gebhart/patrepeval huggingface dataset:
APE1 and XRCC1 Protein Expression Levels Predict Cancer-Specific Survival Following Radical Radiotherapy in Bladder Cancer (2005)

Expression levels of both APE1 and XRCC1 proteins were strongly associated with patient outcome following radiotherapy, separating patients with good outcome from the 50% with poor outcome (82% and 44%, 3-year cause-specific survival, respectively). If prospectively validated, this simple test could be incorporated into clinical practice to select patients likely to respond to radiotherapy and consider alternative forms of therapy for those unlikely to respond.
Simulated annealing and weight decay in adaptive learning: the SARPROP algorithm (1998)

A problem with gradient descent algorithms is that they can converge to poorly performing local minima. Global optimization algorithms address this problem, but at the cost of greatly increased training times. This work examines combining gradient descent with the global optimization technique of simulated annealing (SA). Simulated annealing in the form of noise and weight decay is added to resiliant backpropagation (RPROP), a powerful gradient descent algorithm for training feedforward neural networks. The resulting algorithm, SARPROP, is shown through various simulations not only to be able to escape local minima, but is also able to maintain, and often improve the training times of the RPROP algorithm. In addition, SARPROP may be used with a restart training phase which allows a more thorough search of the error surface and provides an automatic annealing schedule.
Milk Protein intake in the Term infant (1986)

Thirty healthy term infants were studied during the three first months of life. The infants were divided into three feeding groups consisting of 10 infants in each. The feeding regimens were: human milk by breast feeding, a formula (F-I) containing 1.2 g/100 ml of protein and a control formula (F-II) containing 1.6 g protein/100 ml. Both formulas were whey predominant and isocaloric. Protein intake was significantly higher with formula F-II when compared to the human milk group and to formula F-I. No significant differences with respect to weight, length and head circumference were found among the groups, but the rate of growth between 2 to 12 weeks was higher in the control formula (F-II) group. Serum albumin concentrations were normal and similar in all feeding groups. Blood urea nitrogen and urine total nitrogen concentration was significantly lower in the low protein formula I group when compared to the control formula II. After the fourth week of life the low protein formula infants had similar blood urea nitrogen and urine nitrogen concentrations as those of the breast-fed infants. The results indicate that current formulas in use provide excessive protein intakes after the first months of life.
Multi-Dose Container for Nasal and Ophthalmic Drugs: A Preservative Free Future? (2011)

The first nasal spray pumps were developed some 50 years ago and replaced step by step droppers and pipettes. Now they are widely used to moisturize the nasal mucosa using saline solutions (from a regulatory point of view considered medical devices under the EU directive) or as nasal preparations for the administration of topically acting drugs (e.g. nasal decongestants or nasal steroids) or for the non-invasive administration of substances which need to reach systemic circulation (anti-migraine medication, hormones). For chronic diseases like allergic rhinitis, multi-dose devices are very cost effective and convenient and provide the safety and precision regulatory bodies require. To date, most of the medications administered nasally contain a preservative to support long storage times and proper in-use stability. For ophthalmic drugs, there was a similar development from simple droppers to more sophisticated devices. Squeeze bottles without metering function are still widely used for ophthalmic medications especially for chronic conditions. Artificial tears filled in multi-dose bottles are commonly used to relieve dry eye symptoms, these again being medical devices because the mode of action is purely physical. Looking at active drugs, the most successful in the ophthalmic field are drugs (e.g. beta-antagonists and prostaglandine-analogues) for the treatment of glaucoma and anti-histamines to treat allergic conjunctivitis. The reader may wonder why nasal spray pumps together with multi-dose ophthalmic droppers are considered in the very same chapter. The answer is that both device classes share the same blueprint: they use a bottle made of plastic or glass attached to a pump or dropper which generates and delivers a more or less metered dose and on top of this serves as a closure. So the pumps or droppers support two general functions: Sealing of the container and protection of the content during storage and transportation. Delivery of a metered dose of liquid or viscous pharmaceutical formulation. The major challenge during development is to reach a reliable delivery of the metered dose without having any negative impact caused by drug-device interactions.
Confident Phosphorylation Site Localization Using the Mascot Delta Score (2010)

Large scale phosphorylation analysis is more and more getting into focus of proteomic research. Although it is now possible to identify thousands of phosphorylated peptides in a biological system, confident site localization remains challenging. Here we validate the Mascot Delta Score (MD-score) as a simple method that achieves similar sensitivity and specificity for phosphosite localization as the published Ascore, which is mainly used in conjunction with Sequest. The MD-score was evaluated using liquid chromatography-tandem MS data of 180 individually synthesized phosphopeptides with precisely known phosphorylation sites. We tested the MD-score for a wide range of commonly available fragmentation methods and found it to be applicable throughout with high statistical significance. However, the different fragmentation techniques differ strongly in their ability to localize phosphorylation sites. At 1% false localization rate, the highest number of correctly assigned phosphopeptides was achieved by higher energy collision induced dissociation in combination with an Orbitrap mass analyzer followed very closely by low resolution ion trap spectra obtained after electron transfer dissociation. Both these methods are significantly better than low resolution spectra acquired after collision induced dissociation and multi stage activation. Score thresholds determined from simple calibration functions for each fragmentation method were stable over replicate analyses of the phosphopeptide set. The MD-score outperforms the Ascore for tyrosine phosphorylated peptides and we further show that the ability to call sites correctly increases with increasing distance of two candidate sites within a peptide sequence. The MD-score does not require complex computational steps which makes it attractive in terms of practical utility. We provide all mass spectra and the synthetic peptides to the community so that the development of present and future localization software can be benchmarked and any laboratory can determine MD-scores and localization probabilities for their individual analytical set up.
Determination and observation of electronic defect levels in CuInSe2 crystals and thin films (1991)

The effects of heat and surface treatments used in the fabrication of CuInSe2 (CIS) single-crystal and thin-film solar cells are investigated, and the associated dominant defect states are identified using high-resolution photoluminescence (PL) and deep-level transient spectroscopy (DLTS) measurements. The results are correlated with junction electrical characteristics, and comparisons between thin films and single crystals are established. For the first time, direct evidence for several major defect types (Cu vacancies, Cu at In sites, and In at Cu sites) responsible for the majority-carrier type of the CIS is presented based upon spectroscopic atomic imaging of the n- and p-type semiconductor surfaces. Radiative recombination levels of extrinsic origin resulting from the surface processing (including polishing, etching, and annealing) were detected in the near surface region of the CIS single crystals, but not in the thin-film material having the same composition. The energy locations and depth of these states are responsible for the formation of an interfacial layer that is confirmed from frequency-dependent capacitance–voltage (C–V) data. The DLTS measurements on single-crystal and thin-film heterostructure {i.e., [Cd,Zn]S/CIS} devices (of nearly identical chemical compositions) have also confirmed the presence of a dominant trap level in the 270-meV region above the valance band. However, the trap density is some two orders of magnitude lower in the thin-film device, giving evidence that this processing-related defect level is responsible for the inferior performance of the single-crystal solar cells.
Personalization of queries in database systems (2004)

As information becomes available in increasing amounts to a wide spectrum of users, the need for a shift towards a more user-centered information access paradigm arises. We develop a personalization framework for database systems based on user profiles and identify the basic architectural modules required to support it. We define a preference model that assigns to each atomic query condition a personal degree of interest and provide a mechanism to compute the degree of interest in any complex query condition based on the degrees of interest in the constituent atomic ones. Preferences are stored in profiles. At query time, personalization proceeds in two steps: (a) preference selection and (b) preference integration into the original user query. We formulate the main personalization step, i.e. preference selection, as a graph computation problem and provide an efficient algorithm for it. We also discuss results of experimentation with a prototype query personalization system.
Stratum Electricity Markets: Toward Multi-temporal Distributed Risk Management for Sustainable Electricity Provision (2012)

Motivated by the overall challenge of ensuring long-term sustainable electricity service, we view this challenge as a long-term decision making problem under uncertainties. We start by recognizing that, independent of the industry organization, the uncertainties are enormous and often exogenous to the energy service providers. They are multi-dimensional and are result of fundamental drivers, ranging from the supply side, through the demand side, to the regulatory and policy sides. The basic contribution of this thesis comes from the recognition that long-term investments for ensuring reliable and stable electricity service critically depend on how these uncertainties are perceived, valued and managed by the different stakeholders within the complex industry organization such as the electric power industry. We explain several reasons why price signals obtained from current short-term electricity markets alone are not sufficient enough for long-term sustainable provision. Some enhancements are presented in the thesis to improve the short-term electricity market price signals to reflect the true cost of operation. New market mechanisms and instruments are needed to facilitate the stakeholders to better deal with long-term risks. The problems of ensuring long-term stable reliable service in the sense of the traditional resource adequacy requirements are revisited in both the restructuring industry and regulated industry. We introduce a so-called Stratum Electricity Market (SEM) design as the basic market mechanism for solving the problem of long-term reliable electricity service through a series of interactive multi-lateral market exchange platforms for risks communication, management and evaluations over various time horizons and by the different groups of stakeholders. In other words, our proposed SEM is a basic IT-enabled framework for the decision making processes by various parties over different time. Because of the uniqueness of electricity as a commodity, the values for the same amount of energy during different time and at different location can vary dramatically. Moreover, for the same hour, the values for the same amount of power at base load level or at peak load level are different due to the different generation technologies and other non-convex constraints like unit commitment. The multiple market products at zonal/nodal levels with different time horizon and time of use categories are designed to reflect more realistic demand and supply conditions at various temporal and spatial granularities. Detailed market rules, rights and regulations (3Rs) concerning the sub-markets interactions, product hierarchy and financial settlements are also examined.
Biological activities of novel recombinant tumor necrosis factor having N-terminal amino acid sequences derived from cytotoxic factors produced by THP-1 cells. (1988)

Eight species of novel recombinant tumor necrosis factor-S (rTNF-SAM group) were constructed in which N-terminal amino acid sequences were based on that of TNF-S from THP-1 cells with higher basicity than conventional rTNF-alpha. Two of this rTNF-SAM group, denoted as rTNF-SAM1 and rTNF-SAM2, showed more cytocidal activity on A549 lung carcinoma cells and G401 Wilm's tumor cells than did rTNF-alpha. In addition to these cell lines, rTNF-SAM1 revealed strong cytocidal activity on T24 bladder carcinoma cells, which are resistant to rTNF-alpha. Moreover, possible cachectin activity of rTNF-SAM2 seemed to be lower than that of conventional rTNF-alpha, suggesting that rTNF-SAM2 has less side effects. Actually, toxicity as expressed by LD50 value of rTNF-SAM2 as well as others of the rTNF-SAM group was significantly lower than that of conventional rTNF-alpha. Thus, newly constructed rTNF-SAM1 and rTNF-SAM2 should be more promising antitumor reagents for clinical use, since they were shown to be superior to conventional rTNF-alpha both in antitumor effect and in less side effects.
Decision-Directed Fine Synchronization in OFDM Systems (2005)

A new decision-directed (DD) synchronization scheme is proposed for joint estimation of carrier frequency offset (CFO) and sampling clock frequency offset (SFO) in orthogonal frequency-division multiplexing (OFDM) systems. By exploiting the hard decisions, we report accurate estimators of residual CFO and small SFO. The performance analysis and simulation results indicate that the proposed novel DD scheme achieves much better performance than the conventional pilot-based schemes in both additive white Gaussian noise and frequency-selective channels.
MACsec Extension over Software-Defined Networks for in-Vehicle Secure Communication (2018)

The automotive industry has recently introduced Advanced driver assistance systems (ADAS) for safety and better driving. Many Electronic Control Units (ECUs) have been installed in the vehicle to support ADAS, and massive data stream flows over the in-vehicle network. Therefore, the Ethernet backbone, which can guarantee the high bandwidth, has emerged as an in-vehicle communication technology. However, security on automotive Ethernet has not yet been proposed. The IEEE MACsec with IEEE 802.1X Authentication and Key Management (AKM) may be applied for the in-vehicle secure communication, but it has a constraint that its security scope is based on a point-to-point approach. Whenever a frame arrives at the switches in the transmission path, the decryption and re-encryption of the frame are repeated. It may adversely affect the performance of ADAS related to the driver's safety by increasing the end-to-end latency. We therefore propose a new MACsec extension over the Software-Defined Networks (SDN) for an in-vehicle secure communication, which is based on IEEE 802.1X authentication mechanism. The proposed scheme extends the security scope of MACsec from point-to-point to end-to-end by delegating AKM process of ECUs and switches to SDN controller. It could minimize the cryptographic processes of the ECUs and switches without any modification of the existing MACsec standard, and could protect an automotive system from any manipulation by unauthorized third parties. The experimental results show that the proposed scheme is applicable for an in-vehicle secure communication.
Profiling markers of prognosis in colorectal cancer. (2006)

This study has identified an immunohistochemical marker profile of colorectal cancer and showed that it is an independent indicator of prognosis in this type of cancer.
Extracellular Matrix and Oscillatory Mechanics of Rat Lung Parenchyma in Bleomycin-induced Fibrosis (1999)

We investigated in vivo and in vitro oscillatory mechanics in bleomycin-induced fibrotic lungs and correlated these with morphometric changes in the collagen-elastin matrix and contractile cells. Fischer rats received bleomycin sulfate (BLEO,1.5 U) or saline intratracheally. Four weeks later tracheal flow and tracheal and alveolar pressure (using alveolar capsules) were measured in open-chested rats during mechanical ventilation (V T = 8 ml/kg, f = 1 Hz, PEEP = 4 cm H(2)O). Total lung, tissue, and airway resistance (R) and lung elastance (E) were calculated. In addition, excised parenchymal strips (10 x 2 x 2 mm) were studied in the organ bath. Strips were attached to a force transducer at one end and to a servo-controlled lever arm that effected length (L) changes at the other. Sinusoidal oscillations were applied (f = 1 Hz, amplitude = 2. 5% resting L and tension = 0.7 g) and R, E, and hysteresivity (eta) were calculated. Strips were then exposed to acetylcholine (ACh, 10(-)(3) M). The amount of collagen and elastic fibers in the parenchymal strip was assessed semiquantitatively by point-counting in 5-micrometer-thick sections stained with either Sirius Red or Weigert's Resorcin-fuchsin. alpha-Smooth-muscle-specific actin was detected immunohistochemically. Both in vivo and in vitro, R, E, and eta were significantly increased in BLEO rats (p < 0.05). The % increase in R, E and eta after Ach was greater in BLEO rats (p < 0. 01). There was also a significant increase in the volume proportion of collagen, elastic fibers, and actin in the parenchyma (p < 0.01). In BLEO rats, baseline R and E were correlated with the volume proportion of collagen in the parenchyma. We conclude that changes in the collagen-elastin matrix contribute to changes in the viscoelastic properties of bleomycin-treated rat lungs. Dolhnikoff M, Mauad T, Ludwig MS. Extracellular matrix and oscillatory mechanics of rat lung parenchyma in bleomycin-induced fibrosis.
Mass spectrometric and chemical stability of the Asp‐Pro bond in herpes simplex virus epitope peptides compared with X‐Pro bonds of related sequences (2002)

The mass spectrometric analysis of the immunodominant epitope region (273-284) of herpes simplex virus type 1 (HSV-1) glycoprotein D (gD) showed a favoured fission at the Asp-Pro peptide bond. The fast atom bombardment collision induced dissociation (FAB-CID) study of closely related X-Pro peptides documented that neither the length nor the amino acid composition of the peptide has a significant influence on this preferential cleavage. At the same time the DP bond proved to be sensitive to acidic conditions in the course of peptide synthesis. These observations prompted us to compare the chemical and mass spectrometric stability of a new set of nonapeptides related to the 273-284 epitope region of gD, i.e. SALLEDPVG and SALLEXPVG peptides, where X = A, K, I, S, F, E or D, respectively. The chemical stability of these peptides during acidic hydrolysis was investigated by electrospray ionization mass spectrometry (ESI-MS) and the products were identified by ESI-MS and on-line high performance liquid chromatography-mass spectrometry (HPLC-MS). The mass spectrometric fragmentation and bond stability of the untreated peptide samples were also studied using ESI-MS and liquid secondary ion mass spectrometry (LSIMS). Both the chemical hydrolysis and the mass spectrometric fragmentation showed that the Asp-Pro bond could easily be cleaved, while the KP bond proved to be stable under both circumstances. On the other hand, the XP bond (X = A, I, S, F or E) fragmented easily under the mass spectrometric conditions, but was not sensitive to the acidolysis.
Oxygen Reduction Reaction of Ta-C-N Prepared by Reactive Sputtering with Heat Treatment (2007)

Ta-C-N electrocatalysts were prepared by reactive R.F. sputtering with heat treatment in the temperature range from 70 to 800°C. The Ta-C-N was found to have high electrochemical stability in 0.1 mol dm−3 H2SO4. The catalytic activity for the oxygen reduction reaction of the sputtered Ta-C-N increased with the increasing heat treatment temperature. In particular, the current of the ORR on the Ta-C-N with the heat treatment temperature of 800°C was observed at about 0.73 V vs. RHE. It was found that the crystallinity of the Ta-C-N would affect the catalytic activity for the ORR.
Formation and analysis of topographical domains between lipid membranes tethered by DNA hybrids of different lengths (2012)

We recently described a strategy to prepare DNA-tethered lipid membranes either to fixed DNA on a surface or to DNA displayed on a supported bilayer [Boxer et al., J. Struct. Biol., 2009, 168, 190; Boxer et al., Langmuir, 2011, 27, 5492]. With the latter system, the DNA hybrids are laterally mobile; when orthogonal sense-antisense pairs of different lengths are used, the DNA hybrids segregate by height and the tethered membrane deforms to accommodate the height difference. This architecture is particularly useful for modelling interactions between membranes mediated by molecular recognition and resembles cell-to-cell junctions. The length, affinity and population of the DNA hybrids between the membranes are completely controllable. Interesting patterns of height segregation are observed by fluorescence interference contrast microscopy. Diverse behavior is observed in the segregation and pattern forming process and possible mechanisms are discussed. This model system captures some of the essential physics of synapse formation and is a step towards understanding lipid membrane behaviour in cell-to-cell junctions.
Present and future caloric refrigeration and heat-pump technologies (2015)

In recent years, several emerging technologies in the domain of solid-state physics have been investigated as serious alternatives for future refrigeration, heat pumping, air conditioning, or even power generation applications. These technologies relate to what is called caloric energy conversion, i.e., barocalorics, electrocalorics, magnetocalorics, and elastocalorics. Of these technologies, the greatest progress has been observed in the domain of magnetic refrigeration. However, in the recent few years, significant research efforts have also been made in the field of electrocaloric and elastocaloric refrigeration. Many of these technologies suggest the possibility for improvements in energy efficiency, compactness, noise level, as well as a reduction in environmental impacts, so it seems very probable that they will start to fill particular market niches as a replacement for vapor-compression technology in the future.