gebhart/patrepeval huggingface dataset:
Texture-based quantification of lumbar intervertebral disc degeneration from conventional T2-weighted MRI (2011)

Inhomogeneity descriptors could be a valuable tool for tracking the evolution of disc degeneration and monitoring the response to treatment in a simple, precise and repeatable manner.
Design, Synthesis, and Antiviral Activity of Nucleoside and Nucleotide Analogues (1989)

Several categories of antiviral compounds have been designed by exploiting important differences in viral and cellular biochemistry, as well as differences in chemical stability and reactivity between parent "lead" molecules and their modified structures. The synthesis, antiviral activity and mechanism of action of two carbocyclic nucleoside analogues related to the natural product neplanocin A are discussed. While the cytosine carbocycle, cyclopentenyl cytosine (CPE-C, 3), requires activation to form the biologically active nucleotide 5′-triphosphate analogue, a more selective antiviral effect is realized in the purine series by the modified 3-deazaneplanocin A (6c) analogue, due to its resistance to form nucleotide metabolites. In the area of dideoxy nucleoside analogues with anti-HIV activity, dideoxy-fluoro-ara-adenosine (ddF-ara-A, 15) and dideoxy-fluoro-ara-inosine (ddF-ara-I, 16), were designed as hydrolytically stable compounds. Although the beta stereochemistry of the fluorine atom proved not to be essential for chemical stability, it was critical for retaining the potent anti-HIV activity of the parent compounds. In the area of nucleotide analogues which incorporate in their structure an isosteric phosphate group, the complete synthesis of the phosphonate analogue of adenosine-2′-phosphate (26) is discussed. This compound was designed as a hydrolytically stable component of a 2′,5′-oligoadenylate trimer analogue (17) whose synthesis is in progress.
Structure of catabolite gene activator protein at 2.9-A resolution. Incorporation of amino acid sequence and interactions with cyclic AMP. (1982)

The amino acid sequence of the Escherichia coli catabolite gene activator protein has been fit into a 2.9-A resolution electron density map. Each subunit of the dimer consists of two structurally distinct domains. The larger NH2-terminal domain is seen to bind cyclic AMP and forms all of the contacts between the subunits. The cyclic AMP is completely buried between the interior of the "beta roll" structure of the large domain and a long alpha helix; it makes important hydrogen-bonding interactions with residues from both subunits. The guanidinium group of a buried Arg makes an internal salt link with the phosphate of cyclic AMP. The 6-amino group of adenine interacts simultaneously with both subunits. This interaction with both subunits and the fact that cyclic GMP and cyclic IMP do not activate catabolite gene activator protein suggest that the binding of cyclic AMP may alter the relative orientation of the two subunits, which in turn would change the structure of a DNA binding site that is presumed to span the two smaller domains. The distribution and nature of side chains in the small domain do not rule out the possibility that catabolite gene activator protein binds to left-handed B-DNA.
Degradable Poly(β-amino esters):  Synthesis, Characterization, and Self-Assembly with Plasmid DNA (2000)

Poly(β-aminoesters) 1−3 were synthesized via the addition of N,N'-dimethylethylenediamine, piperazine, and 4,4'-trimethylenedipiperidine to 1,4-butanediol diacrylate. Polymerization proceeded exclusively via the conjugate addition of the secondary amines to the bis(acrylate ester). Polymers were isolated in up to 86% yields with molecular weights ranging up to 31 200 relative to polystyrene standards. The polymers degraded hydrolytically in acidic and alkaline media to yield 1,4-butanediol and β-amino acids 4a−6a and the degradation kinetics were investigated at pH 5.1 and 7.4. In general, the polymers degraded more rapidly at pH 7.4 than at pH 5.1. In initial screening assays, both the polymers and their degradation products were determined to be noncytotoxic relative to poly(ethylene imine), a polymer conventionally employed as a synthetic transfection vector. Polymers 1−3 interacted electrostatically with polyanionic plasmid DNA in water and buffer at physiological pH, as determined by agarose gel electrophoresis, quasi-elastic dynamic light scattering (QELS), and ζ-potential measurements. All three polymers condensed DNA into soluble DNA/polymer particles on the order of 50−200 nm. Particles formed from polymers 1 and 2 aggregated extensively, while particles formed from polymer 3 exhibited positive ζ-potentials (e.g., +10 to +15 mV) and did not aggregate for up to 18 h. The nanometer-sized dimensions and reduced cytotoxicities of these DNA/polymer complexes suggest that these types of polymers may be useful as degradable polymeric gene transfer vectors.
Different Modes of Diaminopimelate Synthesis and Their Role in Cell Wall Integrity: a Study with Corynebacterium glutamicum (1998)

In eubacteria, there are three slightly different pathways for the synthesis of m-diaminopimelate (m-DAP), which is one of the key linking units of peptidoglycan. Surprisingly, for unknown reasons, some bacteria use two of these pathways together. An example is Corynebacterium glutamicum, which uses both the succinylase and dehydrogenase pathways for m-DAP synthesis. In this study, we clone dapD and prove by enzyme experiments that this gene encodes the succinylase (M(r) = 24082), initiating the succinylase pathway of m-DAP synthesis. By using gene-directed mutation, dapD, as well as dapE encoding the desuccinylase, was inactivated, thereby forcing C. glutamicum to use only the dehydrogenase pathway of m-DAP synthesis. The mutants are unable to grow on organic nitrogen sources. When supplied with low ammonium concentrations but excess carbon, their morphology is radically altered and they are less resistant to mechanical stress than the wild type. Since the succinylase has a high affinity toward its substrate and uses glutamate as the nitrogen donor, while the dehydrogenase has a low affinity and incorporates ammonium directly, the m-DAP synthesis is another example of twin activities present in bacteria for access to important metabolites such as the well-known twin activities for the synthesis of glutamate or for the uptake of potassium.
Activation of cultured human endothelial cells by recombinant lymphotoxin: comparison with tumor necrosis factor and interleukin 1 species. (1987)

Recombinant human lymphotoxin (LT) was compared with recombinant human tumor necrosis factor (TNF) for direct actions on cultured human endothelial cells (HEC). At equivalent half-maximal concentrations (based on L929 cytotoxicity units) LT and TNF each caused rapid and transient induction (peak 4 to 6 hr) of an antigen associated with leukocyte adhesion (detected by monoclonal antibody H4/18), a rapid but sustained increased expression (plateau 24 hr) of a lymphocyte adhesion structure (ICAM-1), a gradual (plateau 4 to 6 days) increase in expression of HLA-A,B antigens, and gradual (4 to 6 days) conversion of HEC culture morphology from epithelioid to fibroblastoid, an effect enhanced by immune interferon (IFN-gamma). Induction of H4/18 binding by maximal concentrations of LT or TNF could not be augmented by addition of the other cytokine, and 24 hr pretreatment with LT or TNF produced hyporesponsiveness to both mediators for reinduction. H4/18 binding can be transiently induced by tumor-promoting phorbol esters. Pretreatment with either LT or TNF also fully inhibited induction of H4/18 binding by phorbol ester, whereas phorbol ester pretreatment only variably and partially inhibited reinduction by LT or TNF. These actions of LT on endothelium shared with TNF may serve in vivo to promote lymphocyte and inflammatory leukocyte adhesion and transendothelial migration. Recombinant human interleukin 1 species (IL 1 alpha and IL 1 beta) shared many of the actions of LT and TNF and were indistinguishable from each other. However, IL 1 species could be distinguished from LT/TNF by their relative inability to enhance HLA-A,B expression, by their ability to augment H4/18 binding caused by maximally effective concentrations of LT or TNF, and by their inability to inhibit reinduction of H4/18 binding by LT or TNF. In contrast to the actions of LT or TNF, pretreatment with IL 1 alpha or IL 1 beta only partially inhibited induction of H4/18 binding by phorbol ester, and phorbol ester pretreatment consistently, albeit partially, inhibited induction by IL 1 species. These studies suggest that activated T cells through the secretion of LT can in turn activate the local endothelial lining so as to promote homing and extravasation of inflammatory cells. Furthermore, these LT actions can be augmented or complemented by other locally produced mediators such as IFN-gamma or IL 1.
Liposomes: A Novel Topical Delivery System for Pharmaceutical and Cosmetic Applications (1994)

This review will highlight work done in our laboratories evaluating topical liposomal delivery in a wide variety of animal models and human skin using both in vivo and in vitro techniques. The mechanism by which liposomes facilitate deposition of drugs into the skin and some potential applications of topically applied liposomes will be discussed. Particular emphasis will be placed on the development of analytical techniques that allow the quantification of drug levels in the various skin strata and in pilosebaceous structures. Appropriate models of skin representing the two cases, as well as those wherein both routes are available for skin deposition, were examined using a wide variety of liposomal preparations containing radiolabeled and fluorescent molecules as marker compounds.
Effects of long-term administration of pituitary-derived bovine growth hormone and estradiol on growth in steers. (1990)

Sixty-three Friesian steers (9 mo old, 257 kg; n = 15 or 16/treatment) were employed in a 2 x 2 factorial to test bovine growth hormone (bGH) and estradiol (Compudose implant). Steers received daily subcutaneous injections of vehicle or bGH (40 micrograms/kg body weight) for 22 wk. Steers were slaughtered 8 wk after the end of bGH treatment (wk 30). Steers had ad libitum access to silage plus a fixed amount (4 to 5.5 kg/d) of concentrate. Average daily gain (ADG) and feed conversion efficiency (FCE) improved (P less than .05) in response both to bGH and to estradiol during wk 0 to 22. Although bGH did not affect ADG or FCE during wk 23 to 30, estradiol improved (P less than .05) them; bGH and estradiol appeared additive (nonsignificant interactions) during wk 0 to 22. At slaughter, estradiol increased (P less than .05) carcass weight and carcass and leg length while decreasing (P less than .05) conformation score and percentage of kidney, knob and channel fat (KHP); bGH decreased (P less than .05) KHP. Although both bGH and estradiol increased (P less than .01) plasma GH, their effects were not additive. Both bGH and estradiol increased (P less than .01) plasma somatomedin-C and decreased (P less than .01) plasma urea nitrogen concentrations; effects were additive. Estradiol, but not bGH, increased (P less than .05) plasma glucose, whereas neither bGH nor estradiol altered plasma creatinine and nonesterified fatty acids. In summary, both bGH and estradiol improved growth and FCE, and their effects appeared to be additive. It is likely that some of their effects were mediated by somatomedin-C.
Interaction of biotin and biotinyl derivatives with avidin: conformational changes upon binding (2000)

We used FT-Raman and FT-IR spectroscopy to study avidin and its complexes with some biotin and biotinyl derivatives where the COOH group of the pentanoic acid chain is substituted by an ester or amidic group. To investigate the small structural changes due to the binding, the amide I Raman bands of Avidin and its complexes were analysed by two fairly comparable methods. The vibrational results indicate that the interaction with the ligands slightly modifies the secondary structure of the protein, decreasing the β-sheet content and increasing the α-helix percentage. To confirm the results obtained by Raman spectroscopy, we performed Gaussian curve-fitting procedure of the amide I and III infra-red regions of neat avidin and its complexes. The percentages obtained from the analysis of the Raman and IR spectra show the same trend. Thus, IR spectroscopy as an alternative or adjunct to Raman spectroscopy is a useful tool in evaluating small structural modifications produced by a bound ligand on a protein. The structural changes are mainly due to modifications in the hydrogen bonds with the pentanoic acid moiety of the ligand and, probably, are ascribed to conformational modifications in the surface loop which binds the strands of the β-barrel. In fact, biotin-N-succinimidyl ester, as well as biotin hydrazide, which have the same ability in the hydrogen-bond formation compared with biotin, induces avidine conformational changes similar to those observed in the avidin–biotin complex. The terminal group of the biotin derivatives seems to have a slight influence since the structural modifications of the protein observed upon the binding of the long-chain hydrazide-derivative ligands (biotinyl-aminocaproic hydrazide and biocitin hydrazide) are slightly greater than those obtained with the corresponding COOH containing ligands (biotinyl-aminocaproic acid and biocytin). Although the hydrogen bonds formed by the pentanoic acid chain of biotin are not essential to complex formation since they are not directly involved in the active site, the present study confirms that they can interact with the loops that lock biotin in the β-barrels of avidin and modulate the strength of the protein-ligand interaction. Copyright © 2000 John Wiley & Sons, Ltd.
Alignment mechanism of carbon nanofibers produced by plasma-enhanced chemical-vapor deposition (2001)

We report experimental evidence showing a direct correlation between the alignment of carbon nanofibers (CNFs) prepared by plasma-enhanced chemical-vapor deposition and the location of the catalyst particle during CNF growth. In particular, we find that CNFs that have a catalyst particle at the tip (i.e., growth proceeds from the tip) align along the electric-field lines, whereas CNFs with the particle at the base (i.e., growth proceeds from the base) grow in random orientations. We propose a model that explains the alignment process as a result of a feedback mechanism associated with a nonuniform stress (part tensile, part compressive) that is created across the interface of the catalyst particle with the CNF due to electrostatic forces. Furthermore, we propose that the alignment seen recently in some dense CNF films is due to a crowding effect and is not directly the result of electrostatic forces.
β-Secretase Processing in the Trans-Golgi Network Preferentially Generates Truncated Amyloid Species That Accumulate in Alzheimer’s Disease Brain (2002)

The amyloid beta (A beta) peptide that accumulates in Alzheimer's disease brain is derived from the proteolytic processing of the amyloid precursor protein by beta- and gamma-secretase activities. The beta-secretase enzyme beta-site amyloid precursor protein-cleaving enzyme (BACE) generates the N terminus of A beta by cleavage at either Asp(1) (beta-site) or Glu(11) (beta'-site), ultimately leading to the production of full-length A beta 1-40/42 or truncated A beta 11-40/42. The functional significance of this variable cleavage site specificity as well as the relative pathological impact of full-length versus N-terminally truncated A beta remains largely unknown. In our analysis of BACE reactivity in cell culture, we found that the preference of the protease for either beta- or beta'-cleavage was strongly dependent on intracellular localization. Within the endoplasmic reticulum, beta-site proteolysis predominated, whereas in the trans-Golgi network, beta'-cleavage was favored. Furthermore, the contrasting cleavage site specificities of BACE were not simply due to differences in organelle pH or the oligosaccharide composition of the glycoproteins involved. Examination of post-mortem brain specimens revealed significant levels of A beta 11-40/42 within insoluble amyloid pools. Taken together, these data support an important role for beta'-cleavage in the process of cerebral amyloid deposition and localize the processing event to the trans-Golgi network.
GAP1 activity is dependent on cAMP in Saccharomyces cerevisiae (2006)

General amino acid permease (GAP1) activity was evaluated in adenylate cyclase-deficient Saccharomyces cerevisiae to determine the effect of cAMP levels on GAP1 activity. Lowering cAMP concentrations in the culture media led to a decrease in the initial rates of L-citrulline uptake. Kinetics of the amino acid transport system showed a partial loss of transport capacity, with no apparent modifications in permease affinity.
RNA-directed DNA methylation inArabidopsis (2002)

In plants, double-stranded RNA that is processed to short RNAs approximately 21-24 nt in length can trigger two types of epigenetic gene silencing. Posttranscriptional gene silencing, which is related to RNA interference in animals and quelling in fungi, involves targeted elimination of homologous mRNA in the cytoplasm. RNA-directed DNA methylation involves de novo methylation of almost all cytosine residues within a region of RNA-DNA sequence identity. RNA-directed DNA methylation is presumed to be responsible for the methylation observed in protein coding regions of posttranscriptionally silenced genes. Moreover, a type of transcriptional gene silencing and de novo methylation of homologous promoters in trans can occur if a double-stranded RNA contains promoter sequences. Although RNA-directed DNA methylation has been described so far only in plants, there is increasing evidence that RNA can also target genome modifications in other organisms. To understand how RNA directs methylation to identical DNA sequences and how changes in chromatin configuration contribute to initiating or maintaining DNA methylation induced by RNA, a promoter double-stranded RNA-mediated transcriptional gene silencing system has been established in Arabidopsis. A genetic analysis of this system is helping to unravel the relationships among RNA signals, DNA methylation, and chromatin structure.
Detection of infectious prions in urine (2008)

Prions are the infectious agents responsible for prion diseases, which appear to be composed exclusively by the misfolded prion protein (PrP(Sc)). The mechanism of prion transmission is unknown. In this study, we attempted to detect prions in urine of experimentally infected animals. PrP(Sc) was detected in approximately 80% of the animals studied, whereas no false positives were observed among the control animals. Semi-quantitative calculations suggest that PrP(Sc) concentration in urine is around 10-fold lower than in blood. Interestingly, PrP(Sc) present in urine maintains its infectious properties. Our data indicate that low quantities of infectious prions are excreted in the urine. These findings suggest that urine is a possible source of prion transmission.
MicroRNAs as potential biomarkers for gastric cancer (2014)

Gastric cancer is the fourth most common cancer in the world and the second leading cause of cancer-related death. More than 80% of diagnoses occur at the middle to late stage of the disease, highlighting an urgent need for novel biomarkers detectable at earlier stages. Recently, aberrantly expressed microRNAs (miRNAs) have received a great deal of attention as potential sensitive and accurate biomarkers for cancer diagnosis and prognosis. This review summarizes the current knowledge about potential miRNA biomarkers for gastric cancer that have been reported in the publicly available literature between 2008 and 2013. Available evidence indicates that aberrantly expressed miRNAs in gastric cancer correlate with tumorigenesis, tumor proliferation, distant metastasis and invasion. Furthermore, tissue and cancer types can be classified using miRNA expression profiles and next-generation sequencing. As miRNAs in plasma/serum are well protected from RNases, they remain stable under harsh conditions. Thus, potential functions of these circulating miRNAs can be deduced and may implicate their diagnostic value in cancer detection. Circulating miRNAs, as well as tissue miRNAs, may allow for the detection of gastric cancer at an early stage, prediction of prognosis, and monitoring of recurrence and/or lymph node metastasis. Taken together, the data suggest that the participation of miRNAs in biomarker development will enhance the sensitivity and specificity of diagnostic and prognostic tests for gastric cancer.
Herding the Crowd: Using Automated Planning for Better Crowdsourced Planning (2017)

One subclass of human computation applications are those directed at tasks that involve planning (e.g. tour planning) and scheduling (e.g. conference scheduling). Interestingly, work on these systems shows that even primitive forms of automated oversight on the human contributors helps in significantly improving the effectiveness of the humans/crowd. In this paper, we argue that the automated oversight used in these systems can be viewed as a primitive automated planner, and that there are several opportunities for more sophisticated automated planning in effectively steering crowdsourced planning. Straightforward adaptation of current planning technology is however hampered by the mismatch between the capabilities of human workers and automated planners. We identify and partially address two important challenges that need to be overcome before such adaptation of planning technology can occur: (i) interpreting inputs of the human workers (and the requester) and (ii) steering or critiquing plans produced by the human workers, armed only with incomplete domain and preference models. To these ends, we describe the implementation of AI-MIX, a tour plan generation system that uses automated checks and alerts to improve the quality of plans created by human workers.
Silicon ink selective emitter process: Optimization of selectively diffused regions for short wavelength response (2010)

The Innovalight Cougar <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">™</sup> Platform is a portfolio of simple to implement technologies that, when combined with Innova-light Silicon Ink, enables the manufacture of a selective emitter solar cell with a non-masking single-step diffusion. Cell efficiencies of up to 19% have been achieved. Innova-light Silicon Ink is a highly engineered silicon nanoparticle colloidal dispersion, implemented for both high volume ink-jet and screen deposition, and further optimized to be produced and delivered in commercial volumes. A particular feature of the selective emitter structure is its enhanced quantum efficiency in the short wavelength region as result of reduced emitter recombination. In this report we demonstrate how the properties of the selectively doped regions on the front surface of the cell affect the short wavelength response of a Cougar cell. In particular, the importance of the emitter dopant profile for minimizing emitter recombination and the broad processing window of the Cougar cell structure with respect to emitter doping are illustrated. Further, the effect of the ink finger width on the short-wavelength response of the cell and the trade-off between the loss of short circuit current (J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sc</sub> ) and metal-to-ink pattern alignment are demonstrated.