gebhart/patrepeval huggingface dataset:
Treatment of Neonatal Abstinence Syndrome with Clonidine versus Morphine as Primary Therapy (2020)

Background: Maternal opiate use and resulting Neonatal Abstinence Syndrome (NAS) have continued to be a major public health concern in the US. NAS is a result of the abrupt discontinuation of the substances abused or used by the mother during pregnancy. The withdrawal symptoms are seen in about 80% of the neonates exposed to opioids in utero. Pharmacologic treatment is required when the infant fails to respond to supportive care, when scores for withdrawal remain high, if seizures are seen or if withdrawal …
The metabolism of fatty acids in human Bietti crystalline dystrophy. (2001)

BCD is characterized by a lower than normal conversion of FA precursors into n-3 PUFA, whereas there is a higher than normal level of n-6 and n-3 FAs incorporation into TGs in cells from patients with WD. These findings raise the possibility that abnormal lipid metabolism associated with BCD is the result of deficient lipid binding, elongation, or desaturation in contrast to the lysosomal acid lipase deficiency found in Wolman disease.
Clinical features of human prion diseases (2002)

Human prion diseases are rare disorders affecting the central nervous system, characterized by protracted incubation periods, progressive and eventually fatal neurological deficits and the deposition in the brain of prion protein (PrP) (Prusiner, 1994). Scientific interest in this group of diseases has been stimulated by the accumulating evidence in support of the prion hypothesis, which proposes that the transmissible causal agent is a post-translationally modified ‘infectious’ form of a normal host-encoded protein, PrP (Prusiner, 1982) (Chapter 6). There has also been an extraordinary level of public interest in prion diseases following the occurrence of bovine spongiform encephalopathy (BSE) and the proposition that this cattle disease has been transmitted to humans to cause a novel human prion disease, variant Creutzfeldt–Jakob disease (vCJD) (Will et al., 1996).
Camptothecin delivery systems: the antitumor activity of a camptothecin-20-0-polyethylene glycol ester transport form. (1998)

This water soluble transport form of 20-(S)-camptothecin and its underlying technology may have clinical application.
Recent advances in an excimer laser source for microlithography (1991)

This paper describes the advances made in a KrF excimer laser source designed specifically for the deep-UV reduction stepper. Data is presented on key performance aspects that are required for the laser to be used in the next generation of excimer steppers. Major topics discussed will be spectral bandwidth reduction, center wavelength control, pulse-to-pulse energy stability, higher power performance, and the production worthiness of the system. The first generation excimer laser (CX-2LS) for lithography operated at 200 Hz and 3 W, with a spectral bandwidth of 3 pm and a wavelength stability of ±0.5 pm. The new laser (ELS-4000) is designed and engineered to perform at 400 Hz and 4 W with a narrower spectral bandwidth (2 pm) and a wavelength stability of better than ±0.25 pm. In addition, the pulse-to-pulse stability has been improved in stepper-mode operation. The ELS-4000 also employs a new microprocessor controlled gas injection system that permits uninterrupted operation for 10–20 h (7–10 million pulses). This level of performance assures the compatibility of the laser with the requirements of production excimer steppers being developed with higher numerical aperature lenses, larger fields, and higher wafer throughputs.
Whey acidic protein (WAP) regulates the proliferation of mammary epithelial cells by preventing serine protease from degrading laminin (2007)

Whey acidic protein (WAP) is a major whey protein in milk that has structural similarity to the family of serine protease inhibitors with WAP motif domains characterized by a four-disulfide core. We previously reported that enforced expression of the mouse WAP transgene in mammary epithelial cells inhibits their proliferation in vitro and in vivo by means of suppressing cyclin D1 expression (Nukumi et al., 2004, Dev Biol 274: 31-44). This study was conducted in order to clarify the molecular mechanism of the inhibitory function of WAP in HC11 cells, a mammary epithelial cell line. The assembly of laminin, a component in the extracellular matrix, was much more prominent around WAP-clonal HC11 cells that stably expressed the WAP transgene than around mock-clonal HC11 cells, and the proliferation of WAP-clonal HC11 cells was particularly inhibited in the presence of laminin. A laminin degradation assay demonstrated that WAP inhibited the activity of the pancreatic elastase-mediated cleavage of laminin B1 and the phosphorylation of ERK1/2. ERK1/2 phosphorylation was blocked by an inhibitor of the epidermal growth factor (EGF) receptor AG1478. Treatment with pancreatic elastase was found to enhance the proliferation of mock-clonal HC11 cells, but had no effect on that of WAP-clonal HC11 cells. The proliferation of WAP-clonal HC11 cells was recovered by the addition of exogenous EGF. We concluded that WAP plays some role in regulating the proliferation of mammary epithelial cells by preventing elastase-type serine protease from carrying out laminin degradation and thereby suppressing the MAP kinase signal pathway.
Absorptive and Secretory Transport of Selected Artemisinin Derivatives Across Caco-2 Cell Monolayers (2018)

The low permeability of anti-malarial drugs must be borne in mind during development of effective dosage regimens of new drugs.
Integration of Physics-Derived Memristor Models with Machine Learning Frameworks (2022)

Simulation frameworks such MemTorch [1] [2], DNN+NeuroSim [3] [4], and aihwkit [5] are commonly used to facilitate the end-to-end co-design of memristive machine learning (ML) accelerators. These simulators can take device nonidealities into account and are integrated with modern ML frameworks. However, memristors in these simulators are modeled with either lookup tables or simple analytic models with basic nonlinearities. These simple models are unable to capture certain performance-critical aspects of device nonidealities. For example, they ignore the physical cause of switching, which induces errors in switching timings and thus incorrect estimations of conductance states. This work aims at bringing physical dynamics into consideration to model nonidealities while being compatible with GPU accelerators. We focus on Valence Change Memory (VCM) cells, where the switching nonlinearity and SET/RESET asymmetry relate tightly with the thermal resistance, ion mobility, Schottky barrier height, parasitic resistance, and other effects [6]. The resulting dynamics require solving an ODE that captures changes in oxygen vacancies. We modified a physics-derived SPICE-level VCM model [7] [8], integrated it with the aihwkit [5] simulator and tested the performance with the MNIST dataset. Results show that noise that disrupts the SET/RESET matching affects network performance the most. This work serves as a tool for evaluating how physical dynamics in memristive devices affect neural network accuracy and can be used to guide the development of future integrated devices.
Chemistry of bleomycin. XVI. Epi-bleomycin. (1976)

As previously reported1,2), migration of the carbamoyl group from the 3-to the 2-hydroxyl group of the mannose moiety of bleomycin occurs in aqueous alcoholic solution of copper-free bleomycin in the presence of a weak base such as triethylamine until an equilibrium is established. This carbamoyl-migration product has been called iso-bleomycin. Under the same reaction condition, copper-chelated bleomycin does not give iso-bleomycin1), but yields irreversibly another product designated epi-bleomycin. In this communication, the formation, isolation, chemical and biological properties and structure of epi-bleomycin are reported. Preliminary experiments showed that epimerization proceeds slower than isomerization. In order to study the reaction process, liquid chromatography, as shown in Fig. 1, was used for the rapid quantitative determination of the reaction product.
Data from Emerging Role of MicroRNAs as Liquid Biopsy Biomarkers in Gastrointestinal Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;Cancer has emerged as a leading cause of mortality worldwide, claiming more than 8 million lives annually. Gastrointestinal cancers account for about 35% of these mortalities. Recent advances in diagnostic and treatment strategies have reduced mortality among patients with gastrointestinal cancer, yet a significant number of patients still develop late-stage cancer, where treatment options are inadequate. Emerging interests in “liquid biopsies” have encouraged investigators to identify and develop clinically relevant noninvasive genomic and epigenomic signatures that can be exploited as biomarkers capable of detecting premalignant and early-stage cancers. In this context, microRNAs (miRNA), which are small, noncoding RNAs that are frequently dysregulated in cancers, have emerged as promising entities for such diagnostic purposes. Even though the future looks promising, current approaches for detecting miRNAs in blood and other biofluids remain inadequate. This review summarizes existing efforts to exploit circulating miRNAs as cancer biomarkers and evaluates their potential and challenges as liquid biopsy–based biomarkers for gastrointestinal cancers. &lt;i&gt;Clin Cancer Res; 23(10); 2391–9. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Classification based mode decisions for video over network (2001)

A video encoder has to make many mode decisions in order to achieve the goal of a low bit rate, high quality, and fast implementation. We propose a general classification based approach to making such mode decisions accurately and efficiently. We first illustrate the approach using the Intra-Inter coding mode decision. We then focus on the decision to skip or code a frame for rate control of video over networks. Using the classification used approach we show improvement in the rate-distortion sense. We then extend the work to scalable video coding in choosing between scalability modes and examine the performance of our approach over error prone networks, using simulated packet losses.
Abstract 6251: Heat Shock Protein 27 is Localized in Intercalated Discs and is Extensively Modified by Methylglyoxal in Human Hearts (2008)

Hyperglycemia plays an important role in the pathogenesis of diabetic complications including accumulation of methylglyoxal (MG), a highly reactive α-dicarbonyl metabolite of glucose degradation pathways. MG reacts in a non-enzymatic reaction with arginine residues of proteins which results in the formation of argpyrimidine. In several cell lines Hsp27 was found to be the most argpyrimidine containing protein. Whether Hsp27, which is high expressed in cardiac tissue, is also modified in heart, remains unclear. The aim of this investigation was to study the extent of Hsp27-modifications in heart failure and diabetes mellitus. Transmural myocardial samples from the left ventricle of explanted terminal failing hearts (diabetic: n=8; non-diabetic: n=8) and non-failing myocardium (NF) (n=6) without apparent signs of cardiac failure were collected. Cardiac tissue samples and rat cardiomyoblast cells H9c2, which were grown under normal and hyperglycaemic conditions, were investigated for the Hsp27-expression and modification by real-time PCR, western blotting and immunohistology. Hsp27 was significantly decreased (p&lt;0.05) in CM/DM (cardiomyopathy and diabetes mellitus) compared to NF. Relating to Hsp27-expression the MG-modification in diabetic hearts was significantly increased 3-fold (p&lt;0.05) compared to CM (cardiomyopathy) and 9-fold (p&lt;0.05) compared to NF. Consistent with the results in human heart samples, high glucose levels induced a down-regulation of Hsp27 in H9c2-cells in a dose-dependent manner. We also found an increased MG-modification of Hsp27 with higher concentrations of glucose. Noteworthy, we detected Hsp27 in the myocardial intercalated disc and in the M-line of the sarcomer in human cardiac tissue by immunohistology. In summary, we observed an increased argpyrimidine-modification of Hsp27 in the myocardium of patients with terminal heart failure and diabetes in comparison to non-failing donor hearts and explanted hearts from patients with cardiomyopathy. The argpyrimidine-modification of Hsp27 probably results from the diabetic myocardial metabolism and might be of impact for the progress of a cardiomyopathy in patients with diabetes mellitus.
Graphical representation of programs in a demonstrational visual shell—an empirical evaluation (1997)

An open question in the area of Programming by Demonstration (PBD) is how to best represent the inferred program. Without a way to view, edit, and share programs, PBD systems will never reach their full potential. We designed and implemented two graphical representation languages for a PBD desktop similar to the Apple Macintosh Finder. Although a user study showed that both languages enabled nonprogrammers to generate and comprehend programs, the study also revealed that the language that more closely reflected the desktop domain doubled users' abilities to accurately generate programs. Trends suggest that the same language was easier for users to comprehend. These findings suggest that it is possible for a PBD system to enable nonprogrammers to construct programs and that the form of the representation can impact the PBD system's effectiveness. A paper-and-pencil evaluation of the two versions of the PBD desktop prior to the study supported these finding and provided interesting feedback on the interaction between usability evaluations and user studies. In particular, the comparison of the paper-and-pencil evaluation with the empirical evaluation suggested that nonempirical evaluation techniques can provide guidance into how to interpret empirical data and, in particular, that PBD systems need to provide support for programming-strategy selection in order to be successful.
Toward retail product recognition on grocery shelves (2015)

This paper addresses the problem of retail product recognition on grocery shelf images. We present a technique for accomplishing this task with a low time complexity. We decompose the problem into detection and recognition. The former is achieved by a generic product detection module which is trained on a specific class of products (e.g. tobacco packages). Cascade object detection framework of Viola and Jones [1] is used for this purpose. We further make use of Support Vector Machines (SVMs) to recognize the brand inside each detected region. We extract both shape and color information; and apply feature-level fusion from two separate descriptors computed with the bag of words approach. Furthermore, we introduce a dataset (available on request) that we have collected for similar research purposes. Results are presented on this dataset of more than 5,000 images consisting of 10 tobacco brands. We show that satisfactory detection and classification can be achieved on devices with cheap computational power. Potential applications of the proposed approach include planogram compliance control, inventory management and assisting visually impaired people during shopping.
The diversity of receptor recognition in cholesterol‐dependent cytolysins (2014)

Cholesterol-dependent cytolysins (CDCs) are bacterial pore-forming toxins secreted mainly by pathogenic Gram-positive bacteria. CDCs generally recognize and bind to membrane cholesterol to create pores and lyse target cells. However, in contrast to typical CDCs such as streptolysin O, several atypical CDCs have been reported. The first of these was intermedilysin, which is secreted by Streptococcus intermedius and has human cell-specificity, human CD59 (huCD59) being its receptor. In the study reported here, the diversity of receptor recognition among CDCs was investigated and multi-receptor recognition characteristics were identified within this toxin family. Streptococcus mitis-derived human platelet aggregation factor (Sm-hPAF) secreted by S. mitis strain Nm-65 isolated from a patient with Kawasaki disease was previously shown to hemolyze erythrocytes in a species-dependent manner, its maximum activity being in human cells. In the present study, it was found that Sm-hPAF recognizes both membrane cholesterol and huCD59 as receptors for triggering pore-formation. Moreover, vaginolysin (VLY) of Gardnerella vaginalis showed similar characteristics to Sm-hPAF regarding receptor recognition. On the basis of the results presented here, the mode of receptor recognition of CDCs can be categorized into the following three groups: (i) Group I, comprising typical CDCs with high affinity to cholesterol and no or very little affinity to huCD59; (ii) Group II, including atypical CDCs such as ILY, with no or very little affinity to cholesterol and high affinity to huCD59; and (iii) Group III, which contains atypical CDCs such as Sm-hPAF and VLY with affinity to both cholesterol and huCD59.
Health Care Utilization and Costs Associated with Adherence to Clinical Practice Guidelines for Early Magnetic Resonance Imaging among Workers with Acute Occupational Low Back Pain (2013)

Nonadherence to guidelines for early MRI was associated with increased likelihood of lumbosacral injections or surgery and higher costs for out-patient, inpatient, and nonmedical services, and disability compensation.
Torso and heart dimensions of cardiac SPECT patients (2002)

In this work, the range of the patient geometries typically encountered in myocardial perfusion scans was determined. Myocardial patient data was available from two different sources-a database of patient scans from a Picker P2000 SPECT scanner and another database of scans from a 21-slice Posicam PET scanner. These data were sorted into six classes according to sex and weight of the patients. The weight classes were Extra Large (XL), Large (L), and Small/Medium (SM) defined by relative frequencies of 15%, 35% and 50%. From each scan, patient geometry information was condensed into 5 parameters-torso width, torso thickness, and diameter and location of the left ventricle. For each class, a maximum torso was defined and a common volume was defined which contained all left ventricles in the class. These class parameters provide information on field-of-view requirements for cardiac imaging systems, and in particular have applications in the design of SPECT scanners with converging collimators.
600-W single-mode single-frequency thulium fiber laser amplifier (2009)

A four-stage, Tm-doped fiber amplifier chain emitted 608 W of single-frequency (SF) output power with 53 dB gain, 54% slope efficiency, and M<sup>2</sup> = 1.05 beam quality. The output power was limited by available pump power. The final amplifier stage preserved the input &lt;5-MHz linewidth and imposed negligible phase noise above 3 kHz. SBS limits at the 2040-nm operating wavelength were measured by splicing different lengths of passive fiber to the amplifier exit. Thermal limits of the fiber were explored analytically and are consistent with the measured power performance. Comparison of the SBS and thermal limits suggests a maximum SF power of ~750 W from this fiber configuration, with further potential to scale past 1 kW with different fiber parameters. To our knowledge, this is the highest power reported to date from any single-frequency, single-mode fiber laser.
The Conformation of the Activation Peptide of Protein C Is Influenced by Ca2+ and Na+ Binding (2004)

Previous studies have suggested that the conformation of the activation peptide of protein C is influenced by the binding of Ca(2+). To provide direct evidence for the linkage between Ca(2+) binding and the conformation of the activation peptide, we have constructed a protein C mutant in the gamma-carboxyglutamic acid-domainless form in which the P1 Arg(169) of the activation peptide is replaced with the fluorescence reporter Trp. Upon binding of Ca(2+), the intrinsic fluorescence of the mutant decreases approximately 30%, as opposed to only 5% for the wild-type, indicating that Trp(169) is directly influenced by the divalent cation. The K(d) of Ca(2+) binding for the mutant protein C was impaired approximately 4-fold compared with wild-type. Interestingly, the conformation of the activation peptide was also found to be sensitive to the binding of Na(+), and the affinity for Na(+) binding increased approximately 5-fold in the presence of Ca(2+). These findings suggest that Ca(2+) changes the conformation of the activation peptide of protein C and that protein C is also capable of binding Na(+), although with a weaker affinity compared with the mature protease. The mutant protein C can no longer be activated by thrombin but remarkably it can be activated efficiently by chymotrypsin and by the thrombin mutant D189S. Activation of the mutant protein C by chymotrypsin proceeds at a rate comparable to the activation of wild-type protein C by the thrombin-thrombomodulin complex.
Fast and Easy Phage-Tagging and Live/Dead Analysis for the Rapid Monitoring of Bacteriophage Infection (2020)

Use of bacteriophages, which are viruses that kill bacteria, for biocontrol of pathogens and antimicrobial resistant bacteria has become increasingly important in recent years. As traditional culture-based methods are laborious and time-consuming, practicable use of bacteriophages will hinge on development of rapid and high throughput methods to analyze, characterize and screen large bacteriophage libraries. We thus established a novel method to fluorescently tag bacteriophages for virus screening and interaction studies, without the need for complicated and laborious purification procedures or genetic engineering of viruses to express fluorescent proteins. Bacteriophage PMBT14 was tagged using DNA dye Syto 13. Simply by using a membrane filter, tagged bacteriophages can be separated from non-sequestered excess dye rapidly, effortlessly, and cheaply. The procedure takes less than 30 min and makes use of simple laboratory consumables that are already commonly used for bacteriophage preparations. As proof of concept, we present here flow cytometric methods to analyze bacteriophage binding, infection and killing that are very accessible for high throughput analysis. We show that the resulting fluorescently tagged bacteriophage can be used to specifically stain its host bacterium <i>Pseudomonas fluorescens</i> DSM 50090. Individual fluorescent bacteriophages, their binding to and initial infection of bacteria could also be observed using confocal microscopy. The infection process was halted by the metabolic inhibitor sodium azide, suggesting a requirement of host metabolic processes for penetration by PMBT14. Flow cytometric live/dead assays was used as a complementary method to determine bacteriophage infection of its host. We made preliminary efforts to adapt the tagging method to two other bacteriophages and discuss potential pitfalls and solutions in the use of tagged phages. Fluorescent phage tagging has previously been demonstrated to facilitate analysis of bacteriophage-host interactions. The method adopted in this study makes it fast, easy as well as cost effective.
Anti‐tumor necrosis factor receptor and tumor necrosis factor agonist activity by an anti‐idiotypic antibody (1992)

Tumor necrosis factor (TNF) is a cytokine which, among other properties, is a principle mediator of inflammation and septic shock. It acts upon target cells by binding to specific cell surface receptors. A10G10 is a murine monoclonal antibody which recognizes human TNF and neutralizes its activity. A rabbit polyclonal antibody directed at the antigen-binding site of A10G10 was raised and affinity purified over an A10G10 column. The resultant anti-idiotypic antibody recognized not only A10G10 but also both TNF receptors. It showed TNF agonist activity in two different TNF bioassays, and competed with several anti-TNF receptor monoclonal antibodies and TNF itself for binding to cells. These results represent an example of a method for obtaining antibodies to a ligand-specific receptor in the absence of the receptor itself.