gebhart/patrepeval huggingface dataset:
Predicting Cotton Boll Maturation Period Using Degree Days and Other Climatic Factors (2005)

Degree days are often used for cotton ( Gossypium hirsutum L.) growth monitoring and management. The objectives of this research are to determine if 15.5°C is an accurate lower‐threshold temperature to monitor the boll maturation period (BMAP) for cotton in the northern, rainfed region of the U.S. Cotton Belt, to investigate other climatic factors in this cotton region that may improve the accuracy of the current degree day system for cotton, and to evaluate degree day models that include both an upper‐ and lower‐threshold temperature. Cotton was planted at three different timings in 2001 and 2002 to provide different climatic regimes during the BMAP. On 10 typical plants per plot, all first‐position flowers were individually tagged with date of flower opening and were then harvested at full maturity. Daily weather data consisted of maximum, minimum, and average air temperature; maximum and average soil temperature; average soil moisture; maximum and average solar radiation; and maximum and average photosynthetically active radiation. The 17°C degree day model, which used 17°C as the lower threshold, provided the best adjusted r 2 (0.2715) of all the single‐variable models; the degree day 15.5°C model had an adjusted r 2 of 0.2276. The best model using both upper and lower temperature thresholds was DD3017, using 30 and 17°C as the thresholds, and had an adjusted r 2 of 0.2452. Adding average, minimum, and maximum air temperatures to the DD15.5, DD17, and DD3017 models reduced coefficient of variation and mean square error and increased adjusted r 2 values.
Dynamics of the spontaneous emission of an atom into the photon-density-of-states gap: Solvable quantum-electrodynamical model (1993)

We consider the process of spontaneous emission of a two-level atom embedded into a periodic layered dielectric structure. When the resonant atomic frequency lies within the photon-density-of-states gap, of width \ensuremath{\Gamma}, the atom emits light during a time interval t\ensuremath{\Gamma}\ensuremath{\ll}1 until the spontaneous emission becomes fully inhibited. We discuss the enhancing of spontaneous emission by tuning the atomic resonance with a one-mode microcavity. In the \ensuremath{\lambda}/4-shifted distributed feedback microcavities which possess the \ensuremath{\delta}-function-like density of states, in the middle of the gap, the process of spontaneous emission has damped Rabi oscillation behavior; the damping depends on the width of the gap and the height of its walls. A profile of the density-of-states gap can be determined from the experimental data on the temporal behavior of the atomic spontaneous decay.
Engineering and Characterization of an Enzyme Replacement Therapy for Classical Homocystinuria (2017)

Homocystinuria due to loss of cystathionine beta-synthase (CBS) causes accumulation of homocysteine and depletion of cysteine. Current treatments are suboptimal, and thus the development of an enzyme replacement therapy based on PEGylated human truncated CBS (PEG-CBS) has been initiated. Attenuation of potency was observed, which necessitated a screen of several PEG-CBS conjugates for their efficacy to correct and maintain the plasma metabolite profile of murine homocystinuria after repeated administrations interrupted with washouts. We found that CBS coupling with maleimide PEG inconsistently modified the enzyme. In contrast, the PEG-CBS conjugate with 20 kDa N-hydroxysuccinimide-PEG showed very little loss of potency likely due to a reproducible PEGylation resulting in species modified with five PEGs per subunit on average. We developed assays suitable for monitoring the extent of CBS PEGylation and demonstrated a sustainable partial normalization of homocystinuria upon continuous PEG-CBS administration via osmotic pumps. Taken together, we identified the PEG-CBS conjugate suitable for manufacturing and clinical development.
Characterization of the cyanobacterial ycf37: mutation decreases the photosystem I content (2001)

We have constructed and analysed a cyanobacterial mutant that lacks the putative homologue of ycf37, the chloroplast open reading frame 37, which is conserved in different algae, but missing in the plastome of higher plants. In this report we show that Ycf37 of Synechocystis sp. PCC 6803 contains three tetratrico-peptide repeat (TPR) units resembling the structural organization of Ycf3, a protein that has been suggested to function as a chaperone during photosystem (PS) I complex formation. We demonstrate a light-activated transcript accumulation of this gene. Inactivation of ycf37 leads to a lower PSI/PSII ratio and a higher phycocyanin/chlorophyll ratio in Synechocystis cells. The observed alterations in the ycf37 mutants and the structural organization of the gene product suggest a functional role in PSI stability or assembly.
Galvanic corrosion between orthodontic wires and brackets in fluoride mouthwashes (2005)

The aim of this investigation was to determine the influence of fluoride in certain mouthwashes on the risk of corrosion through galvanic coupling of orthodontic wires and brackets. Two titanium alloy wires, nickel-titanium (NiTi) and copper-nickel-titanium (CuNiTi), and the three most commonly used brackets, titanium (Ti), iron-chromium-nickel (FeCrNi) and cobalt-chromium (CoCr), were tested in a reference solution of Fusayama-Meyer artificial saliva and in two commercially available fluoride (250 ppm) mouthwashes, Elmex and Meridol. Corrosion resistance was assessed by inductively coupled plasma-atomic emission spectrometry (ICP-MS), analysis of released metal ions, and a scanning electron microscope (SEM) study of the metal surfaces after immersion of different wire-bracket pairs in the test solutions. The study was completed by an electrochemical analysis. Meridol mouthwash, which contains stannous fluoride, was the solution in which the NiTi wires coupled with the different brackets showed the highest corrosion risk, while in Elmex mouthwash, which contains sodium fluoride, the CuNiTi wires presented the highest corrosion risk. Such corrosion has two consequences: deterioration in mechanical performance of the wire-bracket system, which would negatively affect the final aesthetic result, and the risk of local allergic reactions caused by released Ni ions. The results suggest that mouthwashes should be prescribed according to the orthodontic materials used. A new type of mouthwash for use during orthodontic therapy could be an interesting development in this field.
Constitutive Activation of the Human Vasoactive Intestinal Peptide 1 Receptor, a Member of the New Class II Family of G Protein-coupled Receptors (1998)

The human vasoactive intestinal peptide (VIP) 1 receptor belongs to the new class II subfamily of G protein-coupled receptors. Specific change by mutagenesis of a strictly conserved histidine into arginine at position 178 of the human VIP1 receptor resulted in its constitutive activation with respect to cAMP production. Transfection of the H178R mutant into COS cells resulted in a 3.5-fold increase in the cAMP level as compared with cells transfected with the wild type receptor or the vector alone. This increase was proportional to the amount of transfected cDNA. The H178R mutant exhibited an otherwise normal cAMP response to VIP as well as a dissociation constant similar to that of the wild type receptor. Other mutants at position 178 such as H178K, H178A, and H178D were not constitutively activated. They were otherwise expressed at the cell surface of transfected nonpermeabilized cells. Double mutants were then constructed in which the H178R mutation was associated with a point mutation in the the N-terminal extracellular domain that totally abolished VIP binding or VIP-stimulated cAMP production, i.e. E36A or D68A. The corresponding double mutants H178R/E36A and H178R/D68A were no longer constitutively activated. A control double mutant (H178R/D132A) with an unaltered dissociation constant for VIP and cAMP response to VIP was still constitutively activated. Our findings demonstrate that constitutive activation of the VIP1 receptor by mutation of His178 into R requires the functional integrity of the N-terminal extracellular VIP binding domain. They might provide interesting generalities about the activation process of G protein-coupled receptors.
Recovery Oriented Computing (ROC): Motivation, Definition, Techniques, and Case Studies (2002)

It is time to broaden our performance-dominated research agenda. A four order of magnitude increase in performance since the first ASPLOS in 1982 means that few outside CS&amp;E research community believe that speed is the only problem of computer hardware and software. Current systems crash and freeze so frequently that people become violent. Fast but flaky should not be our 21st century legacy. &lt;p&gt;Recovery Oriented Computing (ROC) takes the perspective that hardware faults, software bugs, and operator errors are facts to be coped with, not problems to be solved. By concentrating on Mean Time to Repair (MTTR) rather than Mean Time to Failure (MTTF), ROC reduces recovery time and thus offers higher availability. Since a large portion of system administration is dealing with failures, ROC may also reduce total cost of ownership. One to two orders of magnitude reduction in cost mean that the purchase price of hardware and software is now a small part of the total cost of ownership. &lt;p&gt;In addition to giving the motivation and definition of ROC, we introduce failure data for Internet sites that shows that the leading cause of outages is operator error. We also demonstrate five ROC techniques in five case studies, which we hope will influence designers of architectures and operating systems. &lt;p&gt;If we embrace availability and maintainability, systems of the future may compete on recovery performance rather than just SPEC performance, and on total cost of ownership rather than just system price. Such a change may restore our pride in the architectures and operating systems we craft
Tumor necrosis factor alpha and interleukin 1 stimulate the human immunodeficiency virus enhancer by activation of the nuclear factor kappa B. (1989)

Binding of peptide hormones to surface membrane receptors leads to the transcription of specific genes within relevant target cells. How these signals are transduced to alter gene expression is largely unknown, but this mechanism probably involves a sequence of enzymatic steps that activate factors in the nucleus that modulate transcription. We now demonstrate that two different peptide hormones, or cytokines, stimulate the human immunodeficiency virus enhancer, and this effect is mediated by nuclear factor (NF) kappa B (nuclear factor that binds the kappa immunoglobulin light chain gene enhancer). These cytokines, tumor necrosis factor alpha and interleukin 1, act on multiple cell types and represent the only naturally occurring activators of this transcription factor among eight cytokines examined. Although NF-kappa B binding can be stimulated by phorbol 12-myristate 13-acetate, tumor necrosis factor alpha acts through an independent mechanism, inducing NF-kappa B binding in HT-2 cells, which did not show increased binding in response to phorbol 12-myristate 13-acetate, and causing superinduction in Jurkat T-lymphoma cells. Tumor necrosis factor alpha is also a more selective activator of T cells than phorbol 12-myristate 13-acetate, having no effect on lymphokine production in EL-4 cells at the same time it induces NF-kappa B. These findings suggest that human immunodeficiency virus gene expression can be induced in T cells without activating lymphokine secretion and that the role of these cytokines in the activation of latent human immunodeficiency virus infection deserves further clinical evaluation. Finally, this link between binding at the surface membrane and stimulation of a specific transcription factor should help define intermediates for these cytokine activation pathways.
In vitro assays used to measure the activity of topoisomerases (1990)

Topoisomerase assays have evolved from simple catalytic assays such as relaxation and supercoiling to those which help to determine the structure-activity relationships of inhibitory agents such as quinolones and some antitumor agents. Topoisomerase assays have found further use in the detection of enzyme fractions during the purification of topoisomerases as well as in studies of mechanisms of antibacterial, antiparasitic, and antitumor agents
Men Talking about Viagra (2004)

The aim of this study was to explore men’s attitudes to Viagra in a social context. Two focus groups were established. The first comprised six members of a sports club; the second included three patients attending a clinic for men with erectile dysfunction, aged between 45 and 65. Each group met for one hour. Interpretative phenomenological analysis was used to identify themes. Analysis indicated the overriding theme for the first group of maintaining a masculine image through denial of any deliberate knowledge of or interest in the topic; for the second group, there was a theme of sadness at being unable to “confess” their problem because of potential loss of masculine image. Men in group contexts talk about Viagra in ways that serve to project a masculine image. Masculine image may be more important to men than their health.
Clonazepam as a therapeutic adjunct to improve the management of depression: a brief review (2009)

Clonazepam, first used for seizure disorders, is now increasingly used to treat affective disorders. We summarize the use of clonazepam to improve the management of depression. Clonazepam is useful for treatment-resistant and/or protracted depression, as well as for acceleration of response to conventional antidepressants. Clonazepam is at this time recommended for use in combination with SSRIs (fluoxetine, fluvoxamine, sertraline) as an antidepressant, and should be used at a dosage of 2.5-6.0 mg/day. If clonazepam is effective, a response should be observed within 2-4 weeks. It is significantly more effective for unipolar than for bipolar depression. Low-dose, long-term treatment with clonazepam exhibits a prophylactic effect against recurrence of depression. Although the mechanism of action of clonazepam has not yet been established, some investigators have been suggested that it involves enhancement of anti-anxiety effects, anticonvulsant effects on subclinical epilepsy, increase in 5-HT/monoamine synthesis or decrease in 5-HT receptor sensitivity mediated through the GABA system, and regulate in GABA activity.
The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium-binding proteins. (1986)

The structure of bovine intestinal calcium-binding protein (ICaBP) has been determined crystallographically at a resolution of 2.3 A and refined by a least squares technique to an R factor of 17.8%. The refined structure includes all 600 non-hydrogen protein atoms, two bound calcium ions, and solvent consisting of one sulfate ion and 36 water molecules. The molecule consists of two helix-loop-helix calcium-binding domains known as EF hands, connected by a linker containing a single turn of helix. Helix-helix interactions are primarily hydrophobic, but also include a few strategic hydrogen bonds. Most of the hydrogen bonds, however, are found in the calcium-binding loops, where they occur both within a single loop and between the two. Examination of the hydrogen bonding patterns in the calcium-binding loops of ICaBP and the related protein, parvalbumin, reveals several conserved hydrogen bonds which are evidently important for loop stabilization. The primary and tertiary structural features which promote the formation of an EF hand were originally identified from the structure of parvalbumin. They are modified in light of the ICaBP structure and considered as they apply to other calcium-binding proteins. The C-terminal domain of ICaBP is a normal EF hand, with ion binding properties similar to those of the calmodulin hands, but the N-terminal domain is a variant hand whose calcium ligands are mostly peptide carbonyls. Relative to a normal EF hand, this domain exhibits a similar KD for calcium binding but a greatly reduced affinity for calcium analogs such as cadmium and the lanthanide series. Lanthanides in particular may be inappropriate models for calcium in this system.
Nimodipine Loaded PLGA Nanoparticles: Formulation Optimization Using Factorial Design,Characterization and In Vitro Evaluation (2007)

The present study was aimed at developing a sustained release formulation of Nimodipine (NIM) nanoparticles using the biodegradable polymers, poly (lactide-co-glycolide) (PLGA 50:50 and 85:15) as carrier. NIM is a widely used calcium channel blocker which has to be administered as an intravenous infusion for a prolonged period of 1-2 weeks in the treatment of cerebral vasospasm. A sustained release biodegradable formulation would serve to replace this conventional therapy of continuous intravenous administration. PLGA nanoparticles were prepared by a modified precipitation method using high pressure homogenizer at 10,000 to 14,000 psi. A 3(2) factorial design was applied for optimization of the formulation parameters and for studying the effect of two independent variables [drug: polymer ratio and concentration of surfactant (Pluronic F 127)] on entrapment efficiency and mean particle size (response variables). Contour plots were plotted which gave a visual representation of the two variables on the dependent variables and also indicated non-linear relationship between them. The nanoparticles had particle size of 131+/-1.9 nm for PLGA 50:50 and 196+/-2.2 nm for PLGA 85:15. Scanning Electron Microscopy studies indicated that nanoparticles had spherical shape with a regular surface. The nanoparticles had high entrapment efficiency (96.42+/-2.09% for PLGA 50:50 and 94.50+/-1.25% for PLGA 85:15). DSC thermograms indicated that NIM was dispersed as an amorphous state in the nanoparticles. In vitro drug release from the lyophilized nanoparticles showed 94.35 +/- 3.8% NIM release from PLGA (50:50) nanoparticles and 63.32 +/- 4.6% release from PLGA (85:15) nanoparticles in 25 days. The release was first ordered and fickian diffusion kinetics in both the cases. These preliminary results indicate that NIM loaded PLGA nanoparticles could be effective in sustaining its release for a prolonged period. However, further studies are needed to confirm its performance in vivo.
Lyme disease: an infectious and postinfectious syndrome. (1994)

Despite recognition and treatment, Lyme disease is associated with significant infectious and postinfectious sequelae.
Muscle Creatine Kinase Sequence Elements Regulating Skeletal and Cardiac Muscle Expression in Transgenic Mice (1989)

Muscle creatine kinase (MCK) is expressed at high levels only in skeletal and cardiac muscle tissues. Previous in vitro transfection studies of skeletal muscle myoblasts and fibroblasts had identified two MCK enhancer elements and one proximal promoter element, each of which exhibited expression only in differentiated skeletal muscle. In this study, we have identified several regions of the mouse MCK gene that are responsible for tissue-specific expression in transgenic mice. A fusion gene containing 3,300 nucleotides of MCK 5' sequence exhibited chloramphenicol acetyltransferase activity levels that were more than 10(4)-fold higher in skeletal muscle than in other, nonmuscle tissues such as kidney, liver, and spleen. Expression in cardiac muscle was also greater than in these nonmuscle tissues by 2 to 3 orders of magnitude. Progressive 5' deletions from nucleotide -3300 resulted in reduced expression of the transgene, and one of these resulted in a preferential decrease in expression in cardiac tissue relative to that in skeletal muscle. Of the two enhancer sequences analyzed, only one directed high-level expression in both skeletal and cardiac muscle. The other enhancer activated expression only in skeletal muscle. These data reveal a complex set of cis-acting sequences that have differential effects on MCK expression in skeletal and cardiac muscle.
Association of reported prostate cancer risk alleles with PSA levels among men without a diagnosis of prostate cancer (2008)

Results from this study may have two important clinical implications. The cumulative effect of six SNPs on PSA levels suggests genetic-specific PSA cutoff values may be used to improve the discriminatory performance of this test for prostate cancer; and the dual associations of these SNPs with PSA levels and prostate cancer risk raise a concern that some of reported prostate cancer risk-associated SNPs may be confounded by the prevalent use of PSA screening.
Vaccination of pediatric solid tumor patients with tumor lysate-pulsed dendritic cells can expand specific T cells and mediate tumor regression. (2001)

Dendritic cells (DCs) have been shown to be a promising adjuvant for inducing immunity to cancer. We evaluated tumor lysate-pulsed DC in a Phase I trial of pediatric patients with solid tumors. Children with relapsed solid malignancies who had failed standard therapies were eligible. The vaccine used immature DC (CD14-, CD80+, CD86+, CD83-, and HLA-DR+) generated from peripheral blood monocytes in the presence of granulocyte/monocyte colony-stimulating factor and interleukin-4. These DC were then pulsed separately with tumor cell lysates and the immunogenic protein keyhole limpet hemocyanin (KLH) for 24 h and then combined. A total of 1 x 10(6) to 1 x 10(7) DC are administered intradermally every 2 weeks for a total of three vaccinations. Fifteen patients (ages 3-17 years) were enrolled with 10 patients completing all vaccinations. Leukapheresis yields averaged 2.8 x 10(8) peripheral blood mononuclear cells (PBMC)/kg, and DC yields averaged 10.9% of starting PBMC. Patients with neuroblastoma, sarcoma, and renal malignancies were treated without obvious toxicity. Delayed-type hypersensitivity (DTH) response was detected in 7 of 10 patients for KLH and 3 of 6 patients for tumor lysates. Priming of T cells to KLH was seen in 6 of 10 patients and to tumor in 3 of 7 patients as demonstrated by specific IFN-gamma-secreting T cells in unstimulated PBMCs. Significant regression of multiple metastatic sites was seen in 1 patient. Five patients showed stable disease, including 3 who had minimal disease at time of vaccine therapy and remain free of tumor with 16-30 months follow-up. Our results demonstrate that it is feasible to generate large numbers of functional DC from pediatric patients even in those highly pretreated and with a large tumor burden. The DC can be administered in an outpatient setting without any observable toxicity. Most importantly, we have demonstrated the ability of the tumor lysate/KLH-pulsed DC to generate specific T-cell responses and to elicit regression of metastatic disease.