gebhart/patrepeval huggingface dataset:
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016)

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
Altered neurometabolite development in HIV-infected children (2004)

These data suggest that normal brain development may be affected in children infected with HIV at birth, particularly evidenced by the lack of age-related increases in the neuronal marker [NAA]. Early, aggressive treatment of infants with HIV before development of encephalopathy is warranted.
Density functional theory and FTIR spectroscopic study of carboxyl group (2005)

Both molecular modelling and FTIR have been used to study carboxyl group among acetic acid, potassium and sodium acetate, glycine, sodium salicylate, salicylic acid and cellulose acetate. Molecular modelling was used to study formic acid. carhoxylic acids R-COOH, monovalent alkali carboxylate CH 3 COO-M, alanine, benzoic acid as well as naphthalene. Each structure was optimized using VWN/DZVP then vibrational spectra were further calculated at the same level of theory. The comparison between both calculated and experimental spectra showed good agreement with each other. Except for formic acid and free carboxyl, the characteristic band is shifted towards lower frequency.
Comparative study of commercially available anti‐α‐synuclein antibodies (2006)

Immunohistochemistry for alpha-synuclein has become the histological technique of choice for the diagnosis for Parkinson's disease, Dementia with Lewy bodies and Multiple System Atrophy (http://www.ICDNS.org). Nevertheless, no standardised protocol has been proposed. We have reviewed 242 of the 270 studies published until June 2005 that mentioned immunohistochemistry for anti-alpha synuclein on human tissue and we found that only 75 (31%) used commercial antibodies. We also noted that protocols, particularly dilution and antigen unmasking, varied between studies, even when the same antibody was employed. In order to establish a standardised protocol for alpha-synuclein immunohistochemistry, which can be applied in diagnostic neuropathology we tested seven commercial monoclonal antibodies in brains of subjects with Parkinson's disease, dementia with Lewy bodies, multiple system atrophy, multiple sclerosis with incidental Lewy bodies and aged-matched normal brain and determined for each antibody the best suited protocol for antigen unmasking. We evaluated the intensity of immunolabelling in Lewy bodies, neuropil threads, dendrites, pre-synaptic terminals, granular cytoplasmic positivity, peri-axonal positivity, glial inclusions and non-specific immunolabelling. Although our results showed that all the antibodies detected alpha-synuclein inclusions, differences were noted between antibodies, particularly with regard to the detection of glial inclusions. From our study, the best antibodies of the seven tested appeared to be those directed against amino acids 116-131 and 15-123 and we suggest them to be used in routine diagnostic practice for alpha-synucleinopathies.
Functional Deficits After Intraneural Injection During Interscalene Block (2010)

Our report suggests that intraneural injection during ultrasound-guided interscalene block carries a risk of neurologic complications.
Molecular Species Specificity of Phospholipid Breakdown in Microsomal Membranes of Senescing Carnation Flowers (1987)

During senescence of cut carnation flowers, there is extensive breakdown of microsomal phospholipid. This is attributable, at least in part, to lipolytic activity associated directly with the microsomal membranes. Evidence indicating that one or more of the lipid-degrading enzymes in these membranes preferentially degrade phospholipid molecular species containing two diunsaturated acyl chains or at least one polyunsaturated acyl chain has been obtained by using radiolabeled phosphatidylcholine substrates. 16:0(*)/16:0(*), 16:0/18:2(*), and 18:1(*)/18:1(*) phosphatidylcholine were degraded only minimally over a 3 hour period by microsomes isolated from senescing flowers. By contrast, [U-(14)C]phosphatidylcholine, which comprises various molecular species including those containing polyunsaturated acyl chains, and 18:0/20:4(*) phosphatidylcholine were extensively degraded. Under identical conditions, but in the absence of added radiolabeled substrate, endogenous 18:2/18:2, 18:1/18:3, and 18:2/18:3 phosphatidylcholine were selectively depleted from the membranes. During natural senescence of the flowers, there was a sharp decline in microsomal 16:0/18:1 and 18:1/18:2 phosphatidylcholine, whereas molecular species containing two diunsaturated acyl chains or at least one polyunsaturated acyl chain remained unchanged or decreased only slightly. The data have been interpreted as indicating that provision of particular molecular species susceptible to lipase attack is a prerequisite to phospholipid catabolism in senescing membranes.
RF MEMS Switches and Applications (INVITED) (2002)

,RF' MEMS are small mechanical devices fabricated by photolithographic processes, which are used for elemental signal processing functions in rf and microwave frequency circuits. The most ,common RF MEMS control component is a microwave transmission line switch, currently under development for applications requiring low insertion loss, high linearity, moderate switching speeds, and low to moderate power. The RF MEMS switch promises integration onto a variety of substrates, including suhs.trates hearing active semiconductor devices. This paper will discuss.some aspects of the operation of RF MEMS switches and how they may be inserted into microwave circuihy to best advantage. [Keywords: RF MEMS, microwave control components, switches]
Toward a Full Theory of Moral Status (2005)

There is much that I like in this essay. I share the conclusion that on this issue (as many others) the President's Council on Bioethics (PCB) has not really delivered the “fair and accurate” accou...
A new view of the spindle checkpoint (2001)

Previous studies of the spindle checkpoint suggested that its ability to prevent entry into anaphase was mediated by the inhibition of the anaphase-promoting complex (APC) ubiquitin ligase by Mad2. Two new studies challenge that view by demonstrating that another checkpoint protein, BubR1, is a far more potent inhibitor of APC function.
Superstructure of self-aligned hexagonal GaN nanorods formed on nitrided Si(111) surface (2012)

We present here the spontaneous formation of catalyst-free, self-aligned crystalline (wurtzite) nanorods on Si(111) surfaces modified by surface nitridation. Nanorods grown by molecular beam epitaxy on bare Si(111) and non-stoichiometric silicon nitride interface are found to be single crystalline but disoriented. Those grown on single crystalline Si3N4 intermediate layer are highly dense c-oriented hexagonal shaped nanorods. The morphology and the self-assembly of the nanorods shows an ordered epitaxial hexagonal superstructure, suggesting that they are nucleated at screw dislocations at the interface and grow spirally in the c-direction. The aligned nanorod assembly shows high-quality structural and optical emission properties.
A trajetória esportiva de dois ex-atletas iniciados precocemente na modalidade de basquetebol: da iniciação ao abandono (2007)

The present qualitative research is a case study which aimed to understand the sporting life course of two athletes who precociously started in early basketball event. Based on interviews with the ex-athletes, their mothers, two coaches, and the analysis of newspaper reports it was verified that stimulation from the family and coaches was the motivation element responsible for the beginning of their sporting careers. Personal success on games and social relationship provided by sports were also essential for continuing on their sporting life. However, the demanding of positive results from family, the difficulty of establishing emotional ties with coaches and other athletes, the dispute for positions in the team, and the search for a new profession led the athletes to give up performance sports, even they were prominent athletes.
Evaluation of antibacterial properties of Barium Zirconate Titanate (BZT) nanoparticle (2014)

So far, the antibacterial activity of some organic and inorganic compounds has been studied. Barium zirconate titanate [Ba(ZrxTi₁-x)O₃] (x = 0.05) nanoparticle is an example of inorganic materials. In vitro studies have provided evidence for the antibacterial activity of this nanoparticle. In the current study, the nano-powder was synthesized by sol-gel method. X-ray diffraction showed that the powder was single-phase and had a perovskite structure at the calcination temperature of 1000 °C. Antibacterial activity of the desired nanoparticle was assessed on two gram-positive (Staphylococcus aureus PTCC1431 and Micrococcus luteus PTCC1625) and two gram-negative (Escherichia coli HP101BA 7601c and clinically isolated Klebsiella pneumoniae) bacteria according to Radial Diffusion Assay (RDA). The results showed that the antibacterial activity of BZT nano-powder on both gram-positive and gram-negative bacteria was acceptable. The minimum inhibitory concentration of this nano-powder was determined. The results showed that MIC values for E. coli, K. pneumoniae, M. luteus and S. aureus were about 2.3 μg/mL, 7.3 μg/mL, 3 μg/mL and 12 μg/mL, respectively. Minimum bactericidal concentration (MBC) was also evaluated and showed that the growth of E. coli, K. pneumoniae, M. luteus and S. aureus could be decreased at 2.3, 14, 3 and 18 μg/mL of BZT. Average log reduction in viable bacteria count in time-kill assay ranged between 6 Log₁₀ cfu/mL to zero after 24 h of incubation with BZT nanoparticle.
Synthesis, properties and analytical application of silica with chemically grafted hydroxamic acid (1985)

A method has been developed for the preparation of a new sorbent based on silica containing chemically grafted hydroxamic acid groups. The sorption of Fe(III), Sc(III), Ti(IV), Zr, Hf, and Th from hydrochloric acid solutions was investigated and it was shown that the extraction of the metal ions is due to the formation of complex compounds with the grafted hydroxamic acid groups. Procedures for concentrating Sc, Zr, and Th, with concentration factors close to 100, and separation of Zr from a 10/sup 4/-fold excess of Fe(III), Sc, or Th, have been developed.
Numerical Analysis of Joule Heating Behavior and Residual Compressive Stress around Crack Tip under High Electric Load (2017)

This paper discusses the Joule heating effect and residual compressive stress near the crack tip under the electro-thermo-structural coupling state. For the crack tip field, the compressive condition is important for retarding or stopping the crack growth.
Ferrocenylsilylation of dendrons: a fast convergent route to redox-stable ferrocene dendrimers (2000)

A 54-ferrocene dendrimer is synthesized by a convergent route and can be used to modify a Pt electrode in CH2Cl2; it can be reversibly oxidized in DMF in a single 54-electron wave (and with NO+).
[The protective effect of an EDTA-sodium-extract-vaccine obtained from swine-pathogenic E. coli in a field trial. 2. Communication: Immunization of weanling piglets (author's transl)]. (1980)

Pentavalent EDTA-Sodium-extract vaccines and monovalent EDTA-Sodium-extract vaccines obtained from swine-pathogenic E. coli were used to test their antiepizootic effect in industrial pig farms, 2929 piglets after weaning were included in this field trial, 1309 were immunized partly orally, partly i.m., 1620 piglets received placebos accordingly. By means of oral immunization the pentavalent vaccine was capable of reducing the morbidity of the vaccinated animals significantly. Intramuscular immunization with the pentavalent vaccines produced significant differences in morbidity too. A monovalent vaccine obtained from E. coli O149 and E. coli O8 was shown to be equally effective, whereas a monovalent vaccine obtained from E. coli O115 was ineffective. But in this stock there were infections with O149 but none with O115 or O8.
Design and Implementation of the Network Server Based on SIP Communication Protocol (2008)

SIP is a kind of application-layer control signaling protocol for creating, modifying and finishing the conversation with one or more participants. It has several advantages such as simple, good expansibility and scalability, and so on. Based on the SIP, in this paper a design and implementation scheme of SIP server system is proposed, and the scheme can realize the functions of IP phone such as calling, billing and so on, and finally based on the standards and interfaces of JainSip API which was provided by SUN company the design scheme is realized.
Photoluminescence optimization and characteristics of the rare-earth element erbium implanted in GaAs, InP, and GaP (1986)

The characteristic 1.54-μm emission from the rare-earth element erbium implanted in GaAs, InP, and GaP was investigated through 10-K photoluminescence essentially as a function of anneal temperature, time, and method. The strip-heater, forming-gas, and quartz-ampoule anneal methods were utilized in the range of 400 to 1000 °C. Erbium-related emissions were observed from 1.48 to 1.64 μm and were observable at emission temperatures of up to 260 K for InP:Er and 296 K for GaP:Er and GaAs:Er. Out of the three semiconductors, GaAs:Er was observed to exhibit the highest optical activation using a square-profile implantation technique. Dependent on the anneal method, optimum Er emissions occurred between 650 and 800 °C for GaAs, for InP between 575 and 625 °C, and for GaP between 800 and 950 °C. In general, the forming-gas anneal method proved most successful; however, maximum luminescence including sharper emission lines was achieved through the strip-heater method. This method, with an anneal time of 10 s, showed also the importance of short-time anneals in GaAs:Er, results which were also paralleled by isothermal anneals of InP:Er. The difference in emissions at different anneal temperatures and times gives preliminary evidence of different Er3+ centers.
2‐Amino‐2,6‐Dideoxy‐D‐Glucose (D‐Quinovosamine): a Constituent of the Lipopolysaccharides of <i>Vibrio cholerae</i> (1973)

From the lipopolysaccharides of Vibrio cholerae strains Inaba and Ogawa, an unusual amino sugar was isolated. By sequential oxidation with sodium metaperiodate and hypoiodide and by oxidation with periodate followed by detection of the acetaldehyde formed, the amino sugar was characterized as a 2‐amino‐dideoxyaldose. The hydrochloride of the amino sugar was compared with those of 2‐amino‐2,6‐dideoxy‐ d ‐glucose, 2‐amino‐2,6‐dideoxy‐ l ‐galactose, 2‐amino‐2,6‐dideoxy‐ d ‐mannose, 2‐amino‐2,6‐dideoxy‐ d ‐gulose, and 2‐amino‐2,6‐dideoxy‐ d ‐allose in an amino acid analyzer. The amino sugar alcohols were studied by paper electrophoresis in molybdate buffer. From the results obtained the amino sugar was identified as 2‐amino‐2,6‐dideoxyglucose (quinovosamine). Its optical rotation indicated it to be of the d ‐configuration.
Mapping Monthly Distribution of Daily Light Integrals across the Contiguous United States (2002)

The daily light integral (DLI) is a measurement of the total amount of photosynthetically active radiation delivered over a 24-hour period and is an important factor influencing plant growth over weeks and months. Contour maps were developed to demonstrate the mean DLI for each month of the year across the contiguous United States. The maps are based on 30 years of solar radiation data for 216 sites compiled and reported by the National Renewable Energy Lab in radiometric units (watt-hours per m -2 ·d -1 , from 300 to 3,000 nm) that we converted to quantum units (mol·m -2 ·d -1 , 400 to 700 nm). The mean DLI ranges from 5 to 10 mol·m -2 ·d -1 across the northern U.S. in December to 55 to 60 mol·m -2 ·d -1 in the southwestern U.S. in May through July. From October through February, the differences in DLI primarily occur between the northern and southern U.S., while from May through August the differences in DLI primarily occur between the eastern and western U.S. The DLI changes rapidly during the months before and after the vernal and autumnal equinoxes, e.g., increasing by more than 60% from February to April in many locations. The contour maps provide a means of estimating the typical DLI received across the U.S. throughout the year.
Atrophy of diaphragm muscle visualized with ultrasound in mechanically ventilated patients (2015)

Mechanical ventilation (MV) induces diaphragmatic muscle atrophy and contractile fibre dysfunction, the so-called ventilator-induced diaphragm dysfunction (VIDD). Although diaphragmatic atrophy can be assessed using ultrasound, the biggest trial in humans published so far included seven patients and only measuring the thickness at two moments during the disease process [1]. We aimed to assess the time course of diaphragm atrophy in a larger cohort of MV patients using ultrasound.
Inhibitory Effects of 150 Plant Extracts on Elastase Activity, and Their Anti‐inflammatory Effects (1999)

The inhibitory effects of 150 medicinal plants on elastase activity were investigated. Among the 150 plants, six plant extracts (final concentration 1 mg/ml in methanol) exhibited more than 65% of inhibition of elastase activity. The inhibitory effects of six active plants, including Areca catechu (IC50, 42.4 mug/ml), Cinnamonum cassia (IC50, 208.7 mug/ml), Myristica fragrans (IC50, 284.1 mug/ml), Curcuma longa (IC50, 398.4 mug/ml), Alpinia katsumadai (IC50, 465.7 mug/ml) and Dryopteris cassirrhizoma (IC50, 714.4 mug/ml) on the activity of human leukocyte elastase, hyaluronidase and lipid peroxidation were examined. In the lipid peroxidation assay, using the TBA method, three of the six plants, including Curcuma longa (IC50, 45.5 mug/ml), Areca catechu (IC50, 51.0 mug/ml) and Alpinia katsumadai (IC50, 116.3 mug/ml) exhibited more than 70% inhibition at the concentration of 1 mug/ml, but only one plant, Areca catechu (IC50, 563 mug/ml) showed high inhibitory effect on hyaluronidase activity. The results suggest that medicinal plants showing several biological activities may be potent inhibitors of the anti-ageing process in skin. This property might be useful for application in cosmetics.
AN EFFICIENT METHOD OF OPERATING THE AIR‐GUN* (1980)

A bstract A new technique is developed for generating a short seismic pulse from the bubble pulses which are radiated by an air‐gun. The new technique, which is useful in well velocity surveys and vertical seismic profiling, can be implemented by firing a single air‐gun several times at the same depth but with different chamber pressures. A record obtained by this procedure from a well‐geophone clamped at a depth of 2450 m gave a maximum peak‐to‐peak amplitude within the first 100 ms of the effective seismic pulse at least ten times any later peak‐to‐peak amplitude.
Applications of homochiral metal‐organic frameworks in enantioselective adsorption and chromatography separation (2014)

Chiral separation is of great importance for drug development, pharmacology, and biology. Chiral metal-organic frameworks (MOFs) is a new class of porous solid materials with high surface area, large pore size, high chemical stability, uniformly structured cavities, and the availability of modification. The excellent properties of MOFs have attracted intense interest to explore their performance and mechanism in chiral separation. This review summarizes three synthetic strategies of chiral MOFs and their applications in enantioselective adsorption and chromatographic separation. All the experimental and molecular simulation results demonstrated that high enantioselectivity was strongly correlated with a close match between the size of the pore and chiral molecules.
Decreasing the sialidase activity of multifunctional <i>Pasteurella multocida</i> α2–3-sialyltransferase 1 (PmST1) by site-directed mutagenesis (2011)

Pasteurella multocida α2-3-sialyltransferase 1 (PmST1) is a multifunctional enzyme which has α2-6-sialyltransferase, α2-3-sialidase, and α2-3-trans-sialidase activities in addition to its major α2-3-sialyltransferase activity. The presence of the α2-3-sialidase activity of PmST1 complicates its application in enzymatic synthesis of α2-3-linked sialosides as the product formed can be hydrolyzed by the enzyme. Herein we show that the α2-3-sialidase activity of PmST1 can be significantly decreased by protein crystal structure-based site-directed mutagenesis. A PmST1 double mutant E271F/R313Y showed a significantly (6333-fold) decreased sialidase activity without affecting its α2-3-sialyltransferase activity. The double mutant E271F/R313Y, therefore, is a superior enzyme for enzymatic synthesis of α2-3-linked sialosides.
Comparison of Bone Products for Phosphorus Availability (1996)

Three bone products (meat and bone meal, steamed bone meal, and bone chips) were compared to a water-soluble P source (monocalcium phosphate) for P availability and enhancement of tomato shoot growth. All bone products were finely ground to pass through a 40-mesh sieve. The products were added to a phosphorus-deficient greenhouse growing medium based on their P concentration with P at 50, 100, 200, and 400 mg·kg −1 . Meat and bone meal produced the least shoot growth in 1992, but all products were similar in 1993. Growth peaked with P at 111 mg·kg −1 in 1992, but in 1993, P at 50 mg·kg −1 was sufficient. Shoot P uptake was in direct proportion to P availability in the soil mix, monocalcium phosphate having the highest shoot P content. Although bone products affected N, Ca, Zn, and Mn content in shoots, the magnitudes of differences were minor and inconsistent from 1992 to 1993. Major consideration for using a bone product are its relative cost of P, fineness of grind, and CaCO 3 equivalent.
Antioxidant Capacity of Tomato Seed Oil in Solution and Its Redox Properties in Cultured Macrophages (2012)

The health benefits of tomato seed oil (TSO) have been suggested to be related to its antioxidant activity, although at the moment not much information is available on the antioxidant effects of TSO in biological systems. In this paper, we evaluated the antioxidant capacity of TSO using different spectrophotometrical antioxidant assays (LPSC, FRAP, αTEAC, DPPH). Moreover, we determined the ability of TSO in inhibiting oxidative stress in human cultured macrophages. The peroxyl radical scavenging LPSC assay was the most sensitive assay to detect the antioxidant capacity of the TSO, followed by the DPPH, FRAP, and αTEAC assay. TSO was able to counteract spontaneous and H₂O₂-induced oxidative stress in human macrophages, limiting intracellular ROS production and controlling oxidative stress signaling. In particular, TSO was able to decrease the phosphorylation of the MAPK ERK1/2, JNK, and p-38, activation of the redox-sensitive NF-kB, and expression of the heat shock proteins 70 and 90. When the antioxidant capacity of TSO was compared with that of purified lycopene, inhibition of ROS production by TSO was remarkably higher. This was due to the high content of other antioxidants in TSO, including (5Z)-, (9Z)-, (13Z)-, and (15Z)-lycopene isomers, β-carotene, lutein, γ-tocopherol, and α-tocopherol.