gebhart/patrepeval huggingface dataset:
Pathogeny and immunological control of toxoplasmosis. (1992)

1. Toxoplasma gondii is a ubiquitous, obligate intracellular parasite of worldwide distribution. In humans, the parasite exists in two forms: the tachyzoite is the rapidly multiplying stage of the parasite which actively invades host cells and represents the principal pathogenic form at the acute phase of the disease; the bradyzoite is the form which multiplies slowly in host cells, resulting in the formation of cysts which persist in tissues. Several antigenic components have been identified, some of which are characteristic for each parasitic stage; particularly, in tachyzoites, the 30 kDa membrane protein represents up to 5% of the total protein content. 2. Toxoplasma infection in humans is usually asymptomatic because of effective immunity involving antibodies, T cells and cytokines. Activated macrophages, CD4 and CD8 lymphocytes and cytokines, such IFN gamma, play a major role in the control of acute infection and the maintenance of infection at the chronic stage. The alteration of immune functions, as observed in congenitally infected children and in HIV-infected patients, may induce the recrudescence of previously latent toxoplasmosis, in relation to disruption of the cyst form of the parasite. The resulting reactivation is responsible for life-threatening infections which are frequently manifested as toxoplasmic encephalitis. 3. In this review, the parasite and immunological factors participating in the pathogenesis of the lesions associated with acute, chronic and reactivated toxoplasmosis are presented.
Microfluidic Agar Device towards High Resolution Electron Microscopy of Bacteria in Culture (2019)

The high-resolution observation of bacteria in culture is one of the promising approaches to discover new action mechanisms of antibacterial agents. Atmospheric scanning electron microscope (SEM) achieved in-liquid observation. We previously improved atmospheric SEM and developed MEMS (Microelectromechanical Systems) liquid cell for the culture of bacteria under SEM observation. MEMS liquid cell required liquid medium for bacterial culture. This caused the low spatial resolution due to the electron scattering and the movement of bacteria due to the medium flow. We developed a microfluidic agar device to culture bacteria without liquid medium. An agar channel of 20 μm in height was fabricated by a PDMS mold, and a hydrophobic pattern was stamped on a glass substrate. By the combination of the agar channel and hydrophobic pattern, dyed water was introduced into the agar channel without the leakage.
Immunogenicity-unwanted immune responses to biological drugs – can we predict them? (2020)

Knowledge of factors capable of influencing the immunogenicity of BAs may help to understand, in a predictive manner and at the single patient level, the presence of risk factors influencing the production of ADAs and their impact on clinical outcomes.
Detection of Extended-Spectrum-β-Lactamase-Producing Escherichia coli ST131 and ST405 Clonal Groups by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (2014)

Escherichia coli sequence type 131 (ST131) and ST405 are important clonal groups, because they are associated with the global increase of extended-spectrum-β-lactamase (ESBL) producers. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is emerging as a rapid, inexpensive, and accurate method for bacterial identification. We investigated the detection performance of MALDI-TOF for the ST131 and ST405 clonal groups using 41 ST131-O25b, 26 ST131-O16, and 41 ST405 ESBL-producing isolates and 41 ESBL-producing isolates frrom other STs. The main spectra representing each clonal group were used for classification with Biotyper (Bruker Daltonics GmbH, Bremen, Germany). The peak that had the highest area under the receiver-operating characteristic curve generated by ClinProTools (Bruker) was detected with FlexAnalysis (Bruker), and an optimal signal-to-noise ratio cutoff was determined. The optimal detection models were generated by ClinProTools. Classification by Biotyper could detect the ST131-whole (O25b and O16 together) group with a sensitivity of 98.5% and a specificity of 93.9%. With FlexAnalysis, a peak of 9,720 Da detected the ST131-whole group with a sensitivity of 97.0% and a specificity of 91.5% at a cutoff value of 8.0. The ClinProTools models exhibited good performance for the detection of the ST131-whole group (sensitivity and specificity, 94.0% and 92.7%, respectively), the ST131-O25b group (95.1% and 98.2%, respectively), and the ST405 group (90.2% and 96.3%, respectively). MALDI-TOF MS had high detection performance for the ST131-whole, ST131-O25b, and ST405 clonal groups. MALDI-TOF MS should be considered as an alternative method to monitor the epidemiology of the ESBL-producing E. coli ST131 and ST405 clonal groups.
Long wavelength GaInAsP/InP laser with automatically formed tunneling aperture (2002)

We have proposed a new current confinement structure for long-wavelength vertical-cavity surface-emitting lasers (VCSELs), i.e., automatically formed tunneling aperture (AFTA). The AFTA can provide a simple current confinement because it can be formed just by electrode annealing. A long wavelength GaInAsP/InP stripe laser with AFTA is fabricated. The annealing condition to form AFTA structure is investigated and optimized. We carried out tunneling electron microscopy (TEM) of the AFTA structure before and after electrode annealing. The TEM image shows the process of destroying tunnel junction.
Large Format HgCdTe Arrays for the James Webb Space Telescope (2006)

The near infrared spectrograph (NIRSpec) will be the James Webb Space Telescope's (JWSTs) primary near-infrared spectrograph. NIRSpec is a multi-object spectrograph with fixed-slit and integral field modes. EADS/Astrium is building NIRSpec for the European Space Agency (ESA), with NASA providing the detector subsystem and programmable multi-aperture mask. In this presentation we present an overview of the detector subsystem (DS)
Multi-level error correcting codes (1992)

This dissertation investigates algebraic block codes with multiple levels of error protection on the information messages, also known as unequal-error-protection (UEP) codes. New constructions of multi-level error correcting linear block codes specified by their generator matrices and by their parity-check matrices are presented and discussed. A family of nonbinary optimal LUEP codes, capable of correcting any t or less random errors affecting the most significant information symbols, while correcting any single random error in the least significant information symbols, is constructed and analyzed. This class of codes is constructed by specifying their parity check matrices, which are combinations of parity check matrices of Reed-Solomon codes and shortened nonbinary Hamming codes. Near optimal binary LUEP codes, constructed by appending (also known as time-sharing) cosets of sub-codes of shorter linear Hamming codes, are proposed and analyzed. This class of LUEP codes is specified by their generator matrices. By computing the Hamming bound on binary LUEP codes with the same dimension and error correcting capabilities as the optimal binary LUEP codes, it is shown that this family of LUEP codes requires at most one additional redundant bit. Furthermore, constructions of LUEP codes by specifying their generator matrices allow the use of multi-stage decoding methods, with reduced decoding complexity, as shown in this work. Certain families of known linear block codes are analyzed to determine their UEP capabilities. We derive conditions for which some shortened Hamming codes, some non-primitive BCH codes and some cyclic codes of composite length are LUEP codes. Bounds on the multi-level error correcting capabilities of these families of linear codes are derived. The error performance of some binary multi-level error-correcting codes over binary symmetric channels and over additive white Gaussian noise channels with BPSK modulation is considered. Some new block coded modulation (BCM) systems using LUEP codes as component codes are presented. It is shown that these schemes offer multiple values of minimum squared Euclidean distances, one for each message part to be protected. In addition, the error performance of a BCM system using LUEP codes and QPSK modulation with Gray mapping between 2-bit symbols and signals, is analyzed. In this dissertation, we also present a new multi-stage soft-decision decoding, based on the trellis structure of LUEP codes.
The effect of a single inhaled dose of a VLA‐4 antagonist on allergen‐induced airway responses and airway inflammation in patients with asthma (2006)

Adhesion molecule very late antigen-4 (VLA-4) is implicated in the recruitment and activation of inflammatory cells in asthma, including eosinophils, T cells and mast cells. VLA-4 antagonists have been proposed as a new anti-inflammatory treatment modality for asthma. Therefore, we investigated whether a single inhaled dose of VLA-4 antagonist GW559090X could protect against allergen-induced changes in airway responses and airway inflammation in patients with asthma. We performed a randomized, double-blind, three-way crossover study with single inhaled doses of 3 mg of GW559090X, 500 microg of fluticasone propionate (FP) or placebo in 15 patients with mild intermittent asthma, controlled with short-acting beta(2)-agonists only. All patients developed a late asthmatic response (LAR) after allergen inhalation during screening. Study medication was administered 30 min prior to allergen challenge. Pre-dose and 24 h post-dose PC20 methacholine and levels of exhaled nitric oxide (eNO) were determined. At the given dose, VLA-4 antagonist GW559090X did not attenuate the early asthmatic response (EAR) when compared with placebo: mean AUC0-2 h(+/-SEM) (%fall h): 27.2+/-3.7 and 21.9+/-3.0 respectively (P=0.33); nor the LAR: mean AUC3-8 h(+/-SEM) (%fall h): 98.8+/-12.9 and 94.8+/-6.8 respectively (P=0.84). However, pretreatment with FP did attenuate both EAR and LAR when compared with placebo: mean AUC0-2 h11.6+/-3.3 (P=0.024) and mean AUC3-8 h 6.3+/-7.6 (P<0.001). None of these treatments had an effect on allergen-induced changes in airway hyper-responsiveness or eNO levels. These findings suggest that VLA-4 may not play a major role in allergen-induced airway responses and inflammation in asthma.
Aspects of Industrial Optics 1968 (1968)

A survey is given of recent developments in optical inspection instruments, particularly those using optical fibres; in holography; and in diffraction methods which lead to a pattern which is the Fourier transform of the original image. The emphasis throughout is on actual or possible applications to industrial or scientific measurement.
Low-Dose Gabapentin Combined with either Lamotrigine or Carbamazepine Can Be Useful Therapies for Trigeminal Neuralgia in Multiple Sclerosis (2000)

Paroxysmal symptoms occur frequently in multiple sclerosis (MS). Usually they are treated with carbamazepine (CBZ) and phenytoin, although these medications are often interrupted due to adverse effects. We report 11 MS patients with trigeminal neuralgia (TN): 6 intolerant to a therapeutic dosage of CBZ, showing serious adverse effects and subsequently treated with a combination of low-dose CBZ and gabapentin (GBP) (group 1); 5 treated with lamotrigine (LMT), showing adverse effects and subsequently treated with GBP (group 2). Subjective pain level and impairment in performing daily activities were rated utilizing a 3-point scale at time 0 and at optimal dosage time (T1). GBP was initiated at 300 mg daily and titrated, until pain control was achieved without new adverse effects, to a maximum dose of 1,200 mg daily. CBZ or LMT were reduced to a level which no longer produced adverse effects, although resulting in a lack of efficacy in relieving pain. Pain control was obtained in all patients but 1, with no side effects. The plasma level analysis, performed in 5 patients, resulted in normal values. The mean dosages at T1 were: group 1 CBZ 400 mg and GBP 850 mg daily; group 2 LMT 150 mg and GBP 780 mg daily. Combining drugs with complementary modes of action may provide a rational pharmacological approach to the management of TN in MS.
Sirtuins: Molecular Traffic Lights in the Crossroad of Oxidative Stress, Chromatin Remodeling, and Transcription (2011)

Transcription is regulated by acetylation/deacetylation reactions of histone and nonhistone proteins mediated by enzymes called KATs and HDACs, respectively. As a major mechanism of transcriptional regulation, protein acetylation is a key controller of physiological processes such as cell cycle, DNA damage response, metabolism, apoptosis, and autophagy. The deacetylase activity of class III histone deacetylases or sirtuins depends on the presence of NAD(+) (nicotinamide adenine dinucleotide), and therefore, their function is closely linked to cellular energy consumption. This activity of sirtuins connects the modulation of chromatin dynamics and transcriptional regulation under oxidative stress to cellular lifespan, glucose homeostasis, inflammation, and multiple aging-related diseases including cancer. Here we provide an overview of the recent developments in relation to the diverse biological activities associated with sirtuin enzymes and stress responsive transcription factors, DNA damage, and oxidative stress and relate the involvement of sirtuins in the regulation of these processes to oncogenesis. Since the majority of the molecular mechanisms implicated in these pathways have been described for Sirt1, this sirtuin family member is more extensively presented in this paper.
white paper The Need for a Universal SmartSensor Network (2003)

The benefits that tagging technologies can bring to enterprises by bridging the gap between the real world and its representation in information systems has clearly been demonstrated by the work of the Auto-ID Centre and in many case studies performed by different companies. While RFID tagging currently receives a lot of attention, it is only one of many different technologies that may be used to get information about objects in the real world. In this paper, we address this much larger set of ‘smart sensor’ technologies. Each of these technologies typically has its own particular strengths and weaknesses in different application areas and under different operating conditions. Therefore, for many applications it seems sensible to integrate the data from a combination of underlying sensors to form a smart sensor network. This paper describes the underlying technologies that may be used to build a smart sensor network and presents the authors’ vision of the network itself, providing several example scenarios to demonstrate its utility. Potential problem areas are also discussed. A framework for a universal smart sensor network is proposed; without such a framework, the effort of integrating all the different sources would be prohibitive, resulting in the continued proliferation of inflexible systems that are unable to adapt to the fast changing business requirements of today’s world. We believe that the time is right for further study of the technology behind smart sensor networks and the applications for them.
APPLICATION OF SOFTWARE ENGINEERING TECHNIQUES TO PROVIDE A FORMAL, REPEATABLE METHODOLOGY TO TEACH PROGRAMMING IN THE FIELD OF STATISTICS AND BUSINESS (2016)

Information about the paper titled "APPLICATION OF SOFTWARE ENGINEERING TECHNIQUES TO PROVIDE A FORMAL, REPEATABLE METHODOLOGY TO TEACH PROGRAMMING IN THE FIELD OF STATISTICS AND BUSINESS" at IATED Digital Library
Mobile capture for wearable computer usability testing (2002)

The-mobility of wearable computers makes usability-testing; difficult. In order to fully understand how a user interacts with the wearable, the researcher must examine, both the user's direct interactions, with the, computer, as well as the external context the user perceives during their interaction. We present, a tool that augments a wearable computer with additional hardware and software to capture the information needed to perform a usability study in the field under realistic conditions. We examine the challenges in doing the capture and present our implementation. We also describe VizWear a tool for examining the captured data. Finally, we present our experiences using the system for a sample user study.
Vasopressin Antagonists for Patients With Acute Heart Failure: Interpreting New Clinical and Translational Data (2013)

Elevated levels of arginine vasopressin (AVP) are associated with a worse prognosis and the development of hyponatremia in patients with heart failure (HF). This observation led to the development of AVP receptor antagonists for the treatment of HF patients. Although AVP receptor antagonists increase serum sodium, their overall benefits in patients with HF have been at best modest, and recent data raise concerns about their safety in patients with acute HF and low serum sodium.
Recycling of hydrophobic polymeric materials in the form of hydrogels and swelling promotion thereof (1994)

Three simultaneous crosslinking and sulfonation reactions were developed, in order to obtain hydrophilic gels from recycled hydrophobic commercial materials. In the first case we employed pulverized fountain pens (Bic) in the absence of solvent. Shaving products (Gillette Blue) and fountain pens (Bic) as well were dissolved in chlorinated solvents and further modified with agents bearing chloromethyl groups in the second and third case respectively. In many cases, the products of these reactions showed high ion-exchange capacities and high swelling degree in water. The swelling behaviour of these resins in solutions of low ionic strength was used so as to increase their ability to swell in water permanently. A swelling ratio of almost 200 was obtained for slightly crosslinked hydrogels according to that treatment at room temperature. The final products may have all the applications of sulfonated polystyrene resins.
REMEDIAL TREATMENTS FOR PREMATURELY CRACKED ASPHALT SURFACINGS --PROCEEDINGS OF THE FOURTH CONFERENCE ON ASPHALT PAVEMENTS FOR SOUTHERN AFRICA, HELD CAPE SUN HOTEL, CAPE TOWN, REPUBLIC OF SOUTH AFRICA, 12-16 MARCH 1984. VOL 1 & VOL 2. (1984)

Premature cracking of asphalt wearing courses is currently attracting much attention, both in South Africa and overseas. This phenomenon can be defined as: unexpected crack initiation on the surface of asphalt wearing courses that is not due to any inadequacy in the structural capacity of the underlying pavement layers. Downward propagation may lead to structural distress. Curative measures may include applications of surfacing rejuvenators or bitumen-rubbers, as well as conventional methods. This paper reports on remedial trials carried out on section 12 of the n3 freeway between alberton and heidelberg where the gap-graded wearing course was exhibiting premature cracking. In these trials, three rejuvenators were used as well as two bitumen-rubber seals, a tar-rubber seal, a slurry followed by a single seal and a conventional surface treatment.(a) for the covering abstract of the conference see IRRD 815702.
Neoadjuvant chemotherapy with MRI monitoring for breast cancer (2017)

NACT allows identification of patient subgroups within TNBC and Her2-positive cohorts with a good prognosis. MRI can be used to identify patients who are responding to treatment.
Seven Challenges for Spatial Analyses of Vector-Borne Diseases (2020)

Abstract Prediction of spatial heterogeneity in disease incidence based on measurable spatial factors is a major goal of spatial epidemiology. There are a number of applied goals of these predictions, including appropriately targeting resources for surveillance and intervention and accurately quantifying disease burden. Although spatial heterogeneity is evident in the epidemiology of many diseases, several aspects of the biology of vector-borne diseases amplify this form of heterogeneity. Here, we review several aspects of this biology, highlighting seven distinct ways in which the biology of vector-borne diseases impacts understanding spatial heterogeneity in disease incidence. Whereas traditional methods place emphasis on spatial regression and other forms of statistical analysis of empirical data, the goal here is to offer a perspective on potential pitfalls of analyses that take data at face value and do not acknowledge the complex, nonlinear, and dynamic relationships between spatial patterns of disease incidence and spatial heterogeneity in transmission.
Systematic analysis of protein targets associated with adverse events of drugs from clinical trials and post-marketing reports (2020)

Abstract Adverse drug reactions (ADRs) are undesired effects of medicines that can harm patients and are a significant source of attrition in drug development. ADRs are anticipated by routinely screening drugs against secondary pharmacology protein panels. However, there is still a lack of quantitative information on the links between these off-target proteins and the risk of ADRs in humans. Here, we present a systematic analysis of associations between measured and predicted in vitro bioactivities of drugs, and adverse events (AEs) in humans from two sources of data: the Side Effect Resource (SIDER), derived from clinical trials, and the Food and Drug Administration Adverse Event Reporting System (FAERS), derived from post-marketing surveillance. The ratio of a drug’s in vitro potency against a given protein relative to its therapeutic unbound drug plasma concentration was used to select proteins most likely to be relevant to in vivo effects. In examining individual target bioactivities as predictors of AEs, we found a trade-off between the Positive Predictive Value and the fraction of drugs with AEs that can be detected, however considering sets of multiple targets for the same AE can help identify a greater fraction of AE-associated drugs. Of the 45 targets with statistically significant associations to AEs, 30 are included on existing safety target panels. The remaining 15 targets include 8 carbonic anhydrases, of which CA5B was significantly associated with cholestatic jaundice. We include the full quantitative data on associations between in vitro bioactivities and AEs in humans in this work, which can be used to make a more informed selection of safety profiling targets.
Learning image registration without images (2020)

We introduce a learning strategy for contrast-invariant image registration without requiring imaging data. While classical registration methods accurately estimate the spatial correspondence between images, they solve a costly optimization problem for every image pair. Learning-based techniques are fast at test time, but can only register images with image contrast and geometric content that are similar to those available during training. We focus on removing this image-data dependency of learning methods. Our approach leverages a generative model for diverse label maps and images that exposes networks to a wide range of variability during training, forcing them to learn features invariant to image type (contrast). This strategy results in powerful networks trained to generalize to a broad array of real input images. We present extensive experiments, with a focus on 3D neuroimaging, showing that this strategy enables robust registration of arbitrary image contrasts without the need to retrain for new modalities. We demonstrate registration accuracy that most often surpasses the state of the art both within and across modalities, using a single model. Critically, we show that input labels from which we synthesize images need not be of actual anatomy: training on randomly generated geometric shapes also results in competitive registration performance, albeit slightly less accurate, while alleviating the dependency on real data of any kind. Our code is available at: this http URL