gebhart/patrepeval huggingface dataset:
Protein structure prediction servers at University College London (2005)

A number of state-of-the-art protein structure prediction servers have been developed by researchers working in the Bioinformatics Unit at University College London. The popular PSIPRED server allows users to perform secondary structure prediction, transmembrane topology prediction and protein fold recognition. More recent servers include DISOPRED for the prediction of protein dynamic disorder and DomPred for domain boundary prediction. These servers are available from our software home page at http://bioinf.cs.ucl.ac.uk/software.html.
General method to derive the relationship between two sets of Zernike coefficients corresponding to different aperture sizes (2006)

Zernike polynomials have been widely used to describe the aberrations in wavefront sensing of the eye. The Zernike coefficients are often computed under different aperture sizes. For the sake of comparison, the same aperture diameter is required. Since no standard aperture size is available for reporting the results, it is important to develop a technique for converting the Zernike coefficients obtained from one aperture size to another size. By investigating the properties of Zernike polynomials, we propose a general method for establishing the relationship between two sets of Zernike coefficients computed with different aperture sizes.
<b>Endovascular Exclusion of Symptomatic Bilateral Common Iliac Artery Aneurysms With Preservation of an Aneurysmal Internal Iliac Artery Via a Reverse-U Stent-Graft</b> (2006)

Endovascular treatment of bilateral CIA aneurysms and combined with a unilateral IIA aneurysm is a technically demanding procedure. An endovascular repair with retrograde (reverse-U stent-graft) hypogastric artery preservation can be considered a first choice until the use of branched iliac stent-grafts becomes more widespread.
Efficacy of common hospital biocides with biofilms of multi-drug resistant clinical isolates (2008)

The hospital environment is particularly susceptible to contamination by bacterial pathogens that grow on surfaces in biofilms. The effects of hospital biocides on two nosocomial pathogens, meticillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, growing as free-floating (planktonic) and adherent biofilm populations (sessile) were examined. Clinical isolates of MRSA and P. aeruginosa were grown as biofilms on discs of materials found in the hospital environment (stainless steel, glass, polyethylene and Teflon) and treated with three commonly used hospital biocides containing benzalkonium chloride (1 % w/v), chlorhexidine gluconate (4 % w/v) and triclosan (1 % w/v). Cell viability following biocide treatment was determined using an XTT assay and the LIVE/DEAD BacLight Bacterial Viability kit. The minimum bactericidal concentration (MBC) of all biocides for planktonic populations of both organisms was considerably less than the concentration recommended for use by the manufacturer. However, when isolates were grown as biofilms, the biocides were ineffective at killing bacteria at the concentrations recommended for use. Following biocide treatment, 0-11 % of cells in MRSA biofilms survived, and up to 80 % of cells in P. aeruginosa biofilms survived. This study suggests that although biocides may be effective against planktonic populations of bacteria, some biocides currently used in hospitals are ineffective against nosocomial pathogens growing as biofilms attached to surfaces and fail to control this reservoir for hospital-acquired infection.
Novel face-detection method under various environments (2009)

We propose a method to detect a face with different poses under various environments. On the basis of skin color information, skin regions are first extracted from an input image. Next, the shoulder part is cut out by using shape information and the head part is then identified as a face candidate. For a face candidate, a set of geometric features is applied to determine if it is a profile face. If not, then a set of eyelike rectangles extracted from the face candidate and the lighting distribution are used to determine if the face candidate is a nonprofile face. Experimental results show that the proposed method is robust under a wide range of lighting conditions, different poses, and races. The detection rate for the HHI face database is 93.68%. For the Champion face database, the detection rate is 95.15%.
Symmetric Nonrandom Two-Liquid Segment Activity Coefficient Model for Electrolytes (2009)

The nonrandom two-liquid segment activity coefficient model (NRTL-SAC) [Chen, C.-C.; Song, Y. Solubility Modeling with a Nonrandom Two-Liquid Segment Activity Coefficient Model. Ind. Eng. Chem. Res. 2004, 43, 8354−8362] has been shown to be a simple and practical thermodynamic model for correlating and predicting phase behavior for complex pharmaceutical molecules. The model was later extended for electrolytes [Chen, C.-C.; Song, Y. Extension of Non-Random Two-Liquid Segment Activity Coefficient Model for Electrolytes. Ind. Eng. Chem. Res. 2005, 44, 8909−8921]. However, the electrolyte model was presented as an unsymmetric activity coefficient model with aqueous phase infinite dilution reference state. Such an unsymmetric model becomes rather cumbersome to use when dealing with nonaqueous solvents. In this work, we present a symmetric electrolyte NRTL-SAC model which simplifies the long-range interaction term. We further examine the utility of the model in predicting salt solubilities in nonaqueous solvents and mixed solvents.
Principles of Warmwater Aquaculture (1979)

Water Systems. Nonconservative Aspects of Water Quality. Conservative Parameters of Water Quality and Physical Aspects of the Aquatic Environment. Feeds, Nutrition, and Growth. Reproduction, Selective Breeding, and Genetics. Disease and Parasitism. Harvesting, Processing and Economics. Minnows, Goldfish, and Sport Fish. Appendices. Glossary. Index.
Practical applications of asset management and comakership business models for FRP bridges (2012)

Fibre Reinforced Polymer (FRP) material and the associated technologies for bridge construction and refurbishment have been proven to be durable and sustainable. Much research and a number of recent projects have demonstrated that FRP bridges can also be cost-effective, provided that the cost and benefits over the lifecycle are considered and the solutions are produced through an efhcient industrialisation chain. These last two aspects very much depend on the integration in the value-chain. Fragmented procurement and business strategies are the existing main barriers of large-scale market implementation of FRP bridges. Previous research in the EU FP7 project Trans-IND has identified the required improvements in the traditional business models and presented the innovative approaches. This paper builds further on the current research outcomes by describing and analysing real project examples where asset management and comakership models are applied by clients, construction companies and suppliers to achieve the optimal value of FRP bridge projects.
Screening of effects of selenomethionine/enriched yeast supplementation on various immunological and chemical parameters of skin and blood in psoriatic patients. (1993)

Selenium (Se) is known to affect the immune system, and decreased Se-levels in blood of patients with moderate or severe psoriasis have been reported. In this study, the effect of Se-supplementation (400 micrograms/day for 6 weeks as Se-yeast, containing about 70% selenomethionine, SeMet) on skin and blood Se-content, on skin glutathione peroxidase activity and on various chemical and immunological parameters of blood and skin was investigated in 7 psoriatic patients. Before the SeMet-supplementation, serum and blood Se-levels were at the normal range, but they increased 42-45% during the Se-dosage, while zinc levels remained unchanged. Se-dependent glutathione peroxidase activity in both normal and lesional psoriatic skin remained unchanged during the trial, although a small net Se-uptake was detected. At the same time, a slight but statistically significant increase in the number of CD4+ T-cells was observed in the reticular dermis of the psoriatic lesions whereas the numbers of CD8+, CD11c+, and CD1+ cells were not significantly altered. Also, a relatively high number of patients (3 out of 7) showed a strongly reduced number of gamma/delta T-lymphocytes or increased CD8+ T-cells (2 patients) in peripheral blood. However, SeMet-supplementation was not related to these abnormalities or to the number of other peripheral blood immunocytes or to serum immunoglobulin levels. In addition, no marked effect on the clinical condition of the patients was observed. This pilot study suggests that SeMet may be able to modulate the immunological mechanism of psoriatic lesions by increasing the number of CD4+ T-cells.
Gynecomastia and Impotence Complications of Spironolactone Therapy (1973)

<h3>To the Editor.—</h3> We wish to report a case history illustrating an unusual complication of spironolactone therapy. <h3>Report of a Case.—</h3> A 49-year-old man suffered increasingly severe headaches. He had been told of hypertension by a physician 11 years previously, but never adhered to treatment. He was a thin, anxious man. The blood pressure was 175/125 mm Hg, and a grade 2 hypertensive retinopathy was present. The heart was not enlarged, and the peripheral pulses were bounding. An x-ray film of the chest revealed a tortuous aorta and a normal-sized heart. Blood urea nitrogen level was 8 mg/100 ml; creatinine level was 1.0 mg/100 ml; and potassium level was 4.8 mEq/liter. The creatinine clearance was 123 ml/minute, and the 24-hour 4-hydroxy-3-methoxymandelic acid (vanillylmandelic acid [VMA]) excretion was 2.4 mg per gram of creatinine. Antihypertensive therapy began with hydrochlorothiazide, 50 mg two times a day, chlordiazepoxide, 10 mg three times a
Knockdown of duplicated zebrafish<i>hoxb1</i>genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention (2002)

We have used a morpholino-based knockdown approach to investigate the functions of a pair of zebrafish Hox gene duplicates, hoxb1a and hoxb1b, which are expressed during development of the hindbrain. We find that the zebrafish hoxb1 duplicates have equivalent functions to mouse Hoxb1 and its paralogue Hoxa1. Thus, we have revealed a 'function shuffling' among genes of paralogue group 1 during the evolution of vertebrates. Like mouse Hoxb1, zebrafish hoxb1a is required for migration of the VIIth cranial nerve branchiomotor neurons from their point of origin in hindbrain rhombomere 4 towards the posterior. By contrast, zebrafish hoxb1b, like mouse Hoxa1, is required for proper segmental organization of rhombomere 4 and the posterior hindbrain. Double knockdown experiments demonstrate that the zebrafish hoxb1 duplicates have partially redundant functions. However, using an RNA rescue approach, we reveal that these duplicated genes do not have interchangeable biochemical functions: only hoxb1a can properly pattern the VIIth cranial nerve. Despite this difference in protein function, we provide evidence that the hoxb1 duplicate genes were initially maintained in the genome because of complementary degenerative mutations in defined cis-regulatory elements.
Low temperature deposition of Ga2O3 thin films using trimethylgallium and oxygen plasma (2012)

Gallium oxide (Ga2O3) thin films were deposited by plasma-enhanced atomic layer deposition (ALD) using trimethylgallium as the gallium precursor and oxygen plasma as the oxidant. A wide ALD temperature window was observed from 100 to 400 °C, where deposition rate was constant at ∼0.53 Å/cycle. X-ray photoelectron spectroscopy survey scans indicated the presence of gallium, oxygen, and carbon elements with concentrations of ∼36, ∼51.8, and ∼12.2 at. %, respectively. As-deposited films were amorphous; upon annealing at 900 °C under N2 atmosphere for 30 min, polycrystalline β-Ga2O3 phase with a monoclinic crystal structure was obtained. Refractive index and root mean square roughness of the annealed Ga2O3 film were higher than those of the as-deposited due to crystallization.
Efficacy of 7‐day treatment with metronidazole+miconazole (Neo‐Penotran®) — a triple‐active pessary for the treatment of single and mixed vaginal infections (2001)

Neo-Penotran provides immediate and effective treatment for vaginitis, irrespective of single or multiple infection, even when the diagnosis may be uncertain.
The Potential and Limitations of a Clustering Approach for the Improved Efficiency of Multiple Endmember Spectral Mixture Analysis in Plant Production System Monitoring (2011)

Due to the subpixel contribution of background soils and shadows, hyperspectral image interpretation in agricultural management is often constrained. In this paper, the potential of multiple endmember spectral mixture analysis (MESMA) to simultaneously extract the subpixel cover fraction and pure spectral signature of the crop component from a mixed hyperspectral signal is evaluated. Radiative transfer models are used to build lookup tables (LUTs) for both the crop and the soil component, but the extensiveness of the LUTs will decrease the efficiency and operational implementation of MESMA. A clustering procedure is therefore presented, allowing a more efficient use of the LUTs in the MESMA model. The performance of MESMA, using clustered and nonclustered LUTs, to extract the cover fraction and the spectral signature of plant canopies was evaluated using 200 simulated mixtures generated from in situ measured hyperspectral data of soil and citrus canopies. Clustering of the LUT resulted in a more efficient and accurate estimation of the pure subpixel vegetation signal ( rmse = 0.097 stabilizing at 40 iterations) compared to a nonclustered LUT (rmse = 0.11 stabilizing at 200 iterations). The subpixel cover fraction estimations, on the other hand, stabilize for both methods around 100 iterations, with an rmse of 0.15 for both approaches. The clustering of the LUT will thus increase both the efficiency and the accuracy of MESMA for estimating the spectral signature of crops while, on average, maintaining the accuracy for the cover fraction estimates. This will enable a more accurate extraction of plant production parameters, which opens up new opportunities regarding precision farming.
Case study : John's wish (2014)

John (pseudonym) is a 56 year old New Zealand Pakeha / European man who was diagnosed with multiple sclerosis 16 years ago. He lives on a rural lifestyle block with his wife Carol (pseudonym) and their two children aged 16 and 14. John and Carol run a business together, which requires them to be away from home for extended periods. John's mobility is severely compromised; he has little movement in his lower limbs and cannot stand unaided. He does have good functional movement and strength in his upper limbs. This enables him to transfer between his self-propelled wheelchair and a bed, with limited assistance. John drives a car which has been modified with hand controls. I first met John when he moved from another DHB to his current home in the area where I work. He was referred to the service for on going continence supplies. John had been receiving a supply of disposable continence pads since 2004. Unfortunately, I received little referral information except his diagnosis and the continence product he was receiving. This case study will high-light some deficiencies in our DHB's policies for the management of chronic urinary retention, bladder scanning and intermittent self-catheterisation.
Functional electrical stimulation for the reduction of spasticity in the hemiplegic hand. (1993)

Functional electrical stimulation can be used to provide hand opening in hemiplegics with spastic finger flexor muscles through stimulation of the extensor digitorum communis (EDC) muscle and the ulnar nerve. Stimulation of the finger extensor muscles in both hemiplegics and nonneurologically impaired individuals does not appear to cause significant reciprocal inhibition of finger flexor muscles. Thus stimulation of the EDC and ulnar nerve may not decrease finger flexor spasticity in the hemiplegic subjects, yet functional hand opening can still be obtained through a direct mechanical effect of the extensor stimulation.
Experimental design for drifting buoy Lagrangian test (1975)

A test of instrumentation fabricated to measure the performance of a free drifting buoy as a (Lagrangian) current meter is described. Specifically it is proposed to distinguish between the trajectory of a drogued buoy and the trajectory of the water at the level of the drogue by measuring the flow relative to the drogue.
Atypical teratoid/rhabdoid tumors: imaging findings of two cases and review of the literature. (2008)

Atypical teratoid/rhabdoid tumor (AT/RT) is a malignant embryonal central nervous system (CNS) tumor, manifesting in children, and composed of rhabdoid cells, with or without fields resembling a classical primitive neuroectodermal tumor (PNET), epithelial tissue and neoplastic mesenchyme. Around 200 cases of CNS AT/RT have been documented in the literature. Although the clinical and pathological findings have been defined in large series previously, and AT/RT has become increasingly recognized, awareness of typical AT/RT is important in making the correct diagnosis of this uncommon but probably underdiagnosed entity. Neuroradiologists rarely mention AT/RT in their differential diagnosis and this paper presents two additional cases in which clinical and pathological findings are combined with neuroradiological presentation.
Treatment of Plasmodium falciparum malaria with quinine in children in Guinea-Bissau: one daily dose is sufficient (2002)

We have earlier obtained good results in falciparum malaria by treating children with low doses of quinine for 7 days in Guinea-Bissau. In order to further simplify treatment, we compared outcome in 100 children with falciparum malaria treated in 1999/2000 for 7 days with 15 mg quinine salt/kg/dose twice daily (group I), 100 children treated with 7.5 mg quinine salt/kg/dose twice daily (group II), and 100 children treated with one single daily dose of 15 mg/kg. One day 28, parasites had reappeared in 12%, 15%, and 9%, respectively. These results are similar to what has been found after previous successful treatment regimens. Apart from a higher incidence of vomiting during the first 24 h of treatment in the groups treated with 15 mg/kg/dose no significant differences in symptoms or side-effects were found between the groups. In patients suffering from uncomplicated malaria, treatment with quinine can be simplified to one single dose of 15 mg/kg bodyweight whenever logistics make 2 daily doses less feasible.
Cellular and molecular mechanisms of goblet cell metaplasia in the respiratory airways (2013)

The mucociliary system, consisting of mucus-secreting goblet cells and ciliated cells, generates a constant overturning layer of protective mucus that lines the airway epithelium. Mucus hypersecretion and the pathophysiological changes associated are hallmarks of many pulmonary diseases including asthma, chronic obstructive pulmonary disease, and cystic fibrosis. Excessive mucus production leads to airway obstruction and, because there is currently no effective treatment, contributes to morbidity and mortality of many patients. Goblet cell differentiation and mucus production are subject to extensive control. An emerging concept is that not all goblet cells are phenotypically identical suggesting that specific molecular pathways orchestrate mucin overproduction. This paper attempts to describe the cellular and molecular mechanisms governing the differentiation of goblet cells in pulmonary diseases, a prerequisite for the development of new therapeutic agents.
Models Cascade for Tree-Structured Named Entity Detection (2011)

Named Entity Recognition (NER) is a well-known Natural Language Processing (NLP) task, used as a preliminary processing to provide a semantic level to more complex tasks. In this paper we describe a new set of named entities having a multilevel tree structure, where base entities are combined to define more complex ones. This definition makes the NER task more complex than previous tasks, even more due to the use of noisy data for the annotation: transcriptions of French broadcast data. We propose an original and effective system to tackle this new task, putting together the strengths of solutions for sequence labeling approaches and syntactic parsing via cascading of different models. Our system was evaluated in the 2011 Quaero named entity detection evaluation campaign and ranked first, with results far better than those of the other participating systems.
Decellularization of placentas: establishing a protocol (2017)

Biological biomaterials for tissue engineering purposes can be produced through tissue and/or organ decellularization. The remaining extracellular matrix (ECM) must be acellular and preserve its proteins and physical features. Placentas are organs of great interest because they are discarded after birth and present large amounts of ECM. Protocols for decellularization are tissue-specific and have not been established for canine placentas yet. This study aimed at analyzing a favorable method for decellularization of maternal and fetal portions of canine placentas. Canine placentas were subjected to ten preliminary tests to analyze the efficacy of parameters such as the type of detergents, freezing temperatures and perfusion. Two protocols were chosen for further analyses using histology, scanning electron microscopy, immunofluorescence and DNA quantification. Sodium dodecyl sulfate (SDS) was the most effective detergent for cell removal. Freezing placentas before decellularization required longer periods of incubation in different detergents. Both perfusion and immersion methods were capable of removing cells. Placentas decellularized using Protocol I (1% SDS, 5 mM EDTA, 50 mM TRIS, and 0.5% antibiotic) preserved the ECM structure better, but Protocol I was less efficient to remove cells and DNA content from the ECM than Protocol II (1% SDS, 5 mM EDTA, 0.05% trypsin, and 0.5% antibiotic).
Technical Aspects of Intra-Arterial Electroencephalogram Recording (1999)

The purpose of this prospective study is to show a technique for recording electroencephalographic activity via an endovascular approach in presurgical evaluation of epileptic patients. Technical aspects and insertion strategy are outlined. Advantages of intra-arterial electroencephalography have been demonstrated. It is a semi-invasive procedure that provides information in temporal lobe and extratemporal epilepsy. It allows a dynamic electroencephalographic recording and patient tolerance is excellent. Risks are practically absent. Disadvantages are: in comparison to ovale electrodes, chronic and multicontact recording is not possible and the recording is only intercritical.
Compatibility of retrieval languages. Introduction to a Forum (1983)

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