gebhart/patrepeval huggingface dataset:
GPS: a comprehensive www server for phosphorylation sites prediction (2005)

Protein phosphorylation plays a fundamental role in most of the cellular regulatory pathways. Experimental identification of protein kinases' (PKs) substrates with their phosphorylation sites is labor-intensive and often limited by the availability and optimization of enzymatic reactions. Recently, large-scale analysis of the phosphoproteome by the mass spectrometry (MS) has become a popular approach. But experimentally, it is still difficult to distinguish the kinase-specific sites on the substrates. In this regard, the in silico prediction of phosphorylation sites with their specific kinases using protein's primary sequences may provide guidelines for further experimental consideration and interpretation of MS phosphoproteomic data. A variety of such tools exists over the Internet and provides the predictions for at most 30 PK subfamilies. We downloaded the verified phosphorylation sites from the public databases and curated the literature extensively for recently found phosphorylation sites. With the hypothesis that PKs in the same subfamily share similar consensus sequences/motifs/functional patterns on substrates, we clustered the 216 unique PKs in 71 PK groups, according to the BLAST results and protein annotations. Then, we applied the group-based phosphorylation scoring (GPS) method on the data set; here, we present a comprehensive PK-specific prediction server GPS, which could predict kinase-specific phosphorylation sites from protein primary sequences for 71 different PK groups. GPS has been implemented in PHP and is available on a www server at http://973-proteinweb.ustc.edu.cn/gps/gps_web/.
EDA in flux (2009)

A crisis is a terrible thing to waste. Quotes like this are often heard by experts in the industry and academia but what does this mean to me? How should I change my professional interests? How should I evolve my career? How is EDA going to evolve? The panel represents multiple points of views on these questions. Four experts will review the current job situation in EDA and provide a historical perspective for previous recessions. The panel will further discuss views on new directions for the Electronics market, how EDA should evolve, and options for career development during the slow down of the industry.
Characterisation of Thin Films Using a Coherence Scanning Interferometry (2015)

Accurate measurement of film thickness and its uniformity are very important to the performance of many coated surfaces and for many applications are critical. Effective inspection of the film thickness and uniformity is the key to high performance. Conventionally, film thickness is meas- ured using a spectrophotometer/reflectometer, ellipsometer or a physical step measurement; however, these techniques all have limitations. Coherence Scanning Interferometry (CSI) is an established method to measure surface topography as this technique offers many advantages such as speed, ease of use and accuracy. The measurement of “thick” films (exceeding ~1.5 μm) which gives rise to clearly separate fringe bunches is a well-established CSI capability. However, a methodology known as the ‘helical complex field’ (HCF) [1] [2] function allows film thickness to be measured down to ~25 nm. This new method, combined with Coherence Correlation Interferometry (CCI) [3] offers film thickness measurements with sub-nanometre vertical resolution and ~1 μm lateral resolution. It is ideally suited for detailed analysis of coated optical surfaces. In this paper, the fundamentals of the techniques are described and some case studies are presented.
Identification and Validation of an Anthracycline/Cyclophosphamide–Based Chemotherapy Response Assay in Breast Cancer (2014)

A formalin-fixed, paraffin-embedded tissue-based assay has been developed and independently validated as a predictor of response and prognosis after anthracycline/cyclophosphamide-based chemotherapy in the neoadjuvant and adjuvant settings. These findings warrant further validation in a prospective clinical study.
Direct prediction of energy digestibility from poultry faeces using near infrared spectroscopy (2007)

In animal production digestibility is an essential factor of the valorization of diets. The main factor of variation of digestibility is the characteristics of the feed itself. In recent experiments we have shown that there are also differences between animals for the ability to digest diets. Such genetic experiments require individual digestibility trials, involving a considerable number of faeces analyses. Therefore we now use routinely NIRS for prediction of faeces chemical composition: DM (Dry matter), GE (Gross energy), Protein, Starch , Fat. A step further in the use of NIRS would be the direct prediction of digestibility by NIRS, because it would avoid the precise registration of feed intake and excreta quantities, which would considerably simplify experimental work. In the framework of an experiment on genetic selection in poultry, we measured DM and GE digestibility values, and the corresponding faeces samples were kept for NIRS analysis. This resulted in 240 faeces samples of known DM (dDM) and 173 of known GE (dGE) digestibilities. Diffuse reflectance NIRS spectra of samples were measured on a FOSS NIRSystem 6500 spectrometer. Calibration equations were built after mathematical pre-processing of spectral data (SNV and detrend with 2nd derivative of spectra) without visible wavelengths. Partial Least Squares regression (modified PLS in WINISI software) was found to be the most efficient method for calibrations. Equations obtained had R2, SEC and SECV values of 0.97, 2.11, 2.67 for dDM and 0.99, 1.31, 1.93 for dGE. The corresponding SD/SECV rations were 4.6 and 5.8 respectively. A validation was run by removing 60 samples (randomly chosen) from the database and predict them with equations developed on remaining samples. SEP values obtained were 3.82 and 2.18 respectively, which shows the robustness of equations. These results confirm that the digestibility of DM and GE can be predicted with a sufficient accuracy directly from poultry faeces in our experiments. It must be underlined that our experimental design aimed to study only the animal part of digestibility, therefore using the same feed for all animals. Prediction of digestibility of different feed is therefore not possible from this particular equation and will have to be calibrated from variable diets.
Molybdenum Disulfide in Oils and Greases Under Boundary Conditions (1973)

A mineral oil and a lithium-based mineral oil grease containing molybdenum disulfide are tested under boundary conditions on the Shell Four Ball Testing Machine and on a modified Reichert Wear Balance. The investigation of the wear tracks by scanning electron microscopy and microprobe analysis shows that a continuous MoS1 film is formed on the metal surface under mild friction conditions. Under extremely severe conditions, however, the MoS2 reacts chemically. It is found that molybdenum diffuses into the steel surface forming intermetallic compounds and carbides which improve the quality of the steel surface. The effect of time and pressure on the thickness of the molybdenum disulfide is determined and the amount of wear reduction by chemical reaction of molybdenum disulfide with the steel surface is compared to that of a traditional EP-additive.
Development Of A Tutorial Software To Serve As A Teaching Aid For Power And Refrigeration Cycles (2020)

The paper presents the development and application of a computer based tutorial software to aid instruction and improve problem solving skills in undergraduate "Thermal Systems and Economics" course offered by the Department of Mechanical Engineering. This course is a required design course in the Mechanical Engineering curriculum and an approved technical elective in the Chemical Engineering curriculum. It is offered during both fall and spring semesters with a class size of about 40 students. The expert tutor serves as a concise data base for key concepts learned in the course, and houses property tables and basic equations to interactively solve problems. The benefits of using this computer based instructional aid include: enhanced use of multimedia course materials, more creative thinking exercises for students, reduced time to master new concepts, and coverage of more materials in the course. The application of computer technology to facilitate interactive learning greatly enhances the instruction process. The concept of an expert tutor can be extended virtually to any engineering or science course at the undergraduate level.
On the Stability of the EPA MPG Adjustment Factors (1985)

&lt;div class="htmlview paragraph"&gt;The offset (sometimes called “shortfall”) between EPA MPG and actual in-use MPG has been shown to be dependent upon vehicle technology and EPA MPG level. If these variables change significantly, there is the potential for the constant EPA MPG adjustment factors (0.90 city, 0.78 highway) to become obsolete.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Trends in passenger car MPG have been used to formulate a model of vehicle technology mixes and MPG levels over the next 15 years, to investigate the degree to which MPG adjustments derived from such a scenario might differ from the promulgated constant adjustment factors.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;As a check on the reasonableness of the future technology scenario, a simple econometric model was constructed independently which relates car class market fractions and MPG levels to gasoline price, and to regulatory requirements: MPG Standards and the Gas Guzzler tax. It is shown that the technology scenario’s fleet MPG is consistent with that of the econometric model, when the latter uses a trend leading to a fuel price of about $2.25/gallon in the year 2000.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;It is shown that, at fleet level, the technology scenario for technology and MPG changes does not obsolete the current MPG adjustment factors.&lt;/div&gt;
Polymer surface patterningvia Diels–Alder trapping of photo-generated thioaldehydes (2012)

An efficient method for polymer surface patterning via Diels-Alder trapping of photo-generated thioaldehydes is presented. It is demonstrated that thioaldehyde end-groups generated by photolysis of phenacyl sulfides can be quantitatively trapped with various dienes. Poly(ethylene glycol) is immobilized on a surface in a spatially controlled fashion via irradiation through a shadow mask.
High efficiency and smooth transition buck-boost converter for extending battery life in portable devices (2009)

This paper presents a high-efficiency and smooth-transition buck-boost (BB) converter to extend the battery life of portable devices. Owing to the usage of four switches, the BB control topology needs to minimize the switching and conduction losses at the same time. Therefore, over a wide input voltage range, the proposed BB converter consumes minimum switching loss like the basic operation of buck or boost converter. Besides, the conduction loss is reduced by means of the reduction of the inductor current level. Especially, the proposed BB converter offers good line/load regulation and thus provides a smooth and stable output voltage when the battery voltage decreases. Simulation results show that the output voltage drops is very small during the whole battery life time and the output transition is very smooth during the mode transition by the proposed BB control scheme.
Trade-off between information gain and fidelity under weak measurements (2015)

It is of general interest how a quantum measurement may disturb a quantum system while it gives information on the state of the system. We study a trade-off relation between the information gain and the output fidelity for a quantum nondemolition measurement scheme for photon numbers. Toward this aim, we obtain general expressions for the information gain and the output fidelity for an arbitrary initial state. We particularly investigate how these two quantities vary with measurement strength for some specific classes of states, through a single measurement or successive measurements.
The Enzymatic Degradation of Heparin and Heparitin Sulfate (1970)

Crude enzyme obtained from heparin-induced flavobacteria has been fractionated into a heparitinase acting on heparitin sulfates and related compounds and a heparinase acting mainly on heparin. Purification achieved for each was from 50 to 100 times that of earlier preparations containing a mixture of the two enzymes. In agreement with previous data both enzymes act as eliminases rather than hydrolases yielding products containing Δ4,5-unsaturated uronic acid. Specificity of the heparitinase appears to require the absence of O-sulfate and the presence of N-acetyl or sulfamido groups. Specificity of the heparinase requires the presence of O-sulfate and sulfamido groups while derivatives containing free amino or N-acetyl are not substrates. The heparinase degrades heparitin sulfate to some extent acting apparently on the heparin-like portion.
Improving self-efficacy in spinal cord injury patients through "design thinking" rehabilitation workshops (2014)

Advances in surgical and medical management have significantly reduced the length of time that patients with spinal cord injury (SCI) have to stay in hospital, but has left patients with potentially less time to psychologically adjust. Following a pilot in 2012, this project was designed to test the effect of "design thinking" workshops on the self-efficacy of people undergoing rehabilitation following spinal injuries. Design thinking is about understanding the approaches and methods that designers use and then applying these to think creatively about problems and suggest ways to solve them. In this instance, design thinking is not about designing new products (although the approaches can be used to do this) but about developing a long term creative and explorative mind-set through skills such as lateral thinking, prototyping and verbal and visual communication. The principles of "design thinking" have underpinned design education and practice for many years, it is also recognised in business and innovation for example, but a literature review indicated that there was no evidence of it being used in rehabilitation or spinal injury settings. Twenty participants took part in the study; 13 (65%) were male and the average age was 37 years (range 16 to 72). Statistically significant improvements were seen for EQ-5D score (t = -3.13, p = 0.007) and Patient Activation Measure score (t = -3.85, p = 0.001). Other outcome measures improved but not statistically. There were no statistical effects on length of stay or readmission rates, but qualitative interviews indicated improved patient experience.
Dual-Polarized Planar Phased Array Antenna With Cavity-Backed Elements (2019)

A planar dual-polarized phased array antenna with cavity-backed elements is proposed in this letter. The array antenna is designed based on a dual-polarized patch antenna element with vertical orthogonal baluns. The antenna element is backed by a compact cavity to reduce the interelement mutual coupling and enhance the scanning performance of the planar array. The proposed array achieves a wide fractional bandwidth of over 20% when scanning up to ±45° in the E- and H-planes. The isolation between the two orthogonal ports in the same element is higher than 30 dB. The validity of a design is verified by simulation and measurements of a 10 × 10 array prototype.
Probabilistic multiscale image segmentation (1997)

A method is presented to segment multidimensional images using a multiscale (hyperstack) approach with probabilistic linking. A hyperstack is a voxel-based multiscale data structure whose levels are constructed by convolving the original image with a Gaussian kernel of increasing width. Between voxels at adjacent scale levels, child-parent linkages are established according to a model-directed linkage scheme. In the resulting tree-like data structure, roots are formed to indicate the most plausible locations in scale space where segments in the original image are represented by a single voxel. The final segmentation is obtained by tracing back the linkages for all roots. The present paper deals with probabilistic (or multiparent) linking. The multiparent linkage structure is translated into a list of probabilities that are indicative of which voxels are partial volume voxels and to which extent. Probability maps are generated to visualize the progress of weak linkages in scale space when going from fine to coarser scale. It is demonstrated that probabilistic linking gives a significantly improved segmentation as compared with conventional (single-parent) linking.
Adapting the mode profile of planar waveguides to single-mode fibers: a novel method (1991)

A novel method for coupling single-mode fibers to planar optical circuits with small waveguide dimensions is proposed. The method eliminates the need to apply microoptics or to adapt the waveguide dimensions within the planar circuit to the fiber dimensions. Alignment tolerances are comparable to those of fiber- fiber coupling. The low loss potential of the method is experimentally demonstrated for A1(2) O(3) waveguides on silicon substrates.
Large‐Scale Ceramic Composite Structures via Near‐Net‐Shape Processing of Carbon Preforms (2000)

Processing of ceramic matrix composites (CMC) presented in this article is based on the conversion of porous carbon preforms into C/SiC-ceramics by reaction infiltration of liquid silicon. For the processing itself as well as for the materials properties of the derived composites, microstructure and architecture of the used preforms play a key role. Composites are fabricated by starting from chopped, carbon short fiber reinforced carbons (C/C) which are machined by conventional CNC milling. Accordingly, very complex component geometries can be shaped. After subsequent reaction infiltration by a silicon melt, silicon carbide (SiC) is formed. In the as-processed composites, remnants of unreacted carbon as well as excess silicon are also present. The infiltration process is accompanied by no significant volume change. This near-net-shape feature allows to fabricate comparatively large components. At the same time also very thin-walled, light-weight structures can be processed. Furthermore, the near-net-shape character of the process allows a joining technique to be applied for the fabrication of multi-segmented components. This contribution presents C/SiC composites for specific applications that are derived from different types of carbon/carbon starting materials. Examples include large-dimensioned optical light-weight structures, large retorts for processing of metals and tube components to be used in combustion technology.
Proposal for an inhibitor of Alzheimer's disease blocking aggregation of amyloid-β peptides:ab initiomolecular simulations (2013)

Aggregation of amyloid-β (Aβ) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with Aβ and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between Aβ and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the Aβ aggregation.
Rear-emitter Si heterojunction solar cells with over 23% efficiency (2015)

We have developed highly crystallized n-type microcrystalline Si layers as window layers for rear emitter Si heterojunction solar cells. We introduce a seed layer between an n-type microcrystalline Si layer and an intrinsic amorphous Si layer to improve the crystallinity of the n-type microcrystalline Si layer. By using this stacked layer instead of an n-type amorphous Si layer, the contact resistance between the n-type thin layer and In2O3:H is reduced without Al-doped ZnO. As a result, we obtain a high short-circuit current and a high fill factor simultaneously, and achieve a solar cell efficiency of 23.43%.
Effects of Digital Noise Reduction on Speech Perception for Children with Hearing Loss (2010)

Consistent with previous findings from studies with adults, results suggest that the form of NR used in this study does not have a negative effect on the overall perception of nonsense syllables, words, or sentences across the age range (5 to 10 yrs) and speech to noise ratios (0, +5, and +10 dB) tested.
TanDEM-X: A Satellite Formation for High Resolution Radar Interferometry (2006)

TanDEM-X (TerraSAR-X add-on for Digital Elevation Measurements) is an innovative spaceborne radar interferometer mission that was approved for full implementation by the German Space Agency in spring 2006. This paper gives an overview of the TanDEM-X mission concept, summarizes the basic products, illustrates the achievable performance, and provides some examples for new imaging modes and applications. Two special aspects are pointed out which are the relative phase referencing and the mutual interference issue.
Machine Learning Prediction for 13X Endurance Enhancement in ReRAM SSD System (2015)

The variable behavior of ReRAM memory cells is modeled with machine learning. Two types of prediction are investigated, reset in the next-cycle and cell fail in the long term. A new proposal, Proactive Bit Redundancy, introduces a ML-traied Prediction Engine into the SSD controller, to predict fail cells and replace them proactively - before actual failure- by redundancy. With the Invalid Masking technique, predicted cells are marked in-place within the page, so that no extra address table is needed. Thus, with ninimal overhead, 2.85x bit error rate reduction or 13x endurance improvement is obtained based on a 50nm AlxOy testchip.
Extraordinary role of Zn in enhancing thermoelectric performance of Ga-doped n-type PbTe (2021)

The discordant Zn and Ga atoms raise the carrier concentration and soften phonon modes, resulting in superior performance nanostructured n-type PbTe.
Differentiation of Na+-K+ pump in rat proximal tubule is modulated by Na+-H+ exchanger (1988)

This study examines the effect of in vivo modulation of Na+-H+ exchange activity on the development of Na+-K+-ATPase in rat kidney proximal convoluted tubule (PCT) segments. To stimulate Na+-H+ exchanger (major entry pathway for Na in PCT), weanling rats were fed NH4Cl for 4 days to induce metabolic acidosis (MA). In vehicle (Vh)-fed rats PCT Na+-K+-ATPase activity (pmol Pi.mm tubule-1.h-1 +/- SE) increased from 481 +/- 78 at 16 days to 1,122 +/- 119 at 20 days. In 20-day-old chronic MA rats, PCT Na+-K+-ATPase activity was 1,717 +/- 109, i.e., significantly higher (P less than 0.01) relative to controls. Chronic MA had no effect on PCT Mg ATPase activity and on Na+-K+-ATPase in the medullary thick ascending limb (MTAL). To inhibit the Na+-H+ exchanger, weanling rats received amiloride (30 micrograms.100 g body wt-1.day-1) via osmotic minipump for 4 days. In Vh-treated rats PCT Na+-K+-ATPase increased from 481 +/- 78 at 16 days to 1,428 +/- 81 at 20 days. In rats given chronic amiloride, PCT Na+-K+-ATPase was significantly lower (858 +/- 75) at 20 days relative to controls but PCT Mg ATPase and MTAL Na+-K+-ATPase activity was the same as in controls. Chronic MA and amiloride had no significant effect on PCT Na+-K+-ATPase activity in adult rats. Acute MA and acute amiloride injection had no significant effect on PCT Na+-K+-ATPase in weanling rats.(ABSTRACT TRUNCATED AT 250 WORDS)