gebhart/patrepeval huggingface dataset:
Growth of GaxIn1−xAs quantum wire heterostructures by the strain-induced lateral-layer ordering process (1995)

GaxIn1−xAs quantum wire (QWR) arrays were grown in situ by molecular beam epitaxy. A lateral composition modulation was achieved in the GaxIn1−xAs material system via the strain-induced lateral layer ordering process occurring spontaneously when (GaAs)n/(InAs)n short-period superlattices are grown on (100)-oriented on-axis InP substrates. The resulting quasiperiodic modulation of the GaxIn1−xAs composition, with a periodicity of 300 Å, offers a lateral quantum confinement along the growth plane. The quantum confinement in the growth direction is provided by sandwiching the thin (∼100 Å) laterally ordered GaxIn1−xAs layer between layers of bulk Al0.24Ga0.24In0.52As. The formation of the QWR array is confirmed by cross-sectional transmission electron microscopy and polarized photoluminescence measurements.
Computation of Aromatic C3N4 Networks and Synthesis of the Molecular Precursor N(C3N3)3Cl6 (2003)

The successful synthesis and structural characterization of molecules that represent segments of extended solids is a valuable strategy for learning metric and stereochemical characteristics of those solids. This approach has been useful in cases in which the solids are particularly difficult to crystallize and thus their atomic connectivity and overall structures become difficult to deduce with X-ray diffraction techniques. One such class of materials is the covalently linked C(x)N(y) extended solids, where molecular analogues remain largely absent. In particular, structures of C(3)N(4) solids are controversial. This report illustrates the utility of a simple molecule, N(C(3)N(3))(3)Cl(6), in answering the question of whether triazine based C(3)N(4) phases are layered or instead they adopt 3D structures. Here, we present density functional calculations that clearly demonstrate the lower stability of graphitic C(3)N(4) relative to 3D analogues.
Use of fumaric acid esters in psoriasis (2007)

Fumaric acid esters (FAE) are chemical compounds derived from the unsaturated dicarbonic acid fumaric acid. The usage of FAEs in treatment of psoriasis was introduced in the late 1950's. In the 1980s more standardized oral preparations of FAEs were developed containing dimethylfumarate (DMF) and salts of monoethylfumarate (MEF) as main compounds. In 1994, Fumaderm an enteric-coated tablet containing DMF and calcium, magnesium and zinc salts of MEF was approved for the treatment of psoriasis in Germany and since then has become the most commonly used systemic therapy in this country. Fumaric acids have been proven to be an effective therapy in patients with psoriasis even though the mechanisms of action are not completely understood. About 50-70% of the patients achieve PASI 75 improvement within four months of treatment and without any long-term toxicity, immunosuppressive effects or increased risk of infection or malignancy. Tolerance is limited by gastrointestinal side effects and flushing of the skin. This article reviews pharmacokinetics, uses, contraindications, dosages and side effects of treatment with FAEs.
African Trypanosomes: Intracellular Trafficking of Host Defense Molecules1 (2006)

Trypanosoma brucei brucei is the causative agent of Nagana in cattle and can infect a wide range of mammals but is unable to infect humans because it is susceptible to the innate cytotoxic activity of normal human serum. A minor subfraction of human high-density lipoprotein (HDL), containing apolipoprotein A-I (APOA1), apolipoprotein L-I (APOL1) and haptoglobin-related protein (HPR) provides this innate protection against T. b. brucei infection. Both HPR and APOL1 are cytotoxic to T. b. brucei but their specific activities for killing increase several hundred-fold when assembled in the same HDL. This HDL is called trypanosome lytic factor (TLF) and kills T. b. brucei following receptor binding, endocytosis, and lysosomal localization. Trypanosome lytic factor is activated in the acidic lysosome and facilitates lysosomal membrane disruption. Lysosomal localization is necessary for T. b. brucei killing by TLF. Trypanosoma brucei rhodesiense, which is indistinguishable from T. b. brucei, is resistant to TLF killing and causes human African sleeping sickness. Human infectivity by T. b. rhodesiense correlates with the evolution of a human serum resistance associated protein (SRA) that is able to ablate TLF killing. When T. b. brucei is transfected with the SRA gene it becomes highly resistant to TLF and human serum. In the SRA transfected cells, intracellular trafficking of TLF is altered and TLF mainly localizes to a subset of SRA containing cytoplasmic vesicles but not to the lysosome. These findings indicate that the cellular distribution of TLF is influenced by SRA expression and may directly determine susceptibility.
The trellis architecture for intelligent monitors (2002)

The process trellis is a software architecture that imposes a simple and regular organization on a complex, diverse set of parallel processes. The organization it imposes is well suited to parallel real-time monitors and expert systems. The trellis architecture is based on a hierarchical graph of decision processes, reflecting the conceptual hierarchy of the problem domain. All processes in the graph execute continuously and concurrently, and they communicate among themselves and with the outside world using a simple and uniform protocol. The trellis is amenable to parallel real-time scheduling strategies, to 'abstraction strategies' that synopsize the structure of complex trellises, and to visualization; it is a highly flexible architecture that seems well suited to a variety of domains. Extensive work on the trellis to date has focused both on design and analytical studies, and on the implementation, using C-Linda, of a substantial prototype trellis for patient monitoring in intensive care units.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Petri Net Modeling and Cycle-Time Analysis of Dual-Arm Cluster Tools With Wafer Revisiting (2012)

There are wafer fabrication processes in cluster tools that require wafer revisiting. If a swap strategy is applied to dual-arm cluster tools handling wafer revisiting, a three-wafer periodical process is formed with three wafers completed in each period. Such a period contains three cycles in a revisiting process and three cycles in a nonrevisiting one. Hence, analysis and scheduling of such tools become very complicated. In this paper, a Petri net (PN) model is developed to describe their operations. Based on it, it is found that, if a swap strategy is applied, such tools are always in a transient state. A systematic method is then presented to analyze their performance. With the help of the proposed PN model, this work, for the first time, derives the optimality conditions of three-wafer period scheduling. Industrial application examples are given to show the results.
Immunodominant CD4+ T-cell epitope within nonstructural protein 3 in acute hepatitis C virus infection (1997)

In acute hepatitis C virus infection, 50 to 70% of patients develop chronic disease. Considering the low rate of spontaneous viral clearance during chronic hepatitis C infection, the first few months of interaction between the patient's immune system and the viral population seem to be crucial in determining the outcome of infection. We previously reported the association between a strong and sustained CD4+ T-cell response to nonstructural protein 3 (NS3) of the hepatitis C virus and a self-limited course of acute hepatitis C infection. In this study, we identify an immunodominant CD4+ T-cell epitope (amino acids 1248 to 1261) that was recognized by the majority (14 of 23) of NS3-specific CD4+ T-cell clones from four of five patients with acute hepatitis C infection. This epitope can be presented to CD4+ T cells by HLA-DR4, -DR11, -DR12, -DR13, and -DR16. HLA-binding studies revealed a high binding affinity for 10 of 13 common HLA-DR alleles. Two additional CD4+ T-cell epitopes, amino acids 1388 to 1407 and amino acids 1450 to 1469, showed a very narrow pattern of binding to individual HLA-DR alleles. Our data suggest that the NS3-specific CD4+ T-cell response in acute hepatitis C infection is dominated by a single, promiscuous peptide epitope which could become a promising candidate for the development of a CD4+ T-cell vaccine.
Atomic structure of a tryptophan-zipper pentamer (2004)

Coiled-coil motifs are ubiquitous mediators of specific protein-protein interactions through the formation of interlocking hydrophobic seams between alpha-helical chains. Residues that form these seams occur at the first (a) and fourth (d) positions of a characteristic 7-aa repeat and are primarily aliphatic. The potential of aromatic residues to promote helix association in a coiled coil was explored by engineering a "Trp-zipper" protein with Trp residues at all 14 a and d positions. The protein forms a discrete, stable, alpha-helical pentamer in water at physiological pH. Its 1.45-A crystal structure reveals a parallel, five-stranded coiled coil, a previously uncharacterized type of "knobs-into-holes" packing interaction between interfacial Trp side chains, and an unusual approximately 8-A-diameter axial channel lined with indole rings that is filled with polyethylene glycol 400 and water and sulfate ion molecules. The engineered Trp-zipper pentamer enlarges current views of coiled-coil assembly, molecular recognition, and protein engineering, and may serve as a soluble model for membrane ion channels.
Efficient Serum-Free Retroviral Gene Transfer into Primitive Human Hematopoietic Progenitor Cells by a Defined, High-Titer, Nonconcentrated Vector-Containing Medium (1998)

Defined serum-free conditions have great conceptual advantages for the biological safety and standardization of clinical gene transfer into hematopoietic stem cells. In the only study reported to date, Sekhar et al. achieved low serum conditions by a complex concentration procedure of a retroviral supernatant initially containing 10% fetal bovine serum. The high cost, small volume, possible coenrichment of serum-derived pathogens, limited recovery of vector particles, and low titer of the final diluted medium restrict the clinical application of this procedure. Transduction of primitive hematopoietic progenitor cells was not demonstrated. In the present study, a defined serum-free medium containing high titers of the pseudotyped retroviral vector PG13/LN was generated from PG13/LN producer cells without requiring a physical enrichment procedure. The transduction of committed hematopoietic progenitor cells in the serum-free vector-containing medium was efficient, and similar to that occurring under serum-containing control conditions. The number of primitive human hematopoietic long-term culture-initiating cell-derived colonies (LTC-IC-derived colonies) generated from CD34+ and CD34+/HLA-DRlo peripheral blood progenitor "stem" cells (PBSCs) increased during 7 days of treatment in this vector-containing medium in the presence of IL-3, SCF, and flt-3 ligand. The described procedure allowed efficient transduction of LTC-IC-derived colonies generated from CD34+, CD34+/HLA-DRlo, and CD34+/CD38lo PBSCs. This is the first report to demonstrate an increase in primitive peripheral blood LTC-IC-derived colonies in vitro as well as their efficient transduction in a high-titer, serum-free vector-containing medium that can be produced exclusively from defined pharmaceutical-grade components, making it ideally suited for applications in clinical gene therapy.
Interaction of vasopressin infusion, corticosteroid treatment, and mortality of septic shock* (2009)

There is a statistically significant interaction between vasopressin and corticosteroids. The combination of low-dose vasopressin and corticosteroids was associated with decreased mortality and organ dysfunction compared with norepinephrine and corticosteroids.
SOIL WATER HYSTERESIS (1975)

The effects of transient temperatures and pressures on soil water hysteresis were studied under controlled laboratory conditions. Variations in ambient pressure and temperature caused small changes in soil water hysteresis. These changes suggest that at least two mechanisms may be present, neither of which is easily rationalized by the classical hourglass-shaped pore liquid jump model. The variation between duplicate samples of a silty clay, a silt loam, and a loamy sand suggested that normal temperature and pressure changes in the field will not cause changes in soil water hysteresis that are larger than those due to natural soil heterogeneity. Consequently, soil water hysteresis curves measured in the laboratory on representative samples may be used in computer models of field situations.
Non-impact printer power and motor control system on a chip (2002)

An integrated circuit chip set has been developed that realizes a color nonimpact printer power supply and motor control system. The two ICs include three switch mode PWM controllers, two unipolar stepper motor drivers, a DC motor H-bridge, a serial control port, and a host of peripheral system functions. Focus is placed on power management and how individual circuits are customized to minimize on-chip power dissipation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Henrietta Lacks, HeLa cells, and cell culture contamination. (2009)

Henrietta Lacks died in 1951 of an aggressive adenocarcinoma of the cervix. A tissue biopsy obtained for diagnostic evaluation yielded additional tissue for Dr George O. Gey's tissue culture laboratory at Johns Hopkins (Baltimore, Maryland). The cancer cells, now called HeLa cells, grew rapidly in cell culture and became the first human cell line. HeLa cells were used by researchers around the world. However, 20 years after Henrietta Lacks' death, mounting evidence suggested that HeLa cells contaminated and overgrew other cell lines. Cultures, supposedly of tissues such as breast cancer or mouse, proved to be HeLa cells. We describe the history behind the development of HeLa cells, including the first published description of Ms Lacks' autopsy, and the cell culture contamination that resulted. The debate over cell culture contamination began in the 1970s and was not harmonious. Ultimately, the problem was not resolved and it continues today. Finally, we discuss the philosophical implications of the immortal HeLa cell line.
Blood-brain barrier permeability measurements by double-indicator method using intravenous injection (1994)

The double-indicator technique with intracarotid bolus injection is useful for the estimation of transfer rates across the human blood-brain barrier. A method using intravenous tracer injection is developed whereby the input is measured at a peripheral artery and the output is measured at the jugular vein. To correct for differences in the brain input of test and reference substances, a five-parameter Dirac impulse response for passage through the cerebrovascular bed is computed from the input and output of the reference substance. This response is then combined with a capillary model of the brain. This is then convoluted with the arterial input curve of the test substance to yield a theoretical test output curve, which is compared with the actual test output curve. On the basis of these two curves and an appropriate mathematical model for the brain, estimates of blood-brain barrier permeability are obtained. In the present study, the techniques are compared in 13 patients in whom alternating intracarotid and intravenous bolus injections were given. For D-glucose, the two techniques yielded similar results. This was also the case for L-phenylalanine, provided that the erythrocyte compartment was taken into account. Data obtained after intravenous injection of leucine and water yielded similar results compared with previous intracarotid data.
Role of chemokines and cytokines in a reactivation model of arthritis in rats induced by injection with streptococcal cell walls (1998)

Intraarticular injection of streptococcal cell wall (SCW) antigen followed by intravenous challenge results in a T cell-mediated monoarticular arthritis ill female Lewis rats. Initial studies showed that this reactivation response to intravenous SCW antigen is dependent on the presence of interleukin-1 (IL-1) and tumor necrosis factor alpha (TNF-alpha) and that the early phase of swelling is neutrophil-dependent. Neutrophil depletion or passive immunization with antibodies to P-selectin or macrophage inflammatory protein-2 reduced the intensity of ankle edema and the influx of neutrophils. After the first few days, however, the arthritic response is mediated primarily by mononuclear cells. Joint tissues showed up-regulation of mRNA for monocyte chemotactic protein-1 (MCP-1), which could be inhibited in part by anti-IL-4; treatment of rats with antibodies to IL-4 or MCP-1 significantly suppressed development of ankle edema and histopathological evidence of inflammation. Antibodies to interferon-gamma or IL-10 had no effect. Treatment with anti-MCP-1 also suppressed influx of (111)In-labeled T cells into the ankle joint. These data suggest that the late, mononuclear-dependent phase of SCW-induced arthritis in female Lewis rats requires cytokines that up-regulate MCP-1, which in turn may facilitate recruitment and extravasation of mononuclear cells into the joint.
Synthetic carbohydrate-based antitumor vaccines: challenges and opportunities (2005)

The development of a clinically effective, carbohydrate-based antitumor vaccine is a longstanding ambition in the prevention and treatment of cancer. This review seeks to provide a discussion of some of the unique challenges facing this particular field of immunology. The authors present a historic account of their ongoing research program devoted to the development of fully synthetic, carbohydrate-based anticancer vaccines of clinical value. As will be seen, remarkable advances in carbohydrate and glycopeptide assembly techniques have allowed for the preparation of synthetic constructs of progressively increasing structural complexity. The authors describe the evolution of their synthetic carbohydrate program from first-generation constructs, which were monovalent in nature, to highly complex unimolecular multivalent vaccines, in which multiple carbohydrate antigens are displayed in the context of a single polypeptide backbone. It is the hope that each generation of vaccines represents a move closer to achieving the ultimate objective of developing broadly useful, robust anticancer vaccines.
Antibodies against oncoproteins E6 and E7 of human papillomavirus types 16 and 18 in patients with head-and-neck squamous-cell carcinoma (2000)

Human papillomaviruses (HPVs) have been recognized as an essential pathogenic factor in anogenital cancer. HPV DNA has also been found in a subgroup of head-and-neck squamous-cell carcinomas (HNSCCs), and a causative role of the virus in the development of these tumors has been suggested by the concomitant inactivation of the tumor-suppressor protein pRb. Using 4 second-generation ELISAs, we found antibodies against at least 1 of the oncoproteins E6 and E7 of the high-risk HPV types 16 and 18 in 11 of 92 sera (12%) taken from HNSCC patients at or near diagnosis, in 1 of 52 sera (2%) taken from HNSCC patients >6 months after diagnosis and in 10 of 288 sera (3. 5%) taken from sex- and age-matched healthy control individuals of the normal population. In 11 of the 12 seropositive HNSCC cases, antibodies were directed against HPV16 proteins. In patients, the HPV16 antibodies were mostly of high titer, and in 6 cases, antibodies against both HPV16 oncoproteins were present. Seven of the 8 HPV16 antibody-positive sera from the control group were of low titer, and none of the 10 antibody-positive sera reacted with both oncoproteins of the same HPV type. The HPV type of the antigens detected by the antibodies in HNSCC patients correlated well with that of the HPV DNA found in the tumor. Of 19 patients known to have HPV16 DNA-positive tumors, 7 (37%) also had HPV16 E6 and/or E7 antibodies. Our finding suggests that the antibodies were formed in an immune response against HPV E6 and E7 proteins expressed in the HNSCC and thus strongly supports the concept of a biologically active role of HPV in the development of a subgroup of HNSCC.
Crustacean parasites associated with hermit crabs from the western Mediterranean Sea, with first documentation of egg predation by the burrowing barnacle Trypetesa lampas (Cirripedia: Acrothoracica: Trypetesidae) (2011)

Parasitic isopods (family Bopyridae) and burrowing barnacles (family Trypetesidae) infesting hermit crabs were investigated from shallow subtidal collections made along the southeastern coast of Spain in 2009. A total of 713 specimens of Clibanarius erythropus (Latreille, 1818) and 82 Calcinus tubularis (L., 1767) were examined. Gastropod shells and worm tubes inhabited by hermit crabs were collected by hand while snorkeling and were cracked to determine host species, size, sex and presence of eggs. Two species of bopyrid isopods were found on C. erythropus: the branchial parasite Bopyrissa fraiseii (Carayon, 1943) and the abdominal parasite Parathelges cardonae Codreanu and Codreanu in Codreanu, 1968. Among all C. erythropus examined, Bopyrissa fraiseii was found on 0.6% of hermit crabs and P. cardonae was found on 0.3%. A redescription of P. cardonae is provided and the species is documented with light and scanning electron microscopy for the first time. No Calcinus tubularis harbored parasitic isopods, but one specimen was parasitized by an unidentified rhizocephalan barnacle of the genus Septosaccus (1.2%). The burrowing barnacle Trypetesa lampas (Hancock, 1849) was found associated with both hermit crab species and evidence of predation on host eggs by this barnacle is shown for the first time. Trypetesa lampas was found in 4.2% of the shells collected. The present study expands our knowledge of the parasite fauna of hermit crabs from the Mediterranean Sea and indicates that additional research is needed to determine the impact of trypetesid egg predators on hermit crab populations.
In Vitro and In Vivo Bacteriolytic Activities of Escherichia coli Phages: Implications for Phage Therapy (2004)

Four T4-like coliphages with broad host ranges for diarrhea-associated Escherichia coli serotypes were isolated from stool specimens from pediatric diarrhea patients and from environmental water samples. All four phages showed a highly efficient gastrointestinal passage in adult mice when added to drinking water. Viable phages were recovered from the feces in a dose-dependent way. The minimal oral dose for consistent fecal recovery was as low as 10(3) PFU of phage per ml of drinking water. In conventional mice, the orally applied phage remained restricted to the gut lumen, and as expected for a noninvasive phage, no histopathological changes of the gut mucosa were detected in the phage-exposed animals. E. coli strains recently introduced into the intestines of conventional mice and traced as ampicillin-resistant colonies were efficiently lysed in vivo by phage added to the drinking water. Likewise, an in vitro phage-susceptible E. coli strain freshly inoculated into axenic mice was lysed in vivo by an orally applied phage, while an in vitro-resistant E. coli strain was not lysed. In contrast, the normal E. coli gut flora of conventional mice was only minimally affected by oral phage application despite the fact that in vitro the majority of the murine intestinal E. coli colonies were susceptible to the given phage cocktail. Apparently, the resident E. coli gut flora is physically or physiologically protected against phage infection.