gebhart/patrepeval huggingface dataset:
MO599COMPARISON OF TOTAL BODY WATER MEASURED BY BIOIMPEDANCE SPECTROSCOPY TO UREA DISTRIBUTION VOLUME ESTIMATED FROM UREA KINETIC MODELING IN HEMODIALYSIS PATIENTS (2021)

Abstract Background and Aims Monitoring of fluid, body composition and nutritional changes is important in clinical nephrology. The Body Composition Monitor (BCM; Fresenius Medical Care, Bad Homburg, Germany) measures whole-body bioimpedance and determines extracellular and intracellular resistance by using the Cole-model to estimate total body water (TBW-BCM) and its partition into extracellular and intracellular water. Both can then be used to define body composition and separate body weight into lean tissue mass, adipose tissue mass, and fluid overload. Urea kinetic modeling (UKM) allows the estimation of dialysis dose (double-pooled Kt/V), urea distribution volume (V-UKM) and dietary protein intake. We studied the bias between estimated V-UKM to anthropometric and measured TBW-BCM (Vant, TBW-BCM). Method Pre-hemodialysis (HD), electrodes for the BCM assessments were placed on the non-arteriovenous access arm and ipsilateral leg, respectively, with the patient in a supine position. Vant was calculated using the Watson equation. In addition to these assessments we entered the specified values from the most recent urea kinetic modeling (UKM) treatment into the online solute-solver calculator (http://ureakinetics.org). We chose a baseline ratio of modeled/anthropometric volume of 0.6 to 1.3 L to exclude values with data entry errors and/or UKM sampling errors. We calculated the post HD TBW-BCM by subtracting the intradialytic weight loss and adjusted these estimates by the differences in post HD weight between sessions to make both estimates comparable. We depicted the comparison between the estimated V-UKM versus the TBW-BCM in a scatter- and Bland-Altman (BA) plot (Figure). For the purpose of error investigation we studied the computed bias (V-UKM minus TBW-BCM) as a function of body mass index (BMI) and stray capacitance (td) in a BA plot. We then calculated the difference between Vant and V-UKM and illustrated the comparison in a scatter and BA plot. Results In a cross-sectional design, we studied 161 stable prevalent HD patients (61.3±14.7 years, 98 (60.9%) males, height of 167.5±10.7 cm) prior to their treatment. The regression plot showed slight agreement (R2= 0.69) and the Bland-Altman plot no systematic trends or proportional error in the main analysis (Figure 1a and b). Neither BMI or td explained bias and variance in the bias between both estimates. Vant and V-UKM plots showed agreement (R2 of 0.68) with a mean bias of -2.3±5.1 and no proportional error. Conclusion Both TBW-BCM and the V-UKM as the “bronze standard” of TBW estimation seemed to agree reasonably well. Neither body composition measurement or kinetic modeling approach showed any significant influence on the accuracy and precision of the estimate. According to BCM availability, estimated V-UKM or measured TBW-BCM could be used alternatively in practice to support clinical decision when pharmacokinetic considerations are concerned.
Optimal Reliability in Energy Harvesting Industrial Wireless Sensor Networks (2016)

For industrial wireless sensor networks, it is essential to reliably sense and deliver the environmental data on time to avoid system malfunction. While energy harvesting is a promising technique to extend the lifetime of sensor nodes, it also brings new challenges for system reliability due to the stochastic nature of the harvested energy. In this paper, we investigate the optimal energy management policy to minimize the weighted packet loss rate under the delay constraint, where the packet loss rate considers the lost packets, both during the sensing and delivering processes. We show that the above-mentioned energy management problem can be modeled as an infinite horizon average reward constraint Markov decision problem. In order to address the well-known curse of dimensionality problem and facilitate distributed implementation, we use the linear value approximation technique. Moreover, we apply stochastic online learning with a post-decision state to deal with the lack of the knowledge of the underlying stochastic processes. A distributed energy allocation algorithm with a water-filling structure and a scheduling algorithm by an auction mechanism are obtained. Experimental results show that the proposed algorithm achieves nearly the same performance as the optimal offline value iteration algorithm while requiring much less computation complexity and signaling overhead, and outperforms various existing baseline algorithms.
Modeling osteoporosis to design and optimize pharmacological therapies comprising multiple drug types (2022)

For the treatment of postmenopausal osteoporosis, several drug classes with different mechanisms of action are available. Since only a limited set of dosing regimens and drug combinations can be tested in clinical trials, it is currently unclear whether common medication strategies achieve optimal bone mineral density gains or are outperformed by alternative dosing schemes and combination therapies that have not been explored so far. Here, we develop a mathematical framework of drug interventions for postmenopausal osteoporosis that unifies fundamental mechanisms of bone remodeling and the mechanisms of action of four drug classes: bisphosphonates, parathyroid hormone analogs, sclerostin inhibitors, and receptor activator of NF-κB ligand inhibitors. Using data from several clinical trials, we calibrate and validate the model, demonstrating its predictive capacity for complex medication scenarios, including sequential and parallel drug combinations. Via simulations, we reveal that there is a large potential to improve gains in bone mineral density by exploiting synergistic interactions between different drug classes, without increasing the total amount of drug administered.
Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism (2012)

Filoviruses, including Marburg virus (MARV) and Ebola virus (EBOV), cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (ds)RNA-binding domain (RBD) of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.
Tunable integrated optical delay lines for time-interleaved polarization multiplexing (2008)

Continuously tunable relative delay between orthogonally polarized data-streams is demonstrated in an integrated ring-resonator CROW. System performance and applications to polarization-division multiplexing transmission systems are discussed.
Biotinylated CdSe/ZnSe nanocrystals for specific fluorescent labeling (2004)

A set of two new surface ligands is presented for the preparation of water-soluble, biotinylated CdSe/ZnSe core/shell nanocrystals, suitable for fluorescent biological labeling. It consists of a thiolated diethyleneglycol derivative and an alkylthiol substituted biotin molecule, which replace the initial capping ligands at the nanocrystal surface. Successful ligand exchange and long-term photostability of the modified nanocrystals as well as their highly specific binding to neuronal cells are demonstrated in different labeling experiments.
Sintered-Tantalum Electrode Modified with Polypyrrole by Electropolymerization (1993)

Abstract Polypyrrole (PPy) formation in the interior of a porous electrode by electropolymerization was considered to be impossible. When a concentrated pyrrole solution was soaked into a sintered-Ta electrode and electrolyzed in a pyrrole-free solution, PPy was formed in the interior. PPy occupied 70% of the inner space, and no defect was observed by SEM.
Testing of Various Solvents for the Preparation of Lipid Samples for Use in Thin Layer Chromatography (2001)

We analyzed the muscular tissue of 6 sheep. Lipid extraction was performed using the Handson and Olley method. TLC separation was performed using 4 separation systems and the best separation method was determined. Visualization was done using a mixture copper acetate and phosphoric acid, at 150 oC.
Deep Learning for In Situ and Real-Time Quality Monitoring in Additive Manufacturing Using Acoustic Emission (2019)

Additive manufacturing (AM) is considered as a revolution in manufacturing. However, the high expectations face technical difficulties that prevent further penetration into wider industries. The main reason is the lack of process reproducibility and the absence of a reliable and cost-effective process monitoring. This paper is a supplement to existing studies in this field and proposes a unique combination of highly sensitive acoustic sensor and machine learning for process monitoring. The acoustic signals from a real powder-bed fusion AM process were collected using a fiber Bragg grating. The process parameters are intentionally tuned to achieve three levels of quality categories, which are related to the porosity contents inside the workpiece. The quality categories are defined as high, medium, and poor quality and their corresponding porosity contents are 0.07%, 0.30%, and 1.42%, respectively. Wavelet spectrograms of the signals and their encoded label representations, obtained from spectral clustering, are taken as features. A deep convolutional neural network is used to classify the features from each category and the classification accuracy ranges between 78% and 91%. Hence, the proposed method has significant industrial potentials for in situ and real-time quality monitoring of AM processes since it requires minimum modifications of commercially available industrial machines.
The Effects of Temperature, Humidity and Aircraft Fluid Exposure on T800H/3900-2 Composites Bonded with AF-555M Adhesive (2010)

Fiber reinforced resin matrix composites and structural adhesives have found increased usage on commercial and military aircraft in recent years. Due to the lack of service history of these relatively new material systems, their long-term aging performance has not been well established. In this study, single lap shear specimens (SLS) were fabricated by secondary bonding of Scotch-Weld(TradeMark) AF-555M between pre-cured adherends comprised of T800H/3900-2 uni-directional laminates. The adherends were co-cured with wet peel-ply for surface preparation. Each bond-line of the SLS specimen was measured to determine thickness and inspected visually using an optical microscope for voids. A three-year environmental aging plan for the SLS specimens at 82 C (180 F) and 85% relative humidity was initiated. SLS strengths were measured for both controls and aged specimens at room temperature and 82 C. The effect of this exposure on lap shear strength and failure modes to date is reported. In addition, the effects of water, saline water, deicing fluid, JP-5 jet fuel and hydraulic fluid on both the composite material and the adhesive bonds were investigated. The up to date results on the effects of these exposures will be discussed.
Molecular Imaging of Conscious, Unrestrained Mice with AwakeSPECT (2013)

These results demonstrate the feasibility of SPECT molecular brain imaging of mice in the conscious, unrestrained state and demonstrate the effects of isoflurane anesthesia on radiotracer uptake.
A Subretinal Cell Delivery Method via Suprachoroidal Access in Minipigs: Safety and Surgical Outcomes (2018)

Palucorcel, pUTC, and vehicle were successfully administered to Göttingen minipigs using a novel subretinal injection cannula via a suprachoroidal surgical approach, with no significant adverse events; therefore, this technique appears to be feasible for further clinical development.
New Catalysts for a Zero-Gap Type Gas-Diffusion Electrode in Chlor-Alkali Membrane Process (2009)

Newly developed gas-diffusion electrodes (GDE) with binary catalyst composed of Ag and Pd were evaluated in a zero-gap type chlor-alkali cell. It was found that the cell voltage was 2.06V at 6kAm-2, which was 120 mV smaller than those of composed of single Ag catalyst or Pd catalyst. The increase of the cell voltage with the binary catalyst after 600 days of operation was only around 20 mV, which is one third of that of Ag catalyst. The particles sizes of the former catalyst were not changed after the electrolysis, but the size of Ag in the latter became large, which quantitatively corresponded to the increase of overvoltage predicted by a porous GDE model calculation. It was suggested that the agglomeration of the Ag catalyst could be inhibited by the existence of Pd.
Adaptive Security and Robust Networks (2003)

This section explores a security protocol that is simultaneously less aggressive and more &apos;intelligent&apos;. The main objective of this work is to promote a vision of information insurance that fits in to the bigger picture and does not disregard structural changes to focus exclusively on minor case-by-case adjustments. When the Internet took off in the mid-1990s, an evolutionary process started that is literally turning networks inside out - no more fixed boundaries to protect, no more convenient access points from where to conduct all security checks.
The Stress Response and Stress Proteins (2020)

The stress response, or heat shock response, is a fundamental molecular mechanism with which organisms compensate for environmentally induced perturbations of cellular function. More than 500 publications examine the relationships between the stress response and the other subjects in this volume (e.g., reactive oxygen species, ischemia-reperfusion injury, inflammation). The stress response initially attracted considerably attention as a model system for investigating gene structure and regulation. In addition, the stress response provided one of the first examples of selective gene expression operating at the level of translation. Diverse aspects of the stress response are consistent with stress proteins serving as molecular chaperones. An essential component of chaperoning activity is thus the ability of stress proteins to “recognize” interactive sites that are normally sequestered in the interior of properly folded proteins. The chapter concludes with examples of engineered stress tolerance to advocate the exploitation of such systems to understand the cell biology of trauma.
Anorexia and Fat Aversion Induced by Vertical Sleeve Gastrectomy Is Attenuated in Neurotensin Receptor 1–Deficient Mice (2021)

Neurotensin (NT) is an anorexic gut hormone and neuropeptide that increases in circulation following bariatric surgery in humans and rodents. We sought to determine the contribution of NT to the metabolic efficacy of vertical sleeve gastrectomy (VSG). To explore a potential mechanistic role of NT in VSG, we performed sham or VSG surgeries in diet-induced obese NT receptor 1 (NTSR1) wild-type and knockout (ko) mice and compared their weight and fat mass loss, glucose tolerance, food intake, and food preference after surgery. NTSR1 ko mice had reduced initial anorexia and body fat loss. Additionally, NTSR1 ko mice had an attenuated reduction in fat preference following VSG. Results from this study suggest that NTSR1 signaling contributes to the potent effect of VSG to initially reduce food intake following VSG surgeries and potentially also on the effects on macronutrient selection induced by VSG. However, maintenance of long-term weight loss after VSG requires signals in addition to NT.
Toward Testing the Hypothesis that Group B Coxsackieviruses (CVB) Trigger Insulin-Dependent Diabetes: Inoculating Nonobese Diabetic Mice with CVB Markedly Lowers Diabetes Incidence (2002)

Insulin-dependent (type 1) diabetes mellitus (T1D) onset is mediated by individual human genetics as well as undefined environmental influences such as viral infections. The group B coxsackieviruses (CVB) are commonly named as putative T1D-inducing agents. We studied CVB replication in nonobese diabetic (NOD) mice to assess how infection by diverse CVB strains affected T1D incidence in a model of human T1D. Inoculation of 4- or 8-week-old NOD mice with any of nine different CVB strains significantly reduced the incidence of T1D by 2- to 10-fold over a 10-month period relative to T1D incidences in mock-infected control mice. Greater protection was conferred by more-pathogenic CVB strains relative to less-virulent or avirulent strains. Two CVB3 strains were employed to further explore the relationship of CVB virulence phenotypes to T1D onset and incidence: a pathogenic strain (CVB3/M) and a nonvirulent strain (CVB3/GA). CVB3/M replicated to four- to fivefold-higher titers than CVB3/GA in the pancreas and induced widespread pancreatitis, whereas CVB3/GA induced no pancreatitis. Apoptotic nuclei were detected by TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) assay in CVB3/M-infected pancreata but not in CVB3/GA-infected pancreata. In situ hybridization detected CVB3 RNA in acinar tissue but not in pancreatic islets. Although islets demonstrated inflammatory infiltrates in CVB3-protected mice, insulin remained detectable by immunohistochemistry in these islets but not in those from diabetic mice. Enzyme-linked immunosorbent assay-based examination of murine sera for immunoglobulin G1 (IgG1) and IgG2a immunoreactivity against diabetic autoantigens insulin and HSP60 revealed no statistically significant relationship between CVB3-protected mice or diabetic mice and specific autoimmunity. However, when pooled sera from CVB3/M-protected mice were used to probe a Western blot of pancreatic proteins, numerous proteins were detected, whereas only one band was detected by sera from CVB3/GA-protected mice. No proteins were detected by sera from diabetic or normal mice. Cumulatively, these data do not support the hypothesis that CVB are causative agents of T1D. To the contrary, CVB infections provide significant protection from T1D onset in NOD mice. Possible mechanisms by which this virus-induced protection may occur are discussed.
Polynomial-based maximum-likelihood technique for synchronization in digital receivers (2002)

Maximum-likelihood estimation theory provides a general framework for developing near-optimum (with respect to the Cramer-Rao bound) synchronization schemes for digital communication systems. A new technique for jointly estimating the symbol timing and carrier phase in digital receivers for linear digital modulations with nonsynchronized sampling is established for both data-aided and nondata-aided systems using a block-based feedforward architecture. This technique is a practical, fully digitally implemented synchronization concept based on a low-order polynomial approximation of the likelihood functions using the Farrow-based interpolator. It is shown that low oversampling, like two samples per symbol, can be used in timing recovery without compromising the system performance. This results in efficient overall receiver implementation. It is also demonstrated that the quality of the interpolator design has a big effect on the performance of the synchronization scheme. Frequency-domain optimized polynomial interpolator designs provide significantly better performance than the well-known Lagrange interpolators.
A single-parasite transcriptional atlas of Toxoplasma Gondii reveals novel control of antigen expression (2020)

<i>Toxoplasma gondii,</i> a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between <i>Toxoplasma</i> and <i>Plasmodium</i> scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Synthesis and Evaluation of a Rationally Designed Click-Based Library for G-Quadruplex Selective DNA Photocleavage (2015)

DNA containing repeating G-rich sequences can adopt higher-order structures known as G-quadruplexes (G4). These structures are believed to form within telomeres and the promoter regions of some genes, particularly in a number of proto-oncogenes, where they may play a role in regulating transcription. Alternatively, G4 DNA may act as a barrier to replication. To investigate these potential biological roles, probes that combine highly selective G4 DNA targeting with photocleavage activity can allow temporal detection of G4 DNA, providing opportunities to obtain novel insights about the biological roles of G4 DNA. We have designed, synthesized, and screened a small library of potential selective G-quadruplex DNA photocleavage agents incorporating the G-quadruplex targeting moiety of 360A with known photocleavage groups linked via "click" chemistry.
DRE-PSA Data Revisited: PSA Sampling Should Precede DREs (1996)

We read with great interest the article entitled "Effect of Digital Rectal Examination [DRE] on Serum Prostate-Specific Antigen [PSA] in a Primary Care Setting,"<sup>1</sup>published by the Internal Medicine Clinic Research Consortium. We take exception with the authors'<sup>1</sup>conclusion that the DRE causes a clinically insignificant increase in the serum PSA level. The Internal Medicine Clinic Research Consortium found that the PSA level increased in 72% of patients, while the expected figure would be 50% if the DRE had no effect. The average increase was about 10% (0.26 μg/L) of the mean level found before DRE. While it is true that a change from 2.0 to 2.3 μg/L is probably of no clinical consequence, the authors showed that the observed increase after DRE tended to be greater for larger basal PSA levels. More impact is therefore expected with patients with borderline values between 3 and 4 μg/L. In