/memory dimension. ROCF scores were significantly correlated with age and years of education, although not with sex. These results are generally supportive of the psychometric quality of the ROCF in an elderly sample. Once adequate normative data become available, the ROCF should prove a useful tool for clinicians in assessing elderly patients.
Salient space detection algorithm for signal extraction from contaminated and distorted spectrum (2018)

An algorithm for signal extraction from a contaminated and distorted spectrum is proposed. First, this algorithm combines the salient space of the spectrum and the statistical characteristics of the noise to detect signal regions at different scales. Second, it extracts signals by subtracting the baseline from the spectrum in the signal regions. The baseline is fitted by segmented polynomial functions. This algorithm has been applied to simulated and experimental data, and the results show that this algorithm can accurately and automatically extract signals with varying widths from a contaminated spectrum. This method minimizes the influence of baseline distortion and exhibits good anti-noise capability and high real-time performance.
Characterizations of Three Major Cysteine Sensors of Keap1 in Stress Response (2015)

The Keap1-Nrf2 system plays a central role in cytoprotection against electrophilic/oxidative stresses. Although Cys151, Cys273, and Cys288 of Keap1 are major sensor cysteine residues for detecting these stresses, it has not been technically feasible to evaluate the functionality of Cys273 or Cys288, since Keap1 mutants that harbor substitutions in these residues and maintain the ability to repress Nrf2 accumulation do not exist. To overcome this problem, we systematically introduced amino acid substitutions into Cys273/Cys288 and finally identified Cys273Trp and Cys288Glu mutations that do not affect Keap1's ability to repress Nrf2 accumulation. Utilizing these Keap1 mutants, we generated stable murine embryonic fibroblast (MEF) cell lines and knock-in mouse lines. Our analyses with the MEFs and peritoneal macrophages from the knock-in mice revealed that three major cysteine residues, Cys151, Cys273, and Cys288, individually and/or redundantly act as sensors. Based on the functional necessity of these three cysteine residues, we categorized chemical inducers of Nrf2 into four classes. Class I and II utilizes Cys151 and Cys288, respectively, while class III requires all three residues (Cys151/Cys273/Cys288), while class IV inducers function independently of all three of these cysteine residues. This study thus demonstrates that Keap1 utilizes multiple cysteine residues specifically and/or collaboratively as sensors for the detection of a wide range of environmental stresses.
Screening of Zinc-Based Sorbents for Hot-Gas Desulfurization (2008)

Highly reactive and attrition-resistant ZnO-based sorbents that are suitable for bubbling fluidized-bed reactors can be produced using the spray-drying method. Most of the ZnO-based sorbents prepared here (ZAC-X, X = 18N−25N) satisfy the physical and chemical criteria for bubbling fluidized-bed application [spherical shape, average particle size, 90−110 µm; size distribution, 40−230 µm; bulk density, 0.9−1.0 g/mL; attrition index (AI), 40−80%; sulfur sorption capacity, 14−17 wt %; sorbent use, 70−80%]. The performance test of the ZAC-C sorbent at Korea Institute of Energy Research (KIER) with a bubbling fluidized-bed for 70 h also demonstrated that it had good sulfidation and regeneration performance (11 wt % sorption capacity and 52% sorbent use) as well as reasonable attrition resistance (1.1% attrition loss for 70 h).
Lot-Release Criteria, Postlicensure Quality Control. and the Haemophilus influenzae Type b Conjugate Vaccines (1995)

In the United States, vaccines are licensed by the Center for Biologics Evaluation and Research (CBER) of the Food and Drug Administration on the basis of their demonstrated safety and efficacy and the demonstrated ability of the manufacturer to produce a consistent product. After licensure, vaccines are generally released to the market on a lot-by-lot basis, following CBER's review of lot-release testing results. A lot is released only if it meets all predefined specifications. A discussion of US vaccine regulation was published recently by Parkman and Hardegree.<sup>1</sup> See also p 849. As reported in this issue ofTHE Journal,<sup>2</sup>during studies of the interchangeability of licensed<i>Haemophilus influenzae</i>type b (Hib) polysaccharide-protein conjugate vaccines, Anderson et al found that a lot of Hib vaccine with the capsular polysaccharide conjugated to the meningococcal outer membrane protein complex (PedvaxHib, Merck and Co, West Point, Pa) produced lower than expected immune
A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large <i>cps</i> Fragment from an Oral Streptococcus (2020)

<i>Streptococcus pneumoniae</i> (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type, named serotype 10D, by determining its unique chemical structure and biosynthetic roles of all capsule synthesis locus (<i>cps</i>) genes. The name 10D reflects its serologic cross-reaction with serotype 10A and appearance of cross-opsonic antibodies in response to immunization with 10A polysaccharide in a 23-valent pneumococcal vaccine. Genetic analysis showed that 10D <i>cps</i> has three large regions syntenic to and highly homologous with <i>cps</i> loci from serotype 6C, serotype 39, and an oral streptococcus strain (<i>S. mitis</i> SK145). The 10D <i>cps</i> region syntenic to SK145 is about 6 kb and has a short gene fragment of <i>wciN</i>α at the 5' end. The presence of this nonfunctional <i>wciN</i>α fragment provides compelling evidence for a recent interspecies genetic transfer from oral streptococcus to pneumococcus. Since oral streptococci have a large repertoire of <i>cps</i> loci, widespread PCV usage could facilitate the appearance of novel serotypes through interspecies recombination.<b>IMPORTANCE</b> The polysaccharide capsule is essential for the pathogenicity of pneumococcus, which is responsible for millions of deaths worldwide each year. Currently available pneumococcal vaccines are designed to elicit antibodies to the capsule polysaccharides of the pneumococcal isolates commonly causing diseases, and the antibodies provide protection only against the pneumococcus expressing the vaccine-targeted capsules. Since pneumococci can produce different capsule polysaccharides and therefore reduce vaccine effectiveness, it is important to track the appearance of novel pneumococcal capsule types and how these new capsules are created. Herein, we describe a new and the 100th pneumococcal capsule type with unique chemical and serological properties. The capsule type was named 10D for its serologic similarity to 10A. Genetic studies provide strong evidence that pneumococcus created 10D capsule polysaccharide by capturing a large genetic fragment from an oral streptococcus. Such interspecies genetic exchanges could greatly increase diversity of pneumococcal capsules and complicate serotype shifts.
Efficient Quantification and Simulation of Modal Dynamics in Multimode Fiber Links (2018)

Sudden environmental effects, such as mechanical vibration, wind, and lightning, impart microsecond-timescale changes to the transmission matrix of multimode optical fibers. We introduce a timescale parameter to characterize the rate of channel changes in mode-division-multiplexed (MDM) links. We show how to efficiently generate continuous unitary matrices that form the basis for a simplified, yet general, dynamic channel model incorporating the effects of modal dispersion, mode-dependent loss, and time-varying mode coupling. We show that fast environmental perturbations can be modeled by deriving the unitary matrices from a linear ramp model, where the ramp slopes depend on the timescale parameter. We discuss the implications of channel dynamics on adaptive multiple-input-multiple-output (MIMO) equalization at the receiver in long-haul MDM links using coherent detection and in short-reach MDM links using direct detection. We show that the channel timescale and the rotation rate of the generalized Stokes vector on the generalized Poincaré sphere are both predictive of adaptive MIMO equalizer misadjustment. Our simplified channel model can be applied to optimize adaptive MIMO equalization algorithms for tracking modal dynamics.
Recent advances in bridging time series and complex networks (2013)

This paper reviews the recent advances in bridging time series analysis and complex network theory. We first introduce the main representative approaches of mapping time series into complex networks with their potential and advantages in applications in a variety of fields, and also report the latest methods to feature complex networks with typical time series after multi-scaling transformation, and to estimate and identify the uncertain connectivity of a complex network. As an example, we show an amplitude-temporal method to fast detect arrhythmia with the indicator of the average degree of associated networks.