gebhart/patrepeval huggingface dataset:
Prediction and Inference With Missing Data in Patient Alert Systems (2019)

We describe the Bedside Patient Rescue (BPR) project, the goal of which is risk prediction of adverse events for non-intensive care unit patients using ∼100 variables (vitals, lab results, assessments, etc.). There are several missing predictor values for most patients, which in the health sciences is the norm, rather than the exception. A Bayesian approach is presented that addresses many of the shortcomings to standard approaches to missing predictors: (i) treatment of the uncertainty due to imputation is straight-forward in the Bayesian paradigm, (ii) the predictor distribution is flexibly modeled as an infinite normal mixture with latent variables to explicitly account for discrete predictors (i.e., as in multivariate probit regression models), and (iii) certain missing not at random situations can be handled effectively by allowing the indicator of missingness into the predictor distribution only to inform the distribution of the missing variables. The proposed approach also has the benefit of providing a distribution for the prediction, including the uncertainty inherent in the imputation. Therefore, we can ask questions such as: is it possible this individual is at high risk but we are missing too much information to know for sure? How much would we reduce the uncertainty in our risk prediction by obtaining a particular missing value? This approach is applied to the BPR problem resulting in excellent predictive capability to identify deteriorating patients. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
Discovery of Trp-His and His-Arg Analogues as New Structural Classes of Short Antimicrobial Peptides (2009)

Naturally occurring antimicrobial peptides contain a large number of amino acid residues, which limits their clinical applicability. In search of short antimicrobial peptides, which represent a possible alternative for lead structures to fight antibiotic resistant microbial infections, a series of synthetic peptide analogues based on Trp-His and His-Arg structural frameworks have been prepared and found to be active against several Gram-negative and Gram-positive bacterial strains as well as against a fungal strain with MIC values of the most potent structures in the range of 5-20 microg/mL ((IC(50) in the range of 1-5 microg/mL). The synthesized peptides showed no cytotoxic effect in an MTT assay up to the highest test concentration of 200 microg/mL. A combination of small size, presence of unnatural amino acids, high antimicrobial activity, and absence of cytotoxicity reveals the synthesized Trp-His and His-Arg analogues as promising candidates for novel antimicrobial therapeutics.
Purification of Monoclonal Antibodies Using High Performance Liquid Chromatography (HPLC) (1984)

Recent increases in the ability to detect low levels of immunofluorescence have shown the need for highly purified primary immunoreagents. There are now reports of purification of monoclonal antibodies using HPLC with reverse phase columns. In this study we have utilized standard size exclusion HPLC to purify both biotinylated and non-biotinylated monoclonal antibodies from hybridoma culture supernatants. Results indicated that both biotinylated and non-biotinylated monoclonal antibodies retained their antigen binding capacity after purification, and were not different in this capacity from commercially available, affinity purified reagents. These findings indicate that size exclusion HPLC may be used in the purification of biologically active monoclonal antibodies, and suggest that this technique may be used in the large scale production of antibodies and their fragments, in antibody purification from ascites fluid, and in antisera quality control.
Genetic algorithm for pattern detection in NIALM systems (2005)

Nonintrusive appliance load monitoring systems (NIALM) require sufficient accurate total load data to separate the load into its major appliances. The most available solutions separate the whole electric energy consumption based on the measurement of all three voltages and currents. Aside from the cost for special measuring devices, the intrusion into the local installation is the main problem for reaching a high market distribution. The use of standard digital electricity meters could avoid this problem with loss of information in the measured data. This paper presents a new NIALM approach to analyse data, collected form a standard digital electricity meter. To disaggregate the consumption of the entire active power into its major electrical end uses, an algorithm consisting of fuzzy clustering methods, a genetic algorithm and a dynamic programming approach is presented.
Plasmacytoid Dendritic Cells Suppress HIV-1 Replication but Contribute to HIV-1 Induced Immunopathogenesis in Humanized Mice (2014)

The role of plasmacytoid dendritic cells (pDC) in human immunodeficiency virus type 1 (HIV-1) infection and pathogenesis remains unclear. HIV-1 infection in the humanized mouse model leads to persistent HIV-1 infection and immunopathogenesis, including type I interferons (IFN-I) induction, immune-activation and depletion of human leukocytes, including CD4 T cells. We developed a monoclonal antibody that specifically depletes human pDC in all lymphoid organs in humanized mice. When pDC were depleted prior to HIV-1 infection, the induction of IFN-I and interferon-stimulated genes (ISGs) were abolished during acute HIV-1 infection with either a highly pathogenic CCR5/CXCR4-dual tropic HIV-1 or a standard CCR5-tropic HIV-1 isolate. Consistent with the anti-viral role of IFN-I, HIV-1 replication was significantly up-regulated in pDC-depleted mice. Interestingly, the cell death induced by the highly pathogenic HIV-1 isolate was severely reduced in pDC-depleted mice. During chronic HIV-1 infection, depletion of pDC also severely reduced the induction of IFN-I and ISGs, associated with elevated HIV-1 replication. Surprisingly, HIV-1 induced depletion of human immune cells including T cells in lymphoid organs, but not the blood, was reduced in spite of the increased viral replication. The increased cell number in lymphoid organs was associated with a reduced level of HIV-induced cell death in human leukocytes including CD4 T cells. We conclude that pDC play opposing roles in suppressing HIV-1 replication and in promoting HIV-1 induced immunopathogenesis. These findings suggest that pDC-depletion and IFN-I blockade will provide novel strategies for treating those HIV-1 immune non-responsive patients with persistent immune activation despite effective anti-retrovirus treatment.
Effect of cyclooxygenase and nitric oxide synthase inhibitors on tumor growth in mouse tumor models with and without cancer cachexia related to prostanoids. (2000)

The potential interaction between cyclooxygenase (Cox) and NO metabolic pathways in the control of local tumor growth was evaluated. Mice bearing either a sarcoma-derived tumor (C57B1; MCG 101) or a malignant melanoma (C3H/HeN; K1735-M2) were used. These models were principally different because they demonstrate, in tumor hosts, conditions with and without cancer cachexia, seemingly related to high and low production of prostanoids, respectively. Cox inhibitors (Cox-1 and Cox-2) decreased tumor growth by 35-40% in MCG 101-bearing mice but had no such effect on melanoma-bearing mice, despite the expression of the Cox-2 protein in melanoma cells. Indomethacin reduced prostanoid production in both tumor (MCG 101) and host tissues and reduced tumor cell proliferation, mainly in vivo. Nitric oxide synthase (NOS) inhibitors (N(omega)-nitro-L-arginine methyl ester and N(omega)-nitro-L-arginine) reduced tumor growth in vivo by approximately 50% in both tumor models. Tumor growth reduction, related to NOS inhibition, was unrelated to prostanoid production and was an in vivo phenomenon in both tumor models. Specific inhibitors of inducible NOS activity, unexpectedly, had no effect in any tumor model, although inducible NOS protein was present in tumor tissues in large amounts. A combination of Cox and NOS inhibitors had no additive effect on tumor growth (MCG 101). Cox inhibition increased tumor tissue (MCG 101) expression of cNOS mRNA but had no significant effect on tumor tissue expression of the transferrin receptor, vascular endothelial growth factor, or basic fibroblast growth factor. NOS inhibition increased tumor tissue content of cNOS mRNA but showed as well a trend to increase mRNA content of the transferrin receptor and vascular endothelial growth factor. Our results suggest that NOS inhibitors can decrease the local growth of tumors that are either responsive or unresponsive to Cox inhibition. This effect may reflect cross-talk between Cox and NOS pathways within or among tumor cells, or it may represent unrelated effects on tumor and host cells. Whether NO inhibition may be used therapeutically in clinical tumors that are unresponsive to eicosanoid intervention remains to be evaluated.
Eupatilin attenuates diabetic nephropathy by upregulating matrix metalloproteinase-9 expression in diabetic rat kidney (2018)

Purpose: To evaluate the nephro-protective effect of eupatilin in diabetic nephropathic (DN) rats.Method: Diabetes was induced by intraperitoneal administration of streptozotocin (STZ, 55 mg/kg) and confirmed by fasting blood glucose results, while DN was determined by measuring serum urea and creatinine levels on day 40 after STZ administration. The eupatilin-treated group received eupatilin at 50 and 100 mg/kg, p.o. for 20 days, after which blood levels of some biochemical parameters, glomerulosclerosis index, eosinophilic cast index, and expression of MMP-9 were determined using standard procedures.Results: Treatment with eupatilin significantly decreased serum levels of glucose, creatinine and urea, and increased creatinine clearance, compared to the negative control group. Moreover, eupatilin attenuated changes in kidney histopathology, and significantly enhanced the expression of MMP-9 in the kidney tissues of the DN rats, relative to negative control group.Conclusion: These results indicate that eupatilin attenuates renal failure in STZ-induced DN rats by upregulating the expression of MMP-9.Keywords: Eupatilin, Streptozotocin, Diabetic nephropathy, MMP-9
TH‐A‐217BCD‐05: Material Decomposition in Spectral Computed Tomography (CT) Using a Likelihood‐Based Method (2012)

Purpose: To investigate the feasibility of accurate quantification of concentrations of mixtures of K‐edge contrast agents in spectral Computed Tomography (CT) imaging based on a novel maximum likelihood based method. Methods: Calcium, gold, and iodine solutions of various concentrations were prepared in vials and placed in phantoms for imaging at 100 kVp with a Cadmium‐Zinc‐Telluride (CZT) photon counting detector. The linear attenuation maps were reconstructed in 5 energy bins, whose boundaries were 22, 34, 60, 80, and 100 keV. A novel maximum likelihood‐based algorithm for material decomposition was developed. Summing over the energy bins, on a pixel‐by‐pixel basis, this procedure takes into account the reconstructed linear attenuation coefficient, its associated noise, and the tabulated mass attenuation coefficient of each material of interest, to determine a cost function. The unknown parameters to be fitted by optimization by the MINUIT optimizer (from CERN) of the cost function are the concentrations of the materials of interest at each pixel. The result is a density map image for upper limits on the concentration of each material. Results: Multiple material decomposition of the spectral CT phantoms according to this method yields reliable estimates of concentrations. The upper limits on concentrations are linearly correlated with known concentrations. Conclusions: This study indicates that the problem of decomposition of multiple materials of interest may be facilitated by optimization in the image domain, based on linear attenuation values, and using log‐likelihood and upper limit techniques. This technique can be used for analysis of the spectral CT data.
Provably Good Batch Reinforcement Learning Without Great Exploration (2020)

Batch reinforcement learning (RL) is important to apply RL algorithms to many high stakes tasks. Doing batch RL in a way that yields a reliable new policy in large domains is challenging: a new decision policy may visit states and actions outside the support of the batch data, and function approximation and optimization with limited samples can further increase the potential of learning policies with overly optimistic estimates of their future performance. Recent algorithms have shown promise but can still be overly optimistic in their expected outcomes. Theoretical work that provides strong guarantees on the performance of the output policy relies on a strong concentrability assumption, that makes it unsuitable for cases where the ratio between state-action distributions of behavior policy and some candidate policies is large. This is because in the traditional analysis, the error bound scales up with this ratio. We show that a small modification to Bellman optimality and evaluation back-up to take a more conservative update can have much stronger guarantees. In certain settings, they can find the approximately best policy within the state-action space explored by the batch data, without requiring a priori assumptions of concentrability. We highlight the necessity of our conservative update and the limitations of previous algorithms and analyses by illustrative MDP examples, and demonstrate an empirical comparison of our algorithm and other state-of-the-art batch RL baselines in standard benchmarks.
Intracellular Delivery of Trehalose for Cell Banking (2018)

Advances in stem cell technology and regenerative medicine have underscored the need for effective banking of living cells. Cryopreservation, using very low temperatures to achieve suspended animation, is widely used to store or bank cells for later use. This process requires the use of cryoprotective agents (CPAs) to protect cells against damage caused by the cooling and warming process. However, current popular CPAs like DMSO can be toxic to cells and must be thoroughly removed from cells before they can be used for research or clinical applications. Trehalose, a nontoxic sugar found in organisms capable of withstanding extreme cold or desiccation, has been explored as an alternative CPA. The disaccharide must be present on both sides of the cellular membrane to provide cryo-protection. However, trehalose is not synthesized by mammalian cells nor has the capability to diffuse through their plasma membranes. Therefore, it is crucial to achieve intracellular delivery of trehalose for utilizing the full potential of the sugar for cell banking. In this review, various methods that have been explored to deliver trehalose into mammalian cells for their banking at both cryogenic and ambient temperatures are surveyed. Among them, the nanoparticle-mediated approach is particularly exciting. Collectively, studies in the literature demonstrate the great potential of using trehalose as the sole CPA for cell banking, to facilitate the widespread use of living cells in modern medicine.
Pregnant and postpartum women requiring intensive care treatment for COVID-19 – first data from the CRONOS-registry (2021)

Background Critical illness during pregnancy puts mother and fetus at serious risks. Current literature regarding the effect of coronavirus 2 (SARS-CoV-2) describes an increased risk for maternal mortality as well as high rates of preterm delivery, however data vary and depend on the respective health care system. We aimed to describe maternal characteristics and clinical presentation of SARS-CoV-2 positive pregnant and postpartum women requiring intensive care treatment for COVID-19 in Germany, in order to explore risk factors for severe COVID-19 courses as well as to provide an overview on treatments applied.
Field Strength Measurements in Resonant Cavities (1952)

It is shown that the frequency of a resonant electromagnetic cavity is perturbed by inserting a metallic sphere, needle, or disk of dimensions small compared to a wavelength by an amount depending upon the local electric and magnetic field at the position of the perturbing object. This perturbation is calculated for ellipsoidal objects of needle-shaped, spherical, and disk-shaped form. The perturbations by the different objects depend upon different components of electric and magnetic fields, and by combining measurements with all three, it is in theory possible to measure all the field components. Experimental checks of the calculations are described, resulting in satisfactory agreement between theory and experiment except with the needles, in which the perturbation is very sensitive to the precise shape of the object, and the needles used were not accurate enough ellipsoids to give satisfactorily quantitative results.
Primary tubulointerstitial nephritis and uveitis syndrome (1993)

Primary acute tubulointerstitial nephritis and uveitis is an uncommon syndrome involving the kidney and eye. Although rare, to date 28 cases having been reported, it is important to recognise this entity to facilitate appropriate investigation and treatment. We report an unusual case of this syndrome in which the patient suffered a relapse of her nephritis concurrently with the onset of the first episode of uveitis. Both responded to treatment, although the uveitis subsequently recurred.
Relaxation Time of the TopologicalT1Process in a Two-Dimensional Foam (2006)

The elementary topological T1 process in a two-dimensional foam corresponds to the flip of one film with respect to the geometrical constraints, and is a process by which the structure of an out-of-equilibrium foam evolves. We study both experimentally and theoretically the T1 dynamics in a dry two-dimensional foam. The dynamics is controlled by the surface viscoelastic properties of the films (surface shear plus dilatational viscosity, mu_{s}+kappa, and Gibbs elasticity ), and is independent of the shear viscosity of the bulk liquid. Moreover, the dynamics of the T1 process provides a tool for measuring the surface rheological properties: we obtained =32+/-8 mN/m and mu_{s}+kappa=1.3+/-0.7 mPa.m.s for sodium dodecyl sulfate, and =65+/-12 mN/m and mu_{s}+kappa=31+/-12 mPa.m.s for bovine serum albumin, in good agreement with literature values.
Ultrashort-pulse laser machining of dielectric materials (1999)

There is a strong deviation from the usual τ1/2 scaling of laser damage fluence for pulses below 10 ps in dielectric materials. This behavior is a result of the transition from a thermally dominated damage mechanism to one dominated by plasma formation on a time scale too short for significant energy transfer to the lattice. This new mechanism of damage (material removal) is accompanied by a qualitative change in the morphology of the interaction site and essentially no collateral damage. High precision machining of all dielectrics (oxides, fluorides, explosives, teeth, glasses, ceramics, SiC, etc.) with no thermal shock or distortion of the remaining material by this mechanism is described.
Aging changes in renal handling of p-aminohippurate (1987)

Aging alterations in the renal transport of p-aminohippurate (PAH) were investigated using cortical slices from C57BL/6 mice and standard clearance techniques in 5-ethyl-5-(1-methylpropyl)-2-thiobarbituric acid (Inactin)-anesthetized Fischer 344 rats. Life-span stages were classified as growth, maturity, and aging. PAH uptake was linear from 0 to 20 min with steady state occurring at 30 min in the growing and mature mouse and 20 min in the aging mouse. Km values for PAH uptake in the growing, mature, and aging mouse were 250, 123, and 643 microM, respectively, and maximal rate of uptake values were 0.756, 0.926, and 0.586 mumol X g-1 X 30 min-1, respectively. The efflux half-life (t 1/2) for PAH was similar in all age groups. The PAH acetylation rate was similar in the growing and mature mouse but decreased by 40% in the aging mouse. There were statistically significant correlations between aging (12-27 mo) and renal plasma flow [(RPF) r2 = 0.33, P less than 0.05] and between aging and tubular maximal (Tm) activity for PAH transport (r2 = 0.84, P less than 0.001). Maximal decreases of 25 and 40% were found for RPF and Tm, respectively, in the aging rat. It is concluded that aging affects PAH transport at the receptor level.
Spiral Growth Manufacturing (SGM) – A Continuous Additive Manufacturing Technology for Processing Metal Powder by Selective Laser Melting (2005)

Spiral growth manufacturing is a new innovative powder based rapid manufacturing technique. The innovation exists in the methodology in which powder layers are deposited. Unlike other pre-placed powder systems, the deposited layers move relative to the location at which they are processed. This is made possible by a rotating build drum into which powder is deposited, in spiralled layers, from a stationary hopper. With this configuration powder can be continuously deposited and levelled and simultaneously processed, eliminating delays in the build cycle. Stainless steel and cobalt-chrome powder is selectively melted using a 100W flash lamp pumped Nd:YAG laser. This paper reports on factors affecting build rate and on build strategies for creating a number of axis-symmetric thin and thick walled cylinders. Experimental results suggest that build rate for thin walled structures bonded to a substrate will ultimately be governed by tangential movements of the powder particles when frictional forces are not sufficient to accelerate the particles along a curved path, provided that enough laser power is available for melting. Even melt pool balling, which is evident when melting one layer at high speeds, diminishes in multiple layer builds due to re-melting and infilling.
Tissue specific expression and developmental regulation of two genes coding for rat fatty acid binding proteins. (1985)

We have examined the tissue distribution and developmental regulation of two low molecular weight cytosolic fatty acid binding proteins. Based on their initial site of isolation, they have been referred to as liver and intestinal fatty acid binding proteins (FABP). Cloned cDNAs were used to probe blots of RNAs extracted from a wide variety of adult rat tissues as well as small intestine and liver RNA obtained from fetal, suckling, and weaning animals. The highest concentrations of "liver" FABP mRNA were found in small intestine and liver. "Intestinal" FABP mRNA is most abundant in small bowel RNA while only trace amounts were encountered in liver. Both mRNAs were detectable in stomach, colon, pancreas, spleen, lung, heart, testes, adrenal, and brain RNA at 1-8% the concentrations observed in small intestine. Accumulation of both mRNAs in the small intestinal epithelium increases during development. The mRNAs are first detectable between the 19th and 21st day of gestation. They undergo a coordinated 3-4-fold increase in concentration within the first 24 h after birth. Thereafter, gut levels of intestinal FABP mRNA remain constant during the suckling period while liver FABP mRNA increases an additional 2-fold. Liver FABP mRNA levels are also induced in hepatocytes during the first postnatal day but subsequently do not change during the suckling and weaning phase, despite marked alterations in hepatic fatty acid metabolism. These observations support the concept that the major role of these proteins is to facilitate the entry of lipids into cells and/or their subsequent intracellular transport and compartmentalization. The data also raise questions about the identity of extragastrointestinal FABPs.