gebhart/patrepeval huggingface dataset:
Syntheses of 2-Modified Phosphatidylinositol 4, 5-Bisphosphates: Putative Probes of Intracellular Signaling (1998)

The first syntheses of phosphatidyl-myo-inositol 4,5-bisphosphates (PtdIns-4,5-P2) modified at the 2-OH are described. Complementary procedures are presented for modification of 2-OH by replacement or derivatization, exemplified by the 2-deoxy-2-fluoro epimer and the 2-O-acetyl derivative, respectively. The products optionally incorporate an ω-aminoalkyl-type residue for conjugation to photoaffinity or other reporter group or solid matrix. These analogues retain the core PtdIns-4,5-P2 structure and stereochemistry, but lack the nucleophilic 2-OH deemed essential for substrate hydrolysis by the mammalian phosphoinositide-specific phospholipase C (PI-PLC). Therefore, the 2-modified analogues are putative structure- and mechanism-based competitive inhibitors of PI-PLC, suitable as comparative probes of PtdIns-4,5-P2-binding to PI-PLC and cellular regulatory proteins.
Complication rates of ablation therapies for hepatocellular carcinoma: a difficult comparison with an easy solution. (2006)

We read the recent debate from Taipei ( Gut 2005; 54 :1151–6) on which is the best image guided ablation therapy for hepatocellular carcinoma (HCC), proposed by Lin and colleagues1 and Huo and colleagues.2 This is an interesting topic for hepatologists and gastroenterologists.

The papers by Lin et al stated that in the treatment of HCC, radiofrequency (RFA) was superior to percutaneous ethanol injection (PEI) and percutaneous acetic acid injection (PAI) with respect to local recurrence, overall survival, and cancer free survival, but RFA also caused more major complications. In contrast, Huo et al stressed that …
Marker PDU Aligned Framing for TCP Specification (2007)

Marker PDU Aligned Framing (MPA) is designed to work as an "adaptation layer" between TCP and the Direct Data Placement protocol (DDP) as described in RFC 5041. It preserves the reliable, in-order delivery of TCP, while adding the preservation of higher-level protocol record boundaries that DDP requires. MPA is fully compliant with applicable TCP RFCs and can be utilized with existing TCP implementations. MPA also supports integrated implementations that combine TCP, MPA and DDP to reduce buffering requirements in the implementation and improve performance at the system level.
Plasma ion sources and ion beam technology inmicrofabrications (2007)

For over decades, focused ion beam (FIB) has been playing a very important role in microscale technology and research, among which, semiconductor microfabrication is one of its biggest application area. As the dimensions of IC devices are scaled down, it has shown the need for new ion beam tools and new approaches to the fabrication of small-scale devices. In the meanwhile, nanotechnology has also deeply involved in material science research and bioresearch in recent years. The conventional FIB systems which utilize liquid gallium ion sources to achieve nanometer scale resolution can no longer meet the various requirements raised from such a wide application area such as low contamination, high throughput and so on. The drive towards controlling materials properties at nanometer length scales relies on the availability of efficient tools. In this thesis, three novel ion beam tools have been developed and investigated as the alternatives for the conventional FIB systems in some particular applications. An integrated focused ion beam (FIB) and scanning electron microscope (SEM) system has been developed for direct doping or surface modification. This new instrument employs a mini-RF driven plasma source to generate focused ion beam with various ion species, a FEI two-lens electron (2LE) column for SEM imaging, and a five-axis manipulator system for sample positioning. An all-electrostatic two-lens column has been designed to focus the ion beam extracted from the source. Based on the Munro ion optics simulation, beam spot sizes as small as 100 nm can be achieved at beam energies between 5 to 35 keV if a 5 μm-diameter extraction aperture is used. Smaller beam spot sizes can be obtained with smaller apertures at sacrifice of some beam current. The FEI 2LE column, which utilizes Schottky emission, electrostatic focusing optics, and stacked-disk column construction, can provide high-resolution (as small as 20 nm) imaging capability, with fairly long working distance (25 mm) at 25 keV beam voltage. Such an integrated FIB/SEM dual-beam system will not only improve the accuracy and reproducibility when performing ion beam sculpting and direct implantation processes, but will also enable researchers to perform cross-sectioning, imaging, and analysis with the same tool. A major advantage of this approach is the ability to produce a wide variety of ion species tailored to the application.
Studies of Spontaneous Fluctuations in Congestion and Nasal Mucosal Microcirculation and the Effects of Oxymetazoline Using Rhinostereometry and Micromanipulator Guided Laser Doppler Flowmetry (1999)

The mucosa of the inferior turbinate was studied using rhinostereometry and micromanipulator-guided laser Doppler flowmetry in 10 healthy volunteers. First, spontaneous fluctuations were studied measuring congestion and multiple microcirculatory parameters simultaneously every 2 minutes. The subjects were then challenged with oxymetazoline using the same measuring technique studying the effects of the challenge during 12 minutes. There were spontaneous variations in congestion of up to 2.1 mm and variations in perfusion from 38% to 175% of average. There was no correlation between congestion in itself, or change in congestion, to perfusion or any other microcirculatory parameter. After challenge with oxymetazoline there was a rapid decrease in perfusion at 3 minutes after which there were no significant changes. The congestion decreased gradually throughout the procedure. Because congestion reflects the filling of the venous sinusoids and the flowmetry the state of the superficial vessels, we conclude that there are spontaneous short-term fluctuations in the sympathetic tone with independent actions on the different vessels. After challenge with a sympathomimetic drug, there was a decrease in both swelling and flow, but not synchronized. The combination of rhinostereometry and micromanipulator-guided laser Doppler flowmetry is a useful tool to study the dynamics of intranasal challenge reactions.
Prostate-localized and androgen-regulated expression of the membrane-bound serine protease TMPRSS2. (1999)

Genes regulated by androgenic hormones are of critical importance for the normal physiological function of the human prostate gland, and they contribute to the development and progression of prostate carcinoma. We used cDNA microarrays containing 1500 cDNAs to profile transcripts regulated by androgens in prostate cancer cells and identified the serine protease TMPRSS2 as a gene exhibiting increased expression upon exposure to androgens. The TMPRSS2 gene is located on chromosome 21 and contains four distinct domains, including a transmembrane region, indicating that it is expressed on the cell surface. Northern analysis demonstrated that TMPRSS2 is highly expressed in prostate epithelium relative to other normal human tissues. In situ hybridization of normal and malignant prostate tissues localizes TMMPRSS2 expression to prostate basal cells and to prostate carcinoma. These results suggest that TMPRSS2 may play a role in prostate carcinogenesis and should be investigated as a diagnostic or therapeutic target for the management of prostate cancers.
Efficient Scalable Accurate Regression Queries in In-DBMS Analytics (2017)

Recent trends aim to incorporate advanced data analytics capabilities within DBMSs. Linear regression queries are fundamental to exploratory analytics and predictive modeling. However, computing their exact answers leaves a lot to be desired in terms of efficiency and scalability. We contribute a novel predictive analytics model and associated regression query processing algorithms, which are efficient, scalable and accurate. We focus on predicting the answers to two key query types that reveal dependencies between the values of different attributes: (i) mean-value queries and (ii) multivariate linear regression queries, both within specific data subspaces defined based on the values of other attributes. Our algorithms achieve many orders of magnitude improvement in query processing efficiency and near-perfect approximations of the underlying relationships among data attributes.
Design, Synthesis, and Evaluation of Phe-Gly Mimetics:  Heterocyclic Building Blocks for Pseudopeptides (1999)

Enantiopure heterocyclic Boc-protected Phe-Gly dipeptidomimetics containing 1,3,4-oxadiazole, 1,2,4-oxadiazole, and 1,2,4-triazole ring systems have been synthesized as building blocks in the synthesis of pseudopeptides. Three derivatives (1-3) have the carboxylic acid function directly bound to the heterocyclic ring, and three derivatives (4-6) have an extra methylene group between the heterocyclic ring and the acid function to allow for an increased conformational flexibility. The mimetics were used as Phe-Gly replacements in the biologically active peptides dermorphin (Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH(2)) and substance P (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-MetNH(2), SP). The pseudopeptide synthesis was performed using solid-phase methodology on a MBHA-resin using Boc-chemistry. The biological evaluation was performed by testing the micro- and delta-opioid receptor affinities of the dermorphin pseudopeptides and the NK(1) receptor affinities of the SP pseudopeptides. The results showed that all mimetics except 3 were excellent replacements of Phe-Gly in dermorphin since they displayed affinities for the micro-receptor (IC(50) = 12-31 nM) in the same range as dermorphin itself (IC(50) = 6.2 nM). The agonist activity of three pseudopeptides at human micro-receptors was also evaluated. It was shown that the tested compounds retained their agonist activity. The SP pseudopeptides showed considerably lower affinities (IC(50) > 1 microM) for the NK(1) receptor than SP itself (IC(50) = 1.5 nM) indicating that the Phe-Gly replacements prevent the pseudopeptides from adopting bioactive conformations.
Lipopolysaccharide and cytokine augmentation of human monocyte IgA receptor expression and function. (1994)

Receptors for IgA (Fc alpha R) are found on phagocytic cells in the peripheral blood and tissues associated with mucosal areas where IgA Abs constitute a major line of defense. Because Fc alpha R are capable of triggering protective functions of monocytes and neutrophils, such as phagocytosis and the oxidative burst, they may be important in amplifying the antimicrobial effects of IgA. Various cytokines play a role in regulating function and FcR expression of monocytes, macrophages, and neutrophils. The present studies examine the modulation of monocyte Fc alpha R by LPS and cytokines. LPS strongly up-regulated monocyte Fc alpha R expression. TNF and IL-1, produced in response to LPS, promoted Fc alpha R increase, as did GM-CSF; whereas IFN-gamma down-regulated Fc alpha R. Increased receptor expression was accompanied by augmented IgA-mediated phagocytosis. An increase in Fc alpha R-specific mRNA was detected in monocytes treated with TNF, IL-1, GM-CSF, and LPS; whereas message was reduced in cells treated with IFN-gamma. Monocyte-derived macrophages and cells of the Monomac 6 monocyte-like line expressed greater numbers of Fc alpha R than monocytes but were less responsive to LPS and TNF. Cell lines THP-1 and U937, which expressed similar or lower levels of Fc alpha R than monocytes, displayed an increase in Fc alpha R in response to LPS and, to various degrees, to TNF, IL-1, and GM-CSF. These results indicate that Fc alpha R on monocytes are modulated by endotoxin and an array of cytokines distinct from those that regulate expression of FcR for IgG.
Two-photon in vivo microscopy of sulfonefluorescein secretion in normal and cystic rat kidneys (2004)

Sulfonefluorescein (SF) is a fluorescent organic anion secreted by kidney proximal tubules. The purposes of this study were 1) to quantify accumulation of SF in normal and cystic rat kidneys in vivo and 2) to test whether SF accumulation could be used as a marker for cysts derived from proximal tubules. Male Munich-Wistar rats, normal Han:SPRD rats, and heterozygous Han:SPRD rats with autosomal-dominant polycystic kidney disease were anesthetized with Inactin and solutions containing SF were administered by constant intravenous infusion. In Munich-Wistar rats, SF fluorescence in the urinary space of Bowman's capsule averaged 0.15 +/- 0.04 (n = 17) times that of glomerular capillary plasma, consistent with extensive plasma protein binding of SF. In normal Han:SPRD rats, steady-state cell cytoplasm SF fluorescence in proximal tubule and distal tubule cells averaged, respectively, 2.7 +/- 1.4 (n = 99 tubules) and 0.2 +/- 0.2 (n = 17) times that of peritubular capillary plasma. No punctate SF fluorescence was seen in proximal tubule cell cytoplasm. Probenecid reduced proximal tubule cell SF fluorescence to 0.64 +/- 0.40 (n = 64) times that of plasma. Ureteral obstruction decreased the proximal tubule cell-to-lumen SF fluorescence gradient, suggesting that tubule fluid flow normally sweeps away secreted SF. In cystic kidneys, cysts derived from proximal tubules could be identified by their uptake of SF, but cell uptake was patchy. We conclude that in vivo two-photon microscopy is a powerful tool for quantifying glomerular and tubular handling of SF, and SF can be used to identify proximal tubule-derived cysts.
Security and privacy requirements analysis within a social setting (2004)

Security issues for software systems ultimately concern relationships among social actors stakeholders, system users, potential attackers - and the software acting on their behalf. We propose a methodological framework for dealing with security and privacy requirements based on i*, an agent-oriented requirements modeling language. The framework supports a set of analysis techniques. In particular, attacker analysis helps identify potential system abusers and their malicious intents. Dependency vulnerability analysis helps detect vulnerabilities in terms of organizational relationships among stakeholders. Countermeasure analysis supports the dynamic decision-making process of defensive system players in addressing vulnerabilities and threats. Finally, access control analysis bridges the gap between security requirement models and security implementation models. The framework is illustrated with an example involving security and privacy concerns in the design of agent-based health information systems. In addition, we discuss model evaluation techniques, including qualitative goal model analysis and property verification techniques based on model checking.
THE EFFECTS OF PRECURSOR LOADING IN THE CEREBRAL METABOLISM OF 5‐HYDROXYINDOLES (1968)

Abstract —Using either tryptophan or 5‐hydroxytryptophan as the precursor, and examining the metabolites in whole rat brain and in brain regions of dog, the pattern of metabolites resembled that found under physiological conditions only after tryptophan administration. From these and other observations on the cerebral 5‐hydroxyindoles the main conclusions are firstly, that there are regional differences within brain in storage, turnover or metabolic fate of 5‐HT. Secondly, that the normal pathway appears to be well localized biochemically with linking of its succeeding steps, and thirdly, that turnover through the system is normally controlled by intracerebral tryptophan 5‐hydroxylase in both rats and dogs although there are differences between the species in the cerebral metabolism of 5‐HT.
A new schedule for decoding low-density parity-check codes (2002)

The best known practical algorithm for the decoding of low-density parity-check (LDPC) codes is the iterative sum-product or belief propagation algorithm, operating on a Tanner graph (TG) of the code. Conventionally, in each iteration, all the symbol nodes and subsequently all the check nodes in the TG pass new messages to their neighbors (the so-called "flooding schedule"). We propose a new message-passing schedule, called "probabilistic schedule". Unlike flooding, the probabilistic schedule operation is based on the structure of the TG, and probabilistically balances the frequency at which different symbol nodes update their outgoing messages in accordance with their girths. Our results show that, particularly for short block lengths, the new schedule offers a much better performance/complexity trade-off. For a particular example of a (1268, 456) code, at no cost in complexity, the probabilistic schedule not only decreases both the bit and message error rates by an order of magnitude, but also reduces the number of undetected errors considerably. This work shows the importance of scheduling in the performance of iterative decoding algorithms and suggests that a schedule which matches the structure of the TG can substantially improve the performance/complexity trade-off in the decoding of short LDPC codes.
High-resolution NMR of encapsulated proteins dissolved in low-viscosity fluids (1998)

The majority of known proteins are too large to be comprehensively examined by solution NMR methods, primarily because they tumble too slowly in solution. Here we introduce an approach to making the NMR relaxation properties of large proteins amenable to modern solution NMR techniques. The encapsulation of a protein in a reverse micelle dissolved in a low-viscosity fluid allows it to tumble as fast as a much smaller protein. The approach is demonstrated and validated with the protein ubiquitin encapsulated in reverse micelles prepared in a variety of alkane solvents.
Effect of molecular weight of hyaluronic acid (HA) on viscoelasticity and particle texturing feel of HA dermal biphasic fillers (2016)

Dermal biphasic HA fillers made from 1058 kDa exhibit suitable elastic moduli (211 to 420 Pa) and particle texturing feel (scale 7 ~ 9).
Stability of Predictive Control in Job Shop System with Reconfigurable Machine Tools for Capacity Adjustment (2019)

Due to changes in individual demand, manufacturing processes have become more complex and dynamic. To cope with respective fluctuations as well as machine breakdowns, capacity adjustment is one of the major effective measures. Instead of labor-oriented methods, we propose a machinery-based approach utilizing the new type of reconfigurable machine tools for adjusting capacities within a job shop system. To economically maintain desired work in process levels for all workstations, we impose a model predictive control scheme. For this method we show stability of the closed-loop for any feasible initial state of the job shop system using a terminal condition argument. For a practical application, this reduces the computation of a suitable prediction horizon to controllability of the initial state. To illustrate the effectiveness and plug-and-play availability of the proposed method, we analyze a numerical simulation of a four workstation job shop system and compare it to a state-of-the-art method.
Fast Negative Photochromism of 1,1′-Binaphthyl-Bridged Phenoxyl–Imidazolyl Radical Complex (2015)

Negative photochromism, in which a thermally stable colored form isomerizes to the transient colorless form by light irradiation and the back reaction occurs thermally, is advantageous in its applications for photoswitching materials because visible light can cause the photochromic color change of the materials. Moreover, the photochromic color change can be induced even on the inside of the materials due to the absence of the reabsorption of the visible excitation light by the photogenerated colorless species. While several negative photochromic compounds have been reported, the time scales of the back reaction are still slower than minutes, and no available fast responsive negative photochromic compounds have been reported. Here, we developed a negative photochromic 1,1'-binaphthyl-bridged phenoxyl-imidazolyl radical complex (BN-PIC) which enables fast photoswitching by visible light. The stable colored BN-PIC shows instantaneous decoloration by visible light irradiation, and the photogenerated colorless form thermally reverts to the initial colored form with a half-life of 1.9 s at room temperature. BN-PIC can also cause the drastic change in the chiroptical properties by the photochromic reaction, and the rate of the thermal back reaction is affected by the chirality of the solvent. Since the negative photochromic reaction can occur on the inside of the materials, the fast negative photochromism is expected to have an impact in the fields of photoresponsive materials of solid states and molecular aggregates.
Portable Wireless Power Transmission System of a Video Capsule Endoscopy: Design and Realization (2012)

Video capsule endoscopy, as a new technology, has brought a revolution in the diagnosis of gastrointestinal tract diseases. However, power limitation has become a great problem that restricts its development and application. Meanwhile, the diagnostic procedure usually lasts more than ten hours or more. So, a portable wireless power transmission system based on inductive coupling is designed for the video capsule endoscopy. The system consists of a double layer solenoid pair primary coil outside and a multiple secondary coils inside the body. At least 150 mW usable power can be transmitted under the worst geometrical conditions, which totally meet requirements of the video capsule endoscopy. On the other hand, the weight of the wireless power transmission system is only 4.98 kg, which realized the portability.
Isolated rupture and repair of the popliteus tendon (1995)

The authors report the case of a 21-year-old woman who sustained a femoral avulsion of the popliteus tendon in a motor vehicle accident. The posterolateral injury was suspected on physical examination and confirmed by magnetic resonance imaging and arthroscopic examination. The popliteus tendon was repaired using two suture anchors. Mild clinical instability was present initially and resolved postoperatively. No residual pain, weakness, or posterolateral instability was noted.
Differences in Reverse Bias Voltage Behavior of n-type and p-type Multicrystalline Solar Cells (2012)

The use of n-type, instead of p-type, silicon wafers for the production of mc-Si solar cells has a clear effect on the pre-breakdown behavior under reverse bias conditions. In p-type solar cells, material related breakdown patterns that are commonly observed in luminescence and thermography images. These patterns do not appear in the investigated n-type mc-Si solar cells, at least not down to a reverse bias of -16 V. To the best of our knowledge, this difference between p-type and n-type mc-Si solar cells has not yet been described in literature before and could provide important information for the understanding of this type of wafer related breakdown.