gebhart/patrepeval huggingface dataset:
pH measurements with an ion sensitive field effect transistor in the mouth of patients with xerostomia (1991)

A transistor pH electrode (ion sensitive field effect transistor), placed in the upper dentures of eleven xerostomia patients and five healthy volunteers, was used to register pH changes in five-, six- and seven-day-old dental plaque. A mouth rinse with a 10% sucrose solution caused a pH fall of about three decades. A significant difference in duration of critical plaque pH was observed: in xerostomia patients, a 10% longer period of pH less than 5.7 was registered during 60 min following a sucrose rinse. Normal oral functions were not influenced by the denture with an integrated electrode. This method is usable for plaque pH registration in xerostomia patients.
Regulation of Myostatin in Vivo by Growth and Differentiation Factor-Associated Serum Protein-1: A Novel Protein with Protease Inhibitor and Follistatin Domains (2003)

Myostatin, a member of the TGFbeta superfamily, is a potent and specific negative regulator of skeletal muscle mass. In serum, myostatin circulates as part of a latent complex containing myostatin propeptide and/or follistatin-related gene (FLRG). Here, we report the identification of an additional protein associated with endogenous myostatin in normal mouse and human serum, discovered by affinity purification and mass spectrometry. This protein, which we have named growth and differentiation factor-associated serum protein-1 (GASP-1), contains multiple domains associated with protease-inhibitory proteins, including a whey acidic protein domain, a Kazal domain, two Kunitz domains, and a netrin domain. GASP-1 also contains a domain homologous to the 10-cysteine repeat found in follistatin, a protein that binds and inhibits activin, another member of the TGFbeta superfamily. We have cloned mouse GASP-1 and shown that it inhibits the biological activity of mature myostatin, but not activin, in a luciferase reporter gene assay. Surprisingly, recombinant GASP-1 binds directly not only to mature myostatin, but also to the myostatin propeptide. Thus, GASP-1 represents a novel class of inhibitory TGFbeta binding proteins.
In Vivo Adulteration: Excess Fluid Ingestion Causes False-Negative Marijuana and Cocaine Urine Test Results (1998)

Drug users can be highly motivated to obtain negative results on urine drug tests and may attempt to subvert the process by in vivo adulteration. The use of herbal products for "flushing" and "detoxification" is frequently advertised as an effective means of passing drug tests. Accordingly, a study was designed to determine the effects of ingestion of two herbal products, Naturally Klean Herbal Tea and Golden Seal root, and a diuretic medication, hydrochlorothiazide. The herbal tea was prepared in 1 gal of water as specified by the manufacturer. All other products were consumed with 1 gal of water. Two control conditions in which the subject consumed only water (1 gal; 12 oz) were included. The 1-gal liquid treatments were divided into 4-qt aliquots, and 1-qt was consumed each hour for 4 h. All treatments were begun approximately 22 h after smoking of a marijuana cigarette (3.58% THC) and 22 h after intranasal administration of cocaine hydrochloride. Following all treatments with excess fluid, creatinine and specific gravity dropped in 1.5-2.0 h to levels indicative of diluted specimens (<20 mg/dL creatinine, <1.003 specific gravity). Marijuana and cocaine metabolite concentrations by immunoassay (EMIT and TDx) also dropped rapidly, and the results frequently switched from positive to negative. By the time subjects had consumed 2 qt of any fluid, they were generally producing false-negative results. For example, ingestion of excess water produced dilute specimens (<20 mg/dL creatinine; <1.003 specific gravity) in an average time plus or minus the standard error of the mean of 1.47 +/- 0.17 h (N = 5) and 1.45 +/- 0.2 h (N = 5) following smoked marijuana and intranasal cocaine, respectively. In comparison, ingestion of Klean Tea produced dilute specimens in 1.36 +/- 0.07 h (N = 4) and 1.39 +/- 0.11 h (N = 4) following marijuana and cocaine administration. Recovery of urine test measures to pre-treatment levels occurred over a period of 8-10 h. Average detection times for marijuana metabolite appeared to be slightly shorter following ingestion of 1 gal of fluids compared with ingestion of 12 oz of water as a result of the time of testing being near the end of the cannabinoid metabolite excretion phase. Consequently, negative cannabinoid results induced by fluid ingestion rarely returned to positive after excess water was eliminated. In contrast, negative cocaine results reverted to positive quickly after the dilution effects disappeared. It was concluded that excess water ingestion can produce false-negative test results, but the claims of herbal products to be an aid in passing a urine test appear to be unfounded.
A MEDIUM FOR THE CULTIVATION OF LACTOBACILLI (1960)

SUMMARY: An improved growth medium for lactobacilli is described. It supports good growth of lactobacilli generally and also is particularly useful for a number of fastidious strains which grow only poorly in other general media. In addition, tomato juice, a highly variable material, is not required. In a slightly modified form, it can also be used as a basal medium for fermentation tests.
A two-dimensional topological compactor with octagonal geometry (1991)

We present a two-dimensional layout compactor with octagonal geometry. We discuss layout optimization algorithms used within a topological framework. We present the results of comparing the compactor against a standard set of benchmarks.
Pulsed light technology: a novel method for food preservation (2014)

With the increase in consumer awareness, demand for minimally processed foods and ecofriendliness, various technologies were developed for food processing and preservation. The conventional thermal food preservation and processing techniques appears to have the shortcoming of adversely affecting the food quality, organoleptic properties and nutrients. However, many non-thermal food preservation technologies were developed to serve the purpose. Many of such technologies are active packaging, pulsed electric field processing, high pressure processing, ultraviolet light processing and pulsed light processing. Pulsed light technology appears to be one of the best alternatives to conventional thermal and chemical decontamination process. Pulsed light processing technique has been commercialized and there have been many reports on the wide spectrum application of this technology. The technology not only decontaminates the food or packaging but also maintains its texture, nutrients etc. The germicidal effect was found to be due to photochemical and photothermal effect. It also has many other applications apart from decontamination, one such being reducing the allergen potent of some naturally occurring foods. The following review article is a compilation of reports on the mechanism of action of the technology and recent application of pulsed light processing.
Simple Quantitative Model for the Reversible Association of DNA Coated Colloids (2009)

We investigate the reversible association of micrometer-sized colloids coated with complementary single-stranded DNA "sticky ends" as a function of the temperature and the sticky end coverage. We find that even a qualitative description of the dissociation transition curves requires the inclusion of an entropic cost. We develop a simple general model for this cost in terms of the configurational entropy loss due to binding and confinement of the tethered DNA between neighboring particles. With this easy-to-use model, we demonstrate for different kinds of DNA constructs quantitative control over the dissociation temperature and the sharpness of the dissociation curve, both essential properties for complex self-assembly processes.
Growth Inhibitor from BSC-1 Cells Closely Related to Platelet Type β Transforming Growth Factor (1984)

Purified growth inhibitor from BSC-1 cells and type beta transforming growth factor from human platelets are shown to have nearly identical biological activity and to compete for binding to the same cell membrane receptor. These findings suggest that the growth inhibitor and the type beta transforming growth factor are similar molecules. The data also show that the same purified polypeptide can either stimulate or inhibit cell proliferation depending on the experimental conditions.
Covalent Inhibition of Digestive Lipases by Chiral Phosphonates (2000)

Designing and synthesizing specific inhibitors is of fundamental value for understanding the molecular mechanisms involved in the interfacial adsorption step as well as the catalytic activity of lipases. In this Account, we will review and discuss results obtained mostly at our laboratory concerning the covalent inhibition of human gastric and human pancreatic lipases by chiral phosphonates. Rather than presenting an exhaustive list of compounds tested so far with lipases of animal and microbial origin, we selected recent experimental data illustrating well the specific problems encountered during the covalent inhibition of these digestive lipases.
Composition of interstitial fluid (1995)

In several previous experiments to determine the composition of interstitial fluid, the results varied depending on the collecting technique, and the electrolyte concentrations differed from those of a hypothetical ultrafiltrate of plasma. In our approach, since a change of position from standing to supine is accompanied by hemodilution with interstitial fluid, we used the changes in hematocrit and composition of plasma in 20 subjects before and after lying down to calculate the composition of added interstitial fluid. The estimated protein concentration was 20.6 g/L, and the concentrations of total calcium and magnesium were low, in accord with a lower concentration of protein-bound calcium and magnesium. The activity of free cations was also lower, in agreement with a Donnan equilibrium potential of 1 mV across the endothelium. The concentration of leukocytes and platelets decreased according to the hemodilution, implying no escape or mobilization of these elements.
Damia: a data mashup fabric for intranet applications (2007)

Damia is a lightweight enterprise data integration service where line of business users can create and catalog high value data feeds for consumption by situational applications. Damia is inspired by the Web 2.0 mashup phenomenon. It consists of (1) a browserbased user-interface that allows for the specification of data mashups as data flow graphs using a set of operators, (2) a server with an execution engine, as well as (3) APIs for searching, debugging, executing and managing mashups. Damia offers a framework and functionality for dynamic entity resolution, streaming and other higher value features particularly important in the enterprise domain. Damia is currently in perpetual beta in the IBM Intranet. In this demonstration, we showcase the creation and execution of several enterprise data mashups, thereby illustrating the architecture and features of the overall Damia system. 1.
Competitive inhibitors and allosteric activators of protein kinase C isoenzymes: a personal account and progress report on transferring academic discoveries to the clinic (2007)

PKC (protein kinase C) isoenzymes are related protein kinases, involved in many signalling events in normal state and in disease. Basic research into identifying the molecular basis of PKC selectivity led to simple strategies to identify selective competitive inhibitor peptides and allosteric agonist peptides of individual PKC isoenzymes. The strategies and rationale used to identify these peptide regulators of protein-protein interaction may be applicable to other signalling events. Importantly, the PKC-regulating peptides proved to be useful pharmacological tools and may serve as drugs or drug leads for a variety of human diseases.
Activity-Adjusted 24-Hour Ambulatory Blood Pressure and Cardiac Remodeling in Children with Sleep Disordered Breathing (2007)

Questions remain as to whether pediatric sleep disordered breathing increases the risk for elevated blood pressure and blood pressure-dependent cardiac remodeling. We tested the hypothesis that activity-adjusted morning blood pressure surge, blood pressure load, and diurnal and nocturnal blood pressure are significantly higher in children with sleep disordered breathing than in healthy controls and that these blood pressure parameters relate to left ventricular remodeling. 24-hour ambulatory blood pressure parameters were compared between groups. The associations between blood pressure and left ventricular relative wall thickness and mass were measured. 140 children met the inclusion criteria. In children with apnea hypopnea index <5 per hour, a significant difference from controls was the morning blood surge. Significant increases in blood pressure surge, blood pressure load, and in 24-hour ambulatory blood pressure were evident in those whom the apnea hypopnea index exceeded 5 per hour. Sleep disordered breathing and body mass index had similar effect on blood pressure parameters except for nocturnal diastolic blood pressure, where sleep disordered breathing had a significantly greater effect than body mass index. Diurnal and nocturnal systolic blood pressure, diastolic blood pressure, and mean arterial blood pressure predicted the changes in left ventricular relative wall thickness. Therefore, sleep disordered breathing in children who are otherwise healthy is independently associated with an increase in morning blood pressure surge, blood pressure load, and 24-hour ambulatory blood pressure. The association between left ventricular remodeling and 24-hour blood pressure highlights the role of sleep disordered breathing in increasing cardiovascular morbidity.
Cloning and Sequencing of the Gene Encoding the Soluble Fumarate Reductase from Saccharomyces cerevisiae (1996)

A gene of the soluble fumarate reductase (FRDS) that binds FAD non-covalently was cloned by polymerase chain reaction (PCR) using degenerate oligonucleotides designed from partial amino acid sequences of highly purified enzyme. The nucleotide sequence of a 0.99-kb amplified product was found to be nearly identical to a partial sequence of an open reading frame (ORF) previously reported (EMBL database accession number S-30830). According to the sequence in the EMBL database, we cloned 1.7-kb fragment containing entire sequence of this ORF by PCR and found that this fragment contained a perfect match to the 0.99-kb sequence amplified with the degenerate primers. From these results, we concluded that this ORF is the FRDS gene. The amino acid sequences of the regions involved in the non-covalent binding of FAD and the active site, which are conserved among the flavoprotein subunits of membrane-bound fumarate reductase and succinate dehydrogenase, were found in FRDS. However, unlike the membrane-bound enzymes, FRDS did not contain the histidine residue that covalently binds the isoalloxazine ring of FAD at or near the corresponding position. FRDS showed high homology to the product of S. cerevisiae OSM1 gene which was reported to be required for growth in hypertonic media.
Wavelength-dispersive properties of glasses for optical fibres: the germania enigma (1978)

A comparative study is made of the wavelength-dispersive properties of germania-doped glass for optical-fibre waveguides and some important discrepancies are revealed. New results are presented for profile dispersion of this material over an extended wavelength range.
Naturally compliant robot-arms actuated by McKibben artificial muscles (2002)

The pneumatic artificial muscle invented in the fifties by J.L. McKibben and recently introduced in robotics under the form of replicas, such as the "Rubbertuator" or the "digit muscle" is analysed. A model of the actuator made of two McKibben artificial muscles is proposed and used to explain the actuator specific natural compliance. Control experiments, both in open-loop and closed-loop, developed on a two DOF SCARA robot prototype actuated by two pairs of McKibben artificial muscles are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Snapshot advantage: a review of the light collection improvement for parallel high-dimensional measurement systems (2012)

The snapshot advantage is a large increase in light collection efficiency available to high-dimensional measurement systems that avoid filtering and scanning. After discussing this advantage in the context of imaging spectrometry, where the greatest effort towards developing snapshot systems has been made, we describe the types of measurements where it is applicable. We then generalize it to the larger context of high-dimensional measurements, where the advantage increases geometrically with measurement dimensionality.
Gaze-Contingent Level Of Detail Rendering (2001)

The contributions of this paper are the development and evaluation of a nonisotropic model-based Level Of Detail (LOD) rendering technique for gaze-contingent viewing of multiresolution meshes. A high resolution portion of the model is rendered at the eye-tracked Point Of Regard (POR). A method is given for converting a closed polygonal mesh to a nonisotropic LOD representation suitable for gaze-contingent viewing. Based on a theoretical model of visual acuity, a three-dimensional spatial degradation function is obtained from human subject experiments in an attempt to render imperceptibly degraded geometric objects. Unlike previous LOD approaches, our resolution degradation method is based on the measurement of visual angle in world coordinates and is applied directly to object geometries prior to rendering. The gaze-contingent technique is evaluated in a Virtual Reality (VR) system integrated with a binocular eye tracker. To our knowledge, this is the first example of a binocular eye-tracked VR system used to evaluate a gaze-contingent modeling technique. Results are reported in terms of rendering performance, indicating an overall 4-fold average frame rate improvement during gaze-contingent viewing. Frame rate improvement ranged from a factor of at least 2, up to a 15-fold gain in performance over full resolution display, varying with the model complexity and the instantaneous direction of the viewer’s gaze.
Advances in the Exon-Intron Database (EID) (2006)

Investigation of exon-intron gene structures is a non-trivial task due to enormous expansions of the eukaryotic genomes, great variety of gene forms, and the imperfectness in sequence data. A number of available informational systems on various gene characteristics complement each other and are indispensable for many genomic studies. Among them, the Exon-Intron Database (EID) is a good choice for large-scale computational examination of exon/intron structure and splicing. It has many internal filters that control for sequence quality, consistency of gene descriptions, accordance to standards, and possible errors. New innovations in EID are described. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. Examples of statistical analyses of gene sequences using EID are provided. We present the latest data on our comparison of intron positions in 11,025 orthologous genes of human, mouse and rat, and find no convincing cases of intron gain. We discuss relevant data-quality issues of genomic databases. In particular, 5% of genes in genomic databases contain internal stop codons. This fact is due to a combination of biological reasons and also to errors in sequence annotations. The EID is freely available at www.meduohio.edu/bioinfo/eid/.
Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss (2017)

Loss of MSH1 is sufficient to cause large-scale regulatory changes in pathways that have been individually linked to one another, but rarely described all together within a single mutant background. This study enforces the recognition of organelles as critical integrators of both internal and external cues, and highlights the relationship between organelle and nuclear regulation in fundamental aspects of plant development and stress signaling. Our findings also encourage further investigation into potential connections between organelle state and genome regulation vis-á-vis small RNA feedback.
A simple device to rapidly prepare whole mounts of murine intestine (2006)

Many mouse models of neoplasia and pre-neoplasia require the examination of whole mounts of the gastrointestinal tract. A simple device has been produced to facilitate the rapid preparation of mouse intestines for subsequent quantification of tumours and pre-neoplastic lesions such as aberrant crypt foci. The device greatly speeds up the production of whole mounts and also provides far more consistent and better-quality preparations.
Understanding the Kinetics of Protein–Nanoparticle Corona Formation (2016)

When a pristine nanoparticle (NP) encounters a biological fluid, biomolecules spontaneously form adsorption layers around the NP, called "protein corona". The corona composition depends on the time-dependent environmental conditions and determines the NP's fate within living organisms. Understanding how the corona evolves is fundamental in nanotoxicology as well as medical applications. However, the process of corona formation is challenging due to the large number of molecules involved and to the large span of relevant time scales ranging from 100 μs, hard to probe in experiments, to hours, out of reach of all-atoms simulations. Here we combine experiments, simulations, and theory to study (i) the corona kinetics (over 10<sup>-3</sup>-10<sup>3</sup> s) and (ii) its final composition for silica NPs in a model plasma made of three blood proteins (human serum albumin, transferrin, and fibrinogen). When computer simulations are calibrated by experimental protein-NP binding affinities measured in single-protein solutions, the theoretical model correctly reproduces competitive protein replacement as proven by independent experiments. When we change the order of administration of the three proteins, we observe a memory effect in the final corona composition that we can explain within our model. Our combined experimental and computational approach is a step toward the development of systematic prediction and control of protein-NP corona composition based on a hierarchy of equilibrium protein binding constants.
The Anti-proliferative Gene TIS21 Is Involved in Osteoclast Differentiation (2002)

The remodeling process of bone is accompanied by complex changes in the expression levels of various genes. Several approaches have been employed to detect differentially-expressed genes in regard to osteoclast differentiation. In order to identify the genes that are involved in osteoclast differentiation, we used a cDNAarray-nylon membrane. Among 1,200 genes that showed a measurable signal, 19 genes were chosen for further study. Eleven genes were up-regulated; eight genes were downregulated. TIS21 was one of the up-regulated genes which were highly expressed in mature osteoclasts. To verify the cDNA microarray results, we carried out RT-PCR and real-time RT-PCR for the TIS21 gene. The TIS21 mRNA level was higher in differentiated-osteoclasts when compared to undifferentiated bone-marrow macrophages. Furthermore, the treatment with 1 mM of a TIS21 antisense oligonucleotide reduced the formation of osteoclasts from the bone-marrow-precursor cells by approximately 30%. These results provide evidence for the potential role of TIS21 in the differentiation of osteoclasts