gebhart/patrepeval huggingface dataset:
Temporal variation of an initial marine biofilm community and its effects on larval settlement and metamorphosis of the tubeworm Hydroides elegans (2005)

Planktonic larvae of many sessile marine invertebrates settle and metamorphose preferentially on surfaces covered by bacterial biofilms. The polychaete tubeworm Hydroides elegans is induced to settle by biofilms and is the primary colonizer of newly submerged surfaces in the succession of macrofouling invertebrates in Pearl Harbor, Hawaii, USA. This study examines the succession of bacterial community composition and cell density of marine biofilms, and how temporal changes in biofilms affect settlement of H. elegans . Settlement assays of H. elegans were conducted on naturally formed biofilms of increasing age from Pearl Harbor. Denaturing gradient gel electrophoresis and epifluoresence microscopy were used to identify community composition and densities of bacterial cells in biofilms. Results of this study suggest that increasing densities of a stable community, rather than a shift in dominant species composition of biofilm bacteria, are probably responsible for the primary colonization of submerged surfaces by H. elegans in Pearl Harbor. However, the current data leave open the question of why larvae of other biofouling invertebrate species known to settle in response to biofilms recruit to surfaces only at later times.
Improved Oxygenation in a Randomized Trial of Inhaled Nitric Oxide for Persistent Pulmonary Hypertension of the Newborn (1997)

Although mortality and ECMO use were similar for both treatment groups using this study size and design, sustained improvement in oxygenation with NO and better oxygenation at initiation of ECMO may have important clinical benefits. We speculate that modification of treatment to include specific lung expansion strategies with NO treatment and recognition that early improvement of oxygenation may be sustained with NO may lead to reduced use of ECMO in NO treated patients compared with controls.
Nucleosides and nucleotides. 97. Synthesis of new broad spectrum antineoplastic nucleosides, 2'-deoxy-2'-methylidenecytidine (DMDC) and its derivatives (1991)

A new type of antineoplastic nucleoside, 2'-deoxy-2'-methylidenecytidine (DMDC) has been synthesized from the corresponding 2'-keto pyrimidine nucleosides 3 and 8 by the Wittig reaction. During the course of the reaction, we found that an intermediate betaine could pick a proton from the excess triphenylphosphonium bromide to form the 2'-phosphonium salts 5 and 10, which could be further converted into the 2'-deoxy-2'-methylidene nucleosides 4 and 9 by treatment with sodium hydride. Various 5-substituted DMDC derivatives 19a-e,h and their uracil congeners 16a-h were also synthesized from the corresponding 5-substituted uridines 12a-f,h. Among them, DMDC as well as 2'-deoxy-2'-methylidene-5-fluorocytidine (19a) showed potent antileukemic activity against murine L1210 cells in culture. The activity of DMDC and 19a toward various human tumor cells in culture compared with 1-beta-D-arabinofuranosylcytosine and 5-fluorouracil was also examined. In vivo antitumor activity of DMDC against L1210 was also described.
Instrumentation for treatment of cancer using proton and light-ion beams (1993)

Clinical trials using accelerated heavy charged-particle beams for treating cancer and other diseases have been performed for nearly four decades. Recently there have been worldwide efforts to construct hospital-based medically dedicated proton or light-ion accelerator facilities. To make such accelerated heavy charged-particle beams clinically useful, specialized instruments must be developed to modify the physical characteristics of the particle beams in order to optimize their biological and clinical effects. This article reviews the beam modifying devices and associated dosimetric equipment developed specifically for controlling and monitoring the clinical beams.
Sarilumab for the treatment of ankylosing spondylitis: results of a Phase II, randomised, double-blind, placebo-controlled study (ALIGN) (2014)

The ALIGN study shows that IL-6Rα blockade with sarilumab was not an effective treatment for AS. Sarilumab was generally well tolerated with a manageable safety profile.
Temporal sequence of major biochemical events during blood bank storage of packed red blood cells. (2012)

Our results demonstrate that changes in the macromolecular organisation of membrane proteins on the RBC occur early in storage and suggest that lipid peroxidation and/or oxidative damage to the membrane are responsible for irreversible morphological changes and loss of function during red cell storage.
Fiber-optic confocal microscope using a MEMS scanner and miniature objective lens (2007)

We designed and constructed a single-fiber-optic confocal microscope (SFCM) with a microelectromechanical system (MEMS) scanner and a miniature objective lens. Axial and lateral resolution values for the system were experimentally measured to be 9.55 mum and 0.83 mum respectively, in good agreement with theoretical predictions. Reflectance images were acquired at a rate of 8 frames per second, over a 140 mum x 70 mum field-of-view. In anticipation of future applications in oral cancer detection, we imaged ex vivo and in vivo human oral tissue with the SFCM, demonstrating the ability of the system to resolve cellular detail.
Brittle-1, an Adenylate Translocator, Facilitates Transfer of Extraplastidial Synthesized ADP-Glucose into Amyloplasts of Maize Endosperms1 (1998)

Amyloplasts of starchy tissues such as those of maize (Zea mays L.) function in the synthesis and accumulation of starch during kernel development. ADP-glucose pyrophosphorylase (AGPase) is known to be located in chloroplasts, and for many years it was generally accepted that AGPase was also localized in amyloplasts of starchy tissues. Recent aqueous fractionation of young maize endosperm led to the conclusion that 95% of the cellular AGPase was extraplastidial, but immunolocalization studies at the electron- and light-microscopic levels supported the conclusion that maize endosperm AGPase was localized in the amyloplasts. We report the results of two nonaqueous procedures that provide evidence that in maize endosperms in the linear phase of starch accumulation, 90% or more of the cellular AGPase is extraplastidial. We also provide evidence that the brittle-1 protein (BT1), an adenylate translocator with a KTGGL motif common to the ADP-glucose-binding site of starch synthases and bacterial glycogen synthases, functions in the transfer of ADP-glucose into the amyloplast stroma. The importance of the BT1 translocator in starch accumulation in maize endosperms is demonstrated by the severely reduced starch content in bt1 mutant kernels.
High-resolution quantitative phase-contrast microscopy by digital holography (2005)

Techniques of digital holography are improved in order to obtain high-resolution, high-fidelity images of quantitative phase-contrast microscopy. In particular, the angular spectrum method of calculating holographic optical field is seen to have significant advantages including tight control of spurious noise components. Holographic phase images are obtained with 0.5 mum diffraction-limited lateral resolution and largely immune from the coherent noise common in other holographic techniques. The phase profile is accurate to about 30 nm of optical thickness. Images of SKOV-3 ovarian cancer cells display intracellular and intranuclear organelles with clarity and quantitative accuracy.
An Expanding Role for CD40L and Other Tumor Necrosis Factor Superfamily Ligands in HIV Infection (2002)

Immunostimulatory members of the tumor necrosis factor (TNF) superfamily (TNFSF) of ligands are known to be important regulators of the immune system. These trimeric molecules interact with members of the TNF receptor superfamily (TNFRSF) to stimulate immune cells. Of the TNFSF molecules, CD40 ligand (CD40L, also called CD154 or TNFSF5) is the most crucial molecule for activating antigen-presenting cells (APCs) and thereby initiating the immune response. Evidence has accrued indicating that HIV infection either selectively depletes those CD4(+) T cells that express CD40L in response to antigen or down-regulates CD40L expression by these cells. Because CD40L expression is necessary for the immune defense against HIV and opportunistic infections, an insufficiency of CD40L could contribute to the progression of AIDS. CD40L contributes to the antiviral mechanisms of the host by inducing anti-HIV beta-chemokines and activating CD8(+) T cells. However, CD40L stimulation can lead to enhanced HIV replication under certain experimental conditions, due to its immune activating properties and the need for cellular activation for high-level HIV production. On balance, it is believed that reversing the relative CD40L deficiency seen in HIV infection will be important for immune restoration in AIDS. In addition, adding CD40L to a therapeutic or preventative vaccine could lead to strengthened antiviral immunity. Because of the complexities in delivering this molecule, a number of forms of CD40L have been developed, and one form of soluble CD40L has been tested in humans. New strategies are being developed to translate the profoundly immunostimulatory effects of CD40L found in animal models to humans with HIV infection.
An extended Doherty amplifier with high efficiency over a wide power range (2001)

An extension of the Doherty amplifier, which maintains high efficiency over a wide range of output power (>6 dB), is presented in this paper. This extended Doherty amplifier is demonstrated experimentally with InGaP/GaAs heterojunction bipolar transistors at 950 MHz. Power-added efficiency (PAE) of 46% is measured at P/sub 1dB/ of 27.5 dBm and 45% is measured at 9 dB backed off from P/sub 1dB/. Additionally, PAE of at least 39% is maintained for over an output power range of 12 dB backed off from P/sub 1dB/. This is an improvement over the classical Doherty amplifier, where high efficiency is typically obtained up to 5-6 dB backed off from P/sub 1dB/. Compared to a single transistor class-B amplifier with similar gain and P/sub 1dB/, the extended Doherty amplifier has PAE 2.6 /spl times/ higher at 10 dB back off and 3 /spl times/ higher at 20 dB back off from P/sub 1dB/. Under different bias and output matching conditions, the amplifier was also evaluated with CDMA signals. At the highest measured power of 25 dBm, the extended Doherty amplifier achieves a PAE of 45% with an adjacent channel power ratio of -42 dBc. Generalized design equations are also derived and the consequences of finite device output impedance on amplifier gain and linearity are explored.
The effect of thermal annealing on GaN nucleation layers deposited on (0001) sapphire by metalorganic chemical vapor deposition (1994)

It has been shown by optical and x-ray measurements that GaN nucleation layers deposited at 540 °C on (0001)-oriented sapphire substrates have a measurable crystalline component, although the x-ray data and the lack of absorbance features near the direct band gap of GaN suggest that the crystallite size is very small. Upon annealing to higher temperatures, the crystallite size increases and the crystal perfection improves markedly, until at temperatures near those empirically determined to be optimum for growth of an epitaxial overlayer, it approaches that of good quality single-crystal material. Most of the recrystallization of the nucleation layer occurs during the ramp from its deposition temperature to the growth temperature of the GaN overlayer, and there appears to be no advantage to prolonged annealing at high temperatures prior to epitaxial growth. In fact, x-ray diffractometer results suggest that the nucleation layer deteriorates after 20 min at temperatures above 1015 °C, under the conditions used in this study.
Stimulation of the Semicircular Canals Via the Rotary Chair as a Means to Test Pharmacologic Countermeasures for Space Motion Sickness (2004)

Results showed a rank order of efficacy of scopolamine > promethazine > placebo > meclizine > lorazepam. Scopolamine significantly increased rotation time, but none of the treatments resulted in a significant delay to onset of symptoms.
Three-dimensional reconstruction of the left ventricle using RP30A GSPECT (2003)

RP30A (2-methoxy isobutyl isonitrile labeled with Tc-99m) is a new myocardial perfusion agent which permits gated single-photon-emission computerized tomography (GSPECT) due to the high count of the Tc-99m. Three-dimensional reconstruction of the left ventricle (LV) from GSPECT with Tc-RP30A was performed on A PDP-11/34 computer and provided useful information about myocardial shape, thickness, and wall motion and visualization of the epicardial and endocardial surfaces in end-diastole and end-systole (ES). Three-dimensional perspective views were generated which could be rotated to view them from different angles. Quantitative wall motion and thickness analysis was performed by measurements along radii emanating from the center of the endocardial long axis in ES. Bull's-eye and four-leaf diagrams were plotted for observing abnormal regions of wall motion and wall thickening or thinning. In addition to its value as a myocardial perfusion agent, three-dimensional reconstruction of the LV with RP30A GSPECT provides a good method for evaluating LV geometry and function by wall motion and thickening analysis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Plasma doping of high aspect ratio structures (2014)

Doping high aspect ratio (HAR) structures poses a major challenge for device manufacturers, particularly in the advanced memory and CMOS image sensor technology spaces. CMOS technology scaling limitations have led to the emergence of vertically integrated cells, which leading-edge chipmakers are already introducing into mass production. Each case involves HAR structures that may require doping to improve or even enable device operation. Meanwhile, scaling is driving CMOS image sensor device challenges in pixel-to-pixel isolation, dark-current reduction, and noise reduction. This study demonstrates the capability of plasma doping as an enabling technology for doping in these challenging HAR structures. Plasma doping process flow optimization and analytical techniques, such as secondary ion mass spectroscopy (SIMS), are demonstrated.
Formation of Sodium Dodecyl Sulfate-stable Fibronectin Multimers (1996)

Fibronectin exists in a soluble form in body fluids and as a fibrillar component of the extracellular matrix. Matrix fibronectin associates as large complexes in SDS unless a reducing reagent is also present. This observation suggests that complex formation is due to interprotomeric disulfides that form by thiol-disulfide exchange. To localize the presumptive new disulfides, we labeled protomeric fibronectin by the chloramine-T method or with 125I-Bolton-Hunter reagent, incorporated 125I-fibronectin into the matrix of cultured fibroblasts, and subjected matrix fibronectin to acid or cyanogen bromide digestion. When cyanogen bromide digests of matrix 125I-fibronectin and protomeric 125I-fibronectin labeled with Bolton-Hunter reagent were analyzed by two-dimensional polyacrylamide gel electrophoresis in SDS, with the first dimension being nonreducing and the second reducing, we were not able to identify any fragments of matrix fibronectin that migrated as high molecular weight complexes in the first dimension. Limited acid digestion of matrix 125I-fibronectin also dissociated the majority of the high molecular weight complexes. Since we could account for all of the parts of fibronectin that contain cysteine or cystine, we conclude that matrix fibronectin is not stabilized by interprotomeric disulfides. We propose, instead, that stabilization is mediated by noncovalent protein-protein interactions that are sensitive to reduction, cyanogen bromide digestion, or limited acid digestion.
A simplified analog control circuit of a maximum power point tracker (2008)

This work proposes an analog maximum power point tracker (MPPT) control circuit for photovoltaic arrays. A clocked auto-oscillation method is used in this control circuit. This control principle is based on sensing the output current to achieve MPPT function. Multiplication of array voltage and current is not needed. The cost and volume of MPPT is reduced and MPPT efficiency is about 94%.
Escherichia coli Open Reading Frame 696 Is idi , a Nonessential Gene Encoding Isopentenyl Diphosphate Isomerase (1999)

Isopentenyl diphosphate isomerase catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In eukaryotes, archaebacteria, and some bacteria, IPP is synthesized from acetyl coenzyme A by the mevalonate pathway. The subsequent isomerization of IPP to DMAPP activates the five-carbon isoprene unit for subsequent prenyl transfer reactions. In Escherichia coli, the isoprene unit is synthesized from pyruvate and glyceraldehyde-3-phosphate by the recently discovered nonmevalonate pathway. An open reading frame (ORF696) encoding a putative IPP isomerase was identified in the E. coli chromosome at 65.3 min. ORF696 was cloned into an expression vector; the 20.5 kDa recombinant protein was purified in three steps, and its identity as an IPP isomerase was established biochemically. The gene for IPP isomerase, idi, is not clustered with other known genes for enzymes in the isoprenoid pathway. E. coli FH12 was constructed by disruption of the chromosomal idi gene with the aminoglycoside 3'-phosphotransferase gene and complemented by the wild-type idi gene on plasmid pFMH33 with a temperature-sensitive origin of replication. FH12/pFMH33 was able to grow at the restrictive temperature of 44 degrees C and FH12 lacking the plasmid grew on minimal medium, thereby establishing that idi is a nonessential gene. Although the V(max) of the bacterial protein was 20-fold lower than that of its yeast counterpart, the catalytic efficiencies of the two enzymes were similar through a counterbalance in K(m)s. The E. coli protein requires Mg(2+) or Mn(2+) for activity. The enzyme contains conserved cysteine and glutamate active-site residues found in other IPP isomerases.
Discovery of AM-7209, a Potent and Selective 4-Amidobenzoic Acid Inhibitor of the MDM2–p53 Interaction (2014)

Structure-based rational design and extensive structure-activity relationship studies led to the discovery of AMG 232 (1), a potent piperidinone inhibitor of the MDM2-p53 association, which is currently being evaluated in human clinical trials for the treatment of cancer. Further modifications of 1, including replacing the carboxylic acid with a 4-amidobenzoic acid, afforded AM-7209 (25), featuring improved potency (KD from ITC competition was 38 pM, SJSA-1 EdU IC50 = 1.6 nM), remarkable pharmacokinetic properties, and in vivo antitumor activity in both the SJSA-1 osteosarcoma xenograft model (ED50 = 2.6 mg/kg QD) and the HCT-116 colorectal carcinoma xenograft model (ED50 = 10 mg/kg QD). In addition, 25 possesses distinct mechanisms of elimination compared to 1.
Human Infection Due to Recombinant Vaccinia–Rabies Glycoprotein Virus (2001)

Rabies is a fatal viral disease transmitted from animals to humans. It causes more than 35,000 human deaths per year.1 Successful application of veterinary vaccines can eliminate canine rabies in an area, but control of rabies in free-ranging carnivores requires other strategies, such as oral vaccination.2 Live viral vaccines containing modified live rabies or recombinant vaccinia–rabies glycoprotein virus, placed in a bait, are used for disease control in Europe and North America.2–5 In the United States, more than 22 million doses of vaccinia–rabies glycoprotein vaccine were distributed from 1990 to 2000, mainly to control rabies in raccoons in the . . .
Molecular orbital studies on the structure of nucleoside analogs. IV. Conformation of 3‐deazapurine nucleosides (1984)

Abstract Conformational properties of 3‐deazapurine nucleosides (namely, 3‐deazaadenosine and 3‐deazaguanosine) have been investigated by the PCILO method. Both C(2′)‐endo and C(3′)‐endo sugar puckers have been considered and the results indicate that the conformational preferences of these nucleoside analogs are quite different from those of their parent nucleosides adenosine and guanosine, respectively. This result has been correlated in terms of the biological inactivity of these nucleoside analogs.
Ten Years’ Experience With Alendronate for Osteoporosis in Postmenopausal Women (2004)

This multinational randomized double-blind trial, the Alendronate Phase III Osteoporosis Treatment Study, examined the results of alendronate therapy in postmenopausal women with osteoporosis who now have been followed for 10 years. A total of 227 women completed all phases of the study. Those participating were assigned to receive 5 or 10 mg of alendronate orally or placebo each day. The primary end point was the change in bone mineral density (BMD) in the lumbar spine. BMD also was measured at the femoral neck, trochanter, total proximal femur, forearm region, and the total body. From 17% to 31% of women in the various treatment groups had preexisting vertebral fractures. BMD continued to increase in the later years of the study in women given 5 or 10 mg of alendronate daily. The mean cumulative increase after 10 years in women taking 10 mg daily was 13.7%. Markers of bone remodeling (urinary N-telopeptides of type I collagen, bone-specific alkaline phosphatase) decreased, and this effect continued through 10 years of treatment. These markers increased within a year after alendronate was discontinued, although mean levels remained below baseline. There were no significant group differences in new vertebral fractures. The 3 groups also had similar safety profiles in the last 3 years of the study. No deaths were ascribed to alendronate therapy. Alendronate therapy continued to be effective over 10 years in these postmenopausal women, as estimated by both BMD measurements and effects on bone remodeling. The antifracture effect of alendronate did not appear to decrease over time.
Specific Deposition of Serum Amyloid A Protein 2 in the Mouse (1987)

The homogenates of amyloid-laden spleens prepared from CBA mice were analysed by SDS-PAGE and immunoblotting employing rat anti-murine monoclonal antibody, MSA 4-26. The results showed that the precursor of amyloid A protein (AA), serum amyloid A protein 2 (SAA2), and SAA intermediates with molecular weights of 10,000, 9000, and 8000 were contained in amyloid-laden tissues. The experiment using sonicated spleen cells and acute phase murine sera showed a delay in the degradation rate of SAA2 on cell fragments and the remains of SAA1 in supernatants. This result can explain disappearance of SAA2 from the murine serum during amyloidogenesis in vivo.