gebhart/patrepeval huggingface dataset:
Interacting Proteins Dictate Function of the Minimal START Domain Phosphatidylcholine Transfer Protein/StarD2 (2007)

The Star (steroidogenic acute regulatory protein)-related transfer (START) domain superfamily is characterized by a distinctive lipid-binding motif. START domains typically reside in multidomain proteins, suggesting their function as lipid sensors that trigger biological activities. Phosphatidylcholine transfer protein (PC-TP, also known as StarD2) is an example of a START domain minimal protein that consists only of the lipid-binding motif. PC-TP, which binds phosphatidylcholine exclusively, is expressed during embryonic development and in several tissues of the adult mouse, including liver. Although it catalyzes the intermembrane exchange of phosphatidylcholines in vitro, this activity does not appear to explain the various metabolic alterations observed in mice lacking PC-TP. Here we demonstrate that PC-TP function may be mediated via interacting proteins. Yeast two-hybrid screening using libraries prepared from mouse liver and embryo identified Them2 (thioesterase superfamily member 2) and the homeodomain transcription factor Pax3 (paired box gene 3), respectively, as PC-TP-interacting proteins. These were notable because the START domain superfamily contains multidomain proteins in which the START domain coexists with thioesterase domains in mammals and with homeodomain transcription factors in plants. Interactions were verified in pulldown assays, and colocalization with PC-TP was confirmed within tissues and intracellularly. The acyl-CoA thioesterase activity of purified recombinant Them2 was markedly enhanced by recombinant PC-TP. In tissue culture, PC-TP coactivated the transcriptional activity of Pax3. These findings suggest that PC-TP functions as a phosphatidylcholine-sensing molecule that engages in diverse regulatory activities that depend upon the cellular expression of distinct interacting proteins.
Enzymic and metabolic adaptations in the gastrocnemius, plantaris and soleus muscles of hypocaloric rats (1989)

1. The effect of hypocaloric feeding (25% of normal food intake for 21 days) of rats on the enzymic and metabolic adaptations in the gastrocnemius, plantaris and soleus muscles was studied. 2. In control and hypocaloric rats the muscle relaxation rates at 100 Hz were 35.76 and 11.38% force loss/10 ms respectively. Control rats exhibited enhanced force of muscle contraction as the frequency of stimulation increased from 10 to 100 Hz, with maximum force being at 100 Hz. Hypocaloric rats exhibited a decrease in the increment of force being exerted at high frequencies, with maintenance of force at lower stimulatory frequencies. 3. In muscles of hypocaloric rats, there were significant decreases in the maximal activities of hexokinase (17.6-37.0%), 6-phosphofructokinase (22.7-34.2%), pyruvate kinase (21.2-36.0%), citrate synthase (34.1-41.5%), oxoglutarate dehydrogenase (29.4-52.4%) and 3-hydroxyacyl-CoA dehydrogenase (26.7-32.1%), whereas the activities of glycogen phosphorylase increased (23.8-43.4%) compared with control values. 4. In soleus-muscle strip preparations of hypocaloric rats, there were significant decreases in the rates of lactate production (28.1%) and glucose oxidation (32.6%) compared with control preparations. 5. Mitochondrial preparations from muscles of hypocaloric rats incubated with various substrates exhibited decreased rates of oxygen uptake compared with control preparations. 6. In muscles of hypocaloric rats (gastrocnemius and soleus), there were significant decreases in the concentrations of glycogen (P less than 0.001) and phosphocreatine (P less than 0.001) and increases in those of pyruvate (P less than 0.001), lactate (P less than 0.001) and ADP (P less than 0.001), whereas those of ATP and AMP remained unchanged. 7. Calculated [lactate]/[pyruvate] and [ATP]/[ADP] ratios exhibited significant increases (P less than 0.05) and decreases (P less than 0.05) in muscles of hypocaloric rats respectively. 8. The results are discussed in relation to the genesis of muscle dysfunction caused by malnutrition.
Bubbles in motion (1993)

An overview of Professor John Davidson's contributions to the study of bubbles and gas-liquid two-phase flows is given, using as an example a new form of gas-liquid contactor which has been developed and applied in the flotation of minerals and wastewaters
Circular Dichroism of Biological Macromolecules (1966)

Circular dichroism, the unequal absorption of right and left circularly polarized light, is a manifestation of optical activity in the vicinity of absorption bands. To the experimental scientist interested in the conformation of macromolecules and in the sensitive response of optical activity to conformational alteration, it offers a relatively new and powerful means of understanding the environment of chromophoric residues. As a tool in the elucidation of electronic spectra, it should be useful to the theoretical scientist in identifying weakly allowed absorption bands as well as in providing rotational parameters which can be compared with the developing theory of optical activity. I have stressed application of circular dichroism, to experimental aspects of protein and nucleic acid conformation in solution. Much is still uncertain in particular quantitative details. However, even these early results shed new light and yield new information on the conformation of these molecules.
Phenotypic change from transformed to normal induced by benzoquinonoid ansamycins accompanies inactivation of p60src in rat kidney cells infected with Rous sarcoma virus. (1986)

Three benzenoid ansamycin antibiotics (herbimycin, macbecin, and geldanamycin) were found to reduce the intracellular phosphorylation of p60src at a permissive temperature (33 degrees C) in a rat kidney cell line infected with a temperature-sensitive mutant of Rous sarcoma virus. This effect was accompanied by morphological changes from the transformed to the normal phenotype. The filamentous staining pattern of actin fibers was observed in the cells treated with these antibiotics at 33 degrees C. Removal of the antibiotics allowed the cells to revert to the transformed morphology. Ansamitocin, another benzenoid ansamycin, and naphthalenoid ansamycins such as streptovaricin and rifamycins did not show this effect. Pulse-labeling of the antibiotic-treated cultures with 32Pi showed a marked reduction of 32P radioactivity incorporated into p60src. A parallel experiment with [35S]methionine showed that synthesis of p60src was slightly inhibited. The immune complex prepared by mixing the herbimycin-treated cell extracts with antibody against p60src was inactive in vitro in phosphorylating the complex itself. On the contrary, the immune complex derived from untreated cells was active in vitro even in the presence of the antibiotics. These results suggest that benzoquinonoid ansamycins have no direct effect on src kinase but destroy its intracellular environment, resulting in an irreversible alteration of p60src and loss of catalytic activity.
Mucositis in patients with hematologic malignancies: an overview (2007)

Mucosal barrier injury (mucositis) is a common complication of many treatments used in hematologic malignancies, affecting most patients whose neoplasms are treated with intensive chemotherapy, and virtually all those receiving myeloablative conditioning regimens prior to hematopoietic stem cell transplantation. Mucositis has been identified as a critical risk factor for infections and is a major driver of analgesic and total parenteral nutrition use. Patients with this complication require careful analgesic therapy, additional nursing care and longer hospitalization. To date, the measures to prevent and treat this potentially devastating complication are inadequate and limited to the control of pain, infections, bleeding and nutrition. Nevertheless, in the last decade, a better insight into the pathogenesis of the mucosal damage has led to the development of novel therapeutic options which potentially could allow a targeted approach to mucositis.
The design, synthesis, and evaluation of compounds that bind to Alzheimer's-related and HIV-1-related amyloids (2012)

Amyloids--misfolded, aggregated peptides--have been implicated in over thirty human diseases. This thesis focused on the study of two different amyloids--A[beta](1- 42) and SEVI (semen-derived enhancer of virus infection)-- associated with two distinct conditions--Alzheimer's Disease (AD) and Acquired Immune Deficiency Syndrome (AIDS), respectively. A[beta] aggregates are a hallmark of AD and may play a central, causative role in the pathogenesis of this disease. A[beta]-amyloid-targeting small molecules have, therefore, attracted wide interest as potential agents for the treatment or diagnosis of AD. This thesis describes the development of a general method to evaluate small molecule-A[beta]-amyloid binding interactions via a modified quantitative ELISA protocol. The implementation of an in vitro model to evaluate the blood-brain barrier permeability of [beta]-amyloid- targeting compounds is also discussed in this thesis. The design and evaluation of a new class of fluorescent probes that bind to A[beta] aggregates is described in this thesis. The advantage of these compounds is that their spectroscopic properties can be altered and fine-tuned via simple synthetic methods. The second portion of this thesis discusses the study of small molecules that bind to SEVI, a naturally abundant amyloid found in semen. SEVI can potentially increase the infectivity of HIV-1 in cells by up to 400,000-fold. Although the mechanism of SEVI- mediated transmission of HIV-1 remains poorly understood, evidence suggests that SEVI binds to both HIV-1 virions and cell membranes, thereby facilitating viral infection. We hypothesized that BTA-EG₆, a derivative of the well- known amyloid-binding compound Thioflavin T, could coat SEVI fibrils, thereby inhibit HIV-1 interactions with SEVI fibrils, and thus, reduce SEVI-mediated enhancement of HIV -1 infectivity. The results of these investigations are presented in this thesis. The final project described in this thesis is the design, synthesis, and evaluation of multivalent analogs of BTA-EG6. The goals of this project were 2-fold : 1) Create compounds that bind with high affinity to both A[beta] fibrils and SEVI fibrils based on the multivalent design strategy and 2) evaluate whether oligomers of the BTA moiety exhibit improved ability over the BTA monomer to inhibit SEVI-mediated enhancement of HIV-1 infectivity. The results of this project are presented in this thesis
Trench CCD image sensor (1989)

The authors describe and present simulation data on the device structure, process flow, and operation of the Trench CCD (charge coupled device), which is being developed to increase the resolution of solid-state image sensors. The device provides larger dynamic range, higher sensitivity, and no image lag together with great packing density. A charge transfer channel formed around a trench eliminates the problem of insufficient dynamic range, which restricts the resolution. Because the Trench CCD occupies a small percentage of the total pixel area, the aperture area is increased, leading to improved sensitivity. Trench fabrication technology is used in dynamic RAM production; hence, further refinements can be expected to enable improvement of CCD image sensor performance parameters other than dynamic range. These features allow the development of a Trench CCD with 2 million pixels for 2/3-in and smaller optical systems, bringing a practical consumer HDTV (high-definition TV) camera closer to reality.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon <i>Sulfolobus solfataricus</i> (2013)

The hyperthermophilic archaeon Sulfolobus solfataricus carries an extensive array of clustered regularly interspaced short palindromic repeats (CRISPR) systems able to mediate DNA degradation of invading genetic elements when complementarity to the small CRISPR-derived (cr)RNAs is given. Studying virus defence in vivo with recombinant viral variants, we demonstrate here that an unexpectedly high number of mutations are tolerated between the CRISPR-derived guide RNAs (crRNAs) and their target sequences (protospacer). Up to 15 mismatches in the crRNA still led to ∼50% of DNA degradation, when these mutations were outside the 'seed' region. More than 15 mutations were necessary to fully abolished interference. Different from other CRISPR systems investigated in vivo, mutations outside the protospacer region indicated no need for a protospacer adjacent motif sequence to confer DNA interference. However, complementarity of only 3 nucleotides between the repeat-derived 5' handle of the crRNA and nucleotides adjacent to the protospacer enabled self-recognition, i.e. protection of the host locus. Our findings show commonalities and differences among the various CRISPR-mediated defence systems and suggest that they should not merely be perceived as a 'first-barrier-defence system' but may be considered to have a broader mechanism that allows host cells to cope with viruses keeping them at reduced levels.
Applying array contraction to a sequence of DOALL loops (2004)

Efficient program execution on multiprocessor computers requires both sufficient parallelism and good data locality. Recent research found that, using a combination of loop shifting, loop fusion, and array contraction, one can reduce the memory required to execute a sequence of serial loops, thereby to improve the cache locality. This paper studies how to extend such a memory-reduction scheme to a sequence of DOALL loops, which are executed in parallel on multiprocessors. Two methods are proposed to overcome difficulties caused by loop-carried dependences. Data copy-in is performed to remove anti-dependences between different parallel threads, and computation duplication is performed to remove flow dependences. Experiments performed on a number of benchmark programs show that the proposed technique improves both cache locality and parallel execution speed for the DOALL loops. The scheme achieves an average speedup of 1.41 for 17 programs on a 4-processor SUN machine.
Stimulated Thermal Rayleigh Scattering in Liquids (1969)

In a previous calculation of the gain factor for stimulated thermal scattering, it has been assumed that the dielectric constant is insensitive to changes in temperature. In our treatment such an approximation has not been made and it is shown that this additional contribution gives rise to a correction of up to 6% to the stimulated thermal Rayleigh peak for liquids commonly used in such experiments. The inadequacy of the Lorentz-Lorenz relation in estimating the magnitude of this correction is also discussed.
A foam single-face pretreatment to modify silk fabric using EBODAC to improve inkjet printing performance (2014)

A novel foam single-face pretreatment was used to modify silk fabrics for improving inkjet printing performance without any washing process. The foams used in pretreatment process were prepared by foaming agent, as Tween 80 and Sodium dodecyl sulfate (SDS). The compatibilities of the cationic modifier ethylene base-double octadecyl dimethyl ammonium chloride (EBODAC) agent with Tween 80 and SDS were investigated by comparing the foam properties at different EBODAC concentrations. The results show that Tween 80 is more compatible with EBODAC. The silk fabric surface is adhered with cationic groups after foam-treated with EBODAC, which improves the inkjet printing performances. The K/S values enhance from 5.84 to 8.21 with the increasing EBODAC concentrations. The printing images of treated fabrics perform more vivid than those of the controlled silk fabrics. The width and edges of practical printing lines become smaller and more definite, respectively. All these indicate that higher color yield and definition are achieved. The hand feeling after foam pretreatment is superior to that after pad pretreatment. The fastnesses are hardly affected after pretreatment. The foam-pretreatment provides a new pathway to improve the inkjet printing performance.
Extending Network Emulation Support in ns-3 using DPDK (2019)

ns-3 network simulator provides support for network emulation by enabling simulated nodes to communicate with real hosts by using a network device called EmuFdNetDevice. Network emulation is an important feature in ns-3 and can be used to validate its models by comparing the emulation results to those obtained from real testbeds. Typically, ns-3 uses raw sockets of host's kernel stack to support network emulation. However, there is an active interest to enhance ns-3's network emulation features by using kernel bypass libraries. Recently, a new network device called NetmapNetDevice has been proposed for ns-3 to enable its interaction with netmap. In this paper, we extend network emulation support in ns-3 by using Data Plane Development Kit (DPDK). DPDK provides a set of fast packet processing libraries to bypass host network stack and obtain a direct access to Network Interface Card (NIC). We propose a new network device in ns-3 called DpdkNetDevice, intermediating between ns-3 Internet stack and DPDK environment to read/write packets from/to the NIC. We validate the working of DpdkNetDevice by performing various experiments and comparing results obtained from it to those obtained from EmuFdNetDevice and NetmapNetDevice. We observe that network emulations using DpdkNetDevice on a Gigabit Ethernet NIC provide higher throughput with significantly lesser CPU cycles per packet.
Interaction of zinc with hemoglobin: binding of zinc and the oxygen affinity (1977)

Stripped human hemoglobin was shown to have a high apparent zinc association constant of 1.3 X 10(7) M-1 with a stoichiometry of one zinc for every two hemes. The saturation of this site produces a dramatic 3.7-fold increase in the oxygen affinity. The effect of zinc on the oxygen affinity is interrelated with the interaction of 2,3-diphosphoglyceric acid (2,3-DPG) and hemoglobin. Thus, a smaller zinc effect is observed in the presence of added 2,3-DPG. Information about the location of the zinc-binding site responsible for the increased oxygen affinity has been obtained by comparing the binding of zinc to various hemoglobins. Blocking the beta93 sulfhydryl group decreases the apparent zinc association constant by an order of magnitude. The substitution of histidine-beta143 in hemoglobin Abruzzo [beta143 (H21) His leads to Arg] and hemoglobin Little Rock [beta143 (H21) His leads to Gln] decreases the apparent zinc association constant by two orders of magnitude. The substitution of histidine-beta143 by other amino acids and the reaction of the beta93 sulfhydryl group are known to produce dramatic increases in the oxygen affinity. The binding of zinc to one or both of these amino acids can, therefore, explain the zinc-induced increase in the oxygen affinity.
Mineralized Bone Allograft-Plug Socket Augmentation: Rationale and Technique (2007)

Background: Socket augmentation allows clinicians to preserve alveolar bone height. This, in turn, could maintain adjacent soft tissue (papillae) height to promote optimal implant esthetics. Materials and Methods: A new regimen for the socket augmentation technique (the mineralized bone allograft-plug technique) is introduced. It uses solvent-preserved mineralized cancellous allografts to fill the sockets up to 1–2 mm below the bone crest. This is covered with a bioabsorbable collagen wound dressing (CollaPlug®; Zimmer Dental, Carlsbad, CA). Illustrations to demonstrate the technique are introduced. A case treated with this approach is presented. Results: This technique is easy to perform with minimal trauma. Both clinical observation and histological results showed excellent bone formation. Conclusion: Our clinical experience, as well as histologic data, suggest that the mineralized bone allograft-plug is a suitable technique for socket augmentation.
<i>In situ</i> chemistry and microbial community compositions in five deep‐sea hydrothermal fluid samples from <scp>I</scp> rina <scp>II</scp> in the <scp>L</scp> ogatchev field (2012)

We present data on the co-registered geochemistry (in situ mass spectrometry) and microbiology (pyrosequencing of 16S rRNA genes; V1, V2, V3 regions) in five fluid samples from Irina II in the Logatchev hydrothermal field. Two samples were collected over 24 min from the same spot and further three samples were from spatially distinct locations (20 cm, 3 m and the overlaying plume). Four low-temperature hydrothermal fluids from the Irina II are composed of the same core bacterial community, namely specific Gammaproteobacteria and Epsilonproteobacteria, which, however, differs in the relative abundance. The microbial composition of the fifth sample (plume) is considerably different. Although a significant correlation between sulfide enrichment and proportions of Sulfurovum (Epsilonproteobacteria) was found, no other significant linkages between abiotic factors, i.e. temperature, hydrogen, methane, sulfide and oxygen, and bacterial lineages were evident. Intriguingly, bacterial community compositions of some time series samples from the same spot were significantly more similar to a sample collected 20 cm away than to each other. Although this finding is based on three single samples only, it provides first hints that single hydrothermal fluid samples collected on a small spatial scale may also reflect unrecognized temporal variability. However, further studies are required to support this hypothesis.
The thermal conductivity of graphite parallel to the basal planes and the velocity of phonons in the ‘out-of-plane’ acoustic mode (1967)

Abstract The thermal conductivity of polycrystalline graphites and pyrolytic graphite parallel to the basal planes varies between 10°K and 80°K as some power of the temperature between 2·3 and 2·8. The conductivity in this temperature range is dominated by the phonon contribution and is believed to be limited by crystallite boundary scattering. In the same temperature range the specific heat is observed to vary as T 2 and thus the behaviour of the conductivity has been held to be anomalous. A calculation of the mean phonon velocity parallel to the basal planes for the ‘out-of-plane’ acoustic mode, as a function of temperature using Komatsu's model of the lattice dynamics of graphite, shows that at least part of this temperature dependence can be accounted for.
Branch parameters validation for state estimation purpose (2008)

In this paper a procedure for validating network branch parameters is proposed. The proposed procedure uses a state estimator based on the normal equations with the inclusion of suspicious branch parameters as state vector here called parameter/state estimator. The idea is to use measurements of several snapshots and to estimate the state variables (bus voltage magnitudes and phase angles), and the suspicious series parameters in a sequential form, taking advantage of the fact that those parameters remain nearly unchanged during a certain time period (time period during which the load remains relatively constant). In order to improve the convergence of the proposed parameter/state estimator, that estimator works in a decoupled way. The performance of the proposed procedure is evaluated on the IEEE-14-bus system.