gebhart/patrepeval huggingface dataset:
Determination of 5-methyl-cytosine and cytosine in tumor DNA of cancer patients (2005)

The determination of the relative methylation in DNA tumor samples, in order to evaluate the activity of some anti-cancer drugs, has become a very important issue in the clinical field. Capillary electrophoresis (CE) applications in this area have been done previously but no good separation for model samples or tumor samples has been reported. In this work, the CE conditions have been optimized in order to obtain baseline separation and efficient peaks for cytosine and 5-methylcytosine in both, standard mixtures and actual tumor samples; other bases (adenine, uracil, guanine, and thymine) have also been integrated in the optimization studies. More efficient peaks and shorter analysis time compared with the already reported conditions have been obtained employing a fused-silica capillary (75 microm inner diameter) of 44.5 cm effective length, 20 mM carbonate buffer (pH 9.6) plus 80 mM sodium dodecyl sulfate, a separation voltage of 20 kV, and detection at 223 nm.
Human PDGFA receptor gene maps to the same region on chromosome 4 as the KIT oncogene (1989)

The gene for the human platelet-derived growth factor (PDGF) A type receptor was assigned to the proximal long arm of chromosome 4 by using in situ hybridization. Of 141 labeled metaphase cells, 74 had grains over chromosome 4, with a distinct peak at bands q11-q12. The presence of the gene on chromosome 4 was also confirmed by hybridization to chromosome specific libraries. This places the PDGFA receptor gene in the same region of chromosome 4 as the KIT oncogene, another member of the PDGF growth factor receptor subfamily. The two other members of this gene family, the PDGFB receptor and the colony stimulating factor-1 (CSF1) receptor, are closely linked on the distal half of the long arm of chromosome 5.
Provocative agents in panic disorder. (1995)

The pharmacological challenge strategy involves giving a provoking agent under controlled rules to clarify some aspect of behavioural or biological function. Various agents such as sodium lactate, carbon dioxide, caffeine, yohimbine, isoprenaline and now cholecystokinin have been used as provoking agents in healthy volunteers as well as in panic patients. Results obtained in this field are updated, with emphasis on the potential mechanisms of action. It is concluded that there may be a final pathway between carbon dioxide, sodium lactate, and cholecystokinin inducing panic attacks.
Effect of Hyperoxia on Vascular Endothelial Growth Factor Levels in a Wound Model (2000)

Increased VEGF production seems to explain in part the angiogenic action of HBO. This supports other data that hypoxia is not necessarily a requirement for wound VEGF production.
Effect of 12-O-tetradecanoylphorbol-13-acetate on the morphology and growth of C3H/10T1/2 mouse embryo cells. (1980)

The effects of the tumor-promoting phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA) on the morphology and growth properties of C3H/10T1/2 clone 8 cells were examined. The morphology of these cells was changed within 30 min following treatment with 0.1 microgram of TPA per ml; they became smaller and refractile with long beady processes. Such changes were observed in both logarithmic and confluent cultures and lasted about 72 hr. Subsequent treatments were much less effective in inducing these changes. Scanning electron microscopy showed cell retraction and rounding as the most significant immediate effects of TPA treatment; many cells remained partially rounded 48 hr afterwards. Long-term surface modifications ascribable to TPA treatment were not detected. TPA had only minor effects on the growth of cultured C3H/10T1/2 cells in the presence of 10% fetal calf serum. Slight increases in plating efficiencies and saturation densities were generally observed in the presence of TPA but not with the related non-tumor-promoting compound phorbol. The cells grew slowly in 1% fetal calf serum and demonstrated serum batch-dependent alterations in their growth properties when exposed to TPA. Under conditions that produce doubling times of 70 hr or greater, TPA, but not phorbol, reduced the doubling time to about 50 hr. Saturation densities were also increased by TPA in 1% fetal calf serum. The effects of TPA on the growth of an oncogenically transformed variant of C3H/10T1/2 were quite different. While minimal effects of TPA were observed quite different. While minimal effects of TPA were observed when transformed cells were treated in the presence of 10% total calf serum, TPA treatment in 1% fetal calf serum significantly inhibited cell growth.
HighSpeed TCP for Large Congestion Windows (2003)

The proposals in this document are experimental. While they may be deployed in the current Internet, they do not represent a consensus that this is the best method for high-speed congestion control. In particular, we note that alternative experimental proposals are likely to be forthcoming, and it is not well understood how the proposals in this document will interact with such alternative proposals.
Intestinal pseudo-obstruction associated with oral morphine (1998)

Morphine is recommended as the strong opioid of choice by the World Health Organization (WHO) for cancer pain management. It is associated with delay in gastro-intestinal transit; as a result, patients may experience marked constipation. We describe a case of intestinal pseudo-obstruction associated with the use of oral morphine in a terminally ill cancer patient.
Botulinum toxin for the treatment of headache: a promising path on a "dead end road"? (2010)

Available preventive treatments for primary headaches such as migraines and tension-type headaches have limited efficacy and often disabling side effects (Schoenen 2004, Schoenen 2000). There is thus room for new more effective and better tolerated therapeutic approaches as long as they can be proven superior to placebo. Based on pilot studies and open trials, botulinum toxin (BT) appeared in the headache armamentarium more than a decade ago and it remains widely used in North America since. The initial enthusiasm for BT was not confirmed by subsequent randomized controlled trials reviewed in this article, neither in tension-type headache, nor in episodic migraine and hence BT was considered a "dead end road" by certain headache experts. A promising "path" for BT may, however, exist. In two recent trials (PREEMPT 1 and 2), OnabotulinumtoxinA (Botox) was found effective in chronic migraine. The therapeutic gain over placebo is modest (+/- 11%), but chronic migraine is most disabling, often drug resistant and a serious public health problem, as it affects 1-2% of people in the general population. Because the PREEMPT trials leave unsolved a number of clinically relevant questions, OnabotulinumtoxinA cannot become yet the pre-emptor of CM treatment. Although the path is promising, it seems wise, at this stage, to restrict its use to specialized headache centres where BT can be included in a multidisciplinary approach for chronic headache patients.
CHEMOPREVENTION OF UROLOGICAL CANCER (1999)

Although there is no incontrovertible proof, numerous studies implicate dietary and nutritional factors in the onset and progression of cancer of the bladder, prostate and kidney. It is possible that the preventive effect of dietary constituents may be in part from consumption with other nutrients and bioactive compounds in whole foods. Further research is needed before vitamins and other nutritional supplements can be advocated as standard therapy but the preponderance of evidence supports increased intake of vitamins A, B6, C, D and E, reduction of animal fat, and increased consumption of fruits and vegetables.
Activity-Dependent Regulation of MEF2 Transcription Factors Suppresses Excitatory Synapse Number (2006)

In the mammalian nervous system, neuronal activity regulates the strength and number of synapses formed. The genetic program that coordinates this process is poorly understood. We show that myocyte enhancer factor 2 (MEF2) transcription factors suppressed excitatory synapse number in a neuronal activity- and calcineurin-dependent manner as hippocampal neurons formed synapses. In response to increased neuronal activity, calcium influx into neurons induced the activation of the calcium/calmodulin-regulated phosphatase calcineurin, which dephosphorylated and activated MEF2. When activated, MEF2 promoted the transcription of a set of genes, including arc and synGAP, that restrict synapse number. These findings define an activity-dependent transcriptional program that may control synapse number during development.
SMART: a web-based tool for the study of genetically mobile domains (2000)

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de ). More than 400 domain families found in signalling, extra-cellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.
Spinal Cord Neuromodulation for Voiding Dysfunction (2000)

A clear understanding of the pathophysiology and neurophysiologic effect of neuromodulation is lacking. Apparently there is a balance of efferent and afferent negative and positive feedback loops that are augmented by external electrical stimulation. This effect may be dramatic even in patients who have have not benefited from virtually every other form of treatment.
Elevated amniotic fluid amino acid levels in fetuses with gastroschisis (2006)

Our objective was to measure maternal plasma and amniotic fluid amino acid concentrations in pregnant women diagnosed as having fetuses with gastroschisis in the second trimester of pregnancy. Twenty-one pregnant women who had fetuses with gastroschisis detected by ultrasonography (gastroschisis group) in the second trimester and 32 women who had abnormal triple screenings indicating an increased risk for Down syndrome but had healthy fetuses (control group) were enrolled in the study. Amniotic fluid was obtained by amniocentesis, and maternal plasma samples were taken simultaneously. The chromosomal analysis of the study and control groups was normal. Levels of free amino acids and non-essential amino acids were measured in plasma and amniotic fluid samples using EZ:fast kits (EZ:fast GC/FID free (physiological) amino acid kit) by gas chromatography (Focus GC AI 3000 Thermo Finnigan analyzer). The mean levels of essential amino acids (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine) and non-essential amino acids (alanine, glycine, proline, and tyrosine) in amniotic fluid were found to be significantly higher in fetuses with gastroschisis than in the control group (P < 0.05). A significant positive correlation between maternal plasma and amniotic fluid concentrations of essential and nonessential amino acids was found only in the gastroschisis group (P < 0.05). The detection of significantly higher amino acid concentrations in the amniotic fluid of fetuses with a gastroschisis defect than in healthy fetuses suggests the occurrence of amino acid malabsorption or of amino acid leakage from the fetus into amniotic fluid.
Structure−Property Relationships of Photopolymerizable Poly(ethylene glycol) Dimethacrylate Hydrogels (2005)

Photopolymerized hydrogels from poly(ethylene glycol) dimethacrylate (PEGDM) and similar derivatives have been extensively used as scaffolds for tissue regeneration and other biological applications. A systematic investigation into the structure and mechanical properties of PEGDM hydrogels was performed to characterize the relationships between the network structure and gel properties. Gels were prepared from oligomers of different molecular masses (1000−8000 g/mol) at various concentrations. Small-angle neutron scattering was used to characterize the structural features of hydrogels with respect to their semidilute solution precursors. A well-defined structural length scale manifested as a maximum in the scattering intensity was observed for hydrogels derived from high molecular mass PEGDMs and/or high oligomer mass fractions. Mechanical testing showed that PEGDM hydrogels are mechanically robust, consistent with gel structures that contain reinforcing cross-linked clusters. Shear moduli were determined for hydrogels swollen to various degrees in water. The concentration dependence of shear modulus for these nonideal hydrogels exhibits a power law behavior with an exponent close to 1/3.
Relation between domain evolution, specificity, and taxonomy of the α‐amylase family members containing a C‐terminal starch‐binding domain (2003)

The alpha-amylase family (glycoside hydrolase family 13; GH 13) contains enzymes with approximately 30 specificities. Six types of enzyme from the family can possess a C-terminal starch-binding domain (SBD): alpha-amylase, maltotetraohydrolase, maltopentaohydrolase, maltogenic alpha-amylase, acarviose transferase, and cyclodextrin glucanotransferase (CGTase). Such enzymes are multidomain proteins and those that contain an SBD consist of four or five domains, the former enzymes being mainly hydrolases and the latter mainly transglycosidases. The individual domains are labelled A [the catalytic (beta/alpha)8-barrel], B, C, D and E (SBD), but D is lacking from the four-domain enzymes. Evolutionary trees were constructed for domains A, B, C and E and compared with the 'complete-sequence tree'. The trees for domains A and B and the complete-sequence tree were very similar and contain two main groups of enzymes, an amylase group and a CGTase group. The tree for domain C changed substantially, the separation between the amylase and CGTase groups being shortened, and a new border line being suggested to include the Klebsiella and Nostoc CGTases (both four-domain proteins) with the four-domain amylases. In the 'SBD tree' the border between hydrolases (mainly alpha-amylases) and transglycosidases (principally CGTases) was not readily defined, because maltogenic alpha-amylase, acarviose transferase, and the archaeal CGTase clustered together at a distance from the main CGTase cluster. Moreover the four-domain CGTases were rooted in the amylase group, reflecting sequence relationships for the SBD. It appears that with respect to the SBD, evolution in GH 13 shows a transition in the segment of the proteins C-terminal to the catalytic (beta/alpha)8-barrel(domain A).
Video Coding With Rate-Distortion Optimized Transform (2011)

Block-based discrete cosine transform (DCT) has been successfully adopted into several international image/video coding standards, e.g., MPEG-2, H.264/AVC, as it can achieve a good tradeoff between performance and complexity. Although DCT theoretically approximates the optimum Karhunen–Loève transform under first-order Markov conditions, one fixed set of transform basis functions (TBF) cannot handle all the cases efficiently due to the non-stationary nature of video contents. To further improve the performance of block-based transform coding, in this paper, we present the design of rate-distortion optimized transform (RDOT) which contributes to both intraframe and interframe coding. The most important property which makes a difference between RDOT and the conventional DCT is that, in the proposed method, transform is implemented with multiple TBF candidates which are obtained from off-line training. With this feature, for coding each residual block, the encoder is capable to select the optimal set of TBF in terms of rate-distortion performance, and better energy compaction is achieved in the transform domain. To obtain an optimum group of candidate TBF, we have developed a two-step iterative optimization technique for the off-line training, with which the TBF candidates are refined at each iteration until the training process becomes converged. Moreover, analysis on the optimal group of candidate TBF is also presented in this paper, with a detailed description of a practical implementation for the proposed algorithm on the latest VCEG key technical area software platform. Extensive experimental results show that, compared with the conventional DCT-based transform scheme adopted into the state-of-the-art H.264/AVC video coding standard, significant improvement of coding performance has been achieved for both intraframe and interframe coding with our proposed method.
Rapid PCR construction of a gene containing Lym-1 antibody variable regions. (1993)

Clinical applications of monoclonal antibodies (mAbs) to tumor-associated antigens provide potential for targeted cancer therapy. Radiolabeled mAb Lym-1 has been used successfully to treat >50 patients with B-cell lymphoma. ~-3) The uptake of Lym-1 in lymphomas is rapid and efficient compared with solid tumors. However, the amount of the radioactive dose injected on these large molecules reaching each gram of tumor is usually <0.1%. When Lym-1 is labeled with radiometal chelates to enhance its tumoricidal effects, there is undesirable accumulation and slow clearance of radioactivity in the liver. Evidence suggests that this is related to receptors for components of the mAb Fc region. (4's) Recent studies (6'7) have demonstrated that two recombinant radio-directed single-chain antigen-binding (SCA) proteins derived from monoclonal antibodies have in vivo tumor-targeting capacity. Although the percent injected dose per gram of tumor is low, the therapeutic index (tumor to normal organ radiation dose) is several times that of the intact mAb, F(ab')2 , or Fab' fragments. ( Furthermore, SCA proteins facilitate development of single or bispecific radioimmunoconjugates, humanized antibodies, or new versions of tumor-reactive molecules for immunotherapy. This may be particularly rewarding for a mAb such as Lym-1 that has already been demonstrated to be successful in clinical radioimmunoconjugate cancer therapy.
Glycoprotein VI Is a Major Collagen Receptor for Platelet Activation: It Recognizes the Platelet-Activating Quaternary Structure of Collagen, Whereas CD36, Glycoprotein IIb/IIIa, and von Willebrand Factor Do Not (1998)

Simple collagen-related peptides (CRPs) containing a repeat Gly-Pro-Hyp sequence are highly potent platelet agonists. Like collagen, they must exhibit tertiary (triple-helical) and quaternary (polymeric) structure to activate platelets. Platelet signaling events induced by the peptides are the same as most of those induced by collagen. The peptides do not recognize the alpha 2 beta 1 integrin. To identify the signaling receptor involved, we have evaluated the response to the CRP, Gly-Lys-Hyp(Gly-Pro-Hyp)10-Gly-Lys-Hyp-Gly of platelets with defined functional deficiencies. These studies exclude a primary recognition role for CD36, von Willebrand factor (vWF), or glycoprotein (GP) IIb/IIIa. Thus, both CD36 and vWF-deficient platelets exhibited normal aggregation, normal fibrinogen binding, and normal expression of CD62 and CD63, measured by flow cytometry, in response to the peptide, and there was normal expression of CD62 and CD63 on thrombasthenic platelets. In contrast, GPVI-deficient platelets were totally unresponsive to the peptide, indicating that this receptor recognizes the Gly-Pro-Hyp sequence in collagen. GPVI-deficient platelets showed some fibrinogen binding in response to collagen but failed to aggregate and to express CD62 and CD63. Collagen, but not CRP-XL, contains binding sites for alpha 2 beta 1. Therefore, it is possible that collagen still induces some signaling via alpha 2 beta 1, leading to activation of GPIIb/IIIa. Our findings are consistent with a two-site, two-step model of collagen interaction with platelets involving recognition of specific sequences in collagen by an adhesive receptor such as alpha 2 beta 1 to arrest platelets under flow and subsequent recognition of another specific collagen sequence by an activatory receptor, namely GPVI.
Human cytomegalovirus UL97 kinase confers ganciclovir susceptibility to recombinant vaccinia virus (1994)

We analyzed whether the phosphotransferase encoded by the UL97 open reading frame of human cytomegalovirus (HCMV) alone is sufficient to confer ganciclovir (GCV) susceptibility to a foreign virus. Two vaccinia virus recombinants (T1 and A5) containing the UL97 open reading frames from a GCV-sensitive HCMV and from a GCV-resistant strain were constructed. T1 exhibited a GCV-sensitive phenotype in plaque reduction assays, whereas A5 did not. Moreover, T1-infected cell cultures showed a strongly increased incorporation of [14C]GCV triphosphate into macromolecular DNA, compared with recombinant A5 or vaccinia virus controls, which could be inhibited by the addition of guanosine. This shows that UL97 kinase is the only additional gene product required to make vaccinia virus susceptible to GCV, and guanosine seems to be one natural substrate for the enzyme. The system described here should be very helpful for fast and detailed functional analyses of UL97 mutations found in GCV-resistant HCMV isolates.
Enhancement of respiratory syncytial virus pulmonary pathology in cotton rats by prior intramuscular inoculation of formalin-inactiva ted virus (1986)

Cotton rats previously inoculated with Formalin-inactivated respiratory syncytial virus (RSV) were challenged intranasally with live RSV to induce an enhancement of RSV disease similar to that observed after the administration of Formalin-inactivated RSV vaccine to human infants 20 years ago. Within 24 h after infection with RSV, cotton rats developed pulmonary lesions that reached a maximum by day 4. Histologically, the lesions resembled an experimental pulmonary Arthus reaction. An action of Formalin on RSV appears to be responsible for this effect, because live virus or virus heated in the absence of Formalin did not induce enhanced immunopathology. Selected epitopes on the fusion (F) or attachment (G) or both RSV surface glycoproteins that are involved in inducing neutralizing antibodies were modified to reduce or ablate their antigenicity. However, other epitopes on the F or G or both glycoproteins were not ablated by Formalin, because cotton rats inoculated parenterally with a Formalin-inactivated virus developed a high level of F and G antibodies measurable by an enzyme-linked immunosorbent assay. At this time, the effect of Formalin on RSV cannot be localized to either the F or G glycoprotein of RSV.
Nucleation and Growth of Noble Metals on Oxide Surfaces Using Atomic Layer Deposition (2007)

Noble metals supported on metal oxide surfaces have broad applications in catalysis, microelectronics and sensing. In most applications it is critical to control the dispersion and morphology of the noble metals to achieve either a smooth, continuous film or isolated particles of controlled size. Here we examine the atomic layer deposition of Pd and Pt films onto a variety of metal oxide surfaces including Al2O3, ZrO2, and TiO2. In situ quartz crystal microbalance measurements and quadrupole mass spectrometry are used to explore the nucleation and growth of the Pd ant Pt on the different metal oxide surfaces. Scanning electron microscopy and X-ray photoelectron spectroscopy are used to examine the morphology and surface state of the resulting Pt and Pd coatings. By varying the support material and the deposition conditions, we can control the morphology of the ALD noble metal coatings to yield agglomerated particles or continuous films.