gebhart/patrepeval huggingface dataset:
Comparative Study on Programmable Robots as Programming Educational Tools (2015)

Computational Thinking skills are basic and important to manipulate computers. Currently, several systems exist to provide an effective way to learn programming that use computers, smartphones, tablets, or programmable robots. Although studies have reported improved programming skills and motivation to learn programming using an on-screen application
CTCF-dependent enhancer blockers at the upstream region of the chicken -globin gene domain (2004)

The eukaryotic genome is partitioned into chromatin domains containing coding and intergenic regions. Insulators have been suggested to play a role in establishing and maintaining chromatin domains. Here we describe the identification and characterization of two separable enhancer blocking elements located in the 5' flanking region of the chicken alpha-globin domain, 11-16 kb upstream of the embryonic alpha-type pi gene in a DNA fragment harboring a MAR (matrix attachment region) element and three DNase I hypersensitive sites (HSs). The most upstream enhancer blocking element co-localizes with the MAR element and an erythroid-specific HS. The second enhancer blocking element roughly co-localizes with a constitutive HS. The third erythroid-specific HS present within the DNA fragment studied harbors a silencing, but not an enhancer blocking, activity. The 11 zinc-finger CCCTC-binding factor (CTCF), which plays an essential role in enhancer blocking activity in many previously characterized vertebrate insulators, is found to bind the two alpha-globin enhancer blocking elements. Detailed analysis has demonstrated that mutation of the CTCF binding site within the most upstream enhancer blocking element abolishes the enhancer blocking activity. The results are discussed with respect to special features of the tissue-specific alpha-globin gene domain located in a permanently open chromatin area.
Targeting multiple opioid receptors – improved analgesics with reduced side effects? (2017)

This article is part of a themed section on Emerging Areas of Opioid Pharmacology. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.14/issuetoc.
Krüppel-like Factor 4 Is Acetylated by p300 and Regulates Gene Transcription via Modulation of Histone Acetylation (2007)

Colon cancer is the second leading cause of cancer death in the United States. Krüppel-like factor 4 (KLF4) is a transcription factor involved in both proliferation and differentiation in the colon. It is down-regulated in both mouse and human colonic adenomas and has been implicated as a tumor suppressor in the gut, whereas in breast cancer, KLF4 is an oncogene. KLF4 is also involved in reprogramming differentiated cells into pluripotent stem cells. KLF4 can act as a transcriptional activator or repressor, but the underlying mechanisms are poorly understood. We found that p300, a CREB-binding protein-related protein, interacts with KLF4 both in vitro and in vivo and activates transcription. We further made the novel observation that endogenous KLF4 is acetylated by p300/CBP in vivo and that mutations of the acetylated lysines resulted in a decreased ability of KLF4 to activate target genes, suggesting that acetylation is important for KLF4-mediated transactivation. Furthermore, we found that KLF4 differentially modulates histone H4 acetylation at the promoters of target genes. Co-transfection of KLF4 and HDAC3 resulted in a synergistic repression of a cyclin B(1) reporter construct. Our results suggest that KLF4 might function as an activator or repressor of transcription depending on whether it interacts with co-activators such as p300 and CREB-binding protein or co-repressors such as HDAC3.
The Enantioselective Synthesis of Conformationally Constrained Cyclic &#946;- Amino Acids (2005)

Enantiomerically pure and conformationally constrained cyclic β-amino acids have been the subject of a vast amount of research across the chemical, biological, and medicinal disciplines. These valuable molecules are synthetic precursors for a wide variety of useful compounds that include natural products and modified peptides. Many methods have been developed to prepare chiral cyclic β-amino acids in high optical purity. This mini-review will discuss some of the most recent and successful approaches.
Multiple 3' ends of mRNA encoding vaccinia virus growth factor occur within a series of repeated sequences downstream of T clusters (1986)

Analysis of the 5' ends of six apparently full-length cloned cDNA copies of the vaccinia virus growth factor gene suggested precise transcriptional initiation at the first purine following a run of five pyrimidines in the noncoding strand. By contrast, the 3' ends exhibited heterogeneity and were distributed over a 46-base-pair region. In each of the six cDNAs, the nucleotide immediately preceding the retained copy of the poly(A) tail corresponded to the first or second T of a TATGT repeat. Clusters of Ts occurred upstream of the 3' ends, but the AATAAA polyadenylation consensus sequence of higher eucaryotes was absent. Determination of the complete sequence of one cDNA revealed exact correspondence with the vaccinia virus growth factor gene, indicating the absence of internal RNA processing.
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans (2010)

Bloodstream infection by highly antibiotic-resistant bacteria, such as vancomycin-resistant Enterococcus (VRE), is a growing clinical problem that increasingly defies medical intervention. Identifying patients at high risk for bacterial sepsis remains an important clinical challenge. Recent studies have shown that antibiotics can alter microbial diversity in the intestine. Here, we characterized these effects using 16s rDNA pyrosequencing and demonstrated that antibiotic treatment of mice enabled exogenously administered VRE to efficiently and nearly completely displace the normal microbiota of the small and large intestine. In the clinical setting, we found that intestinal domination by VRE preceded bloodstream infection in patients undergoing allogeneic hematopoietic stem cell transplantation. Our results demonstrate that antibiotics perturb the normal commensal microbiota and set the stage for intestinal domination by bacteria associated with hospital-acquired infections. Thus, high-throughput DNA sequencing of the intestinal microbiota could identify patients at high risk of developing bacterial sepsis.
Glycogen synthase kinase-3 in insulin and Wnt signalling: a double-edged sword? (2004)

Glycogen synthase kinase-3 is an unusual protein serine/threonine kinase that, unlike most of its 500-odd relatives in the genome, is active under resting conditions and is inactivated upon cell stimulation. The two mammalian isoforms, GSK-3alpha and beta, play largely overlapping roles and have been implicated in a variety of human pathologies, including Type II diabetes, Alzheimer's disease, bipolar disorder and cancer. Recently, the modes of regulation of this enzyme have been elucidated through a combination of structural and cell biological studies. A series of relatively selective small molecules have facilitated chemical manipulation of the enzyme in intact cells and tissues, and new roles for the protein kinase in embryonic stem cell differentiation and motility have emerged. Despite these advances, the therapeutic value of this enzyme as a drug target remains clouded by uncertainty over the potential of antagonists to promote tumorigenesis. This article describes the state of understanding of this intriguing enzyme, and weighs current evidence regarding whether there is a therapeutic window for amelioration of diseases in which it is implicated, in the absence of inducing new pathologies.
The Prevalence of Premonitory Symptoms in Migraine: A Questionnaire Study in 461 Patients (2006)

Migraine attacks are often preceded by premonitory symptoms. Prevalence rates of migraine patients reporting one or more premonitory symptoms show considerable variability and rates range between 12% and 79%. Sources of variability might be differences in study population or research design. Using a questionnaire, we retrospectively studied the prevalence of 12 predefined premonitory symptoms in a clinic-based population. Of 461 migraine patients, 374 (81%) responded. At least one premonitory symptom was reported by 86.9% and 71.1% reported two or more. The most frequently reported premonitory symptoms were fatigue (46.5%), phonophobia (36.4%) and yawning (35.8%). The mean number of premonitory symptoms per person was 3.2 (+/- 2.5). Women reported 3.3 premonitory symptoms compared with 2.5 symptoms in men (P = 0.01). Age, education, migraine subtype (with or without aura) and mean attack frequency had no effect on the mean number of symptoms per individual. In conclusion, premonitory symptoms are frequently reported by migraine patients. Sensitivity and specificity of premonitory symptoms for migraine need to be assessed using prospective methods.
Transient expression of interleukin 2 receptors. Consequences for T cell growth. (1983)

T lymphocyte mitosis results from the interaction of interleukin 2 (IL-2) with specific receptors that appear only after appropriate immune stimulation. To assess the potential role of IL-2 receptor levels in determining the rate and magnitude of T cell proliferation, the expression of IL-2 receptors by lectin-stimulated human peripheral blood T cells was examined and correlated with T cell growth. Using biosynthetically radiolabeled IL-2 and anti-Tac, a monoclonal antibody that blocks IL-2 receptor binding, IL-2 receptors were found to accumulate slowly and asynchronously among lectin-stimulated T cells and to precede the onset of DNA synthesis. Moreover, a critical threshold of IL-2 receptor density appeared to be required before the commitment to cell cycle progression, as analyzed quantitatively by tritiated thymidine incorporation and flow cytometric analysis of cellular DNA content. Once maximal IL-2 receptor expression occurred, continued proliferation was IL-2 concentration dependent as assessed using homogenous immunoaffinity-purified IL-2. Upon removal of the activating lectin, IL-2 receptor levels progressively declined, and, in parallel, the rate of proliferation diminished. The decay of IL-2 receptors could not be attributed to IL-2-mediated down-regulation. Instead, renewed IL-2 receptor expression was dependent upon the reintroduction of the initial activating signal. Repetitive exposure to lectin resulted in a more rapid reexpression of maximal IL-2 receptor levels, which was then followed by an accelerated resumption of proliferation. Thus, the extent of T cell proliferation after immune stimulation depends upon the interplay of the IL-2 concentration available and the density of IL-2 receptors expressed, both of which are ultimately determined by antigen/lectin stimulation. The awareness of the transience and the antigen/lectin dependence of IL-2 receptor expression, together with the capacity to monitor T cell cultures for IL-2 receptor levels, should facilitate the initiation and maintenance of cloned, antigen-specific T cells in long-term culture. In addition, these findings suggest that, in vivo, the rapidity of acquisition of maximum IL-2 receptor levels by activated T cells and the duration of IL-2 receptor expression may well direct the magnitude of T cell clonal expansion and resultant immune responses.
Fast polarization modulated ellipsometer using a microprocessor system for digital Fourier analysis (1982)

A new type of spectroscopic automatic ellipsometer using a piezobirefringent element for polarization modulation at 50 kHz is described. Instead of lock-in amplifiers the data-acquisition system consists of a 12.8-MHz digital sampling of the detected signal with a high word rate 8-bit ADC, followed by on line Fourier transformation of the accumulated data with a short instruction cycle (∼200 ns) microprocessor, driven by a commercial microcomputer. The absolute minimum time required for measuring one set of Fourier coefficients is thus reduced to the modulation period of 20 μs. For digital error reduction purposes and signal-to-noise ratio improvement a basic 5 ms sequence of 256 accumulated periods per point is chosen. At this data-acquisition rate a precision of 5×10−4 is obtained. Further accumulation over 10 s leads to 10−5 precision capability. A detailed analysis of various sources of inaccuracy leads to an estimate of 0.5° maximum systematic error on the ellipsometric angles and ψ and Δ. Applications to the in situ study of a-Si:H plasma deposited films are also presented.
Impaired production of gamma-interferon by newborn cells in vitro is due to a functionally immature macrophage. (1985)

The decreased production of gamma-(PHA-induced) interferon (IFN) by leukocytes of normal newborns could be due to functionally immature T cells, macrophages, or both. We studied gamma-IFN production by macrophages and T cells, alone and in combination, obtained from 50 cord blood samples and 14 adult blood samples in a series of experiments. Adherent macrophages were cultivated for 7 days before the addition of T cells. After 48 hr, PHA-stimulated macrophage-T cell supernatants were harvested and assayed for IFN by a microassay. Macrophage-T cell cultures of autologous and nonautologous cells in 14 adults showed enhanced IFN production (GMT 121 +/- 5 IU) as compared with Ficoll-Hypaque mononuclear cells (GMT 42 +/- 5 IU). No IFN was detected in supernatants from PHA-stimulated Ficoll-Hypaque cord cells alone or macrophage-T cord combined cultures. Combined cord macrophages and adult T cells produced minimal IFN (GMT 13 +/- 3 IU); however, cord T cells combined with adult macrophages showed enhanced IFN production (GMT 195 +/- 47 IU). This cord macrophage dysfunction was not due to an inhibitor and improved with the time of in vitro cultivation. These results indicate that the neonatal macrophage is primarily responsible for the impaired gamma-IFN response by the newborn cells.
Cerebellin: a quantifiable marker for Purkinje cell maturation. (1985)

The cerebellum-specific hexadecapeptide cerebellin has been localized by immunocytochemical means to the perikarya and dendrites of cerebellar Purkinje cells. Biochemical analysis using ion-pairing HPLC shows cerebellin to first appear 5 days after birth, whereafter levels rise to a maximum at 25 days postpartum, and then decline to stable adult values. This same pattern of development occurs with a lag of approximately 5 days for the major metabolite of cerebellin, des-Ser1-cerebellin. The immunocytochemical picture of cerebellin in developing Purkinje cells mirrors the biochemical data. These results show that cerebellins represent unique quantifiable markers for the investigation of Purkinje cell maturation and lend support to the feasibility of using unique endogenous peptides to chart neurodevelopment.
Diagnosis and Management of Cystic Neoplasms of the Pancreas: An Evidence-Based Approach (2008)

Katz, Matthew H.G. MD; Mortenson, Melinda M. MD; Wang, Huamin MD, PhD; Hwang, Rosa MD; Tamm, Eric P. MD; Staerkel, Gregg MD; Lee, Jeffrey H. MD; Evans, Douglas B. MD, FACS; Fleming, Jason B. MD, FACS Author Information
Fine-specificity of cytotoxic T lymphocytes which recognize conserved epitopes of the Gag protein of human immunodeficiency virus type 1 (1996)

Human immunodeficiency virus type 1 (HIV-1) Gag-specific cytotoxic T lymphocyte (CTL) responses were studied in seven seropositive long-term asymptomatic individuals (CDC A1) with stable CD4 counts for more than 8 years. Using a set of partially overlapping peptides covering the whole Gag, five 15-20-mer peptides were found to contain CTL epitopes. Further characterization of these epitopes revealed a new HLA-A25-restricted CTL epitope in p24, p24(203-212) ETINEEAAEW. This region of Gag is highly conserved in clades B and D of HIV-1. Naturally occurring amino acid sequences, containing p24(203)D (consensus HIV-1 clades A, C, F, G and H) or p24(204)I (HIV-2ROD) were not recognized by CTL recognizing the index peptide. No virus variants with mutations in this sequence were found in peripheral blood mononuclear cells from the HIV-1-infected individual concerned during the 8 year observation period, indicating that the virus had not escaped from the observed CTL response.
Chronic Pelvic Pain in Women. (2016)

Chronic pelvic pain in women is defined as persistent, noncyclic pain perceived to be in structures related to the pelvis and lasting more than six months. Often no specific etiology can be identified, and it can be conceptualized as a chronic regional pain syndrome or functional somatic pain syndrome. It is typically associated with other functional somatic pain syndromes (e.g., irritable bowel syndrome, nonspecific chronic fatigue syndrome) and mental health disorders (e.g., posttraumatic stress disorder, depression). Diagnosis is based on findings from the history and physical examination. Pelvic ultrasonography is indicated to rule out anatomic abnormalities. Referral for diagnostic evaluation of endometriosis by laparoscopy is usually indicated in severe cases. Curative treatment is elusive, and evidence-based therapies are limited. Patient engagement in a biopsychosocial approach is recommended, with treatment of any identifiable disease process such as endometriosis, interstitial cystitis/painful bladder syndrome, and comorbid depression. Potentially beneficial medications include depot medroxyprogesterone, gabapentin, nonsteroidal anti-inflammatory drugs, and gonadotropin-releasing hormone agonists with add-back hormone therapy. Pelvic floor physical therapy may be helpful. Behavioral therapy is an integral part of treatment. In select cases, neuromodulation of sacral nerves may be appropriate. Hysterectomy may be considered as a last resort if pain seems to be of uterine origin, although significant improvement occurs in only about one-half of cases. Chronic pelvic pain should be managed with a collaborative, patient-centered approach.
Disc Degeneration in the Rabbit: A Biochemical and Radiological Comparison Between Four Disc Injury Models (2005)

In the first experiment, the 21-gauge 3-puncture and the 18-gauge 1-puncture models produced the most consistent disc degeneration in the rabbit lumbar spine. When these 2 models were again studied in the second experiment, the 21-gauge 3-puncture technique was superior in producing disc degeneration over a shorter period of time.
Creating the bluegene/l supercomputer from low-power SoC ASICs (2005)

An overview of the design aspects of the BlueGene/L chip, the heart of the BlueGene/L supercomputer, is presented. Following an SoC approach, processors, memory and communication subsystems are integrated into one low-power chip. The high-density system packaging of the BlueGene/L system provides better power and cost performance.
On zero-error coding of correlated sources (2003)

The authors consider the following simple encoding scenario, which they term successive encoding: /spl phi//sub x/ performs lossless encoding of X, at rate H(X), and /spl phi//sub y/ is designed assuming that the decoder has recovered X. For coding with vanishing error probability, the results of Slepian and Wolf (1973) show that time-sharing of the two possible successive encoding scenarios (obtained by interchanging the roles of X and Y) is optimal, in that all achievable rate pairs can be achieved via this strategy. But time-sharing combined with successive encoding may not be an optimal strategy in the case of zero-error coding. The authors construct a simple example for this suboptimality phenomenon.
The Indoleamine-2,3-Dioxygenase (IDO) Inhibitor 1-Methyl-D-tryptophan Upregulates IDO1 in Human Cancer Cells (2011)

1-methyl-D-tryptophan (1-D-MT) is currently being used in clinical trials in patients with relapsed or refractory solid tumors with the aim of inhibiting indoleamine-2,3-dioxygenase (IDO)-mediated tumor immune escape. IDO is expressed in tumors and tumor-draining lymph nodes and degrades tryptophan (trp) to create an immunsuppressive micromilieu both by depleting trp and by accumulating immunosuppressive metabolites of the kynurenine (kyn) pathway. Here we show that proliferation of alloreactive T-cells cocultured with IDO1-positive human cancer cells paradoxically was inhibited by 1-D-MT. Surprisingly incubation with 1-D-MT increased kyn production of human cancer cells. Cell-free assays revealed that 1-D-MT did not alter IDO1 enzymatic activity. Instead, 1-D-MT induced IDO1 mRNA and protein expression through pathways involving p38 MAPK and JNK signalling. Treatment of cancer patients with 1-D-MT has transcriptional effects that may promote rather than suppress anti-tumor immune escape by increasing IDO1 in the cancer cells. These off-target effects should be carefully analyzed in the ongoing clinical trials with 1-D-MT.
bcl-x is expressed in embryonic and postnatal neural tissues and functions to prevent neuronal cell death. (1995)

Previous studies have implicated the bcl-2 protooncogene as a potential regulator of neuronal survival. However, mice lacking functional bcl-2 exhibited normal development and maintenance of the central nervous system (CNS). Since bcl-2 appears dispensable for neuronal survival, we have examined the expression and function of bcl-x, another member of the bcl-2 family of death regulatory genes. Bcl-2 is expressed in neuronal tissues during embryonic development but is down-regulated in the adult CNS. In contrast, Bcl-xL expression is retained in neurons of the adult CNS. Two different forms of bcl-x mRNA and their corresponding products, Bcl-xL and Bcl-x beta, were expressed in embryonic and adult neurons of the CNS. Microinjection of bcl-xL and bcl-x beta cDNAs into primary sympathetic neurons inhibited their death induced by nerve growth factor withdrawal. Thus, Bcl-x proteins appear to play an important role in the regulation of neuronal survival in the adult CNS.
Methods for automatic multiparameter analysis of fluorescence in situ hybridized specimens with a laser scanning cytometer (1997)

Multiparameter laser scanning cytometry has been applied to the automatic counting of probe spots and the simultaneous measurement of cellular DNA for fluorescence in situ hybridization (FISH) prepared specimens counterstained with propidium iodide. Relatively low resolution imaging, highly variable probe fluorescence, spectral overlap of probe with counterstain fluorescence, and autofluorescence required the development of an image processing method to detect and isolate FISH probe spots. Inability to properly apportion detected probe spots because of overlapping probe spot images in the same cell required development of a method to eliminate cell data whenever spots in that cell could not be reliably isolated. Laser scanning cytometry incorporating these methods to determine per cell probe spot count and DNA is demonstrated on tissue cultures and peripheral blood cells using different centromeric FISH probes with either FITC or Spectrum Green labeling.