gebhart/patrepeval huggingface dataset:
Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host (2006)

Probiotics are deliberately ingested preparations of live bacterial species that confer health benefits on the host. Many of these species are associated with the fermentation of dairy products. Despite their increasing use, the molecular details of the impact of various probiotic preparations on resident members of the gut microbiota and the host are generally lacking. To address this issue, we colonized germ-free mice with Bacteroides thetaiotaomicron, a prominent component of the adult human gut microbiota, and Bifidobacterium longum, a minor member but a commonly used probiotic. Simultaneous whole genome transcriptional profiling of both bacterial species in their gut habitat and of the intestinal epithelium, combined with mass-spectrometric analysis of habitat-associated carbohydrates, revealed that the presence of B. longum elicits an expansion in the diversity of polysaccharides targeted for degradation by B. thetaiotaomicron (e.g., mannose- and xylose-containing glycans), and induces host genes involved in innate immunity. Although the overall transcriptome expressed by B. thetaiotaomicron when it encounters B. longum in the cecum is dependent upon the genetic background of the mouse (as assessed by a mixed analysis of variance [ANOVA] model of co-colonization experiments performed in NMRI and C57BL/6J animals), B. thetaiotaomicron's expanded capacity to utilize polysaccharides occurs independently of host genotype, and is also observed with a fermented dairy product-associated strain, Lactobacillus casei. This gnotobiotic mouse model provides a controlled case study of how a resident symbiont and a probiotic species adapt their substrate utilization in response to one another, and illustrates both the generality and specificity of the relationship between a host, a component of its microbiota, and intentionally consumed microbial species.
Yeast Cells Provide Insight into Alpha-Synuclein Biology and Pathobiology (2003)

Alpha-synuclein is implicated in several neurodegenerative disorders, such as Parkinson's disease and multiple system atrophy, yet its functions remain obscure. When expressed in yeast, alpha-synuclein associated with the plasma membrane in a highly selective manner, before forming cytoplasmic inclusions through a concentration-dependent, nucleated process. Alpha-synuclein inhibited phospholipase D, induced lipid droplet accumulation, and affected vesicle trafficking. This readily manipulable system provides an opportunity to dissect the molecular pathways underlying normal alpha-synuclein biology and the pathogenic consequences of its misfolding.
Thermodynamics of the binding of biotin and some analogues by avidin (1966)

1. The reaction between avidin and biotin was found to be exothermic, DeltaH being -20.3kcal./mole of biotin bound. The corresponding value of DeltaH for streptavidin was -23kcal./mole. 2. The heat evolved was independent of the pH (between 5 and 9), of the buffer (borate or ammonia) and of the fractional saturation of the avidin with biotin. 3. The entropy change for the reaction was zero, and it is suggested that the entropy increase to be expected from hydrophobic interactions was counterbalanced by a decrease in entropy accompanying the formation of buried hydrogen bonds. 4. Modification of the potential hydrogen-bonding sites of the imidazolidone ring led to a decreased heat output and a positive entropy of reaction.
Targeting Sites within HIV-1 cDNA with a DNA-Cleaving Ribozyme (1996)

A variant of the Tetrahymena ribozyme that efficiently cleaves single-stranded DNA under simulated physiological conditions [Tsang, J., & Joyce, G. F. (1994) Biochemistry 33, 5966-5973] was evaluated as a potential therapeutic agent on the basis of its ability to cleave synthetic oligonucleotide substrates corresponding to conserved target sites within HIV-I cDNA. In order to increase the sequence selectivity of the ribozyme, its substrate recognition domain was extended from 6 to 12 nucleotides, allowing base pairing with substrate nucleotides that lie both upstream and downstream of the cleavage site. The sequence of the extended recognition domain could be changed to allow cleavage of a variety of different DNA targets. The ribozyme exhibited a high degree of sequence specificity, discriminating by a factor of 10(2) to more than 10(4) against substrates that form a single-base mismatch with the ribozyme's recognition domain. Mismatches that occurred close to the cleavage site led to a greater decrease in activity compared to those that occurred farther away.
A note on efficient zero-knowledge proofs and arguments (extended abstract) (1992)

In this note, we present new zero-knowledge interactive proofs and arguments for languages in NP. To show that x ε L, with an error probability of at most 2-k, our zero-knowledge proof system requires O(|x|c1)+O(lgc2|x|)k ideal bit commitments, where c1 and c2 depend only on L. This construction is the first in the ideal bit commitment model that achieves large values of k more efficiently than by running k independent iterations of the base interactive proof system. Under suitable complexity assumptions, we exhibit zero knowledge arguments that require O(lgc|x|kl bits of communication, where c depends only on L, and l is the security parameter for the prover. This is the first construction in which the total amount of communication can be less than that needed to transmit the NP witness. Our protocols are based on efficiently checkable proofs for NP[4].
One-step synthesis of a sulfur-impregnated graphene cathode for lithium–sulfur batteries (2012)

A practical route is introduced for synthesizing a sulfur-impregnated graphene composite as a promising cathode material for lithium–sulfur batteries. Sulfur particles with a size of a few microns are successfully grown in the interior spaces between randomly dispersed graphene sheets through a heterogeneous crystal growth mechanism. The proposed route not only enables the control of the particle size of active sulfur but also affords quantitative yields of composite powder in large quantities. We investigate the potential use of the sulfur-impregnated graphene composite as a cathode material owing to its advantages of confining active sulfur, preventing the dissolution of soluble polysulfides, and providing sufficient electrical conduction. A high discharge capacity of 1237 mA h g−1 during the first cycle and a good cyclic retention of 67% after 50 cycles are attained in a voltage range of 1.8–2.6 V vs. Li/Li+. These results emphasize the importance of tailoring cathode materials for improving the electrochemical properties of lithium–sulfur batteries. Our results provide a basis for further investigations on advanced lithium batteries.
Cats discriminate between cholecalciferol and ergocalciferol* (2002)

A comparison was made of the ability of ergocalciferol and cholecalciferol to elevate plasma concentrations of vitamin D and 25-hydroxyvitamin D in cats. Cholecalciferol, given as an oral bolus in oil, resulted in a rapid elevation of plasma concentration of cholecalciferol followed by a rapid decline. In contrast, 25-hydroxyvitamin D concentration in plasma increased until day 3 after administration and remained elevated for a further 5 days. When 337 microg of both cholecalciferol and ergocalciferol in oil were given as an oral bolus to 10 cats, the peak plasma concentrations of cholecalciferol and ergocalciferol occurred at 8 or 12 h after administration. Peak concentrations of cholecalciferol were over twice those of ergocalciferol (570 +/- 80 vs. 264 +/- 42 nmol/l). The area under the curve 0-169 h for cholecalciferol was also more than twice that for ergocalciferol. When ergocalciferol and cholecalciferol were administered in a parenteral oil-based emulsion, higher concentrations of 25-hydroxyvitamin D3 than 25-hydroxyvitamin D2 were maintained in plasma. When both vitamins were included in the diet in the nutritional range, plasma concentrations of 25-hydroxyvitamin D2 were 0.68 of those of 25-hydroxyvitamin D3. Discrimination against ergocalciferol by cats appears to result from differences in affinity of the binding protein for the metabolites of the two forms of vitamin D. These results indicate that cats discriminate against ergocalciferol, and use it with an efficiency of 0.7 of that of cholecalciferol to maintain plasma 25-hydroxyvitamin D concentration.
Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication (2004)

Bacterial communities use "quorum sensing" (QS) to coordinate their population behavior through the action of extracellular signal molecules, such as the N-acyl-l-homoserine lactones (AHLs). The versatile and ubiquitous opportunistic pathogen Pseudomonas aeruginosa is a well-studied model for AHL-mediated QS. This species also produces an intercellular signal distinct from AHLs, 3,4-dihydroxy-2-heptylquinoline (PQS), which belongs to a family of poorly characterized 4-hydroxy-2-alkylquinolines (HAQs) previously identified for their antimicrobial activity. Here we use liquid chromatography (LC)/MS, genetics, and whole-genome expression to investigate the structure, biosynthesis, regulation, and activity of HAQs. We show that the pqsA-E operon encodes enzymes that catalyze the biosynthesis of five distinct classes of HAQs, and establish the sequence of synthesis of these compounds, which include potent cytochrome inhibitors and antibiotics active against human commensal and pathogenic bacteria. We find that anthranilic acid, the product of the PhnAB synthase, is the primary precursor of HAQs and that the HAQ congener 4-hydroxy-2-heptylquinoline (HHQ) is the direct precursor of the PQS signaling molecule. Significantly, whereas phnAB and pqsA-E are positively regulated by the virulence-associated transcription factor MvfR, which is also required for the expression of several QS-regulated genes, the conversion of HHQ to PQS is instead controlled by LasR. Finally, our results reveal that HHQ is itself both released from, and taken up by, bacterial cells where it is converted into PQS, suggesting that it functions as a messenger molecule in a cell-to-cell communication pathway. HAQ signaling represents a potential target for the pharmacological intervention of P. aeruginosa-mediated infections.
Achieving efficient delivery of morpholino oligos in cultured cells (2001)

One of the many features that make morpholino oligos unique among the antisense structural types is an uncharged backbone. While this feature eliminates the nonspecific interactions of traditional S-oligos, it also renders the morpholino undeliverable via the traditional lipid-based delivery systems. This article describes a highly efficient method of delivering morpholino oligos into adherent and nonadherent cultured cells. In this system, a nonionic morpholino oligo is paired to a complementary DNA "carrier." The DNA is then bound electrostatically to a partially ionized, weakly-basic ethoxylated polyethylenimine (EPEI). This morpholino/DNA/EPEI complex is efficiently endocytosed, and when the pH drops within the endosome, the EPEI more fully ionizes, resulting in permeabilization of the endosomal membrane and release of the morpholino into the cytosol. This article describes optimization of delivery in HeLa cells and provides the basis for delivery in any cultured endocytic cell type. genesis 30:94--102, 2001.
Elevated expression of carcinoembryonic antigen-related cell adhesion molecule 1 promotes progression of non-small cell lung cancer. (2003)

The absence of CEACAM-1 in normal lung tissue and its expression in tumor cells argues against a tumor-suppressive role of CEACAM-1 in NSCLC. The correlation between elevated CEACAM-1 expression and an unfavorable prognosis indicates rather that CEACAM-1 might promote lung cancer progression.
Monensin Inhibits Canonical Wnt Signaling in Human Colorectal Cancer Cells and Suppresses Tumor Growth in Multiple Intestinal Neoplasia Mice (2014)

The Wnt signaling pathway is required during embryonic development and for the maintenance of homeostasis in adult tissues. However, aberrant activation of the pathway is implicated in a number of human disorders, including cancer of the gastrointestinal tract, breast, liver, melanoma, and hematologic malignancies. In this study, we identified monensin, a polyether ionophore antibiotic, as a potent inhibitor of Wnt signaling. The inhibitory effect of monensin on the Wnt/β-catenin signaling cascade was observed in mammalian cells stimulated with Wnt ligands, glycogen synthase kinase-3 inhibitors, and in cells transfected with β-catenin expression constructs. Furthermore, monensin suppressed the Wnt-dependent tail fin regeneration in zebrafish and Wnt- or β-catenin-induced formation of secondary body axis in Xenopus embryos. In Wnt3a-activated HEK293 cells, monensin blocked the phoshorylation of Wnt coreceptor low-density lipoprotein receptor related protein 6 and promoted its degradation. In human colorectal carcinoma cells displaying deregulated Wnt signaling, monensin reduced the intracellular levels of β-catenin. The reduction attenuated the expression of Wnt signaling target genes such as cyclin D1 and SP5 and decreased the cell proliferation rate. In multiple intestinal neoplasia (Min) mice, daily administration of monensin suppressed progression of the intestinal tumors without any sign of toxicity on normal mucosa. Our data suggest monensin as a prospective anticancer drug for therapy of neoplasia with deregulated Wnt signaling.
Cd-Doped InGaN Films Grown on GaN Films (1993)

Cd-doped InGaN films were grown for the first time at temperatures between 810°C and 780°C. Room-temperature photoluminescence (PL) showed strong blue emissions which had peak wavelengths between 424 nm and 495 nm, depending on the indium mole fraction, and full width at half-maximum (FWHM) of about 60 nm. These blue emissions had a peak wavelength at an energy level 0.5 eV lower than the band-gap energy of each InGaN. The intensity of the Cd-related emission was almost the same as that of the band-edge (BE) emission of Si-doped InGaN.
Studies of the low-pressure inductively-coupled plasma etching for a larger area wafer using plasma modeling and Langmuir probe (1998)

As semiconductor wafer size increases (from the current 200 to 300 mm), scaling up a process chamber to meet the same or even more stringent requirements becomes difficult due to complexity of the nonequilibrium plasmas. Designing 300 mm etching reactors can be costly and time consuming for developers without an understanding of fundamental physical and chemical processes. To expedite development and reduce cost, plasma modeling and plasma diagnostics are used to gain insight and assist the 300 mm etching reactor development. In this article, it is demonstrated that plasma modeling and Langmuir probe measurement can be used to study various plasma properties including the effects of inductively coupled power, chamber pressure, aspect ratio, and coil configuration, for a planar inductively-coupled plasma. The results from these studies are used to optimize an inductively-coupled plasma R&amp;D chamber capable of etching 300 mm wafers.
Enhancement of spontaneous recombination rate in a quantum well by resonant surface plasmon coupling (2002)

Using time-resolved photoluminescence measurements, the recombination rate in an ${\mathrm{In}}_{0.18}{\mathrm{Ga}}_{0.82}\mathrm{N}/\mathrm{GaN}$ quantum well (QW) is shown to be greatly enhanced when spontaneous emission is resonantly coupled to a silver surface plasmon. The rate of enhanced spontaneous emission into the surface plasmon was as much as 92 times faster than QW spontaneous emission into free space. A calculation, based on Fermi's golden rule, reveals that the enhancement is very sensitive to silver thickness and indicates even greater enhancements are possible for QW's placed closer to the surface metal coating.
Phosphorylation of hepatitis C virus-encoded nonstructural protein NS5A (1995)

Two proteins, a 56-kDa protein (p56) and a 58-kDa protein (p58), are produced from the hepatitis C virus (HCV) nonstructural region 5A (NS5A). Recently, we found that both proteins are phosphorylated at serine residues and that p58 is a hyperphosphorylated form of p56. Furthermore, hyper-phosphorylation depends on the production of an intact form of the HCV NS4A protein. To clarify the nature of NS5A phosphorylation, pulse-chase analysis was performed with a transient protein production system in cultured cells. The study indicated that basal and hyperphosphorylation of NS5A occurred after proteolytic production of NS5A was complete. In an attempt to identify the location of the hyperphosphorylation sites in p58, proteins with sequential deletions from the C-terminal region of NS5A and with mutations of possible phosphorylated serine residues to a neutral amino acid, alanine, were constructed. The deleted or mutated proteins were then tested for hyperphosphorylation in the presence of the NS4A product. Here, we report that serine residues 2197, 2201, and/or 2204 are important for hyper-phosphorylation. Important sites for basal phosphorylation were identified in the region from residues 2200 to 2250 and in the C-terminal region of the NS5A product. A subcellular localization study showed that most of the NS5A products were localized in the nuclear periplasmic membrane fraction.
[Problem of fetal arrhythmias--a case report]. (1985)

A fetal congenital complete AV-block was detected in the 30th week of gestation. After close sonographic and cardiotocographic follow-up examinations premature labor occurred in the 37th week of gestation. The interpretation of the fetal heart rate pattern was difficult. The bradycardia was accompanied by late decelerations (dip II), only different from familiar hypoxia-patterns by the bradycardia. Caesarean section therefore was immediately done. A partial abruptio placentae was found as causing hypoxia. The child developed well after insertion of a temporary transvenous pacemaker. The AV-block is still persisting. At the age of three months the child fell ill of an acute cutaneous lupus erythematosus. The symptoms disappeared after unspecific treatment. Antinuclear antibodies pathognomonic for lupus erythematosus were traceable in the symptomless mother. There are other observations of motherly autoantibodies passing the placental barrier impairing the fetal heart conduction.
Alpha-synuclein cortical Lewy bodies correlate with dementia in Parkinson’s disease (2000)

CLBs detected by alpha-synuclein antibodies in patients with PD are a more sensitive and specific correlate of dementia than the presence of Alzheimer's pathology, which was present in a minority of the cases in this series.
Improving Mouse Dynamics Biometric Performance Using Variance Reduction via Extractors With Separate Features (2010)

The European standard for access control imposes stringent performance requirements on commercial biometric technologies that few existing recognition systems are able to meet. In this correspondence paper, we present the first mouse dynamics biometric recognition system that fulfills this standard. The proposed system achieves notable performance improvement by developing separate models for separate feature groups involved. The improvements are achieved through the use of a fuzzy classification based on the Learning Algorithm for Multivariate Data Analysis and using a score-level fusion scheme to merge corresponding biometric scores. Evaluation of the proposed framework using mouse data from 48 users achieves a false acceptance rate of 0% and a false rejection rate of 0.36%.
Phenotypic Screening of Small Molecule Libraries by High Throughput Cell Imaging (2003)

We have developed high throughput fluorescence cell imaging methods to screen chemical libraries for compounds with effects on diverse aspects of cell physiology. We describe screens for compounds that arrest cells in mitosis, that block cell migration, and that block the secretory pathway. Each of these screens yielded specific inhibitors for research use, and the mitosis screen identified Eg5 as a potential target protein for cancer chemotherapy. Cell imaging provides a large amount of information from primary screening data that can be used to distinguish compounds with different effects on cells, and together with automated analysis, to quantitate compound effects.
DNA-Templated Native Chemical Ligation of Functionalized Peptide Nucleic Acids: A Versatile Tool for Single Base-Specific Detection of Nucleic Acids (2013)

Single base-specific detection of DNA/RNA sequences is of importance in the diagnosis of disease-associated genetic disorders or early stage cancer. This chapter introduces DNA-templated native chemical PNA ligation as a potentially useful tool for the sequence specific detection of nucleic acids. The template-induced alignment of PNA-thioesters and 1,2-aminothiol-PNAs in close proximity leads to an increase in their effective molarities. This facilitates PNA ligation to proceed at concentrations where no reaction would be possible in absence of the template. Moreover, hybridization of the rather short PNA conjugates with non-complementary DNA/RNA is disfavored, which prevents PNA ligation to occur on single base-mismatched templates. Different readout strategies of the ligation reaction such as HPLC, MALDI-TOF-MS and fluorecence monitoring are discussed, and examples for the detection of a point mutation within single stranded and PCR-amplified double stranded DNA are provided.
Syndrome comorbidity in patients with major depression or dysthymia: prevalence and temporal relationships (1990)

The authors administered the Structured Clinical Interview for DSM-III-R to 260 patients with principal diagnoses of depressive disorders. Approximately two-thirds of these patients were given at least one additional concurrent axis I disorder. The most common comorbid diagnoses were anxiety disorders. The depressive disorders preceded the anxiety disorders in most patients. The authors not only point out the scientific and clinical implications of psychiatric comorbidity in view of the patterns of comorbidity found in this and previous studies but also discuss issues in comorbidity research.
Presence of activin signal transduction in normal ovarian cells and epithelial ovarian carcinoma (2000)

In this study, we have investigated the expression of inhibin subunits and activin receptors (ActRs) in normal and malignant ovarian cells. Each product of the inhibin subunits (α, βa, βb) and activin receptors (ActRs) amplified by reverse transcription polymerase chain reaction were detected as a single band in human granulosa cells, surface epithelial cells (OSE), and the ovarian cancer cell lines OVCAR 3 and SKOV 3. Western blot analysis was performed using polyclonal antibodies against ActR IIa or IIb peptides based on 13 COOH-terminal amino acids; cultured human granulosa cells were used as a positive control. Using ActR IIa antibody, one major band corresponding to approximately 80 kDa and one minor band corresponding to 105 kDa were observed in the samples. One single band at approximately 60 kDa was detected in OVCAR 3 and a 50 kDa band was detected with ActR IIb antibody in cultured granulosa cell, OSE and SKOV 3. Although no detectable change was induced in Smad 4 mRNA in OVCAR 3, Smad 2 mRNA levels were increased during 48 h treatment with activin A (50 ng ml−1). These data provide a better understanding as the first step in the mechanism of action of the activin in the epithelial ovarian carcinoma. © 2000 Cancer Research Campaign