gebhart/patrepeval huggingface dataset:
A Perspective on the Trends and Challenges Facing Porphyrin‐Based Anti‐Microbial Materials (2016)

The emergence of multidrug resistant bacterium threatens to unravel global healthcare systems, built up over centuries of medical research and development. Current antibiotics have little resistance against this onslaught as bacterium strains can quickly evolve effective defense mechanisms. Fortunately, alternative therapies exist and, at the forefront of research lays the photodynamic inhibition approach mediated by porphyrin based photosensitizers. This review will focus on the development of various porphyrins compounds and their incorporation as small molecules, into polymers, fibers and thin films as practical therapeutic agents, utilizing photodynamic therapy to inhibit a wide spectrum of bacterium. The use of photodynamic therapy of these porphyrin molecules are discussed and evaluated according to their electronic and bulk material effect on different bacterium strains. This review also provides an insight into the general direction and challenges facing porphyrins and derivatives as full‐fledged therapeutic agents and what needs to be further done in order to be bestowed their rightful and equal status in modern medicine, similar to the very first antibiotic; penicillin itself. It is hoped that, with this perspective, new paradigms and strategies in the application of porphyrins and derivatives will progressively flourish and lead to advances against disease.
Chirality Transfer from Guanidinium Ylides to 3-Alkenyl (or 3-Alkynyl) Aziridine-2-carboxylates and Application to the Syntheses of (2<i>R</i>,3<i>S</i>)-3-Hydroxyleucinate and <scp>d</scp>-<i>e</i><i>rythro</i>-Sphingosine (2005)

[Reaction: see text]. Reaction of chiral guanidinium ylides with alpha,beta-unsaturated aldehydes gives 3-(alpha,beta-unsaturated) aziridine-2-carboxylates in high diastereo- and enantioselectivities (up to 93% diastereomeric excess and 98% enantiomeric excess). 3-(1-methylvinyl)- and 3-[(E)-pentadec-1-enyl]aziridine-2-carboxylates were successfully employed to prepare (2R,3S)-3-hydroxyleucinate and d-erythro-sphingosine, respectively.
Controllable plasmonic antennas with ultra narrow bandwidth based on silver nano-flags (2012)

We show theoretically plasmonic antennas based on two-step chemical synthesized silver nano-flags constructed by a silver nanowire and a nanoplate. The silver nano-flag antennas exhibit high polarization sensitivity and diversity of spectral signatures dependent on the structural parameters arising from the observed mode competition. With specific configuration engineering, the antennas show controllable electric-field enhancement and ultra narrow bandwidths down to about 2 nm. These nano-antennas promise exciting applications in lasing spaser, optical modulation, and enhanced nonlinear processes.
Unique features in the ribosome binding site sequence of the gram-positive Staphylococcus aureus beta-lactamase gene. (1981)

The base sequence of the ribosome binding site region of the Gram-positive Staphylococcus aureus beta-lactamase gene has been determined. The leader peptide sequence of 24 amino acids which precedes the NH2 terminus of extracellular S. aureus beta-lactamase has also been established. This initiation site possesses two unique features not observed for most initiation sites recognized by Escherichia coli ribosomes. A novel initiation codon, UUG, initiates protein synthesis with methionine; and a very strong Shine-Dalgarno complementarity containing five G-C base pairs precedes the UUG initiation codon. The strong Shine-Dalgarno complementarity may explain the reduced translational dependence on initiation factor IF-3 function that has been observed for the beta-lactamase mRNA and other mRNAs from Gram-positive bacteria. We suggest that this extent of complementarity between the mRNA and this extent of complementarity between the mRNA and the ribosome may be a requirement for efficient initiation by Bacillus subtilis and other Gram-positive ribosomes, and may provide the basis for the observed inability of the Gram-positive systems to translate most of the mRNAs from Gram-negative bacteria.
Strategies for Expanding Structural Diversity Available from Olefin Isomerization−Claisen Rearrangement Reactions (2006)

Boron-substituted di(allyl) ethers provide an efficient conduit for expanding the structural diversity available from olefin isomerization-Claisen rearrangement (ICR) reactions. Easily prepared allyl propargyl ethers undergo chemoselective Zr(IV)-catalyzed hydroboration to afford the boron-substituted ICR substrates. The boron-substituted allyl residue undergoes chemoselective Ir(I)-catalyzed olefin isomerization and in situ Claisen rearrangement to afford stereodefined beta-boryl aldehyde products. Functionalization of the C-B linkage by oxidation or Suzuki cross-coupling provides a route to Claisen adducts previously inaccessible from the ICR methodology.
Insights into chaperonin function from studies on archaeal thermosomes (2011)

It is now well understood that, although proteins fold spontaneously (in a thermodynamic sense), many nevertheless require the assistance of helpers called molecular chaperones to reach their correct and active folded state in living cells. This is because the pathways of protein folding are full of traps for the unwary: the forces that drive proteins into their folded states can also drive them into insoluble aggregates, and, particularly when cells are stressed, this can lead, without prevention or correction, to cell death. The chaperonins are a family of molecular chaperones, practically ubiquitous in all living organisms, which possess a remarkable structure and mechanism of action. They act as nanoboxes in which proteins can fold, isolated from their environment and from other partners with which they might, with potentially deleterious consequences, interact. The opening and closing of these boxes is timed by the binding and hydrolysis of ATP. The chaperonins which are found in bacteria are extremely well characterized, and, although those found in archaea (also known as thermosomes) and eukaryotes have received less attention, our understanding of these proteins is constantly improving. This short review will summarize what we know about chaperonin function in the cell from studies on the archaeal chaperonins, and show how recent work is improving our understanding of this essential class of molecular chaperones.
Substrate range of benzylsuccinate synthase from Azoarcus sp. strain T (1999)

Benzylsuccinate synthase, which catalyzes the anaerobic addition of the methyl carbon of toluene to fumarate, has recently been reported in several denitrifying and sulfate-reducing, toluene-degrading bacteria. In substrate range studies with partially purified benzylsuccinate synthase from denitrifying Azoarcus sp. strain T, benzylsuccinate analogs were observed as a result of fumarate addition to the following toluene surrogates: xylenes, monofluorotoluenes, benzaldehyde, and 1-methyl-1-cyclohexene (but not 4-methyl-1-cyclohexene or methylcyclohexane). Benzylsuccinate was also observed as a result of toluene addition to maleate, but no products were observed from assays with toluene and either crotonate or trans-glutaconate. Toluene-maleate addition, like toluene-fumarate addition, resulted in highly stereospecific formation of the (+)-benzylsuccinic acid enantiomer [(R)-2-benzyl-3-carboxypropionic acid]. The previously reported finding that the methyl H atom abstracted from toluene is retained in the succinyl moiety of benzylsuccinate was found to apply to several toluene surrogates. The implications of these observations for the mechanism of benzylsuccinate synthase will be discussed.
State Policies Affecting Cities and Counties in 1992 (1993)

Most states did not make major changes in their policies affecting cities and counties in 1992. California and Maryland are the two leading exceptions. As many states continued to experience fiscal stress, fourteen states cut aid to local governments, while ten states increased aid. Some important changes also occurred in local revenue authority, sorting out responsibilities, and restrictions on unfunded mandates.
A Molded-Plastic Technique for Connecting and Splicing Optical-Fiber Tapes and Cables (1975)

We describe a new technique for optical-fiber cable connecting and splicing. Preliminary tests with multimode fibers produced splices with an average loss of less than 0.1 dB and a peak loss of 0.18 dB.
Interpretation and Semiparametric Efficiency in Quantile Regression under Misspecification (2015)

Allowing for misspecification in the linear conditional quantile function, this paper provides a new interpretation and the semiparametric efficiency bound for the quantile regression parameter β ( τ ) in Koenker and Bassett (1978). The first result on interpretation shows that under a mean-squared loss function, the probability limit of the Koenker–Bassett estimator minimizes a weighted distribution approximation error, defined as \(F_{Y}(X'\beta(\tau)|X) - \tau\), i.e., the deviation of the conditional distribution function, evaluated at the linear quantile approximation, from the quantile level. The second result implies that the Koenker–Bassett estimator semiparametrically efficiently estimates the quantile regression parameter that produces parsimonious descriptive statistics for the conditional distribution. Therefore, quantile regression shares the attractive features of ordinary least squares: interpretability and semiparametric efficiency under misspecification.
Front end x-ray beam position monitors at the Canadian Light Source (2006)

Bacteria belonging to <i>Staphylococcus</i> genus, in particular methicillin-resistant <i>Staphylococcus aureus</i> and multidrug-resistant <i>Staphylococcus epidermidis</i>, together with <i>Cutibacterium acnes</i> are the main strains involved in skin disease. The increase in multidrug-resistant bacteria has revived attention on natural compounds as alternative agents for the treatment management. Among these, hop extract, a hydroalcoholic solution obtained from experimental crops of <i>Humulus lupulus</i> L. variety <i>cascade</i> (hop), displays diverse biological properties including an antimicrobial one. The aim of this study was to evaluate the antimicrobial activity and the capacity to inhibit the biofilm formation of a characterized hop extract against <i>S. aureus</i> and <i>S. epidermidis</i> multidrug-resistant strains and against a <i>C. acnes</i> strain. The hop extract was characterized by (i) phytochemical analysis through a reversed-phase high-performance liquid chromatography (HPLC)-fluorimetric method, (ii) biocompatibility test with <i>Artemia salina</i> L., (iii) cytotoxicity against two cell lines, (iv) docking analysis, and (v) antimicrobial and antibiofilm activities by detection of zones inhibition, minimal inhibitory concentrations (MICs), biomass quantification, and cell viability. The hop extract was biocompatible and non-cytotoxic at all tested concentrations. HPLC analysis revealed significant levels of gallic acid, resveratrol, and rutin. This last compound was the most representative displaying a high affinity against PBP2a and KAS III (Ki values in the submicromolar range). The characterized hop extract showed a good antimicrobial action with MICs ranging from 1 to 16 μg/mL and was able to inhibit the biofilm formation of all tested strains, except for two <i>S. aureus</i> strains. The biofilm formed in presence of the hop extract was significantly reduced in most cases, even when present at a concentration of 1/4 MIC. The live/dead images showed a remarkable inhibition in the biofilm formation by hop extract with a weak killing action. Overall, the tested hop extract is a good candidate to further explore for its use in the prevention of infection particularly, by multidrug-resistant Gram-positive pathogens.
HCN channels are expressed differentially in retinal bipolar cells and concentrated at synaptic terminals (2003)

Hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels codetermine the integrative behaviour of neurons and shape their response to synaptic stimulation. We used immunohistochemistry and patch-clamp recording to study the composition and distribution of HCN channels in the rat retina. All four HCN channel isoforms (HCN1-4) are expressed differentially in the retina. In particular, different classes of bipolar cells have a different inventory of HCN channels. We found no evidence for the formation of heterooligomeric HCN channels. HCN channels are densely clustered at synaptic terminals of bipolar cells and photoreceptors. This suggests that HCN channels are involved in the control of transmitter release.
Gastrointestinal tolerability of extended-release metformin tablets compared to immediate-release metformin tablets: results of a retrospective cohort study (2004)

In this retrospective chart review, patients switched from immediate-release metformin to metformin-XR experienced fewer GI side effects on comparable doses of the extended-release metformin.
Monitoring Network Evolution using MDL (2008)

Given publication titles and authors, what can we say about the evolution of scientific topics and communities over time? Which communities shrunk, which emerged, and which split, over time? And, when in time were the turning points? We propose TimeFall, which can automatically answer these questions given a social network/graph that evolves over time. The main novelty of the proposed approach is that it needs no user-defined parameters, relying instead on the principle of minimum description length (MDL), to extract the communities, and to find good cut-points in time when communities change abruptly: a cut-point is good, if it leads to shorter data description. We illustrate our algorithm on synthetic and large real datasets, and we show that the results of the TimeFall agree with human intuition.
Metabolic engineering of <i>Corynebacterium glutamicum</i> for production of 1,5‐diaminopentane from hemicellulose (2011)

In the present work, the bio-based production of 1,5-diaminopentane (cadaverine), an important building block for bio-polyamides, was extended to hemicellulose a non-food raw material. For this purpose, the metabolism of 1,5-diaminopentane-producing Corynebacterium glutamicum was engineered to the use of the C(5) sugar xylose. This was realized by heterologous expression of the xylA and xylB genes from Escherichia coli, mediating the conversion of xylose into xylulose 5-phosphate (an intermediate of the pentose phosphate pathway), in a defined diaminopentane-producing C. glutamicum strain, recently obtained by systems metabolic engineering. The created mutant, C. glutamicum DAP-Xyl1, exhibited efficient production of the diamine from xylose and from mixtures of xylose and glucose. Subsequently, the novel strain was tested on industrially relevant hemicellulose fractions, mainly containing xylose and glucose as carbon source. A two-step process was developed, comprising (i) enzymatic hydrolysis of hemicellulose from dried oat spelts, and (ii) biotechnological 1,5-diaminopentane production from the obtained hydrolysates with the novel C. glutamicum strain. This now opens a future avenue towards bio-based 1,5-diaminopentane and bio-polyamides thereof from non-food raw materials.
<title>Far-Infrared Reflectance Spectra Of Optical Black Coatings</title> (1983)

Far-infrared specular reflectance spectra of six optically black coatings near normal incidence are presented. The spectra were obtained using nine bandpass transmission filters in the wavelength range between 12 and 300 μm. Data on the construction, thickness, and rms surface roughness of the coatings are also presented. The chemical composition of two coatings can be distinguished from that of the others by a strong absorption feature between 20 and 40 μm which is attributed to amorphous silicate material. Inverse relationships between these spectra and coating roughness and thickness are noted and lead to development of a reflecting-layer model for the measured reflectance. The model is applied to the spectra of several coatings whose construction falls within its constraints.
Water Disinfection: A Practical Approach to Calculating Dose Values for Preharvest and Postharvest Applications (2001)

Clean, disinfected water is necessary to minimize the potential transmission of pathogens from water to produce, from healthy to infected produce within a lot, and from one lot to another over time. Waterborne microorganisms, including postharvest plant pathogens and agents of human illness, can be rapidly acquired and taken up on plant surfaces. Natural plant surface contours, natural openings, harvest and trimming wounds, and scuffing can be points of entry as well as safe harbor for microbes. In these protected sites, microbes are largely unaffected by common or permitted doses of postharvest water treatments, such as chlorine, chlorine dioxide, ozone, peroxide, and peroxyacetic acid. Therefore, it is essential that enough sanitizer is maintained in water to kill microbes before they attach or become internalized in produce. This is important in some preharvest water uses and in all postharvest procedures involving water, including washing, cooling, water-mediated transport (flumes), and postharvest drenching.
Enhancement of the Performance of Low-Efficiency HVAC Filters Due to Continuous Unipolar Ion Emission (2006)

Our novel concept utilizing continuous emission of unipolar ions, which has been recently proven to enhance the efficiency of facepiece respirators, was applied to conventional HVAC filters. Laboratory study demonstrated that the air ion emission in the vicinity of a low-efficiency HVAC filter significantly improves its performance. For example, the collection efficiency of two commercial HVAC filters challenged with 1μm PSL particles jumped from 5–15% (measured with no ion emission) to 40–90% (when the ion output rate was ∼ 1012 e−/sec). The enhancement effect depends on the filter type and, generally, on the distance from the ion emitter to the filter surface. The results were explained as follows. The air ions with high mobility are deposited on the fibers forming a macroscopic electric field, which shield out some incoming unipolarly charged particles due to repelling forces. The field estimate has shown that this explanation is feasible. The enhancement effect seems to have a good potential to be employed in industrial and residential ventilation systems as it enhances the aerosol collection efficiency of a low-efficiency HVAC filter while not affecting its pressure drop.
A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition (2003)

A rhodium(III) complex, rac-[Rh(bpy)(2)phzi](3+) (bpy, 2,2'-bipyridine; phzi, benzo[a]phenazine-5,6-quinone diimine) has been designed as a sterically demanding intercalator targeted to destabilized mismatched sites in double-helical DNA. The complex is readily synthesized by condensation of the phenazine quinone with the corresponding diammine complex. Upon photoactivation, the complex promotes direct strand scission at single-base mismatch sites within the DNA duplex. As with the parent mismatch-specific reagent, [Rh(bpy)(2)(chrysi)](3+) [chrysene-5,6-quinone diimine (chrysi)], mismatch selectivity depends on the helix destabilization associated with mispairing. Unlike the parent chrysi complex, the phzi analogue binds and cleaves with high affinity and efficiency. The specific binding constants for CA, CC, and CT mismatches within a 31-mer oligonucleotide duplex are 0.3, 1, and 6 x 10(7) M(-1), respectively; site-specific photocleavage is evident at nanomolar concentrations. Moreover, the specificity, defined as the ratio in binding affinities for mispaired vs. well paired sites, is maintained. The increase in affinity is attributed to greater stability in the mismatched site associated with stacking by the heterocyclic aromatic ligand. The high-affinity complex is also applied in the differential cleavage of DNA obtained from cell lines deficient in mismatch repair vs. those proficient in mismatch repair. Agreement is found between photocleavage by the mismatch-specific probes and deficiency in mismatch repair. This mismatch-specific targeting, therefore, offers a potential strategy for new chemotherapeutic design.
Distortion compensation techniques for large reflector antennas (2002)

The high-frequency limit of reflector antennas is usually governed by the magnitude of the surface error. Whereas little can be done for the high-spatial frequency portion of this error, there are various techniques that can be employed to compensate for large-scale surface errors due to gravity induced distortions for ground antennas or thermally induced distortions for spacecraft antennas. This somewhat tutorial paper describes various techniques that can be utilized to compensate for the gain-loss due to these distortions. The techniques described are 1) main reflector compensation 2) subreflector compensation 3) use of a deformable flat plate in the optics path and 4) an array feed compensation system. Examples are given for the use of each technique along with an estimate of the expected performance improvement.
Second-Tier Test for Quantification of Alloisoleucine and Branched-Chain Amino Acids in Dried Blood Spots to Improve Newborn Screening for Maple Syrup Urine Disease (MSUD) (2008)

The LC-MS/MS method can reliably measure allo-Ile in dried blood spots for the diagnosis of MSUD. Applied to newborn screening as a second-tier test, it will reduce false-positive results, which produce family anxiety and increase follow-up costs. The assay also appears suitable for use in monitoring treatment of MSUD patients.
Psikolojik Danışman Adaylarının Duygusal Farkındalık Düzeylerinin Belirleyicileri (2015)

Ruh sagligini korumayi ve iyilestirmeyi hedefleyen, psikolojik danisman ile danisan arasinda kurulan profesyonel iliskinin, baska deyisle terapotik iliskinin temelinde duygularin farkinda olma ve duygulari ifade etme yatmaktadir. Psikolojik danismanlarin kendilerinin ve digerlerinin duygularini fark edip ifade edebilmeleri mesleki bir beceri olarak ele alinmaktadir. Bu sebeple, bu calisma kapsaminda psikolojik danisman adaylarinin duygusal farkindalik duzeyleri cinsiyet, sinif duzeyi, algilanan sosyal destek (aile destegi ve arkadas destegi) degiskenleri acisindan incelenmistir. Psikolojik Danisma ve Rehberlik Lisans programina devam eden 181 aday uzerinde yapilan bu calismada, ogrencilerin duygusal farkindaliklarini olcmek amaciyla Duygusal Farkindalik Duzeyi Olcegi (DFDO), algiladiklari sosyal destek duzeylerini olcmek amaciyla Algilanan Sosyal Destek Olcegi (ASDO) ve demografik bilgilerini belirlemek icin Demografik Bilgi Formu (DBF) kullanilmistir. Elde edilen veriler SPSS ile analiz edilmistir. Arkadastan ve aileden algilanan sosyal destek ile cinsiyet ve sinif duzeyinin, bireylerin kendi ve digerlerinin duygularini anlamadaki yordama gucleri, dogrusal regresyon analiziyle incelenmistir. Arastirmadan elde edilen bulgulara gore, cinsiyetin ve sinif duzeyinin duygusal farkindalik duzeyini etkiledigi; algilanan sosyal destegin de duygusal farkindaligi etkilemedigi sonucuna ulasilmistir. Arastirmadan elde edilen bulgular literatur isiginda tartisilmistir.