gebhart/patrepeval huggingface dataset:
Gene Therapy for HIV-1 Infection (2011)

The introduction of the highly active antiretroviral therapy (HAART) for the treatment of HIV-1-infection has dramatically improved the quality of life and the survival of HIVinfected patients. HAART can effectively suppress virus replication and thereby helps to preserve immune functions. However, as HIV-1 persists in latently infected reservoirs (Finzi et al., 1997), complete eradication of the virus by antiretroviral drugs has never been achieved and life-long treatment is required. Moreover, emerging viral resistance and drug toxicity restrict long-term therapeutic efficacy (Brinkman et al., 1999; Vigouroux et al., 1999). As a consequence, HAART has not had a major impact on the global prevalence of HIVinfection and there is no vaccine in sight that could prevent further virus spread. In addition to HAART and vaccines, gene therapy approaches for HIV-1 infection have been under investigation for more than two decades. Gene therapy could theoretically overcome the limitations of standard antiretroviral drug therapy and facilitate sustained suppression of virus replication after only few treatment cycles. Moreover, the choice of adequate genes or combinations of genes and expression systems could greatly reduce toxicity and prevent the generation of resistant virus strains. Although gene therapy is an expensive and technically challenging therapy today, future developments could simplify the procedures involved and bring down costs. Two basic gene therapeutic strategies for immune reconstitution of AIDS patients have been developed and the safety and efficacy of different approaches have been examined in preclinical and clinical studies. The first strategy aims to specifically kill HIV-infected cells by enhancing the antiviral host immune responses. The second approach, termed ‘intracellular immunization’, is based on the expression of antiviral genes that prevent HIV-1 replication in its target cells. Furthermore, therapeutic or prophylactic vaccination strategies that aim to enhance anti-HIV immunity and use DNA or viral vectors to express the viral antigens can formally be classified as gene therapy approaches. However, such vaccination strategies are not in the scope of this review.
New Forms of Insulin (1972)

This paper reviews some recent developments in insulin purification and formulation. Neutral Regular insulin (unbuffered Regular insulin with pH adjusted to neutrality, designated NRI) maintained nearly full potency when stored at room temperature for twelve months, while the potency of acid Regular (“commercial”) insulin (ARI) had dropped 20 per cent. When NRI and ARI were administered in combination with NPH or Ultralente insulin, comparable time activity responses were elicited. In fasted normal subjects subcutaneous doses of NRI and ARI gave similar blood glucose responses. Thirty-seven patients with allergy to commercially available insulin were treated with one or both of two highly purified insulins (single peak and single component pork insulin). Improvement occurred in 78 per cent. Single component insulin was usually, but not always, superior to single peak insulin when both were tested in the same patient. Insulin was administered orally with an absorption promoter, Brij 98, to twenty normal and thirteen diabetic fasted subjects in crossover studies. Under optimum conditions, definite responses were observed in about 50 per cent of subjects. Serum insulin measurements in the normals and diabetics revealed that increased concentrations were not necessarily associated with falls in blood glucose concentrations in spite of delivery of the insulin by the portal route. Because of the amounts of insulin required, the limitations of test conditions, and a high incidence of nausea, this project has been discontinued.
Hypophosphatemia (2007)

Current evidence regarding the clinical consequences of hypophosphatemia is not straightforward. Given the potentially different implications of hypophosphatemia among various patient groups, this commentary touches on patients with low serum phosphate after acute hospitalization, those with chronic ambulatory hypophosphatemia, and those with hypophosphatemia in the setting of advanced renal disease. Finally, this commentary examines the evidence regarding how best to replete phosphorous in the hypophosphatemic patient.
Efficiency of removal of nitrogen, phosphorus, and zinc from domestic wastewater by a constructed wetland system in rural areas: a case study (2008)

The effluent from the combined household wastewater treatment facilities used in unsewered areas of Japan is generally high in nitrogen (N) and phosphorus (P). In Japan, environmental quality standards for zinc (Zn) pollution were enacted recently because of the toxicity of Zn to aquatic ecosystems. In 2004 a fallow paddy field at the Koibuchi College of Agriculture and Nutrition was converted into a surface-water-flow constructed wetland (500 m(2)) to clean the effluent from the combined household wastewater treatment facility of a dormitory (100 residents) before discharge to a pond. We evaluated N and P removal efficiencies and the fate of soluble Zn in the wetland from April 2006 to March 2007. Wetland influent contained an average of 18.3 mg L(-1) total N and 1.86 mg L(-1) total P. In the effluent from the wetland, average total N concentration was 10.3 mg L(-1) and average total P was 0.90 mg L(-1). Average removal rates were 0.37 g m(-2) d(-1) for total N and 0.050 g m(-2) d(-1) for total P (percentage removal rates of 40% and 48%, respectively). Soluble Zn concentration decreased from 0.041 in the influent to 0.023 mg L(-1) after passing through the wetland. The average Zn removal rate during the year was 0.0007 g m(-2) d(-1) (percentage removal rate 37%).
CyDNA: Synthesis and Replication of Highly Cy-Dye Substituted DNA by an Evolved Polymerase (2010)

DNA not only transmits genetic information but can also serve as a versatile supramolecular scaffold. Here we describe a strategy for the synthesis and replication of DNA displaying hundreds of substituents using directed evolution of polymerase function by short-patch compartmentalized self-replication (spCSR) and the widely used fluorescent dye labeled deoxinucleotide triphosphates Cy3-dCTP and Cy5-dCTP as substrates. In just two rounds of spCSR selection, we have isolated a polymerase that allows the PCR amplification of double stranded DNA fragments up to 1kb, in which all dC bases are substituted by its fluorescent dye-labeled equivalent Cy3- or Cy5-dC. The resulting "CyDNA" displays hundreds of aromatic heterocycles on the outside of the DNA helix and is brightly colored and highly fluorescent. CyDNA also exhibits significantly altered physicochemical properties compared to standard B-form DNA, including loss of silica and intercalating dye binding, resistance to cleavage by some endonucleases, an up to 40% increased apparent diameter as judged by atomic force microscopy and organic phase partitioning during phenol extraction. CyDNA also displays very bright fluorescence enabling significant signal gains in microarray and microfluidic applications. CyDNA represents a step toward a long-term goal of the encoded synthesis of DNA-based polymers of programmable and evolvable sequence and properties.
Electronic structure of anatase TiO2 oxide (1994)

Photoemission spectromicroscopy was used to investigate the electronic structure of TiO2 anatase single crystals and polycrystalline thin films. The stoichiometry and the degree of oxidation of as-grown crystals, as-deposited films, as well as of thermally annealed samples in different atmospheres, were analyzed, based on the Ti 2p and O 1s core levels, with an energy resolution of 0.4 eV. The experimental density of states (DOS) was found to be in agreement with the theoretical DOS reported in the literature for anatase crystals, and shows some characteristics similar to the experimental DOS reported for rutile crystals. In reduced samples, the experimental DOS is characterized by intense emission in the region of O 2p bonding orbitals, and does not exhibit an appreciable density of states in the band gap. As-grown crystals exhibit small band gap emission (a few percent of the valence band VB signal) at about 0.8 eV, which is attributed to Ti3+ (3d) defect states. Annealing the crystals at high temperatures in O2 or subsequent thermal reduction in an Ar–H2 mixture (95%–5%) produces nearly stoichiometric surfaces with smaller or undetectable density of Ti3+ states. In addition, some redistribution of the spectral weight is observed in the VB spectra.
Gradient of RGD-dependent entry of adenoviral vector in nasal and intrapulmonary epithelia: implications for gene therapy of cystic fibrosis. (1996)

The efficiency with which adenoviral vectors infect airway epithelial cells in vivo is unclear despite extensive preclinical and clinical studies. Our hypothesis is that gene transfer is limited by vector internalization which is mediated by binding of a fiber with a cellular receptor and the RGD motif of the penton base of the virus with cellular alpha v beta integrin. Experiments in mice demonstrate an anatomical gradient of susceptibility to adenoviral vector-mediated gene transfer with epithelia of proximal structures, such as nose and trachea, much less infectable than the distal noncartilaginous airway. Throughout the airway, gene transfer is dependent on RGD-mediated interactions which are rate limiting in the distal lung. A panel of tissues from cystic fibrosis and non-cystic fibrosis patients was analyzed for expression of alpha v beta 5 integrin which is capable of mediating RGD-dependent uptake of vector. Luminal epithelial cells of the nose and trachea were void of alpha v beta 5 expression whereas abundant expression of this integrin was present in virtually all epithelial cells of distal conducting airway. These findings could explain difficulties we and others have had in correcting the functional deficit of cystic fibrosis nasal epithelia and suggest that gene transfer efficiency may be greater in distal human lung.
Electrical properties of SbSI crystals in the vicinity of the ferroelectric curie point (1986)

The electrical properties of SbSI crystals have been studied with particular reference to the ferroelectric phase transition. The dielectric constant along the c-axis obeys the Curie-Weiss law with C = 2.54 × 105 K and T0 = 15.2°C. The coefficients in the Gibbs free energy expanded by the electric polarization have been determined to be ξ = -3.02 × 108 Vm5C-3 and ζ = 6.99 × 109 Vm9C-5 by using the temperature dependence of the dielectric constant and the spontaneous polarization. An anomaly in the electric conductivity has been found at the Curie point. Effects of substitution of Bi for Sb in SbSI on the behavior of the phase transition have been also studied. The Curie point decreases with increasing Bi concentration x according to the relation Tc(x) = Tc(0) - 520x (°C). The phase transition, which is a first-order for pure SbSI, becomes a second-order between x = 0.10 and 0.17.
Trends in Prostate Cancer in the United States (2012)

In the United States, prostate cancer is the most commonly diagnosed non-skin cancer and the second leading cause of cancer death. The American Cancer Society estimates that 241 740 American men will be diagnosed with the disease and 28 170 men will die of it in 2012. Prostate cancer demographics have changed dramatically over the past 30 years. The prostate cancer age-adjusted incidence rate increased through the 1980s and peaked in the early to mid-1990s. The incidence rate has declined since. American mortality rates rose through the 1980s and peaked in 1991. Today, the American incidence rates are below 1975 levels. Both the incidence rate and the 5-year survival rates are heavily influenced by the introduction of serum prostate-specific antigen test and the widespread use of it in cancer screening. The effect of screening on prostate cancer mortality is less certain. Screening has caused a dramatic increase in the number and proportion of men diagnosed with localized disease. Outcomes studies among men treated with radical prostatectomy show that greater than 30% serum prostate-specific antigen relapse rates are common. This suggests that many men who are diagnosed with "localized early stage disease" actually have "apparently localized early stage disease," which is really low-volume metastatic disease.
The Kramers–Kronig Receiver (2017)

This tutorial reviews the operation principles and the various implementations of the Kramers–Kronig receiver, which has been recently shown to offer unprecedented opportunities in the design of high performance and reduced complexity optical transceivers.
An Expeditious Synthesis of Isofagomine (2007)

An expeditious synthesis of isofagomine, from d-arabinose, is reported.
Halogenated Boron Subphthalocyanines as Light Harvesting Electron Acceptors in Organic Photovoltaics (2011)

By tuning the frontier orbital energies through selective halogenation of the periphery of the organic framework, new light harvesting electron acceptors based on boron subphthalocyanine chloride (SubPc) have been made. Planar heterojunction organic photovoltaics made using a Cl6-SubPc acceptor deliver an exceptionally high open-circuit voltage (∼1.3 V), good power conversion efficiency (∼2.7%) and improved operational stability in comparison to similar devices made using C60 as the acceptor material. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mechanical, cellular, and molecular factors interact to modulate circulating endothelial cell progenitors (2004)

It appears that there are two classes of human circulating endothelial cell (EC) progenitors, CD34+ and CD34-CD14+ cells. Attention has focused on CD34+ cells, yet CD34-CD14+ monocytic cells are far more abundant and may represent the most common class of circulating EC progenitor. Little is known about molecular or physiological factors that regulate putative CD34-CD14+ EC progenitor function, although factors secreted by other blood and cardiovascular cells to which they are exposed probably affect their behavior. Hypoxia and stretch are two important physiological stimuli known to trigger growth factors in cardiovascular cells and accordingly may modulate EC progenitors. To investigate the impact of these environmental parameters on EC progenitors, EC production in CD34-CD14+ cultures was evaluated. Our data indicate that neither stretch nor hypoxia alters EC production by EC progenitors directly but do so indirectly through their effects on cardiovascular cells. Conditioned media (CM) from coronary artery smooth muscle cells inhibit EC production in culture, and this inhibition is stronger if the coronary smooth muscle cells have been subjected to cyclic stretch. In contrast, cardiomyocyte CM increases EC cell number, an effect that is potentiated if the myocytes have been subjected to hypoxia. Significantly, EC progenitor responses to CM are altered by the presence of CD34-CD14- peripheral blood mononuclear cells (PBMCs). Moreover, CD34-CD14- PBMCs attenuate EC progenitor responsiveness to the angiogenic factors basic fibroblast growth factor (FGF-2), vascular endothelial cell growth factor-A165, and erythropoietin while inducing EC progenitor death in the presence of transforming growth factor-beta1 in vitro
Foreword (1995)

This special issue of ZAMP is published to honor Paul M. Naghdi for his contributions to mechanics over the last forty years and more. It is offered in celebration of his long, productive career in continuum mechanics, a career which has been marked by a passion for the intrinsic beauty of the subject, an uncompromising adherence to academic standards, and an untiring devotion to our profession.
Treating Diabetes and Obesity with an FGF21-Mimetic Antibody Activating the βKlotho/FGFR1c Receptor Complex (2012)

Fibroblast growth factor 21 (FGF21) is a distinctive member of the FGF family with potent beneficial effects on lipid, body weight, and glucose metabolism and has attracted considerable interest as a potential therapeutic for treating diabetes and obesity. As an alternative to native FGF21, we have developed a monoclonal antibody, mimAb1, that binds to βKlotho with high affinity and specifically activates signaling from the βKlotho/FGFR1c (FGF receptor 1c) receptor complex. In obese cynomolgus monkeys, injection of mimAb1 led to FGF21-like metabolic effects, including decreases in body weight, plasma insulin, triglycerides, and glucose during tolerance testing. Mice with adipose-selective FGFR1 knockout were refractory to FGF21-induced improvements in glucose metabolism and body weight. These results in obese monkeys (with mimAb1) and in FGFR1 knockout mice (with FGF21) demonstrated the essential role of FGFR1c in FGF21 function and suggest fat as a critical target tissue for the cytokine and antibody. Because mimAb1 depends on βKlotho to activate FGFR1c, it is not expected to induce side effects caused by activating FGFR1c alone. The unexpected finding of an antibody that can activate FGF21-like signaling through cell surface receptors provided preclinical validation for an innovative therapeutic approach to diabetes and obesity.
Synthesis of cinchona alkaloid sulfonamide polymers as sustainable catalysts for the enantioselective desymmetrization of cyclic anhydrides (2016)

Mizoroki–Heck polymerization of cinchona sulfonamide gave chiral polymers, which are active catalysts for enantioselective desymmetrization of cyclic anhydrides to give chiral hemiesters in high yield with high enantioselectivities.
Gene Expression Profile in Skeletal Muscle of Type 2 Diabetes and the Effect of Insulin Treatment (2002)

Type 2 diabetes is characterized by muscle insulin resistance. Nondiabetic first-degree relatives of type 2 diabetic patients have also been reported to have insulin resistance. A polygenic basis for pathogenesis of type 2 diabetes has been proposed. A gene expression profile was evaluated in the skeletal muscle of patients with type 2 diabetes while not on treatment for 2 weeks and after 10 days of intensive insulin treatment. Comparison of gene expression pattern with age-, sex-, and BMI-matched people with no family history of diabetes was performed using a microarray technique (Hu6800 arrays; Affymetrix, Santa Clara, CA). Only those gene transcripts showing > or =1.9-fold changes and an average difference in fluorescence intensity of > or =1,000 in all subjects are reported. Insulin sensitivity (SI) was measured using an intravenous glucose tolerance test. Of 6,451 genes surveyed, transcriptional patterns of 85 genes showed alterations in the diabetic patients after withdrawal of treatment, when compared with patterns in the nondiabetic control subjects. Insulin treatment reduced the difference in patterns between diabetic and nondiabetic control subjects (improved) in all but 11 gene transcripts, which included genes involved in structural and contractile functions, growth and tissue development, stress response, and energy metabolism. These improved transcripts included genes involved in insulin signaling, transcription factors, and mitochondrial maintenance. However, insulin treatment altered the transcription of 29 additional genes involved in signal transduction; structural and contractile functions; growth and tissue development; and protein, fat, and energy metabolism. Type 2 diabetic patients had elevated circulating insulin during the insulin-treated phase, although their blood glucose levels (98.8 +/- 6.4 vs. 90.0 +/- 2.9 mg/dl for diabetic vs. control) were similar to those of the control subjects. In contrast, after withdrawal of treatment, the diabetic patients had reduced SI and elevated blood glucose (224.0 +/- 26.2 mg/dl), although their insulin levels were similar to those of the nondiabetic control subjects. This study identified several candidate genes for muscle insulin resistance, complications associated with poor glycemic control, and effects of insulin treatment in people with type 2 diabetes.
Use of Instrumented Dynamic Cone Penetrometer in Pavement Characterization (2000)

The dynamic cone penetrometer data had been conventionally used for estimating the base and subgrade California bearing ratio. In recent years, a need for developing mechanistic pavement design procedures has been emphasized. However to develop mechanistic pavement design procedures, measuring engineering properties of pavement layers is essential. Two modifications to the existing dynamic cone penetrometer have been proposed in this paper for obtaining engineering properties of pavement layers. First, an ordinary dynamic cone penetrometer was instrumented with a load cell and an accelerometer to determine the energy imparted to the ground, the resistance to the penetration, and the penetration of the device into the base and subgrade. A second device consisting of a three-dimensional accelerometer embedded in a DCP-like rod was developed to measure modulus and Poisson's ratio of the base and subgrade layers. This device can be placed in the same hole drilled for the first device, thus, requiring minimum coring. Although both devices are proven to be feasible, further analysis is needed for reliably extracting information from these measurements.
A comparison of standard, “MAST” -augmented, and open-chest CPR in dogs (1980)

Hemodynamic, respiratory, and cerebral variables during 2 h of standard external CPR were studied in 5 dogs. In an additional 12 dogs, possible augmentation of these variables by Military Anti-Shock Trousers (MAST) was evaluated. In 9 dogs, external and internal cardiac massage were compared. During ventricular fibrillation (VF) and after 2 min of circulatory arrest, standard CPR basic life support (without drug support) could sustain only borderline values: systolic arterial pressure (SAP) remained at 70--80 mm Hg and mean arterial pressure (MAP) at 35--45 mm Hg. Sternal compressions increased central venous pressure (CVP) to near SAP, and also increased intracranial pressure (ICP), but less than CVP. Thus, systemic perfusion pressures (SPP, i.e., MAP-mean CVP) control value 130 mm Hg) were only 11--15 mm Hg; and cerebral perfusion pressures (CPP, i.e., MAP-ICP) were 20--32 mm Hg during CPR. Common carotid arterial blood flow (CCABF) remained at an average of 8--20% of control values. Normalization of aerobic metabolism proved impossible (final pHa of 7.1). During external CPR, MAST inflation moderately increased MAP, SAP, SPP, and CPP; and significantly increased CCABF from 6.8 to 13.2% of prearrest control. The MAST failed to improve cerebral venous PO2, pupil signs, and EEG activity. With fixed pressure IPPV/100% O2, the MAST decreased tidal volumes and PaO2 (increased shunting); and increased PaCO2 and acidemia. Epinephrine 1 mg iv improved arterial pressures but not flows. A switch to open-chest (internal) cardiac massage (OCCM) after 2 h of external CPR significantly increased arterial and perfusion pressures (decreased venous pressures) and more than doubled CCABF; and resulted in a return of EEG activity and pupillary constriction. Prolonged standard CPR, and to a lesser extent MAST-augmented CPR, seem unlikely to maintain adequate oxygen transport for vital organ systems viability, particularly the brain. OCCM might better sustain viability.