gebhart/patrepeval huggingface dataset:
Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law (2015)

Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is not enough to predict the behavior of designed circuits and thus, a costly trial-error process is eventually required. In this work, we provide a new theoretical framework for the predictive treatment of the genetic load. We mathematically and experimentally demonstrate that dependences among genes follow a quantitatively predictable behavior. Our theory predicts the observed reduction of the expression of a given synthetic gene when an extra genetic load is introduced in the circuit. The theory also explains that such dependence qualitatively differs when the extra load is added either by transcriptional or translational modifications. We finally show that the limitation of the cellular resources for gene expression leads to a mathematical formulation that converges to an expression analogous to the Ohm's law for electric circuits. Similitudes and divergences with this law are outlined. Our work provides a suitable framework with predictive character for the design process of complex genetic devices in synthetic biology.
[Heart arrest caused by ventricular fibrillation in acute biliary pancreatitis: a case report and etiopathogenetic hypothesis]. (2000)

Acute pancreatitis and/or gallbladder disease precipitating angina pectoris, or producing arrhythmias or ST-T wave changes on electrocardiography in the absence of coronary artery disease, have frequently been mentioned. Many attempts have been made to explain the etiology of these findings. To the authors' knowledge, this report is the most dramatic expression of pathogenetic mechanisms which are still considered hypothetical.
The physiological effects of salmon lice infection on post‐smolt of Atlantic salmon (1996)

The physiological effects of salmon lice infections on post‐smolt of Atlantic salmon were examined by experimentally infecting hatchery reared post‐smolts with infective copepodids. Even at high infection intensities, ranging from 30–250 lice per fish, early chalimus stages did not have severe, physiological effects on the fish. There was a sudden increase in fish mortality after the appearance of preadult I stages. Infected fish were then suffering due to lesions and osmoregulatory failure. Plasma chloride level increased significantly and total protein, albumin and haematocrit decreased significantly in infected compared to uninfected fish. All infected fish became moribund before adult lice appeared. Infection intensities above 30 salmon lice larvae per fish thus appear to cause death of Atlantic salmon post‐smolt soon after the lice reach their pre‐adult stage.
Dual-Function Detector–Modulator Smart-Pixel Module (1997)

We describe a smart-pixel circuit that permits the use of a GaAs/AlGaAs multiple quantum well diode to be used both as a detector for data input and a modulator for data output. The module provides the ability to double the number of inputs or outputs to the array and is well suited to cascaded optoelectronic system architectures that require bidirectional communition.
Optical coherence tomography imaging of cardiac substrates (2019)

Cardiovascular disease is the leading cause of morbidity and mortality in the United States. Knowledge of a patient's heart structure will help to plan procedures, potentially identifying arrhythmia substrates, critical structures to avoid, detect transplant rejection, and reduce ambiguity when interpreting electrograms and functional measurements. Similarly, basic research of numerous cardiac diseases would greatly benefit from structural imaging at cellular scale. For both applications imaging on the scale of a myocyte is needed, which is approximately 100 µm × 10 µm. The use of optical coherence tomography (OCT) as a tool for characterizing cardiac tissue structure and function has been growing in the past two decades. We briefly review OCT principles and highlight important considerations when imaging cardiac muscle. In particular, image penetration, tissue birefringence, and light absorption by blood during <i>in vivo</i> imaging are important factors when imaging the heart with OCT. Within the article, we highlight applications of cardiac OCT imaging including imaging heart tissue structure in small animal models, quantification of myofiber organization, monitoring of radiofrequency ablation (RFA) lesion formation, structure-function analysis enabled by functional extensions of OCT and multimodal analysis and characterizing important substrates within the human heart. The review concludes with a summary and future outlook of OCT imaging the heart, which is promising with progress in optical catheter development, functional extensions of OCT, and real time image processing to enable dynamic imaging and real time tracking during therapeutic procedures.
Inheritance and Linkage of Tomato Mottle Virus Resistance Genes Derived from Lycopersicon chilense Accession LA 1932 (2001)

Tomato mottle virus (ToMoV) is a silverleaf whitefly ( Bemisia argentifolii Bellows and Perring n. sp.) transmitted, bipartite geminivirus that infects tomatoes ( Lycopersicon esculentum Mill.). Inbred lines resistant to ToMoV were derived from Lycopersicon chilense Dunal accession LA 1932. Inheritance was studied using a family developed from the crossing of a resistant inbred with a susceptible tomato inbred over two seasons. The F 1 had resistance intermediate to the parents and generation means analysis of F 1 and F 2 , backcross and parental populations suggested that the action of at least two additive genes with high heritability (h 2 n.s. = 0.87) controlled ToMoV resistance. When data from the two seasons were combined, an acceptable fit to an additive-dominance genetic model was obtained. Single plant comparisons, bulk comparisons, and tailends of F 2 populations segregating for ToMoV resistance derived from LA 1932 identified randomly amplified polymorphic DNA (RAPD) markers using eight hundred 10-mer oligonucleotide primers. The F 2 populations used for inheritance studies were screened for polymorphic markers, and 12 RAPD markers associated with the ToMoV resistant line were linked to the morphological markers self-pruning ( sp ) and potato leaf ( c ) on chromosome 6. RAPD markers that were associated with ToMoV resistance segregated into two linked regions flanking either side of the sp and c loci. The molecular studies suggested that the action of at least two additive regions controlled ToMoV resistance which supported the inheritance analysis.
Induction of Deoxyribonucleic Acid Synthesis in the Liver of the Intact Animal (1972)

Abstract Based in part on observations made in blood-mixing experiments with intact and 70 and 90% hepatectomized rats, a mixture of chemicals has been devised that induces nuclear DNA formation and mitosis in the parenchymal liver cells of the unoperated animal. The mixture (TAGH solution) contains 3,3',5-triiodo-l-thyronine (triiodothyronine), amino acids, glucagon, and heparin. Each component of the stimulatory solution contributes to the enhancement in DNA synthesis but triiodothyronine is the single most important constituent. Given with the AGH solution (amino acids, glucagon, and heparin), as little as 2 µg of the hormone has a detectable effect and 10 µg is about two-thirds as effective as 100 µg or 2 mg. The time curve of the response of unoperated rats to the TAGH solution is the same as after 70% hepatectomy. With both stimuli, liver DNA formation begins at 14 hours. Unoperated rats can be initially treated with triiodothyronine, however, so that DNA synthesis is already high at 10 hours from the start of the infusion of the AGH solution. Several pieces of evidence are given to show that the TAGH solution does not induce DNA replication by damaging some of the cells of the intact liver. The TAGH solution, just as 70% hepatectomy, causes in the liver an increase in the rate of ribosome formation, an accumulation of glycerides, and changes in fatty acid composition. Unlike partial hepatectomy, however, the solution does not produce rises in the rates of synthesis of serum albumin or of total hepatic protein.
Joint torque control by a direct feedback for industrial robots (1983)

Based on the experimental findings of Wu and Paul [17], two joints of an industrial robot have been redesigned and fabricated to include torque sensing capability by means of strain gauges. The resulting control systems reduced the effective frictional torques of the joints from 1072 oz.in to 33.5 oz.in. The stability of the closed-loop systems was analyzed by means of the describing function for limit cycles exhibited in the system, which can be removed by an insertion of phased-lead series compensating networks.
Role of the PDZ Domain-Binding Motif of the Oncoprotein E6 in the Pathogenesis of Human Papillomavirus Type 31 (2004)

A number of PDZ domain-containing proteins have been identified as binding partners for the oncoprotein E6 of the high-risk type human papillomaviruses (HPVs). These include hDlg, hScrib, MAGI-1, MAGI-2, MAGI-3, and MUPP1. The PDZ domain-binding motif (-X-T-X-V) at the carboxy terminus of E6 is essential for targeting PDZ proteins for proteasomal degradation. The presence of this motif only in the high-risk HPVs suggests its possible role in HPV-induced oncogenesis. To investigate the role of the PDZ domain-binding motif of E6 in the HPV life cycle, two mutant HPV31 genomes were constructed: E6ValDelta, with a deletion of the last amino acid residue of E6 (valine), and E6ETQVDelta, with a deletion of the entire PDZ domain-binding motif of E6 (ETQV). Three human foreskin keratinocyte (HFK) cell lines were established which maintained transfected wild-type HPV31 or either of two mutant genomes. Cells containing either of two mutant genomes were significantly retarded in their growth rates and reduced in their viral copy numbers compared to those transfected with wild-type genomes. Western analysis did not reveal any significant changes in the levels of PDZ proteins following stable transfection of any HPV31 genomes into HFKs. Although the E6ETQVDelta-transfected HFKs exhibited a pattern of morphological differentiation that appeared different from the HPV31 wild-type-transfected HFKs in organotypic raft cultures, immunohistochemical analysis failed to identify substantial changes in the differentiation-dependent membrane localization of hDlg proteins. These results suggest that binding of E6 to PDZ proteins modulates the early viral functions such as proliferation and maintenance of the viral copy number in undifferentiated cells.
Mechanism of Inactivation of γ-Aminobutyric Acid Aminotransferase by (1<i>S</i>,3<i>S</i>)-3-Amino-4-difluoromethylene-1-cyclopentanoic Acid (CPP-115) (2015)

γ-Aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that degrades GABA, the principal inhibitory neurotransmitter in mammalian cells. When the concentration of GABA falls below a threshold level, convulsions can occur. Inhibition of GABA-AT raises GABA levels in the brain, which can terminate seizures as well as have potential therapeutic applications in treating other neurological disorders, including drug addiction. Among the analogues that we previously developed, (1S,3S)-3-amino-4-difluoromethylene-1-cyclopentanoic acid (CPP-115) showed 187 times greater potency than that of vigabatrin, a known inactivator of GABA-AT and approved drug (Sabril) for the treatment of infantile spasms and refractory adult epilepsy. Recently, CPP-115 was shown to have no adverse effects in a Phase I clinical trial. Here we report a novel inactivation mechanism for CPP-115, a mechanism-based inactivator that undergoes GABA-AT-catalyzed hydrolysis of the difluoromethylene group to a carboxylic acid with concomitant loss of two fluoride ions and coenzyme conversion to pyridoxamine 5'-phosphate (PMP). The partition ratio for CPP-115 with GABA-AT is about 2000, releasing cyclopentanone-2,4-dicarboxylate (22) and two other precursors of this compound (20 and 21). Time-dependent inactivation occurs by a conformational change induced by the formation of the aldimine of 4-aminocyclopentane-1,3-dicarboxylic acid and PMP (20), which disrupts an electrostatic interaction between Glu270 and Arg445 to form an electrostatic interaction between Arg445 and the newly formed carboxylate produced by hydrolysis of the difluoromethylene group in CPP-115, resulting in a noncovalent, tightly bound complex. This represents a novel mechanism for inactivation of GABA-AT and a new approach for the design of mechanism-based inactivators in general.
Effects of dexamethasone treatment on insulin-stimulated rates of glycolysis and glycogen synthesis in isolated incubated skeletal muscles of the rat (1987)

1. Rats were treated with dexamethasone for 4 days before measurement of the rates of lactate formation [which is an index of hexose transport; see Challiss, Lozeman, Leighton & Newsholme (1986) Biochem. J. 233, 377-381] and glycogen synthesis in response to various concentrations of insulin in isolated incubated soleus and extensor digitorum longus muscle preparations. 2. The concentration of insulin required to stimulate these processes half-maximally in soleus and extensor digitorum longus muscles isolated from control rats was about 100 muunits/ml. 3. Dexamethasone increases the concentration of insulin required to stimulate glycolysis half-maximally in soleus and extensor digitorum longus preparations to 250 and 300 muunits/ml respectively. The respective insulin concentrations necessary to stimulate glycogen synthesis half-maximally were about 430 and 370 muunits/ml for soleus and extensor digitorum longus muscle preparations isolated from steroid-treated rats. 5. Dexamethasone treatment did not change the amount of insulin bound to soleus muscle.
Metabolic and Thermoregulatory Responses to a Simulated American Football Practice in the Heat (2007)

Energy cost is a major factor influencing the tolerable thermal load, particularly during exercise in the heat. However, no data exist on the metabolic cost of football practice, although a value of 35% of maximal aerobic capacity (VO(2)max) has been estimated. The energy cost and thermoregulatory response of offensive linemen (OL) was measured wearing different American football ensembles during a simulated half of football practice in the heat. Five collegiate offensive linemen (133 kg, 20% fat, 42 ml x kg(-1) x min(-1) maximal oxygen uptake) completed each of four 60-minute test sessions in an environmental chamber (28 degrees C, 55% relative humidity [RH]) wearing shorts (S), helmet (H), helmet and shoulder pads (HS), and full gear (FUL). Core temperature in the digestive tract (TGI) was obtained using an ingestible sensor. During simulated football drills (e.g., repetitions of drive blocking), exercise intensity ranged from 30 to 81% VO(2)max but averaged 55%VO(2)max (6.7 METS) overall. Blood lactate remained >5 mmol x L(-1), and heart rate (HR) averaged 79%HRmax. Equipment had a significant effect on %VO(2)max but only during recovery between drills with HS (61.4 +/- 3.7%) compared with H (53.3 +/- 6.9%) and S (40.1 +/- 8.5%). The TGI was higher (p < 0.05) with HS compared with H at several time-points after 30 minutes. Football practice for OL elicits a significantly higher overall metabolic cost (>6 METS, >50%VO(2)max) than assumed in previous studies. The addition of shoulder pads increases core temperature and energy cost, especially during recovery between active drills in unacclimatized linemen.
A Hierarchy of Support Vector Machines for Pattern Detection (2006)

We introduce a computational design for pattern detection based on a treestructured network of support vector machines (SVMs). An SVM is associated with each cell in a recursive partitioning of the space of patterns (hypotheses) into increasingly finer subsets. The hierarchy is traversed coarse-to-fine and each chain of positive responses from the root to a leaf constitutes a detection. Our objective is to design and build a network which balances overall error and computation. Initially, SVMs are constructed for each cell with no constraints. This “free network ” is then perturbed, cell by cell, into another network, which is “graded” in two ways: first, the number of support vectors of each SVM is reduced (by clustering) in order to adjust to a pre-determined, increasing function of cell depth; second, the decision boundaries are shifted to preserve all positive responses from the original set of training data. The limits on the numbers of clusters (virtual support vectors) result from minimizing the mean computational cost of collecting all detections subject to a bound on the expected number of false positives. When applied to detecting faces in cluttered scenes, the patterns correspond to poses and the free network is already faster and more accurate than applying a single pose-specific SVM many times. The graded network promotes very rapid processing of background regions while maintaining the discriminatory power of the free network.
Tunable absorption resonances in the ultraviolet for InP nanowire arrays (2014)

The ability to tune the photon absorptance spectrum is an attracting way of tailoring the response of devices like photodetectors and solar cells. Here, we measure the reflectance spectra of InP substrates patterned with arrays of vertically standing InP nanowires. Using the reflectance spectra, we calculate and analyze the corresponding absorptance spectra of the nanowires. We show that we can tune absorption resonances for the nanowire arrays into the ultraviolet by decreasing the diameter of the nanowires. When we compare our measurements with electromagnetic modeling, we generally find good agreement. Interestingly, the remaining differences between modeled and measured spectra are attributed to a crystal-phase dependence in the refractive index of InP. Specifically, we find indication of significant differences in the refractive index between the modeled zinc-blende InP nanowires and the measured wurtzite InP nanowires in the ultraviolet. We believe that such crystal-phase dependent differences in the refractive index affect the possibility to excite optical resonances in the large wavelength range of 345 < λ < 390 nm. To support this claim, we investigated how resonances in nanostructures can be shifted in wavelength by geometrical tuning. We find that dispersion in the refractive index can dominate over geometrical tuning and stop the possibility for such shifting. Our results open the door for using crystal-phase engineering to optimize the absorption in InP nanowire-based solar cells and photodetectors.
Effects of Mg Additive on Inhibition of Ag Agglomeration in Ag-Based Ohmic Contacts on p-GaN (2010)

We investigate the effect of Mg additive on the inhibition of Ag agglomeration in Ag contacts on p-GaN. The Mg-containing Ag contact shows low contact resistivity of 6.3 x 10(-5) Omega cm(2), high reflectance of 85.5% at 460 nm wavelength, and better thermal stability than the Ag contact after annealing in air ambient. Synchrotron radiation photoemission spectroscopy revealed that Mg atoms dissolving in the Ag contact reacted with oxygen atoms to form Mg oxides and increases the work function via decreasing the Schottky barrier height for hole injection. This leads to the inhibition of Ag atoms from lattice diffusion in the contact and to the suppression of the formation of Ag agglomeration, leading to enhanced light reflectance and thermal stability. (C) 2010 The Electrochemical Society. [DOI: 10.1149/1.3355164] All rights reserved.
The effects of source temperature and characteristics on the optical emission from a gallium liquid metal ion source (1989)

The light emitted from the region close to the tip of an emitting liquid metal ion source has been observed. It is shown that at high currents the light intensity rises almost as the cube of the current, but that the optical emission also depends on the source characteristics. A model based on the break-up of charged droplets is proposed to account for these results, thermal evaporation being found to be insignificant. Measurements of the effects of source temperature on light emission are also presented. From these measurements it is demonstrated that field ionisation cannot be responsible for the distortion of the total ion energy distribution seen at elevated temperatures.
Nocturnal cough in patients with chronic bronchitis and emphysema. (1984)

Patients with respiratory disease commonly report that their sleep is disrupted by nocturnal cough. We have recorded cough during the night in 10 patients with severe chronic bronchitis and emphysema (forced expiratory volume in one second, 1.0 +/- SEM 0.1/L) who complained of nocturnal cough and correlated cough with electroencephalographic sleep stage and arterial oxygenation. Cough was recorded using a directional microphone and an auto-editing tape recorder system. Each cough was subsequently verified by a listener. There was a mean of 14.6 +/- 4.5 bouts of coughing per patient per night, each bout lasting on average 3.9 +/- 0.2 s. Eighty-five percent of coughing bouts occurred during electroencephalographically confirmed wakefulness (p less than 0.02 versus sleep), and coughs during true sleep were rare, with only 1 patient coughing during rapid eye movement sleep and none during Stages 3 and 4 sleep. Cough was only once followed by arousal. There was no correlation between cough and either apneas or hypoxemia during sleep. We conclude that spontaneous cough is suppressed during sleep and only rarely awakens patients.
Damage Mechanisms Avoided or Managed for NIF Large Optics (2016)

After every other failure mode has been considered, in the end, the high-performance limit of all lasers is set by optical damage. The demands of inertial confinement fusion (ICF) pushed lasers designed as ICF drivers into this limit from their very earliest days. The first ICF lasers were small, and their pulses were short. Their goal was to provide as much power to the target as possible. Typically, they faced damage due to high intensity on their optics. As requests for higher laser energy, longer pulse lengths, and better symmetry appeared, new kinds of damage also emerged, some of them anticipated and others unexpected. This paper will discuss the various types of damage to large optics that had to be considered, avoided to the extent possible, or otherwise managed as the National Ignition Facility (NIF) laser was designed, fabricated, and brought into operation. It has been possible for NIF to meet its requirements because of the experience gained in previous ICF systems and because NIF designers have continued to be able to avoid or manage new damage situations as they have appeared.