gebhart/patrepeval huggingface dataset:
Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface. (1996)

Barnase and barstar are trivial names of the extracellular RNase and its intracellular inhibitor produced by Bacillus amyloliquefaciens. Inhibition involves the formation of a very tight one-to-one complex of the two proteins. With the crystallographic solution of the structure of the barnase-barstar complex and the development of methods for measuring the free energy of binding, the pair can be used to study protein-protein recognition in detail. In this report, we describe the isolation of suppressor mutations in barstar that compensate for the loss in interaction energy caused by a mutation in barnase. Our suppressor search is based on in vivo selection for barstar variants that are able to protect host cells against the RNAse activity of those barnase mutants not properly inhibited by wild-type barstar. This approach utilizes a plasmid system in which barnase expression is tightly controlled to keep the mutant barnase gene silent. When expression of barnase is turned on, failure to form a complex between the mutant barnase and barstar has a lethal effect on host cells unless overcome by substitution of the wild-type barstar by a functional suppressor derivative. A set of barstar suppressors has been identified for barnase mutants with substitutions in two amino acid positions (residues 102 and 59), which are critically involved in both RNase activity and barstar binding. The mutations selected as suppressors could not have been predicted on the basis of the known protein structures. The single barstar mutation with the highest information content for inhibition of barnase (H102K) has the substitution Y30W. The reduction in binding caused by the R59E mutation in barnase can be partly reversed by changing Glu-76 of barstar, which forms a salt bridge with the Arg-59 in the wild-type complex, to arginine, thus completing an interchange of the two charges.
REPAIR OF CRANIOTOMY DEFECTS USING BONE MARROW STROMAL CELLS (1998)

These studies demonstrate that mitotically expanded bone marrow cells can serve as an abundant source of osteoprogenitor cells that are capable of repairing craniofacial skeletal defects in mice without the addition of growth or morphogenetic factors.
Biosynthesis of xyloglucan in suspension-cultured soybean cells. Occurrence and some properties of xyloglucan 4-beta-D-glucosyltransferase and 6-alpha-D-xylosyltransferase. (1981)

A particulate enzyme fraction that catalyzes the transfer of glucose from UDP-[14C]glucose and of xylose from UDP-[14C]xylose into a xyloglucan has been isolated from suspension-cultured soybean cells. The incorporation of radioactivity from [14C]xylose into the polysaccharide was dependent on the presence of UDP-glucose in the incubation mixture, and that from [14C]glucose was dependent on the concentration of UDP-xylose in the mixture. Mn2+ was required for the incorporation of xylose and the optimum concentration of Mn2+ was about 10 mM. This reaction showed a pH optimum at 6.5 to 7.0 in 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer and was inhibited by phosphate buffer and Tris buffer. On hydrolysis with Trichoderma endoglucanase, the polysaccharide synthesized in vitro gave a pentasaccharide, a hepatasaccharide, and a small amount of non-asaccharide. Based on the results from fragmentation and methylation analyses, the following structures were proposed for the penta- and the heptasaccharides from the xyloglucan synthesized in vitro: (formula, see text).
Purification of the mRNAs for Ewe αs‐Casein and β‐Casein by Immunoprecipitation of Polysomes (1976)

Specific polysomes synthesizing alphas-casein and beta-casein were immunoprecipitated from total polysomes of the lactating ewe mammary gland. The polysome - anti-casein complex was immunoprecipitated by anti-immunoglobulins. 22%, 32% and 10% of polysomes were immunoprecipitated with saturating amounts of anti-alphas-casein, anti-beta-casein and anti-chi-casein respectively. Poly(U)-Sepharose chromatography of the immunoprecipitated RNAs permitted the isolation of the corresponding poly(A)-containing RNA which migrated as one major band in polyacrylamide gel electrophoresis. As judged by the contamination with the messenger activity for one of the other caseins, the purity of the mRNA for alphas-casein as well as for beta-casein was estimated to be between 75% and 80%.
Mutant Huntingtin Expression in Clonal Striatal Cells: Dissociation of Inclusion Formation and Neuronal Survival by Caspase Inhibition (1999)

Neuronal intranuclear inclusions are found in the brains of patients with Huntington's disease and form from the polyglutamine-expanded N-terminal region of mutant huntingtin. To explore the properties of inclusions and their involvement in cell death, mouse clonal striatal cells were transiently transfected with truncated and full-length human wild-type and mutant huntingtin cDNAs. Both normal and mutant proteins localized in the cytoplasm, and infrequently, in dispersed and perinuclear vacuoles. Only mutant huntingtin formed nuclear and cytoplasmic inclusions, which increased with polyglutamine expansion and with time after transfection. Nuclear inclusions contained primarily cleaved N-terminal products, whereas cytoplasmic inclusions contained cleaved and larger intact proteins. Cells with wild-type or mutant protein had distinct apoptotic features (membrane blebbing, shrinkage, cellular fragmentation), but those with mutant huntingtin generated the most cell fragments (apoptotic bodies). The caspase inhibitor Z-VAD-FMK significantly increased cell survival but did not diminish nuclear and cytoplasmic inclusions. In contrast, Z-DEVD-FMK significantly reduced nuclear and cytoplasmic inclusions but did not increase survival. A series of N-terminal products was formed from truncated normal and mutant proteins and from full-length mutant huntingtin but not from full-length wild-type huntingtin. One prominent N-terminal product was blocked by Z-VAD-FMK. In summary, the formation of inclusions in clonal striatal cells corresponds to that seen in the HD brain and is separable from events that regulate cell death. N-terminal cleavage may be linked to mutant huntingtin's role in cell death.
Defining the Epithelial Stem Cell Niche in Skin (2003)

Many adult regenerative cells divide infrequently but have high proliferative capacity. We developed a strategy to fluorescently label slow-cycling cells in a cell type-specific fashion. We used this method to purify the label-retaining cells (LRCs) that mark the skin stem cell (SC) niche. We found that these cells rarely divide within their niche but change properties abruptly when stimulated to exit. We determined their transcriptional profile, which, when compared to progeny and other SCs, defines the niche. Many of the >100 messenger RNAs preferentially expressed in the niche encode surface receptors and secreted proteins, enabling LRCs to signal and respond to their environment.
Approximate Nearest Neighbors: Towards Removing the Curse of Dimensionality (1998)

The nearest neighbor problem is the following: Given a set of n points P = fp1�:::�p ng in some metric space X, preprocess P so as to e ciently answer queries which require nding the point inP closest to a query point q 2 X. We focus on the particularly interesting case of the d-dimensional Euclidean space where X = &amp;lt; d under some l p norm. Despite decades of e ort, the current solutions are far from satisfactory � in fact, for large d, in theory or in practice, they provide little improvement over the brute-force algorithm which compares the query point to each data point. Of late, there has been some interest in the approximate nearest neighbors problem, which is: Find a point p 2 P that is an-approximate nearest neighbor of the query q in that for all p 0 2 P, d(p � q) (1 +)d(p 0 �q). We present two algorithmic results for the approximate version that signi cantly improvethe known bounds: (a) preprocessing cost polynomial in n and d, and a truly sublinear query time� and, (b) query time polynomial in log n and d, and only a mildly exponential preprocessing cost ~O(n) O(1 = ) d.Further, applying a classical geometric lemma on random projections (for which we give a simpler proof), we obtain the rst known algorithm with polynomial preprocessing and query time polynomial in d and log n. Unfortunately, for small, the latter is a purely theoretical result since the exponent depends on 1 =. Experimental results indicate that our rst algorithm o ers orders of magnitude improvement on running times over real data sets. Its key ingredient is the notion of locality-sensitive hashing which maybeofindependentinterest� here, we give applications to information retrieval, pattern recognition, dynamic closest-pairs, and fast clustering algorithms.
Novel Nitride Devices Based on Polarization Fields (2000)

A key property of the nitrides is the fact that they possess large spontaneous and piezoelectric polarization fields that allow a significant tailoring of the carrier dynamics and optical properties of nitride devices. In this paper, based on first-principles calculations of structural and electronic properties of bulk nitrides and their heterostructure, we investigate the potential of this novel material class for modern device applications by performing self-consistent Monte Carlo simulations. We demonstrate that the internal electric fields have a significant and favorable influence on the transistor characteristics.
A lambda 3' enhancer drives active and untemplated somatic hypermutation of a lambda 1 transgene. (1998)

Somatic hypermutation is a highly regulated process that targets mutations to the rearranged Ig genes. Little is known about the cis-elements required for somatic hypermutation of the lambda light chain gene. We have studied somatic hypermutation of a rearranged lambda 1 transgene under the control of either a lambda 2-4 or kappa 3' enhancer. The mutations in the transgenes were analyzed by sequencing DNA amplified from hypermutating Peyer's patch B cells. The results indicate that the lambda 3' enhancer can drive active hypermutation of a lambda 1 transgene in Peyer's patch cells. The lambda 1 transgene under analysis carried two marked V lambda 2 genes immediately upstream that could serve as sequence donors in possible gene conversion events. There was no evidence of sequence transfer to the hypermutated lambda 1 gene, suggesting that gene conversion is not a major mechanism for somatic hypermutation in mice.
Rapid identification of Candida species in blood cultures by a clinically useful PCR method (1997)

Widespread use of fluconazole for the prophylaxis and treatment of candidiasis has led to a reduction in the number of cases of candidemia caused by Candida albicans but has also resulted in the emergence of candidemias caused by innately fluconazole-resistant, non-C. albicans Candida species. Given the fulminant and rapidly fatal outcome of acute disseminated candidiasis, rapid identification of newly emerging Candida species in blood culture is critical for the implementation of appropriately targeted antifungal drug therapy. Therefore, we used a PCR-based assay to rapidly identify Candida species from positive blood culture bottles. This assay used fungus-specific, universal primers for DNA amplification and species-specific probes to identify C. albicans, C. krusei, C. parapsilosis, C. tropicalis, or C. glabrata amplicons. It also used a simpler and more rapid (1.5-h) sample preparation technique than those described previously and used detergent, heat, and mechanical breakage to recover Candida species DNA from blood cultures. A simple and rapid (3.5-h) enzyme immunosorbent assay (EIA)-based format was then used for amplicon detection. One hundred fifty blood culture bottles, including 73 positive blood culture bottle sets (aerobic and anaerobic) from 31 patients with candidemia, were tested. The combined PCR and EIA methods (PCR-EIA) correctly identified all Candida species in 73 blood culture bottle sets, including bottles containing bacteria coisolated with yeasts and 3 cultures of samples from patients with mixed candidemias originally identified as single-species infections by routine phenotypic identification methods. Species identification time was reduced from a mean of 3.5 days by routine phenotypic methods to 7 h by the PCR-EIA method. No false-positive results were obtained for patients with bacteremias (n = 18), artificially produced non-Candida fungemias (n = 3), or bottles with no growth (n = 20). Analytical sensitivity was 1 cell per 2-microl sample. This method is simpler and more rapid than previously described molecular identification methods, can identify all five of the most medically important Candida species, and has the potential to be automated for use in the clinical microbiology laboratory.
Interneuronal Transfer and Distal Action of Tetanus Toxin and Botulinum Neurotoxins A and D in Central Neurons (2016)

Recent reports suggest that botulinum neurotoxin (BoNT) A, which is widely used clinically to inhibit neurotransmission, can spread within networks of neurons to have distal effects, but this remains controversial. Moreover, it is not known whether other members of this toxin family are transferred between neurons. Here, we investigate the potential distal effects of BoNT/A, BoNT/D, and tetanus toxin (TeNT), using central neurons grown in microfluidic devices. Toxins acted upon the neurons that mediated initial entry, but all three toxins were also taken up, via an alternative pathway, into non-acidified organelles that mediated retrograde transport to the somato-dendritic compartment. Toxins were then released into the media, where they entered and exerted their effects upon upstream neurons. These findings directly demonstrate that these agents undergo transcytosis and interneuronal transfer in an active form, resulting in long-distance effects.
The pharmacological bases of the antiangiogenic activity of paclitaxel (2013)

In the mid 1990s, researchers began to investigate the antiangiogenic activity of paclitaxel as a possible additional mechanism contributing to its antineoplastic activity in vivo. In the last decade, a number of studies showed that paclitaxel has antiangiogenic activity that could be ascribed to the inhibition of either tubule formation or cell migration, and to an antiproliferative effect towards activated endothelial cells. Furthermore, paclitaxel was shown to downregulate VEGF and Ang-1 expression in tumor cells, and to increase the secretion of TSP-1 in the tumor microenvironment. Moreover, the new pharmaceutical formulations of paclitaxel (such as liposome-encapsulated paclitaxel, ABI-007, and paclitaxel entrapped in emulsifying wax nanoparticles) enhanced the in vivo antiangiogenic activity of the drug. Thus, the preclinical data of paclitaxel may be exploited to implement a novel and rational therapeutic strategy to control tumor progression in patients.
Silencing of the thrombomodulin gene in human malignant melanoma (2005)

The loss of thrombomodulin (TM) expression is associated with tumour growth, infiltration and lymph node metastasis in human tumours. In melanoma cell lines, TM is reported to mediate cell adhesion, and its introduction into TM-negative melanoma cell lines suppresses their growth. In this study, we analysed TM expression in surgical melanoma specimens and the role of its promoter methylation in the loss of its expression. In 15 (75%) of the 20 specimens (five from a primary site and 15 from metastatic sites), melanoma cells lacked TM immunoreactivity. Methylation of the TM promoter region was detected in 10 (67%) of the 15 TM-negative specimens by methylation-specific polymerase chain reaction, whereas methylation was detected in two (40%) of the five TM-positive specimens. In cell lines, complete methylation of the TM promoter CpG island was detected in six (46%) of 13 melanoma cell lines, whereas no methylation was detected in two cultured normal melanocytes. There was a good correlation between the methylated status of the CpG island and the loss of TM messenger RNA (mRNA) expression. Treatment of melanoma cell lines with a demethylating agent, 5-aza-2'-deoxycytidine, induced demethylation of the promoter CpG island and the restoration of mRNA and protein expression. These findings suggest that most human melanomas lack TM expression, and that methylation of the promoter CpG island is one of the mechanisms responsible.
Generation of embryos directly from embryonic stem cells by tetraploid embryo complementation reveals a role for GATA factors in organogenesis (2005)

Gene targeting in ES (embryonic stem) cells has been used extensively to study the role of proteins during embryonic development. In the traditional procedure, this requires the generation of chimaeric mice by introducing ES cells into blastocysts and allowing them to develop to term. Once chimaeric mice are produced, they are bred into a recipient mouse strain to establish germline transmission of the allele of interest. Although this approach has been used very successfully, the breeding cycles involved are time consuming. In addition, genes that are essential for organogenesis often have roles in the formation of extra-embryonic tissues that are essential for early stages of post-implantation development. For example, mice lacking the GATA transcription factors, GATA4 or GATA6, arrest during gastrulation due to an essential role for these factors in differentiation of extra-embryonic endoderm. This lethality has frustrated the study of these factors during the development of organs such as the liver and heart. Extraembryonic defects can, however, be circumvented by generating clonal mouse embryos directly from ES cells by tetraploid complementation. Here, we describe the usefulness and efficacy of this approach using GATA factors as an example.
A New Method for Measuring Daytime Sleepiness: The Epworth Sleepiness Scale (1991)

The development and use of a new scale, the Epworth sleepiness scale (ESS), is described. This is a simple, self-administered questionnaire which is shown to provide a measurement of the subject's general level of daytime sleepiness. One hundred and eighty adults answered the ESS, including 30 normal men and women as controls and 150 patients with a range of sleep disorders. They rated the chances that they would doze off or fall asleep when in eight different situations commonly encountered in daily life. Total ESS scores significantly distinguished normal subjects from patients in various diagnostic groups including obstructive sleep apnea syndrome, narcolepsy and idiopathic hypersomnia. ESS scores were significantly correlated with sleep latency measured during the multiple sleep latency test and during overnight polysomnography. In patients with obstructive sleep apnea syndrome ESS scores were significantly correlated with the respiratory disturbance index and the minimum SaO2 recorded overnight. ESS scores of patients who simply snored did not differ from controls.
The structure and substrate specificity of human Cdk12/Cyclin K (2014)

Phosphorylation of the RNA polymerase II C-terminal domain (CTD) by cyclin-dependent kinases is important for productive transcription. Here we determine the crystal structure of Cdk12/CycK and analyse its requirements for substrate recognition. Active Cdk12/CycK is arranged in an open conformation similar to that of Cdk9/CycT but different from those of cell cycle kinases. Cdk12 contains a C-terminal extension that folds onto the N- and C-terminal lobes thereby contacting the ATP ribose. The interaction is mediated by an HE motif followed by a polybasic cluster that is conserved in transcriptional CDKs. Cdk12/CycK showed the highest activity on a CTD substrate prephosphorylated at position Ser7, whereas the common Lys7 substitution was not recognized. Flavopiridol is most potent towards Cdk12 but was still 10-fold more potent towards Cdk9. T-loop phosphorylation of Cdk12 required coexpression with a Cdk-activating kinase. These results suggest the regulation of Pol II elongation by a relay of transcriptionally active CTD kinases.
The Effect of Lactose Derivatives on Intestinal Lactic Acid Bacteria (1999)

Nine strains of lactic acid bacteria were studied for growth and fermentation end products on lactulose, lactitol, and lactobionic acid. In addition, human fecal and biopsy isolates were screened for new potential by probiotic strains utilizing lactose derivatives, and one new isolate of Lactobacillus rhamnosus was enriched. The utilization of lactose derivatives and the effect on the fermentation end products were dependent on strain. Typical mixed-acid fermentations were observed with Lb. rhamnosus and Lactococcus lactis. Microbiota enriched from fecal and biopsy samples using modified MRS medium consisted mainly of enterococci and streptococci. The adhesion of tested strains to Caco-2 cells was not dependent on carbon source. The new Lb. rhamnosus strain VTT E-97800 has potential for further probiotic studies.
A tree algorithm for nearest neighbor searching in document retrieval systems (1978)

The problem of finding nearest neighbors to a query in a document collection is a special case of associative retrieval, in which searches are performed using more than one key. A nearest neighbors associative retrieval algorithm, suitable for document retrieval using similarity matching, is described. The basic structure used is a binary tree, at each node a set of keys (concepts) is tested to select the most promising branch. Backtracking to initially rejected branches is allowed and often necessary. Under certain conditions, the search time required by this algorithm is 0(log 2 N) k . N is the number of documents, and k is a system-dependent parameter. A series of experiments with a small collection confirm the predictions made using the analytic model; k is approximately 4 in this situation. This algorithm is compared with two other searching algorithms; sequential search and clustered search. For large collections, the average search time for this algorithm is less than that for a sequential search and greater than that for a clustered search. However, the clustered search, unlike the sequential search and this algorithm, does not guarantee that the near neighbors found are actually the nearest neighbors.
The Clinical Opiate Withdrawal Scale (COWS) (2003)

The clinical opiate withdrawal scale (COWS) is a clinician-administered, pen and paper instrument that rates eleven common opiate withdrawal signs or symptoms. The summed score of the eleven items can be used to assess a patient's level of opiate withdrawal and to make inferences about their level of physical dependence on opioids. With increasing use of opioids for treatment of pain and the availability of sublingual buprenorphine in the United States for treatment of opioid dependence, clinical assessment of opiate withdrawal intensity has received renewed interest. Buprenorphine, a partial opiate agonist at the mu receptor, can precipitate opiate withdrawal in patients with a high level of opioid dependence who are not experiencing opioid withdrawal. Since development of the first opiate withdrawal scale in the mid-1930s, many different opioid withdrawal scales have been used in clinical and research settings. This article reviews the history of opiate withdrawal scales and the context of their initial use. A template version of the COWS that can be copied and used clinically is appended. PDF formatted versions of the COWS are also available from the websites of the American Society of Addiction Medicine, the California Society of Addiction Medicine, the UCLA Integrated Substance Abuse Programs, and AlcoholMD.com.