gebhart/patrepeval huggingface dataset:
Detection of Staphylococcus aureus by polymerase chain reaction amplification of the nuc gene (1992)

Synthetic oligonucleotide primers of 21 and 24 bases, respectively, were used in the polymerase chain reaction (PCR) to amplify a sequence of the nuc gene, which encodes the thermostable nuclease of Staphylococcus aureus. A DNA fragment of approximately 270 bp was amplified from lysed S. aureus cells or isolated DNA. The PCR product was detected by agarose gel electrophoresis or Southern blot analysis by using a 33-mer internal nuc gene hybridization probe. With S. aureus cells the lower detection limit was less than 10 CFU, and with the isolated target the lower detection limit was 0.69 pg of DNA. The primers recognized 90 of 90 reference or clinical S. aureus strains. Amplification was not recorded when 80 strains representing 16 other staphylococcal species were tested or when 20 strains representing 9 different nonstaphylococcal species were tested. Some of the non-S. aureus staphylococci produced thermostable nucleases but were PCR negative. The PCR product was generated when in vitro-cultured S. aureus was used to prepare simulated clinical specimens of blood, urine, cerebrospinal fluid, or synovial fluid. No PCR product was generated when the sterile body fluids were tested. However, the sensitivity of the PCR was reduced when S. aureus in blood or urine was tested in comparison with that when bacteria in saline were tested. With the bacteria in blood, the detection limit of the PCR was 10(3) CFU. A positive PCR result was recorded when a limited number of clinical samples from wounds verified to be infected with S. aureus were tested, while the PCR product was not detected in materials from infections caused by other bacteria. Generation of PCR products was not affected by exposure of S. aureus to bactericidal agents, including cloxacillin and gentamicin, prior to testing, but was affected by exposure to UV radiation. The PCR for amplification of the nuc gene has potential for the rapid diagnosis of S. aureus infections by direct testing of clinical specimens, including specimens from patients with ongoing antimicrobial therapy.
Interfacial reactions between nickel thin films and GaN (1997)

Thin Ni films on GaN were annealed at temperatures between 400 and 900 °C in N2, Ar, and forming gas and were analyzed using glancing angle x-ray diffraction and Auger depth profiling. The first indication of an interfacial reaction was found after an anneal at 600 °C for 1 h, after which Ga was observed to be dissolved in the face-centered cubic Ni film. The extent of dissolution increased with continued annealing. After annealing at 750 °C for 1 hr in either N2 or Ar, greater intermixing occurred. The reaction product was either Ni3Ga or face-centered cubic Ni with dissolved Ga. Annealing at 900 °C resulted in the formation of the B2 phase NiGa. It was clear from Auger depth profiles that the reacted film contained significantly more Ga than N and that N2 gas was released to the annealing environment, even when the samples were annealed in N2 gas at 1 atm. Thus, a trend of increasing Ga content in the reacted films was observed with increasing temperature. The observed reactions are consistent with the thermodynamics of the Ni–Ga–N system.
A tutorial on computer-aided analysis of switched-capacitor circuits (1983)

In this paper, various formulation techniques for analyzing switched-capacitor circuits have been described and compared. Some basic pcoperties of the time-, z-, and frequency-domain solutions have been presented. Analysis techniques for handling nonideal op-amps, switch resistances, and noise and distortion effects are discussed. Methods for sensitivity analysis have been briefly mentioned and, finally, an overview of computer-aided analysis techniques has been given.
Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition. (1991)

Arginine-rich sequences are found in many RNA-binding proteins and have been proposed to mediate specific RNA recognition. Fragments of the HIV-1 Tat protein that contain the arginine-rich region of Tat bind specifically to a 3-nucleotide bulge in TAR RNA. To determine the amino acid requirements for specific RNA recognition, we synthesized a series of mutant Tat peptides spanning this domain (YGRKKRRQRRRP) and measured their affinity and specificity for TAR RNA. Several corresponding mutations were introduced into the full-length Tat protein, and trans-activation activity was measured. Systematic substitution of arginine residues with alanines or lysines suggested that overall charge density is important but did not point to any specific residues as being essential for binding. A glutamine-to-alanine substitution had no effect on binding. Remarkably, peptides with scrambled or reversed sequences showed the same affinity and specificity for TAR RNA as the wild-type peptide. Trans-activation activity of the mutant Tat proteins correlated with RNA binding. Arginine-rich peptides from SIV Tat and from HIV-1 Rev, which can functionally substitute for the basic region of HIV-1 Tat, also bound specifically to TAR. Circular dichroism spectra suggest that the arginine-rich region of Tat is unstructured in the absence of RNA, becomes partially or fully structured upon binding, and induces a conformational change in the RNA. These results suggest that arginine-rich RNA-binding domains have considerable sequence flexibility, reminiscent of acidic domains found in transcriptional activators, and that RNA structure may provide much of the specificity for the interaction.
A Promoter Haplotype of the Immunoreceptor Tyrosine-Based Inhibitory Motif-Bearing FcγRIIb Alters Receptor Expression and Associates with Autoimmunity. I. Regulatory FCGR2B Polymorphisms and Their Association with Systemic Lupus Erythematosus (2004)

FcgammaRIIb, the immunoreceptor tyrosine-based inhibitory motif-containing receptor for IgG (Mendelian Inheritance in Man no. 604590), plays an important role in maintaining the homeostasis of immune responses. We have identified 10 novel single-nucleotide polymorphisms in the promoter region of human FCGR2B gene and characterized two functionally distinct haplotypes in its proximal promoter. In luciferase reporter assays, the less frequent promoter haplotype leads to increased expression of the reporter gene in both B lymphoid and myeloid cell lines under constitutive and stimulated conditions. Four independent genome-wide scans support linkage of the human FcgammaR region to the systemic lupus erythematosus (SLE; Online Mendelian Inheritance in Man no. 152700) phenotype. Our case-control study in 600 Caucasians indicates a significant association of the less frequent FCGR2B promoter haplotype with the SLE phenotype (odds ratio = 1.65; p = 0.0054). The FCGR2B haplotype has no linkage disequilibrium with previously identified FCGR2A and FCGR3A polymorphisms, and after adjustment for FCGR2A and FCGR3A, FCGR2B showed a persistent association with SLE (odds ratio = 1.72; p = 0.0083). These results suggest that an expression variant of FCGR2B is a risk factor for human lupus and implicate FCGR2B in disease pathogenesis.
Long-term growth of malignant thymocytes in vitro (1989)

We report a new methodology for the long-term growth of malignant T- lymphoblasts from patients with T-cell acute lymphoblastic leukemia (T- ALL) and T-cell lymphoblastic lymphoma (T-LL). When malignant cells were cultured in the presence of insulin-like growth factor I under hypoxic conditions, cellular proliferation occurred that resulted in the establishment of immortal cell lines from ten of 12 patient tumors. Authenticity of each cell line was verified by a direct comparison of the immunophenotype, karyotype, and immunogenotype with the patient's tumor cells. This improved method of cell culture permits frequent establishment of cell lines from patients with T-ALL/T-LL, thereby aiding in analysis of thymocyte transformation and neoplasia.
Approaches using virtual environments with mosaic (1994)

This paper describes two ways to use a computer generated environment with Mosaic. Two approaches are taken. The first is to allow the user to interact with an environment displayed as part of the Mosaic document, an in-line image. The second is to create an independent process with which the user can have high bandwidth interaction, i.e. real time manipulations, which can drive Mosaic remotely. In the first case an in-line picture of a space can be “walked-through ” by allowing the user to select buttons which move the point-of-view of the user forward, backward, left or right. Each user selection causes a network request to the Mosaic server which renders a new scene and/or loads a new HTML page. This method has the advantage of being a pure Mosaic application and issues of portability are minimized, however at the cost of performance. Using the second method, creating an independent process, a user is allowed to interact with a graphical process running on the user’s workstation. At appropriate times in the interaction the user selects an object. Objects can have a URL associated which causes the Mosaic process to go to that URL using the remote control facility in the X version
Pharmacokinetic Studies with a Dual-Release Formulation of Levodopa, a Novel Principle in the Treatment of Parkinson’s Disease (1998)

The objectives of the two studies reported here were the investigation of the influence of tablet breaking and food on the pharmacokinetics of levodopa and 3-O-methyldopa (3-OMD) after administration of a new levodopa/benserazide formulation with a biphasic drug delivery profile (Madopar DR). Both studies had an open-label, randomised, two-way crossover design and were conducted in 12 healthy young subjects. The pharmacokinetics of levodopa and 3-OMD after one intact or two halved tablets were very similar with average Cmax and tmax 1.9 mg x l(-1) and 1.2 h, respectively. Administration of the formulation after a standard breakfast did not influence the extent of levodopa absorption but increased the absorption rate. Cmax and tmax were on average 2.1 mg x l(-1) and 1.3 h, respectively, in the fed condition and 1.5 mg x l(-1) and 2.5 h in the fasted condition. The presence of food did not markedly affect the plateau in levodopa levels between about 1 and 3 h after intake. In conclusion, the release characteristics in healthy subjects of the new levodopa/benserazide formulation are influenced only to a minor extent by concomitant intake of food or by tablet breaking.
TATA-binding Protein Residues Implicated in a Functional Interplay between Negative Cofactor NC2 (Dr1) and General Factors TFIIA and TFIIB (1995)

The TATA-binding protein (TBP) plays a key role in transcription initiation. Several negative cofactors (NC1, NC2, and Dr1) are known to interact with TBP in a manner that prevents productive interactions of transcription factors TFIIA and TFIIB with promoter-bound TBP. To gain insights into the regulatory interplay on the surface of TBP, we have employed mutant forms of TBP to identify amino acid residues important for interactions with the negative regulatory cofactor NC2 and the general factor TFIIB. The results show the involvement of distinct domains of TBP in these interactions. Residues (Lys-133, Lys-145, and Lys-151) in the basic repeat region are important for interactions with NC2, as well as with TFIIA (Buratowski, S., and Zhou, H. (1992) Science 255, 1130-1132; Lee, D. K., DeJong, J., Hashimoto, S., Horikoshi, M., and Roeder, R. G. (1992) Mol. Cell. Biol. 12, 5189-5196), whereas a residue (Leu-189) in the second stirrup-like loop spanning S2' and S3' is required for interaction with TFIIB. In addition, we demonstrate that NC2 is identical to the previously cloned negative cofactor Dr1. The implications of these results for TBP structure and function are discussed.
Multicenter Evaluation of a Candida albicans Peptide Nucleic Acid Fluorescent In Situ Hybridization Probe for Characterization of Yeast Isolates from Blood Cultures (2005)

We evaluated aliquots from 244 clinical blood culture bottles that demonstrated yeasts on Gram stain using a Candida albicans peptide nucleic acid (PNA) fluorescent in situ hybridization (FISH) probe. The sensitivity, specificity, positive predictive value, and negative predictive value of the C. albicans PNA FISH test in this study were 99%, 100%, 100%, and 99.3%, respectively.
Enhanced Fidelity of 3TC-Selected Mutant HIV-1 Reverse Transcriptase (1996)

Monotherapy with (-)2',3'-dideoxy-3'-thiacytidine (3TC) leads to the appearance of a drug-resistant variant of human immunodeficiency virus-type 1 (HIV-1) with the methionine-184 --> valine (M184V) substitution in the reverse transcriptase (RT). Despite resulting drug resistance, treatment for more than 48 weeks is associated with a lower plasma viral burden than that at baseline. Studies to investigate this apparent contradiction revealed the following. (i) Titers of HIV-neutralizing antibodies remained stable in 3TC-treated individuals in contrast to rapid declines in those treated with azidothymidine (AZT). (ii) Unlike wild-type HIV, growth of M184V HIV in cell culture in the presence of d4T, AZT, Nevirapine, Delavirdine, or Saquinavir did not select for variants displaying drug resistance. (iii) There was an increase in fidelity of nucleotide insertion by the M184V mutant compared with wild-type enzyme.
Pharmacological antagonism of the actions of group II and III mGluR agonists in the lateral perforant path of rat hippocampal slices (1996)

1. An understanding of the physiological and pathological roles of metabotropic glutamate receptors (mGluRs) is currently hampered by the lack of selective antagonists. Standard extracellular recording techniques were used to investigate the activity of recently reported mGluR antagonists on agonist-induced depressions of synaptic transmission in the lateral perforant path of hippocampal slices obtained from 12-16 day-old rats. 2. The group III specific mGluR agonist, (S)-2-amino-4-phosphonobutanoate (L-AP4) depressed basal synaptic transmission in a reversible and dose-dependent manner. The mean (+/-s.e. mean) depression obtained with 100 microM L-AP4 (the maximum concentration tested) was 74 +/- 3% and the IC50 value was 3 +/- 1 microM (n = 5). 3. The selective group II mGluR agonists, (1S,3S)-1-aminocyclopentane-1, 3-dicarboxylate ((1S,3s)-ACPD) and (2S, 1'R, 2'R, 3'R)-2-(2',3'-dicarboxycyclopropyl)glycine (DCG-IV) also depressed basal synaptic transmission in a reversible and dose-dependent manner. The mean depression obtained with 200 microM (1S,3S)-ACPD was 83 +/- 8% and the IC50 value was 12 +/- 3 microM (n = 5). The mean depression obtained with 1 microM DCG-IV was 73 +/- 7% and the IC50 value was 88 +/- 15 nM (n = 4). 4. Synaptic depressions induced by the actions of 20 microM (1S,3S)-ACPD and 10 microM L-AP4 were antagonized by the mGluR antagonists (+)-alpha-methyl-4-carboxyphenylglycine ((+)-MCPG), (S)-2-methyl-2-amino-4-phosphonobutanoate (MAP4), (2S,1'S,2'S)-2-methyl-2(2'-carboxycyclopropyl)glycine (MCCG), (RS)-alpha-methyl-4-tetrazolylphenylglycine (MTPG), (RS)-alpha-methyl-4-sulphonophenylglycine (MSPG) and (RS)-alpha-methyl-4-phosphonophenylglycine (MPPG) (all tested at 500 microM). 5. (+)-MCPG was a weak antagonist of both L-AP4 and (1S,3S)-ACPD-induced depressions. MCCG was selective towards (1S,3S)-ACPD, but analysis of its effects were complicated by apparent partial agonist activity. MAP4 showed good selectivity for L-AP4-induced effects. 6. The most effective antagonist tested against 10 microM L-AP4 was MPPG (mean reversal 90 +/- 3%; n = 4). In contrast, the most effective antagonist tested against 20 microM (1S,3S)-ACPD induced depressions was MTPG (mean reversal 64 +/- 4%; n = 4). Both antagonists produced parallel shifts in agonist dose-response curves. Schild analysis yielded estimated KD values of 11.7 microM and 27.5 microM, respectively. Neither antagonist had any effect on basal transmission or on depressions induced by the adenosine receptor agonist, 2-chloroadenosine (500 nM; n = 3). 7. We conclude that both group II and group III mGluRs can mediate synaptic depressions induced by mGluR agonists in the lateral perforant path. The mGlur antagonists MTPG, MPPG and MAP4 should be useful in determining the roles of group II and III mGluRs in the central nervous system.
Human adipose tissue‐derived mesenchymal stromal cells as salvage therapy for treatment of severe refractory acute graft‐vs.‐host disease in two children (2007)

Severe GVHD is a lethal complication to ASCT, and a number of approaches are therefore being evaluated. Recently, Le Blanc et al. reported a case of grade IV therapy-resistant acute GVHD of the gut and liver that showed rapid improvement after infusion of mesenchymal stem cells. Here we describe two pediatric patients who developed severe refractory acute GVHD following ASCT and were successfully treated with AMSC from HLA-mismatched unrelated donors.
<title>Extracting multidimensional signal features for content-based visual query</title> (1995)

Future large visual information systems (such as image databases and video servers) require effective and efficient methods for indexing, accessing, and manipulating images based on visual content. This paper focuses on automatic extraction of low-level visual features such as texture, color, and shape. Continuing our prior work in compressed video manipulation, we also propose to explore the possibility of deriving visual features directly from the compressed domain, such as the DCT and wavelet transform domain. By stressing at the low-level features, we hope to achieve generic techniques applicable to general applications. By exploring the compressed-domain content extractability, we hope to reduce the computational complexity. We also propose a quad-tree based data structure to bind various signal features. Integrated feature maps are proposed to improve the overall effectiveness of the feature-based image query system. Current technical progress and system prototypes are also described. Part of the prototype work has been integrated into the Multimedia/VOD testbed in the Advanced Image Lab of Columbia University.
The Metabolism of Cyclohexanol by Acinetobacter NCIB 9871 (1975)

Acinetobacter NCIB 9871 was isolated by elective culture on cyclohexanol and grows with this compound as sole source of carbon. It displays a restricted growth spectrum, being unable to grow on a wide range of alternative alicyclic alcohols and ketones. Cyclohexanol‐grown cells oxidize the growth substrate at a rate of 230 μl of O 2 /h per mg dry wt with the consumption of 5.65 μmot of O 2 /μmol substrate. Cyclohexanone is oxidized at a similar rate with the consumption of 4.85 μmol of O 2 /μmol. 1 ‐Oxa‐2‐oxocycloheptane and 6‐hydroxyhexanoate are both oxidized at the same slow rate of 44 μl of O 2 /h per mg dry wt and adipate is not oxidized. Studies with cell extracts reveal the presence of inducible dehydrogenases for cyclohexanol, 6‐hydroxyhexanoate and 6‐oxohexanoate and a monooxygenase, that in conjunction with a lactonase converts cyclohexanone to 6‐hydroxyhexanoate. The monooxygenase is therefore presumed to be of the lactone‐forming type and the pathway for conversion of cyclohexanol to adipate; cyclohexanol → cyclohexanone → 1‐oxa‐2‐oxocycloheptane → 6‐hydroxyhexanoate → 6‐oxohexanoate → adipate; for which key intermediates have been identified chromatographically, is identical with the route for the oxidation of cyclohexanol by Nocardia globerula CL1.
DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization (2015)

The circadian transcriptional repressors cryptochrome 1 (Cry1) and 2 (Cry2) evolved from photolyases, bacterial light-activated DNA repair enzymes. In this study, we report that while they have lost DNA repair activity, Cry1/2 adapted to protect genomic integrity by responding to DNA damage through posttranslational modification and coordinating the downstream transcriptional response. We demonstrate that genotoxic stress stimulates Cry1 phosphorylation and its deubiquitination by Herpes virus associated ubiquitin-specific protease (Hausp, a.k.a Usp7), stabilizing Cry1 and shifting circadian clock time. DNA damage also increases Cry2 interaction with Fbxl3, destabilizing Cry2. Thus, genotoxic stress increases the Cry1/Cry2 ratio, suggesting distinct functions for Cry1 and Cry2 following DNA damage. Indeed, the transcriptional response to genotoxic stress is enhanced in Cry1-/- and blunted in Cry2-/- cells. Furthermore, Cry2-/- cells accumulate damaged DNA. These results suggest that Cry1 and Cry2, which evolved from DNA repair enzymes, protect genomic integrity via coordinated transcriptional regulation.
Gerstmann‐Sträussler‐Scheinker disease: Immunohistological and experimental studies (1988)

The older brother of the patient from whom the Fukuoka-1 strain was isolated was found to have numerous kuru plaques, the main finding common to both siblings. Other clinicopathological features including spongiform change were absent in the older brother. Immunostaining using anti-kuru plaque core protein and anti-beta-protein peptide revealed many kuru plaques and a few senile plaques in the older brother. Experimental transmission of the disease to laboratory animals was successful, using tissues from both siblings, through inoculation of fresh brain homogenates, purified prion protein, and formalin-fixed brain homogenates. Prion protein fractions from the patient's brain shortened the incubation periods and formalin-fixed mouse brains did not lengthen the periods. The disease in the two brothers can be classified as Gerstmann-Sträussler-Scheinker disease, a familial variant of Creutzfeldt-Jakob disease. Gerstmann-Sträussler-Scheinker disease manifests a variety of clinicopathological features. Immunohistological verification of kuru plaques has major diagnostic value in assessing dementia.
Monoclonal Antibodies in Chronic Lymphocytic Leukemia (2000)

For decades, alkylating agents have been the mainstay of treatment of chronic lymphocytic leukemia CLL), achieving a modest response. Recently, fludarabine has been shown to induce higher and long‐lasting responses, and has, in many institutions, replaced the alkylating agents as the first‐line agent in the treatment of CLL. However, the goal of achieving higher complete responses that might translate into an improved overall survival in CLL still remains elusive. Antibody‐mediated therapy has emerged as an effective modality in the treatment of low‐grade B‐cell malignancies. Monoclonal antibodies McAb) against specific lymphocyte markers, including CD52 Campath‐1H) and CD20 rituximab), are currently being actively studied in the treatment of CLL. Initial results with Campath‐1H and rituximab in previously treated and untreated patients with CLL have been promising. We present a review of the current status of McAb and their potential role in the future for the treatment of CLL.