gebhart/patrepeval huggingface dataset:
Thermodynamics of G-tetraplex formation by telomeric DNAs (1993)

Telomeres are structures at the ends of eukaryotic chromosomes, the DNA of which contains stretches of tandemly repeated sequences with G clusters along one strand. Model telomeric G-rich DNAs can form different tetraplex structures, stabilized by cyclic hydrogen bonding of four guanines in the presence of metal ions such as Na+ or K+. Oligonucleotides with a single copy of the Oxytricha sequence dT4G4 form a tetramer, with a parallel-stranded, right-handed helical structure. Additional copies favor folded-back structures that associate to form an antiparallel dimer. The parallel-stranded tetramer has all G's in the anti configuration, while the folded-back dimer has alternating syn and anti nucleotide conformations along each strand. Here we have constructed two G-tetraplex structures, containing identical G-tetrad base pairs, from oligonucleotides. One has the truncated telomeric sequence from Oxytricha, dG4T4G4, which forms an antiparallel G-quartet structure; the second is constrained to form a parallel G-strand arrangement by insertion of a 5'-p-5' linkage between two dT2G4 sequences. Each oligomer forms a defined G-tetraplex dimeric structure in the presence of Na+. The standard-state enthalpies, entropies, and free energy for formation of these tetraplexes have been determined. The parallel strand structure is thermodynamically more stable than the antiparallel one, primarily because of both greater enthalpy and entropy of formation. In addition, the two molecules differ in their interaction with sodium ions, reflecting a difference in ion binding and therefore in structure between the two forms.
Erythropoietin Delivery by Genetically Engineered Bone Marrow Stromal Cells for Correction of Anemia in Mice with Chronic Renal Failure (2006)

The goal of this research was to develop a strategy to couple stem cell and gene therapy for in vivo delivery of erythropoietin (Epo) for treatment of anemia of ESRD. It was shown previously that autologous bone marrow stromal cells (MSCs) can be genetically engineered to secrete pharmacologic amounts of Epo in normal mice. Therefore, whether anemia in mice with mild to moderate chronic renal failure (CRF) can be improved with Epo gene-modified MSCs (Epo+MSCs) within a subcutaneous implant was examined. A cohort of C57BL/6 mice were rendered anemic by right kidney electrocoagulation and left nephrectomy. In these CRF mice, the hematocrit (Hct) dropped from a prenephrectomy baseline of approximately 55% to 40% after induction of renal failure. MSCs from C57BL/6 donor mice were genetically engineered to secrete murine Epo at a rate of 3 to 4 units of Epo/10(6) cells per 24 h, embedded in a collagen-based matrix, and implanted subcutaneously in anemic CRF mice. It was observed that Hct increased after administration of Epo+MSCs, according to cell dose. Implants of 3 million Epo+MSCs per mouse had no effect on Hct, whereas 10 million led to a supraphysiologic effect. The Hct of CRF mice that received 4.5 or 7.5 million Epo+MSCs rose to a peak 54+/-4.0 or 63+/-5.5%, respectively, at 3 wk after implantation and remained above 48 or 54% for >19 wk. Moreover, mice that had CRF and received Epo+MSCs showed significantly greater swimming exercise capacity. In conclusion, these results demonstrate that subcutaneous implantation of Epo-secreting genetically engineered MSCs can correct anemia that occurs in a murine model of CRF.
Analyzing protein circular dichroism spectra for accurate secondary structures (1999)

We have developed an algorithm to analyze the circular dichroism of proteins for secondary structure. Its hallmark is tremendous flexibility in creating the basis set, and it also combines the ideas of many previous workers. We also present a new basis set containing the CD spectra of 22 proteins with secondary structures from high quality X-ray diffraction data. High flexibility is obtained by doing the analysis with a variable selection basis set of only eight proteins. Many variable selection basis sets fail to give a good analysis, but good analyses can be selected without any a priori knowledge by using the following criteria: (1) the sum of secondary structures should be close to 1.0, (2) no fraction of secondary structure should be less than -0.03, (3) the reconstructed CD spectrum should fit the original CD spectrum with only a small error, and (4) the fraction of alpha-helix should be similar to that obtained using all the proteins in the basis set. This algorithm gives a root mean square error for the predicted secondary structure for the proteins in the basis set of 3.3% for alpha-helix, 2.6% for 3(10)-helix, 4.2% for beta-strand, 4.2% for beta-turn, 2.7% for poly(L-proline) II type 3(1)-helix, and 5.1% for other structures when compared with the X-ray structure.
File server scaling with network-attached secure disks (1997)

By providing direct data transfer between storage and client, network-attached storage devices have the potential to improve scalability for existing distributed file systems (by removing the server as a bottleneck) and bandwidth for new parallel and distributed file systems (through network striping and more efficient data paths). Together, these advantages influence a large enough fraction of the storage market to make commodity network-attached storage feasible. Realizing the technology's full potential requires careful consideration across a wide range of file system, networking and security issues. This paper contrasts two network-attached storage architectures---(1) Networked SCSI disks (NetSCSI) are network-attached storage devices with minimal changes from the familiar SCSI interface, while (2) Network-Attached Secure Disks (NASD) are drives that support independent client access to drive object services. To estimate the potential performance benefits of these architectures, we develop an analytic model and perform trace-driven replay experiments based on AFS and NFS traces. Our results suggest that NetSCSI can reduce file server load during a burst of NFS or AFS activity by about 30%. With the NASD architecture, server load (during burst activity) can be reduced by a factor of up to five for AFS and up to ten for NFS.
Inhibition by memantine of the development of persistent oral dyskinesias induced by long‐term haloperidol treatment of rats (1996)

1. Tardive dyskinesia (TD) is a serious side-effect of long-term treatment with neuroleptics. To investigate if neuroleptic-induced excessive stimulation of striatal glutamate receptors may underlie TD development, the effect of the NMDA antagonist, memantine (1-amino-3,5-dimethyladamantane), was studied in a rat model of TD. 2. In an acute experiment, six groups of rats were treated daily for 1 week with either vehicle or memantine 20 or 40 mg kg-1 day-1, and on the seventh day they received one injection of either haloperidol 1.0 mg kg-1 i.p. or saline i.p. In a subsequent long-term experiment lasting 20 weeks, the same treatment was continued, except that haloperidol was injected i.m. as decanoate (38 mg kg-1 every 4 weeks) and control rats received sesame oil. The behaviour was videotaped and scored at intervals during both experiments, and for 16 weeks after cessation of the long-term treatment. 3. In the acute experiment, haloperidol decreased motor activity and memantine increased moving and tended to attenuate the immobility induced by haloperidol. Memantine also enhanced the haloperidol-induced increase in the putative TD-analogue vacuous chewing movements (VCM). 4. In the long-term experiment, the most marked effect of haloperidol was a gradual increase in VCM and the increase persisted significantly for 12 weeks after cessation of treatment. Memantine dose-dependently increased VCM and moving during long-term treatment. However, only one week after stopping treatment, both these effects of memantine disappeared. In contrast to rats previously treated with haloperidol alone, rats co-treated with memantine (both doses) and haloperidol had VCM at the level of controls two weeks after stopping treatment. The blood levels of drugs were within the therapeutic range achieved in human subjects. 5. These results suggest that long-lasting changes induced by haloperidol are prevented by memantine, which supports the theory that excessive NMDA receptor stimulation may be a mechanism underlying the development of persistent VCM in rats and maybe also TD in human subjects.
R1, a Novel Repressor of the Human Monoamine Oxidase A (2005)

Monoamine oxidase catalyzes the oxidative deamination of a number of neurotransmitters. A deficiency in monoamine oxidase A results in aggressive behavior in both humans and mice. Studies on the regulation of monoamine oxidase A gene expression have shown that the Sp1 family is important for monoamine oxidase A expression. To search for novel transcription factors, the sequences of three Sp1 sites in the monoamine oxidase A core promoter were used in the yeast one-hybrid system to screen a human cDNA library. A novel repressor, R1 (RAM2), has been cloned. The R1 cDNA encodes a protein with 454 amino acids and an open reading frame at the 5'-end. The transfection of R1 in a human neuroblastoma cell line, SK-N-BE (2)-C, inhibited the monoamine oxidase A promoter and enzymatic activity. The degree of inhibition of monoamine oxidase A by R1 correlated with the level of R1 protein expression. R1 was also found to repress monoamine oxidase A promoter activity within a natural chromatin environment. A gel-shift assay indicated that the endogenous R1 protein in SK-N-BE (2)-C cells interacted with the R1 binding sequence. R1 also bound directly to the natural monoamine oxidase A promoter in vivo as shown by chromatin immunoprecipitation assay. Immunocytochemical analysis showed that R1 was expressed in both cytosol and nucleus, which suggested a role for R1 in transcriptional regulation. Northern blot analysis revealed the presence of endogenous R1 mRNA in human brain and peripheral tissues. Taken together, this study shows that R1 is a novel repressor that inhibits monoamine oxidase A gene expression.
Analysis of the error surface of the XOR network with two hidden nodes (1996)

Protein arginine methyltransferase 5 (PRMT5), a histone methyltransferase responsible for the symmetric dimethylation of histone H4 on Arg 3 (H4R3me2s), is an enzyme that participates in tumor cell progression in a variety of hematological malignancies. However, the biological functions of PRMT5 in multiple myeloma (MM) and the underlying molecular mechanisms remain unclear. In this study, we conducted a bioinformatics analysis and found that PRMT5 expression was significantly upregulated in MM. In vitro and in vivo phenotypic experiments revealed that knockdown of PRMT5 expression enhanced cell pyroptosis in MM. Moreover, we found that CASP1 expression was negatively correlated with PRMT5 expression, and repressing PRMT5 expression rescued both the phenotype and expression markers (N-GSDMD, IL-1b, and IL-18). Inhibition of PRMT5 activity increased CASP1 expression and promoted MM cell pyroptosis. Finally, high expression of PRMT5 or low expression of CASP1 was correlated with poor overall survival in MM. Collectively, our results provide a mechanism by which PRMT5 regulates cell pyroptosis by silencing CASP1 in MM.
Polarized Raman Study of Aligned Multiwalled Carbon Nanotubes (2000)

Polarized Raman spectra of high purity aligned arrays of multiwalled carbon nanotubes, prepared on silica substrates from the thermal decomposition of a ferrocene-xylene mixture, show a strong dependence of the graphitelike G band and the disorder-induced D band on the polarization geometry employed in the experiments. The experimental G-band intensity exhibits a minimum at straight theta(m) = 55 degrees in the VV configuration, in good agreement with theoretical predictions of a characteristic minimum at 54.7 degrees for A(1g) modes in single wall nanotubes, where straight theta(m) denotes the angle between the polarization direction and the nanotube axis.
Two-Component Response Regulators from Arabidopsis thaliana Contain a Putative DNA-Binding Motif (1998)

An expression sequence tag database of higher plants was screened by in silico profile analysis for response regulators of the two-component regulatory system. Two closely related clones (ARR1 and ARR2), corresponding to one of the extracted candidates, were isolated from Arabidopsis thaliana. The two genes were comparably expressed in all tissues, and at higher levels in the roots. The amino-terminal half of their translation products was highly conserved. This is where a phosphate receiver domain with the landmark aspartate residue and a putative DNA-binding domain were located. Their carboxyl-terminal halves, although less similar to each other, included glutamine-rich and proline-rich regions characteristic of the transcriptional activation domain of eukaryotes. This architecture resembles that of typical bacterial response regulators serving as transcription factors.
Italian Protestants: Religion, Ethnicity, and Assimilation (2000)

Early in the twentieth century, Italian Protestants in the United States comprised a religious minority in the Italian Catholic community and an ethnic minority in the American one. Because the assimilation of Protestants from heavily Catholic countries is little studied, I examine the life cycle of three Italian Protestant churches in three denominations in Rochester, New York in order to explain why they disappeared earlier than did their Catholic counterparts. When the second generation Italian Protestants attained adolescence, religious identity with American Protestants overrode ethnic identity, accelerating their assimilation. The Italian Protestant churches had become middle‐class American organizations save for the use of Italian, a fatal contradiction. By 1960,all three churches had died, but all of the ethnic Catholic and national Orthodox parishes had survived.
Modeling of 3-D Surface Roughness Effects With Application to $\mu$-Coaxial Lines (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Effects of 3-D surface roughness on the propagation constant of transverse electromagnetic transmission lines are calculated using finite-element method software by solving for the fields inside conductors. The modeling is validated by comparison with available literature results for the special case of 2-D surface roughness and by simulations using the finite-integration technique. Results for cubical, semiellipsoidal, and pyramidal indentations, as well as rectangular, semicircular, and triangular grooves in conductor surfaces are presented. A developed surface roughness model is applied to rectangular <formula formulatype="inline"><tex>$\mu$</tex></formula>-coaxial lines. It is shown that roughness contributes up to 9.2% to their overall loss for frequencies below 40 GHz. </para>
Fast search in Hamming space with multi-index hashing (2012)

There has been growing interest in mapping image data onto compact binary codes for fast near neighbor search in vision applications. Although binary codes are motivated by their use as direct indices (addresses) into a hash table, codes longer than 32 bits are not being used in this way, as it was thought to be ineffective. We introduce a rigorous way to build multiple hash tables on binary code substrings that enables exact K-nearest neighbor search in Hamming space. The algorithm is straightforward to implement, storage efficient, and it has sub-linear run-time behavior for uniformly distributed codes. Empirical results show dramatic speed-ups over a linear scan baseline and for datasets with up to one billion items, 64- or 128-bit codes, and search radii up to 25 bits.
An Essential Role for Ectodomain Shedding in Mammalian Development (1998)

The ectodomains of numerous proteins are released from cells by proteolysis to yield soluble intercellular regulators. The responsible protease, tumor necrosis factor-alpha converting enzyme (TACE), has been identified only in the case when tumor necrosis factor-alpha (TNFalpha) is released. Analyses of cells lacking this metalloproteinase-disintegrin revealed an expanded role for TACE in the processing of other cell surface proteins, including a TNF receptor, the L-selectin adhesion molecule, and transforming growth factor-alpha (TGFalpha). The phenotype of mice lacking TACE suggests an essential role for soluble TGFalpha in normal development and emphasizes the importance of protein ectodomain shedding in vivo.
Spectroscopic Properties of a Family of Mono‐ to Trinuclear Lanthanide Complexes (2017)

A series of mono‐, di‐, and trinuclear complexes of Eu and Tb was designed to study the influence of the number of Ln emitting centers on the luminescence properties of discrete polynuclear complexes. The complexes are based on a cyclen scaffold, functionalized by two picolinic acid pendant arms. These coordinating units are separated by a 1,3‐dimethylbenzene spacer for the dinuclear complex and a 1,3,5‐trimethylbenzene bridge in the case of the trinuclear complex. The synthesis and characterization of the ligands are presented, together with the preparation and spectroscopic characterization of the complexes. The luminescence properties of the complexes were determined by UV/Vis absorption spectroscopy and steady‐state and time‐resolved luminescence spectroscopy in buffered aqueous solutions. Comparison of the electronic absorption spectra showed that the absorption properties can almost be considered as extensive parameters within experimental error, as expected for electronically non‐conjugated systems. A small drop of both the excited state luminescence lifetimes and the luminescence quantum yields was observed for the trinuclear complexes in the case of Tb. To understand this behavior, theoretical HF (Hartree–Fock) calculations were performed for the three complexes. Models indicate that the average intermetallic distance in the dinuclear complex is almost the same as in the trinuclear one, disfavoring a possible distance dependence of the observed phenomena.
Apoptosis is rapidly triggered by antisense depletion of MCL-1 in differentiating U937 cells (2000)

Abstract Mcl-1 is a member of the Bcl-2 protein family, which has been shown to delay apoptosis in transfection and/or overexpression experiments. As yet no gene knockout mice have been engineered, and so there is little evidence to show that loss of Mcl-1 expression is sufficient to trigger apoptosis. U937 cells constitutively express the antiapoptotic protein Bcl-2; but during differentiation, in response to the phorbol ester PMA (phorbol 12 β-myristate 13 α-acetate), Mcl-1 is transiently induced. The purpose of this investigation was to determine the functional role played by Mcl-1 in this differentiation program. Mcl-1 expression was specifically disrupted by chimeric methylphosphonate/phosphodiester antisense oligodeoxynucleotides to just 5% of control levels. The depletion of Mcl-1 messenger RNA (mRNA) and protein was both rapid and specific, as indicated by the use of control oligodeoxynucleotides and analysis of the expression of otherBCL2 family members and PMA-induced tumor necrosis factor–α (TNF-α). Specific depletion of Mcl-1 mRNA and protein, in the absence of changes in cellular levels of Bcl-2, results in a rapid entry into apoptosis. Levels of the proapoptotic protein Bax remained unchanged during differentiation, while Bak expression doubled within 24 hours. Apoptosis was detected within 4 hours of Mcl-1 antisense treatment by a variety of parameters including a novel live cell imaging technique allowing correlation of antisense treatment and apoptosis in individual cells. The induction of Mcl-1 is required to prevent apoptosis during differentiation of U937 cells, and the constitutive expression of Bcl-2 is unable to compensate for the loss of Mcl-1.
Total Synthesis Guided Structure Elucidation of (+)‐Psychotetramine (2011)

Solving the puzzles: Total synthesis played a key role in the elucidation of the stereochemistry and verification of the constitution of the complex polymeric natural product psychotetramine. The route features three powerful assembly processes that enabled four rounds of total synthesis-guided structure determination. The pursuit of this alkaloid also led to an improved procedure for indole–aniline coupling and a highly efficient enantioselective synthesis of psychotrimine. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
MeCP2 and MBD2 expression in human neoplastic and non-neoplastic breast tissue and its association with oestrogen receptor status (2003)

This study analysed mRNA expression of two members of the methyl-CpG-binding protein family - MeCP2 and MBD2 - in human non-neoplastic (n=11) and neoplastic (n=57) breast tissue specimens using a quantitative real-time PCR method. We observed higher expression levels of MeCP2 mRNA in neoplastic tissues than in non-neoplastic tissues (P=0.001), whereas no significant differences for MBD2 were detected. When studying the relations between the most important clinicopathologic features of breast cancer and the mRNA expression level of both MBDs, we found that oestrogen receptor (OR)-positive breast cancer specimens contained higher levels of MeCP2 mRNA than did OR-negative cancers (P=0.005). Furthermore, we observed statistically significantly higher levels of MeCP2 in non-neoplastic tissues expressing high levels of OR as compared to those expressing low levels (P=0.017). Finally, using a linear regression model, we identified a statistically significant association between OR expression and MeCP2 mRNA expression in neoplastic and non-neoplastic breast tissue specimens (P=0.003). In conclusion, we were able to demonstrate for the first time that there exists a strong association between OR status and MeCP2 mRNA expression. Furthermore, we speculate that MeCP2, regulated by OR, plays a key role in the differentiation processes in human breast tissues.
An unusual presentation of renal cell carcinoma with deep vein thrombosis of the calf. (1996)

Renal cell carcinoma is a malignant tumour that involves the vena cava in 4% to 10% of patients undergoing radical nephrectomy. Of these only a third to half presented with symptoms of vena caval involvement. We present a case of renal cell carcinoma with vena caval involvement that presented with just a swollen right leg. The patient was staged and had a nephrectomy and resection of the inferior vena cava. Due to extensive collateral venous drainage renal function was not compromised and he was discharged well.
Inhibition of anaerobic glycolysis in Ehrlich ascites tumor cells by 2-deoxy-D-glucose. (1958)

This investigation was supported in part by American Cancer Society Institutional Grants and material was taken from part
 of Nirenberg's dissertation at the University of Michigan. The article reports on the process of anaerobic glycolysis
 in Ehrlich ascites tumors exposed to glucose.