gebhart/patrepeval huggingface dataset:
Autophagy facilitates macrophage depots of sustained-release nanoformulated antiretroviral drugs (2017)

Long-acting anti-HIV products can substantively change the standard of care for patients with HIV/AIDS. To this end, hydrophobic antiretroviral drugs (ARVs) were recently developed for parenteral administration at monthly or longer intervals. While shorter-acting hydrophilic drugs can be made into nanocarrier-encased prodrugs, the nanocarrier encasement must be boosted to establish long-acting ARV depots. The mixed-lineage kinase 3 (MLK-3) inhibitor URMC-099 provides this function by affecting autophagy. Here, we have shown that URMC-099 facilitates ARV sequestration and its antiretroviral responses by promoting the nuclear translocation of the transcription factor EB (TFEB). In monocyte-derived macrophages, URMC-099 induction of autophagy led to retention of nanoparticles containing the antiretroviral protease inhibitor atazanavir. These nanoparticles were localized within macrophage autophagosomes, leading to a 4-fold enhancement of mitochondrial and cell vitality. In rodents, URMC-099 activation of autophagy led to 50-fold increases in the plasma drug concentration of the viral integrase inhibitor dolutegravir. These data paralleled URMC-099-mediated induction of autophagy and the previously reported antiretroviral responses in HIV-1-infected humanized mice. We conclude that pharmacologic induction of autophagy provides a means to extend the action of a long-acting, slow, effective release of antiretroviral therapy.
First-Trimester Diagnosis of Conjoined Twins (1997)

Two cases of conjoined twins were diagnosed during first-trimester endovaginal ultrasound and were confirmed by embryoscopy performed prior to the termination of pregnancy. An early and accurate diagnosis of this anomaly, obtained by the combined use of ultrasound and endoscopy, may enable adequate counselling and an earlier termination of pregnancy associated with minimal maternal risks.
In Vitro Skin Penetration and Degradation of Peptides and Their Analysis Using a Kinetic Model. (2000)

The main purpose of this study was to estimate the net percutaneous absorption of physiologically active peptides in vitro. The degradation of two peptides, Leu-enkephalin (Enk) and Tyr-Pro-Leu-Gly amide (TPLG), during skin penetration and on the dermal side following penetration, and the prevention of degradation by some protease inhibitors, were investigated using rat skin in vitro. In addition, these permeation and degradation data were analyzed using a kinetic model. These peptides were rapidly degraded in the receptor fluid of a Franz diffusion cell (rate constant: 0.977 h(-1) for Enk and 0.250 h(-1) for TPLG). The addition of phenylmethylsulfonyl fluoride (PMSF) and phenanthroline and the pretreatment of skin with these inhibitors prevented almost completely any degradation in the receptor fluid and skin, respectively. The pretreatment of skin with PMSF and phenanthroline had no effect on the penetration of dextran (1000 Da). The degradation rate constant during skin penetration, calculated from the difference in the penetration rate constants via pretreated and untreated skins, was also high (0.037 h(-1) for Enk and 0.050 h(-1) for TPLG). A kinetic model including an input rate (zero-order), the permeation rate across the viable skin (first-order) and the degradation rate in skin (first-order) was sufficient to describe the apparent steady-state flux of the peptides through skin. We have, thus, established a method for measuring the true flux of peptides across skin in vitro and a kinetic model which simply describes the skin penetration of peptides.
The Human Poly(A)-binding Protein 1 Shuttles between the Nucleus and the Cytoplasm (1998)

We have studied the intracellular localization of poly(A)-binding protein 1 (PABP1) by indirect immunofluorescence as well as by tagging with the green fluorescent protein (GFP) in living cells. We show that PABP1 is able to enter the nucleus. Accumulation of PABP1 in the nuclei was observed upon transcription inhibition, suggesting that active transcription is required for PABP1 export. The nuclear import of PABP1 is an energy-dependent process since PABP1 fails to enter the nucleus upon ATP depletion and at low temperature. Transfection of PABP1 or PABP1-GFP resulted in heterogeneity of intracellular distribution of the protein. In the low expressing cells, PABP1 was localized in the cytoplasm, whereas in the high expressors, we observed accumulation of the protein in the nucleus. Nuclear PABP1 observed either after overexpression or after transcription inhibition was found in speckles and colocalized with splicing factor SC35. The ability of PABP1 to shuttle between nucleus and cytoplasm was also shown by heterokaryon formation upon cell fusion. Deletion mutagenesis showed that the minimal part of PABP1 retaining the ability to shuttle consists of the first two RNA-binding domains. This mutant interacted with poly(A) RNA with high affinity and accumulated in the nucleus. Deletion mutants exhibiting reduced RNA binding affinity did not accumulate in the nucleus. PABP1 has been proposed to participate at various steps of mRNA utilization. Our results suggest involvement of PABP1 in nuclear events associated with the formation and transport of mRNP to the cytoplasm and identify a new trafficking pattern for RNA-binding proteins.
Power Converter Integration Design Based on Evaluation Platform Concept (2006)

A power converter evaluation platform has been proposed to quantify the correlation between converter factors such as semiconductor power devices, the conversion circuit, passive components and the control system. One of features of the proposed platform is that various parameters of the converter can be varied arbitrarily by the parameter adjustable circuit board and the digital controller. Correlations between converter factors are quantified empirically in the platform, and optimal converter parameters to realize the high output power density converter are extracted.
Comment on “Modified full-field optical coherence tomography: A novel tool for rapid histology of fresh tissues” (2011)

Optical coherence tomography (OCT) is one of several three-dimensional microscopy techniques that may revolutionize pathology practice.[1] These techniques essentially create histology-like images without glass microscope slides. This type of imaging can even be performed in vivo,[2] and represents a tremendous opportunity for pathology as a medical specialty. Not only can we pathologists revolutionize our workflow to drastically decrease turn-around time; we can also begin to project our substantial microscopic diagnostic expertise into realms that were previously off limits (i.e., in vivo diagnostics).

Mukherjee et al.[1] present an excellent report of their experience with a novel “full-field” OCT-based imaging platform. They demonstrate high quality images that resemble low-to-medium magnification histopathology photomicrographs. This is extremely exciting, and one can imagine potential applications for such images: enhanced specimen grossing; reduced need for frozen sections during intraoperative consultation; perhaps even sign-out of specific surgical pathology tests such as postpartum tubal ligation specimens. This last may seem controversial, but existing OCT images may already be of high enough quality to permit assessment for the presence of complete cross sections of fallopian tube tissue.[3]

It is likely that image quality will continue to increase, perhaps to the extent that it may rival what is possible with traditional microscopy (i.e., “routine” diagnostic work). Maturation of 3D histopathology may push OCT and related techniques far beyond glass-based methods, especially with computer-assisted diagnostic tools.[4] It is very possible that diagnostic-quality in vivo images may even make traditional biopsy obsolete, especially in certain situations (i.e., surveillance of Barrett's esophagus). Mukherjee's experience is also interesting because they are reporting on a system that it is commercially available, designed for use with histopathology specimens, and produces DICOM-compatible images that by definition can be incorporated into existing image management infrastructure such as radiology PACS systems.

The rise of three-dimensional microscopic imaging modalities represents a fabulous opportunity for Pathology, but it also may foreshadow the end of traditional microscope-based practice. The stakes are very high, and we may have to compete with other specialties for “turf”. We should do so vigorously, leveraging our strong advantages related to existing microscopic morphology expertise, our culture of providing definitive diagnosis (vs. “impressions”), and possibly even cost. If we do not seize this opportunity we may be left in a passive role as these technologies develop around us, perhaps even rendering our old microscopic techniques obsolete. Mukherjee et al have provided us with a tantalizing glimpse of the future, and it is bright.
Interaction Between Cyclosporine and Grapefruit Juice Requires Long‐Term Ingestion in Stable Renal Transplant Recipients (1998)

A drug interaction exists between cyclosporine and grapefruit juice, and it is likely at the level of intestinal drug absorption.
Direct Smelting of Metallurgical Dusts and Ore Fines in a 125t DC‐HEP Furnace (2004)

In the metallurgical plant of LARCO at Larymna, approximately 200000t/y of nickelferrous dust are collected in the gas cleaning systems of the Rotary Kilns (R/Ks) corresponding to an annual production of 100000t FeNi20%. In addition, a stockpile of one million tons of old R/K dust lies close to the plant and the community of Larymna. A “one‐stage” environmentally friendly process has been developed for the recycling of this dust by direct reduction smelting in a DC arc furnace. The industrial adaptation of this process was tested in the 125t DC‐HEP (Direct Current — Hollow Electrode Powder) furnace at Georgsmarienhütte steelwork (GMH) in Germany. About 70t of dust were directly smelted by injection through the hollow electrode of the furnace. The nickel recovery in the metal bath was 93‐99.9%. Final products were low nickel alloyed steel grades and slag suitable for special cement types production. Main cause of the dust generation in the R/Ks is the disintegration of laterite and the ore fines fraction after the ore crushing. Their separation, collection and metallurgical exploitation prior to their feeding in the R/Ks would significantly reduce the amount of the generated dust. Therefore, the smelting of untreated laterite ore fines in the DC‐HEP furnace was also indicatively tested. Thus, a zero residues industrial production process was developed for the recycling of nickel bearing dust and ore fines by smelting in a DC‐arc furnace, since the finally produced FeNi‐alloy and slag are 100% utilized in the steel and cement industry respectively.
Quantitative Assessment of Pore Blockage in Supported Catalysts: Comparing Differential Scanning Calorimetry and Physisorption (2012)

Mesoporous materials are commonly used as supports for a guest phase, such as catalytically active transition metal nanoparticles. N2 physisorption at 77 K is the standard technique to characterize mesoporosity; however, it is not always suitable to assess pore blockage caused by the guest phase. Here we report on the qualitative and quantitative assessment of pore blockage comparing N2 physisorption with two alternative techniques: differential scanning calorimetry (DSC) of the freezing and melting of confined water and physisorption of Ar at 77 K. A set of well-defined model catalyst nanostructures with varying degrees of pore blockage was synthesized using ordered mesoporous supports and different nanoparticle sizes. Pore blockage was detected with sorption techniques by analyzing the delayed gas desorption. For the first time we report the analysis of nanoparticle induced constrictions with DSC by studying the delayed freezing of water in the constricted pores. Both DSC and argon sorption provided information which cannot be accessed by standard N2 physisorption. Therefore, both techniques are advocated for the analysis of complex porous structures.
Human balancing of an inverted pendulum: position control by small, ballistic-like, throw and catch movements (2002)

In standing, there are small sways of the body. Our interest is to use an artificial task to illuminate the mechanisms underlying the sways and to account for changes in their size. Using the ankle musculature, subjects balanced a large inverted pendulum. The equilibrium of the pendulum is unstable and quasi-regular sway was observed like that in quiet standing. By giving full attention to minimising sway subjects could systematically reduce pendulum movement. The pendulum position, the torque generated at each ankle and the soleus and tibialis anterior EMGs were recorded. Explanations about how the human inverted pendulum is balanced usually ignore the fact that balance is maintained over a range of angles and not just at one angle. Any resting equilibrium position of the pendulum is unstable and in practice temporary; movement to a different resting equilibrium position can only be accomplished by a biphasic ‘throw and catch’ pattern of torque and not by an elastic mechanism. Results showed that balance was achieved by the constant repetition of a neurally generated ballistic-like biphasic pattern of torque which can control both position and sway size. A decomposition technique revealed that there was a substantial contribution to changes in torque from intrinsic mechanical ankle stiffness; however, by itself this was insufficient to maintain balance or to control position. Minimisation of sway size was caused by improvement in the accuracy of the anticipatory torque impulses. We hypothesise that examination of centre of mass and centre of pressure data for quiet standing will duplicate these results.
Use of multichannel electrogastrography for noninvasive assessment of gastric myoelectrical activity in dogs (2009)

Electrogastrography may be useful in assessing gastric myoelectrical activities in awake dogs with naturally occurring gastrointestinal disease, including gastric dilatation-volvulus.
Modulation method for measuring specific heat (1973)

In the avian salt gland carbachol (CCh) evokes oscillations in K+ and Cl- current that are sufficient to fully activate secretory activity. Employing the perforated patch-clamp technique, we demonstrate that beta-adrenergic receptor activation stimulates a sustained adenosine 3',5'-cyclic monophosphate (cAMP)-dependent Cl- current with no increase in K+ current. This evokes only a modest increase in secretory activity. However, application of isoproterenol in the presence of a threshold dose of CCh results in maximal secretory activity. Membrane potential measurements demonstrate that isoproterenol stimulates a sustained membrane depolarization from approximately -45 mV to the Cl- equilibrium potential (ECl), whereas CCh evokes oscillations in membrane potential to levels more negative than ECl, representing a mixture of K+ and Cl- conductances. We conclude that, in agreement with current models of fluid secretion, maximal stimulation can only be achieved with simultaneous activation of both K+ and Cl- currents. Because isoproterenol fails to stimulate a K+ current, Cl- secretion is reduced as the driving force for Cl- secretion is dissipated. However, if a driving force is imposed by increasing K+ channel activity (by coadministering CCh), Cl- efflux is sustained. These results could provide a basis for the marked potentiation of Ca(2+)-mediated secretion by agonists that increase cAMP seen in in vivo studies of salivary glands and other exocrine tissues.
Performance analysis of accelerated image registration using GPGPU (2009)

This paper presents a performance analysis of an accelerated 2-D rigid image registration implementation that employs the Compute Unified Device Architecture (CUDA) programming environment to take advantage of the parallel processing capabilities of NVIDIA's Tesla C870 GPU. We explain the underlying structure of the GPU implementation and compare its performance and accuracy against a fast CPU-based implementation. Our experimental results demonstrate that our GPU version is capable of up to 90x speedup with bilinear interpolation and 30x speedup with bicubic interpolation while maintaining a high level of accuracy. This compares favorably to recent image registration studies, but it also indicates that our implementation only reaches about 70% of theorectical peak performance. To analyze our results, we utilize profiling data to identify some of the underlying limitations of CUDA that prohibit peak performance. At the end, we emphasize the need to manage memory resources carefully to fully utilize the GPU and obtain maximum speedup.
Comparison of competing fiber optic probes for tissue fluorescence analysis (2000)

Several fiber optic probes attached single- or multi-fiber light delivery systems have been competitively examined for purposes of in vivo tissue fluorescence spectroscopy with endoscopic technique use. The effects of the probes' designs and excitation/receiving fiber geometry on fluorescence spectra are analyzed with the sensor optical efficiency (SOE) coefficient and the tip coupling efficiency (TCE) one calculated by means of ray tracing. The profiles of the excitation beam as well as fluorescence profiles were simulated with uniform and Gaussian cross power distributions, whereas the diameter of the tissue surface area from which fluorescence light was collected was taken as five diameter of the tissue surface area directly illuminated by the excitation beam. The plots of the SOE-coefficients versus changeable probe-tissue gap simulated possible peristaltic tissue movement during clinical in situ spectroscopic optical biopsy would be a helpful tool for specialists to design novel endoscopic fiber optic catheters to differentiate normal and pathologic tissues.
Bismacrocyclic Inhibitors of Hepatitis C NS3/4a Protease (2008)

Zeit gespart: Der Bismakrocyclus 2 wurde aus 1 mithilfe einer selektiven doppelten Ringschlussmetathese (RCM) zur gleichzeitigen Bildung der 18- und der 15-gliedrigen Ringe gebildet. Das Derivat 3 zeigt ausgezeichnete Aktivität gegen die NS3/4a-Protease. 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.
A film technique for the determination of output factors and end effect times for the Leksell Gamma Knife (2001)

The relative output factors of the four helmets for a model B Leksell Gamma Knife and the end effect times for each helmet have been measured. For the three helmets with the smallest-diameter collimators a technique employing Kodak XV-2 film was used. The measured output factors are in good agreement with the values recommended by the manufacturer. The end effect times vary with the collimator size, with the shorter time occurring with the smaller collimator.
Rational, yet simple, design and synthesis of an antifreeze-protein inspired polymer for cellular cryopreservation (2015)

Antifreeze (glyco) proteins AF(G)Ps are potent ice recrystallization inhibitors, which is a desirable property to enhance cryopreservation of donor tissue/cells. Here we present the rational synthesis of a new, biomimetic, ice-recrystallization inhibiting polymer derived from a cheap commodity polymer, based on an ampholyte structure. The polymer is used to enhance the cryopreservation of red blood cells, demonstrating a macromolecular solution to tissue storage.
Distinct epigenetic profiles in children with perinatally-acquired HIV on antiretroviral therapy (2019)

Perinatally-acquired HIV has persistent effects on long-term health outcomes, even after early treatment. We hypothesize that epigenetic indicators, such as DNA methylation, may elucidate cellular processes that explain these effects. Here, we compared DNA methylation profiles in whole blood from 120 HIV-infected children on antiretroviral therapy (ART) and 60 frequency age-matched HIV-uninfected children aged 4-9 years in Johannesburg, South Africa. Using an individual CpG site approach, we found 1,309 differentially-methylated (DM) CpG sites between groups, including 1,271 CpG sites that were hyper-methylated in the HIV-infected group and 38 CpG sites that were hypo-methylated in the HIV-infected group. Six hyper-methylated CpG sites were in EBF4, which codes for a transcription factor involved in B-cell maturation. The top hypomethylated site was in the promoter region of NLRC5, encoding a transcription factor that regulates major histocompatibility complex (MHC) class I molecule expression. Using a differentially-methylated region (DMR) approach, we found 315 DMRs between groups, including 28 regions encompassing 686 CpG sites on chromosome 6. A large number of the genes identified in both the CpG site and DMR approaches were located in the MHC region on chromosome 6, which plays an important role in the adaptive immune system. This study provides the first evidence that changes in the epigenome are detectable in children with perinatally-acquired HIV infection on suppressive ART started at an early age.
Development of Microporous Covered Stents: Geometrical Design of the Luminal Surface (2005)

To reduce in-stent restenosis rates we have developed newly designed covered stents, in which a stent strut is buried into a microporous elastomeric cover film to provide a physical barrier against tissue ingrowth and a pharmacological reservoir for drug-eluting. The covered stents were prepared by dip-coating balloon expandable stents mounted on a stainless steel rod in a segmented polyurethane (SPU) solution, and were subsequently subjected to laser-processed microporing (pore diameter, 100 microm; interpore distance, 200 microm). The covered stents, which possessed flat luminal surfaces and micropores that were homogeneously arranged on the whole surface of the covering film, were deployed into the bilateral common carotid arteries of normal New Zealand white rabbits. Angiography after one month of implantation showed all stents were patent with little thrombus formation. The mean thickness of the formed neointimal layers was 292 +/- 177 microm (n=8), which was close to the size in non-covered bare stent (231 +/- 58 microm, n=7), but markedly decreased (about 2/3) from that in the previously developed wrapping-type covered stents (415 +/- 173 microm, P<0.01, n=8).
Intraoperative ventilatory management (2014)

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1 6LoWPAN Extension for IPsec (2012)

Abstract—Real-world deployments of wireless sensor networks (WSNs) require secure communication. Recently, WSNs and traditional IP networks are more tightly integrated using IPv6 and 6LoWPAN. Available IPv6 protocol stacks can use IPsec to secure data exchange. Thus, it is desirable to extend 6LoWPAN such that IPsec communication with IPv6 nodes is possible. It is beneficial to use IPsec because the existing end-points on the Internet do not need to be modified to communicate securely with the WSN. We propose a 6LoWPAN extension for IPsec. Our extension supports both IPsec’s Authentication Header (AH) and Encapsulation Security Payload (ESP). Thus, communication endpoints are able to authenticate, encrypt, and check the integrity of messages using standardized and established IPv6 mechanisms. I.