gebhart/patrepeval huggingface dataset:
A Monolayer of Primary Colonic Epithelium Generated on a Scaffold with a Gradient of Stiffness for Drug Transport Studies (2018)

Animal models are frequently used for in vitro physiologic and drug transport studies of the colon, but there exists significant pressure to improve assay throughput as well as to achieve tighter control of experimental variables than can be achieved with animals. Thus, development of a primary in vitro colonic epithelium cultured as high resistance with transport protein expression and functional behavior similar to that of a native colonic would be of enormous value for pharmaceutical research. A collagen scaffold, in which the degree of collagen cross-linking was present as a gradient, was developed to support the proliferation of primary colonic cells. The gradient of cross-linking created a gradient in stiffness across the scaffold, enabling the scaffold to resist deformation by cells. mRNA expression and quantitative proteomic mass spectrometry of cells growing on these surfaces as a monolayer suggested that the transporters present were similar to those in vivo. Confluent monolayers acted as a barrier to small molecules so that drug transport studies were readily performed. Transport function was evaluated using atenolol (a substrate for passive paracellular transport), propranolol (a substrate for passive transcellular transport), rhodamine 123 (Rh123, a substrate for P-glycoprotein), and riboflavin (a substrate for solute carrier transporters). Atenolol was poorly transported with an apparent permeability ( P<sub>app</sub>) of <5 × 10<sup>-7</sup> cm s<sup>-1</sup>, while propranolol demonstrated a P<sub>app</sub> of 9.69 × 10<sup>-6</sup> cm s<sup>-1</sup>. Rh123 was transported in a luminal direction ( P<sub>app,efflux</sub>/ P<sub>app,influx</sub> = 7) and was blocked by verapamil, a known inhibitor of P-glycoprotein. Riboflavin was transported in a basal direction, and saturation of the transporter was observed at high riboflavin concentrations as occurs in vivo. It is anticipated that this platform of primary colonic epithelium will find utility in drug development and physiological studies, since the tissue possesses high integrity and active transporters and metabolism similar to that in vivo.
Two beta‐alanyl‐CoA:ammonia lyases in <i>Clostridium propionicum</i> (2005)

The fermentation of beta-alanine by Clostridium propionicum proceeds via activation to the CoA-thiol ester, followed by deamination to acryloyl-CoA, which is also an intermediate in the fermentation of l-alanine. By shifting the organism from the carbon and energy source alpha-alanine to beta-alanine, the enzyme beta-alanyl-CoA:ammonia lyase is induced 300-fold (approximately 30% of the soluble protein). The low basal lyase activity is encoded by the acl1 gene, whereas the almost identical acl2 gene (six amino acid substitutions) is responsible for the high activity after growth on beta-alanine. The deduced beta-alanyl-CoA:ammonia lyase proteins are related to putative beta-aminobutyryl-CoA ammonia lyases involved in lysine fermentation and found in the genomes of several anaerobic bacteria. beta-Alanyl-CoA:ammonia lyase 2 was purified to homogeneity and characterized as a heteropentamer composed of 16 kDa subunits. The apparent K(m) value for acryloyl-CoA was measured as 23 +/- 4 microm, independent of the concentration of the second substrate ammonia; k(cat)/K(m) was calculated as 10(7) m(-1) x s(-1). The apparent K(m) for ammonia was much higher, 70 +/- 5 mm at 150 microm acryloyl-CoA with a much lower k(cat)/K(m) of 4 x 10(3) m(-1) x s(-1). In the reverse reaction, a K(m) of 210 +/- 30 microM was obtained for beta-alanyl-CoA. The elimination of ammonia was inhibited by 70% at 100 mm ammonium chloride. The content of beta-alanyl-CoA:ammonia lyase in beta-alanine grown cells is about 100 times higher than that required to sustain the growth rate of the organism. It is therefore suggested that the enzyme is needed to bind acryloyl-CoA, in order to keep the toxic free form at a very low level. A formula was derived for the calculation of isomerization equilibra between L-alanine/beta-alanine or D-lactate/3-hydroxypropionate.
Baking, Extrusion and Frying (2005)

This chapter contains sections titled: Baking Bread General Principles Methods of Bread Production Bulk Fermentation Chorleywood Bread Process The Baking Process Mixing Fermentation (Proof) Baking Gluten Polymer Structure, Rheology and Baking Baking Quality and Rheology Extrusion General Principles The Extrusion Process Advantages of the Extrusion Process Extrusion Equipment Single-Screw Extruders Twin-Screw Extruders Comparison of Single- and Twin-Screw Extruders Effects of Extrusion on the Properties of Foods Extrusion of Starch-Based Products Nutritional Changes Flavour Formation and Retention During Extrusion Frying General Principles The Frying Process Fried Products Frying Equipment Batch Frying Equipment Continuous Frying Equipment Oil-Reducing System Frying Oils Potato Chip and Potato Crisp Production Potato Chip Production Potato Crisp Production Heat and Mass Transfer During Deep-Fat Frying Modelling Deep-Fat Frying Kinetics of Oil Uptake Factors Affecting Oil Absorption Microstructural Changes During Deep-Fat Frying
Optimization of noisy fitness functions by means of genetic algorithms using history of search with test of estimation (2003)

The authors discuss optimization of functions with uncertainty by means of genetic algorithms (GAs). In practical application of such GAs, the possible number of fitness evaluations is quite limited. The authors have proposed a GA utilizing history of search (Memory-based Fitness Evaluation GA: MFEGA) so as to reduce the number of fitness evaluations for such applications of GAs. However, it is also found that the MFEGA faces difficulty when the optimum resides outside of the region where population covers because the MFEGA uses the history of search for estimation of fitness values. The authors propose the tested-MFEGA, an extension of the MFEGA that tests validity of the estimated fitness value so as to overcome the aforesaid problem. Numerical experiments show that the proposed method outperforms a conventional GA of sampling fitness values several times even when the original MFEGA fails.
A Phase II Trial of Didemnin B (NSC #335319) in Patients with Previously Treated Epithelial Ovarian Cancer A Gynecologic Oncology Group Study (1993)

Sixteen evaluable patients with advanced or recurrent epithelial ovarian carcinoma following progression on combination chemotherapy were treated with 4.2 mg/m2 of Didemnin B (NSC #325319) intravenously every 28 days until progression of disease. All patients had prior cisplatin-containing chemotherapy. There were no responders. Seven patients had stable disease (43.7%) and nine (53.3%) had increasing disease. The toxicities were significant, consisting of nausea and vomiting in seven patients (44%), one grade 3 hepatic toxicity, and three instances of grade 4 toxicities (1 leukopenia, 1 GI, and 1 GU). When used with this schedule Didemnin B is ineffective in patients with previously treated epithelial ovarian cancer.
Specificity of Mycobacterium tuberculosis antigen 5 determined with mouse monoclonal antibodies (1984)

Four mouse monoclonal antibodies have been developed which react with Mycobacterium tuberculosis antigen 5. Each of these monoclonal antibodies has been used to prepare immunoabsorbents, and antigen has been isolated from unheated M. tuberculosis H37Ra culture filtrate by affinity chromatography with these absorbents. Antigen thus obtained was found to be similar in tuberculin reactivity and in enzyme-linked immunosorbent assays to antigen 5 isolated from polyclonal immunoabsorbents, and the protein yields from the monoclonal immunoabsorbents were similar to those from polyclonal absorbents. Antigen recovered from monoclonal absorbents cross-reacted with antigens of Mycobacterium kansasii in delayed skin tests. Immunoelectrophoresis demonstrated that the major component of the antigens eluted from the monoclonal immunoabsorbents was mycobacterial arabinomannan. Antigen 5 was not identified in the eluates by immunoelectrophoresis. These observations support the hypothesis that antigen 5 and M. tuberculosis arabinomannan contain a single major shared epitope.
Density Ratio Estimation in Machine Learning (2012)

Machine learning is an interdisciplinary field of science and engineering that studies mathematical theories and practical applications of systems that learn. This book introduces theories, methods and applications of density ratio estimation, which is a newly emerging paradigm in the machine learning community. Various machine learning problems such as non-stationarity adaptation, outlier detection, dimensionality reduction, independent component analysis, clustering, classification and conditional density estimation can be systematically solved via the estimation of probability density ratios. The authors offer a comprehensive introduction of various density ratio estimators including methods via density estimation, moment matching, probabilistic classification, density fitting and density ratio fitting as well as describing how these can be applied to machine learning. The book provides mathematical theories for density ratio estimation including parametric and non-parametric convergence analysis and numerical stability analysis to complete the first and definitive treatment of the entire framework of density ratio estimation in machine learning.
Design and Implementation of a Smart LED Lighting System Using a Self Adaptive Weighted Data Fusion Algorithm (2013)

This work aims to develop a smart LED lighting system, which is remotely controlled by Android apps via handheld devices, e.g., smartphones, tablets, and so forth. The status of energy use is reflected by readings displayed on a handheld device, and it is treated as a criterion in the lighting mode design of a system. A multimeter, a wireless light dimmer, an IR learning remote module, etc. are connected to a server by means of RS 232/485 and a human computer interface on a touch screen. The wireless data communication is designed to operate in compliance with the ZigBee standard, and signal processing on sensed data is made through a self adaptive weighted data fusion algorithm. A low variation in data fusion together with a high stability is experimentally demonstrated in this work. The wireless light dimmer as well as the IR learning remote module can be instructed directly by command given on the human computer interface, and the reading on a multimeter can be displayed thereon via the server. This proposed smart LED lighting system can be remotely controlled and self learning mode can be enabled by a single handheld device via WiFi transmission. Hence, this proposal is validated as an approach to power monitoring for home appliances, and is demonstrated as a digital home network in consideration of energy efficiency.
Underlying causes of hygroscopic stability in high-quality replicated composite optics (2019)

As next-generation space-based telescopes require larger mirrors, replicated composite optics are gaining increased attention due to limitations in scalability of conventional glass optics. Replication is the process of transferring an optical surface to a thin polymeric film supported by a CFRP substrate, offering weight savings, cost reductions, and faster manufacturing times. These optical surfaces require both dimensional precision (RMS < 32nm) and dimensional stability in a variety of environments. In our previous work, high quality replications were fabricated with UV-cured epoxy resin. Our work showed that the class of resin material as well as the processing route chosen had significant effects on the final stability of the composite optic. However, the fundamental material properties governing the behavior are not yet fully understood. In this paper, we will investigate how varying amounts of photoinitiator concentration on a UV-cured epoxy affect inherent material properties. The influence of these properties on the hygroscopic stability of the resin will be discussed.
The Multi-Purpose Camera: A New Anterior Eye Segment Analysis System (1990)

A new device for the analysis of the anterior eye segment was developed. With this device, a Scheimpflug slit image and a retroillumination image can be taken separately using a CCD camera. The quality of the images obtained was satisfactory enough for analysis. The data obtained were stored and analyzed on an almost real-time level using an on-line computer. The menu for the data analysis provided for this device includes multilinear densitometry, with planimetry, area densitometry, measurement of anterior chamber depth and thickness of lens layers, determination of chamber angle and positioning of implanted intraocular lenses, and measurement of opaque areas in the retroillumination image.
Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors (1997)

The complete nucleotide sequence of the 5936 bp cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 was determined. Based on the characteristics of its putative replication genes, repA and repB, pFAJ2600 was assigned to the family of pAL5000-related small replicons identified in Mycobacterium (pAL5000), Corynebacterium (pXZ10142), Brevibacterium (pRBL1), Bifidobacterium (pMB1) and Neisseria (pJD1). The replication systems of these plasmids show striking similarities to the ones used by the ColE2 family of plasmids from Enterobacteria with respect to both trans-acting factors and ori sequences. Two possible plasmid stabilization systems are encoded on pFAJ2600: a site-specific recombinase (PmrA) related to the Escherichia coli Xer proteins for plasmid multimer resolution and an ATPase (ParA) related to the A-type of proteins in sop/par partitioning systems. The proposed replication termination region of pFAJ2600 has features in common with the Ter loci of Bacillus subtilis. Chimeras composed of a pUC18-Cmr derivative inserted in the parA-repA intergenic region of vector pFAJ2600 produced vectors that could be shuttled between Escherichia coli and several Rhodococcus species (R. erythropolis, R. fascians, R. rhodochrous, R. ruber). The pFAJ2600-based shuttle vector pFAJ2574 was stably maintained in R. erythropolis and R. fascians growing under non-selective conditions.
Narrow-beam aluminum-mirrored fiber optical-taps with controllable tapped power (1996)

A fiber optical-tap has been fabricated and tested. Two separate fiber tips were polished with an angle of 45/spl deg/, and one of the tips was coated with aluminum inside a vacuum deposition unit. Then, the coated and uncoated polished tips were spliced together using a fusion splicer to form a fiber optical-tap. The power of the tapped light is controllable by controlling the thickness of the aluminum coating during vacuum deposition. As the aluminum coating thickness increases, the amount of tapped light increases and consequently the power transmitted after the fiber optical-tap decreases. For the same aluminum coating thickness, the tapped beam power from a single-mode fiber tap is higher than that from a multimode fiber tap. In addition to the feasibility of tapping a narrow light beam and controlling its power, the fabricated optical tap has a short length, which means that it can be integrated easily in optical signal-processing circuits. The mechanical strength of the tap has been tested in the laboratory and found to be capable of supporting between 75 and 180 g before breaking.
Atypical kinetics of immobilized firefly luciferase (1986)

The kinetic properties of collagen-bound firefly luciferase have been investigated. Under definite hydrodynamic conditions with low agitation in the reaction medium, the observed behavior is modified compared to the enzyme free in solution: reducing the stirring rate decreases the observed enzymatic activity. But diffusional resistances alone cannot account for these atypical kinetics though mass transfer may certainly play an important role during the transient state of the bioluminescent reaction. After immobilization, the time necessary to reach the steady state increased from 300 ms to 3 min and the two substrates, luciferin and ATP, behave differently with respect to the enzyme: The nature of the saturating substrate first in contact with the bound enzyme is not indifferent suggesting that immobilization can reveal behaviors or mechanisms which are not visualized with the free enzyme.
Human RAGE GLY82SER dimorphism and HLA class II DRB1‐DQA1‐DQB1 haplotypes in type 1 diabetes (1999)

Abstract Advanced glycation end products (AGEs) are believed to play an important role in the development of diabetic complications. AGEs increase in diabetes and modulate cellular functions through binding to a specific cell surface receptor (RAGE). The RAGE gene maps to chromosome 6p in the HLA class III area and is telomeric to the class II region at 250 kb from DRA. A recent report described the characterization of a major RAGE gene variant as a biallelic single base polymorphism (G/A 557) in the exon 3 sequence leading to a change of a glycine to a serine at position 82. Using DGGE and PCR‐RFLP, we have investigated the distribution of this dimorphism in conjunction with HLA class II genes in large populations of type 1 diabetic patients and healthy subjects. Although no association of this RAGE gene polymorphism with disease susceptibility was found, we report a strong linkage disequilibrium between the variant carrying the serine amino acid at position 82 and two HLA‐DR2 and HLA‐DR4 specificities. In particular, we describe two major extensive HLA class II haplotypes associated with this serine variant and identified as DRB1*0401‐DQA1*0301‐DQB1*0301 in the diabetic group and DRB1*1501‐DQA1*0102‐DQB1*0602 in control individuals. These data were partially confirmed by family transmission analysis.
A New Floating-gate Radiation Sensor and Readout Circuit in Standard Single-Poly 130-nm CMOS Technology (2019)

This paper describes a new dosimeter, which is composed of a Floating-Gate-Radiation-Field-Effect-Transistor (FGRADFET) sensor and novel absorbed-dose and a dose-rate readout circuit. It is a single-chip implementation employing a standard single-poly 130-nm CMOS technology. The FGRADFET extends the floating-gate (FG) as an extra silicon-area (60 μm × 200 μm) of poly-over-field-oxide (FOX) that acts as a catchment to sense the radiation from the environment. There is also a parallel array of 16 pMOS transistors (1 μm × 2 μm each) at the edge of the FOX catchment-area to charge the FG by the Fowler-Nordheim tunneling effect prior to the sensor deployment. Thus, no bias voltage is needed for the FG transistors during the irradiation. A cascode current-mirror, a reference FGRADFET, and 16 reference pMOS transistors are employed to compensate temperature effects and read the FG voltage of the FGRADFET sensor, which is proportional to the total absorbed dose. A further processing circuit for the FG voltage output is also designed to extract the slope of the FG voltage (the dose-rate). These circuits include differentiator, preamplifier buffer, chopper-amplifier, low-pass filter, and double-ended-tosingle-ended output amplifier. The measured average sensitivity of around 3.86 mV/rad was achieved for X-ray irradiation. It consumes 320 μW in detecting the dose-rate with a 1-10 rad/min measurement range corresponding to the single-ended output ranging from 220 to 960 mV.
Hole Transfer Equilibrium in Rigidly Linked Bichromophoric Molecules (1999)

Two bichromophoric molecules consisting of anthracene and diphenylpolyene moieties linked by two fused norbornyl bridges undergo photoionization upon ultraviolet (UV) pulsed laser irradiation. The simultaneous observation of the cation radicals of both anthracene and polyene groups points to a rapid (nanosecond or faster) intramolecular hole transfer equilibrium between the two chromophores. The existence of an equilibrium is supported by the results of one- and two-laser transient absorption and electrochemical experiments. Equilibrium constants (293 K) were determined by both transient absorption and cyclic voltammetry measurements and were independent of the method used within experimental error. For A-sp-VB, which contains anthracene and vinyldiphenylbutadiene chromophores, Keq = 4.0 ± 2 (transient absorption) and 3.2 ± 2 (electrochemical), favoring the anthracene cation radical. For A-sp-VS, containing anthracene and vinylstilbene groups, Keq = 70 ± 30 (transient absorption) and 105 ± 50 (electrochemical), favoring the anthracene cation radical.
Interaction Between<i>Mas</i>and the Angiotensin AT1 Receptor in the Amygdala (2000)

The Mas-protooncogene is a maternally imprinted gene encoding an orphan G protein-coupled receptor expressed mainly in limbic structures of the rodent CNS. Because Mas and the product of the Mas-related gene enhance the effects of angiotensins on cells expressing angiotensin receptors of the AT1 subtype, we first compared the distribution of cells expressing AT1 receptors in different limbic and thalamic brain structures in Mas-knockout mice and in wildtype mice by an immunohistochemical approach. No significant differences could be found between the two strains. The Mas-protooncogene seems to be implicated in the signal transduction of angiotensin receptors and is expressed in the amygdala. Therefore we then analyzed whether field potentials are altered by angiotensin II in brain slices of the basolateral amygdala. An opposite action of angiotensin II was obtained in mice lacking the Mas-protooncogene in comparison to wildtype mice. The use of different angiotensin receptor antagonists provides the first in vitro evidence for a functional interaction between the Mas-protooncogene and the AT1 receptor.
Scrotal Liposarcoma - A Rare Extratesticular Tumour (2011)

Scrotal and inguinal masses are common patient complaints that prove diagnostically challenging due to the multiple anatomic structures found in the confined space of the scrotum.1

History and adequate examination is the cornerstone in diagnosing scrotal pathology. Ultrasonography is the principle radiologic study used to evaluate scrotal masses. This can locate the site of a mass, and differentiate between solid and cystic lesions. The Doppler feature can also be used to evaluate blood flow. Occasionally CT or MRI is used if ultrasound is inconclusive, and usually precedes scrotal exploration.1

Scrotal masses can be testicular or paratesticular. Paratesticular masses are usually benign, with adenomatoid tumours being the most common, representing 30% of paratesticular masses and 77% of benign tumours arising from the epididymis.2 They usually occur in the 20–40-year age group but can present at any age, are 0.5–5 cm in size, and slow-growing. Papillary cystadenomas and leiomyomas account for most of the other benign solid tumours.2

Primary malignancies of the epididymis or paratesticular structures are extremely rare in adults. These are adenocarcinomas, and sarcomas including rhabdomyosarcoma, leiomyosarcomas and liposarcomas.3

Liposarcoma is the second most common soft tissue tumour in adults, with an incidence ranging from 9.8–16.0%.4 According to the 2002 World Health Organization (WHO) histological classification of tumours, liposarcoma can be divided into five categories: atypical lipomatous tumour/well-differentiated; dedifferentiated; myxoid; pleomorphic; and mixed-type liposarcoma. Liposarcoma of the spermatic cord is however a rare condition, representing about 7% of paratesticular sarcomas.5
Rufinamide for generalized seizures associated with Lennox–Gastaut syndrome (2008)

Rufinamide was an effective and well-tolerated treatment for seizures associated with Lennox-Gastaut syndrome.