gebhart/patrepeval huggingface dataset:
Role for Cathepsin F in Invariant Chain Processing and Major Histocompatibility Complex Class II Peptide Loading by Macrophages (2000)

The major histocompatibility complex (MHC) class II-associated invariant chain (Ii) regulates intracellular trafficking and peptide loading of MHC class II molecules. Such loading occurs after endosomal degradation of the invariant chain to a approximately 3-kD peptide termed CLIP (class II-associated invariant chain peptide). Cathepsins L and S have both been implicated in degradation of Ii to CLIP in thymus and peripheral lymphoid organs, respectively. However, macrophages from mice deficient in both cathepsins S and L can process Ii and load peptides onto MHC class II dimers normally. Both processes are blocked by a cysteine protease inhibitor, indicating the involvement of an additional Ii-processing enzyme(s). Comparison of cysteine proteases expressed by macrophages with those found in splenocytes and dendritic cells revealed two enzymes expressed exclusively in macrophages, cathepsins Z and F. Recombinant cathepsin Z did not generate CLIP from Ii-MHC class II complexes, whereas cathepsin F was as efficient as cathepsin S in CLIP generation. Inhibition of cathepsin F activity and MHC class II peptide loading by macrophages exhibited similar specificity and activity profiles. These experiments show that cathepsin F, in a subset of antigen presenting cells (APCs), can efficiently degrade Ii. Different APCs can thus use distinct proteases to mediate MHC class II maturation and peptide loading.
Pervasive diagnosis: the integration of diagnostic goals into production plans (2008)

In model-based control, a planner uses a system description to create a plan that achieves production goals (Fikes &amp; Nilsson 1971). The same description can be used by model-based diagnosis to infer the condition of components in a system from partially informative sensors. Prior work has demonstrated that diagnosis can be used to adapt the con-trol of a system to changes in its components. However diagnosis must either make inferences from passive obser-vations of production, or production must be halted to take diagnostic actions. We observe that the declarative nature of model-based control allows the planner to achieve pro-duction goals in multiple ways. This flexibility can be ex-ploited with a novel paradigm we call pervasive diagnosis which produces diagnostic production plans that simultane-ously achieve production goals while uncovering additional information about component health. We present an effi-cient heuristic search for these diagnostic production plans and show through experiments on a model of an industrial digital printing press that the theoretical increase in infor-mation can be realized on practical real-time systems. We obtain higher long-run productivity than a decoupled com-bination of planning and diagnosis.
TU‐AB‐BRA‐03: Atlas‐Based Algorithms with Local Registration‐Goodness Weighting for MRI‐Driven Electron Density Mapping (2016)

Purpose: To develop image‐analysis algorithms to synthesize CT with accurate electron densities for MR‐only radiotherapy of head & neck (H&N) and pelvis anatomies. Methods: CT and 3T‐MRI (Philips, mDixon sequence) scans were randomly selected from a pool of H&N (n=11) and pelvis (n=12) anatomies to form an atlas. All MRIs were pre‐processed to eliminate scanner and patient‐induced intensity inhomogeneities and standardize their intensity histograms. CT and MRI for each patient were then co‐registered to construct CT‐MRI atlases. For more accurate CT‐MR fusion, bone intensities in CT were suppressed to improve the similarity between CT and MRI. For a new patient, all CT‐MRI atlases are deformed onto the new patients’ MRI initially. A newly‐developed generalized registration error (GRE) metric was then calculated as a measure of local registration accuracy. The synthetic CT value at each point is a 1/GRE‐weighted average of CTs from all CT‐MR atlases. For evaluation, the mean absolute error (MAE) between the original and synthetic CT (generated in a leave‐one‐out scheme) was computed. The planning dose from the original and synthetic CT was also compared. Results: For H&N patients, MAE was 67±9, 114±22, and 116±9 HU over the entire‐CT, air and bone regions, respectively. For pelvis anatomy, MAE was 47±5 and 146±14 for the entire and bone regions. In comparison with MIRADA medical, an FDA‐approved registration tool, we found that our proposed registration strategy reduces MAE by ∼30% and ∼50% over the entire and bone regions, respectively. GRE‐weighted strategy further lowers MAE by ∼15% to ∼40%. Our primary dose calculation also showed highly consistent results between the original and synthetic CT. Conclusion: We've developed a novel image‐analysis technique to synthesize CT for H&N and pelvis anatomies. Our proposed image fusion strategy and GRE metric help generate more accurate synthetic CT using locally more similar atlases (Support: Philips Healthcare). The research is supported by Philips HealthCare
Saddle-point construction in the design of lithographic objectives, part 1: method (2008)

The multidimensional merit function space of complex optical systems contains a large number of local minima. We illustrate a method to find new local minima by constructing saddle points, with examples of deep and extreme UV objectives. The central idea of the method is that, at certain positions in a system with N surfaces that is a local minimum, a thin meniscus lens or two mirror surfaces can be introduced to construct a system with N+2 surfaces that is a saddle point. When optimization rolls down on the two sides of the saddle point, two minima are obtained. Often one of these two minima can also be reached from several other saddle points constructed in the same way. With saddle-point construction we can obtain new design shapes from existing ones in a simple, efficient, and systematic manner that is suitable for complex designs such as those for lithographic objectives.
Emitter wrap-through solar cell (2002)

The authors present a new solar cell concept (emitter wrap-through or EWT) for a back-contact cell. The cell has laser-drilled vias to wrap the emitter on the front surface to contacts on the back surface and uses a potentially low-cost process sequence. Modeling calculations show that efficiencies of 18 and 21% are possible with large-area solar-grade multi- and monocrystalline silicon EWT cells, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Joint multi-label multi-instance learning for image classification (2008)

In real world, an image is usually associated with multiple labels which are characterized by different regions in the image. Thus image classification is naturally posed as both a multi-label learning and multi-instance learning problem. Different from existing research which has considered these two problems separately, we propose an integrated multi-label multi-instance learning (MLMIL) approach based on hidden conditional random fields (HCRFs), which simultaneously captures both the connections between semantic labels and regions, and the correlations among the labels in a single formulation. We apply this MLMIL framework to image classification and report superior performance compared to key existing approaches over the MSR Cambridge (MSRC) and Corel data sets.
Analysis of Mutual Flux Linkage in Switched Reluctance Machines (2018)

Although switched reluctance machines (SRM) are usually modeled and analyzed on per-phase basis, knowledge of mutual coupling between phases might be very important in cases where some sophisticated control algorithms have to be applied, as for example torque sharing functions (TSF) for torque ripple reduction. These algorithms require simultaneous conduction of several SRM phases, in which case mutual coupling can't be neglected. This paper aims to give an overview of the shape and magnitude of the mutual flux linkage between SRM phases for the several SRM configurations with the different combination of stator and rotor poles. All results are obtained by magnetostatic 2D FEM simulations by exciting one phase and calculating the flux in another unexcited phase. By examining the obtained results, conclusions are derived for the certain types of SRM configurations that express the similar mutual flux linkage pattern.
Measuring and optimizing a system for persistent database sessions (2002)

High availability for both data and applications is rapidly becoming a business requirement. While database systems support recovery, providing high database availability, applications may still lose work because of server outages. When a server crashes, any volatile state associated with the application's database session is lost and the application may require an operator-assisted restart. This exposes server failures to end-users and always degrades application availability. Our Phoenix/ODBC system supports persistent database sessions that can survive a database crash without the application being aware of the outage, except for possible timing considerations. This improves application availability and eliminates the application programming needed to cope with database crashes. Phoenix/ODBC requires no changes to the database system, data access routines or applications. Hence, it can be deployed in any application that uses ODBC to access a database. Further, our generic approach can be exploited for a variety of data access protocols. In this paper, we describe the design of Phoenix/ODBC and introduce an extension to optimize the response time and to reduce overhead for OLTP workloads. We present a performance evaluation using the TPC-C and TPC-H benchmarks that demonstrate Phoenix/ODBC's extra overhead is modest.
Structural Analysis, Plastid Localization, and Expression of the Biotin Carboxylase Subunit of Acetyl-Coenzyme A Carboxylase from Tobacco (1995)

Acetyl-coenzyme A carboxylase (ACCase, EC 6.4.1.2) catalyzes the synthesis of malonyl-coenzyme A, which is utilized in the plastid for de novo fatty acid synthesis and outside the plastid for a variety of reactions, including the synthesis of very long chain fatty acids and flavonoids. Recent evidence for both multifunctional and multisubunit ACCase isozymes in dicot plants has been obtained. We describe here the isolation of a tobacco (Nicotiana tabacum L. cv bright yellow 2 [NT1]) cDNA clone (E3) that encodes a 58.4-kD protein that shares 80% sequence similarity and 65% identity with the Anabaena biotin carboxylase subunit of ACCase. Similar to other biotin carboxylase subunits of acetyl-CoA carboxylase, the E3-encoded protein contains a putative ATP-binding motif but lacks a biotin-binding site (methionine-lysine-methionine or methionine-lysine-leucine). The deduced protein sequence contains a putative transit peptide whose function was confirmed by its ability to direct in vitro chloroplast uptake. The subcellular localization of this biotin carboxylase has also been confirmed to be plastidial by western blot analysis of pea (Pisum sativum), alfalfa (Medicago sativa L.), and castor (Ricinus communis L.) plastid preparations. Northern blot analysis indicates that the plastid biotin carboxylase transcripts are expressed at severalfold higher levels in castor seeds than in leaves.
Peptide-based carrier devices for stellate cells and other cell-types involved in chronic inflammatory and fibrotic disorders (2004)

The present invention relates to a compound comprising a carrier molecule, said carrier molecule being linked to a further molecule, said further molecule being at least one cyclic peptide, said cyclic peptide comprising in the cyclic peptide portion thereof at least one sequence encoding a cell receptor recognising peptide (RRP) and with the proviso that the compound is not a naturally occuring receptor agonist or antagonist. Preferably, the RRP is of a receptor specific for Hepatic Stellate Cells (HSC) or a receptor that is upregulated on HSC during disease. In particular, the RRP may be of a receptor selected from the group of PDGF receptor, collagen type VI receptor, cytokine receptor(s) such as TGF?, IFN? and interleukin 1?. Preferably, the cyclic portion of the cyclic peptide comprises at least the amino acid sequence RGD or KPT.
Correction of translation-induced artifacts in wrist MRI scans using orthogonal acquisitions (2002)

Correction of motion artifacts in MRI due to interview in-plane 2-D rigid body translations is possible using only the raw data of two standard 2DFT images acquired of the same object with phase encode direction swapped. Previous techniques simply use multiple or orthogonal images to reduce artifacts by ghost interference or geometric averaging. The orthogonal k-space phase difference (ORKPHAD) provides an overdetermined system of linear equations that can be solved directly to compensate for the phase errors caused by the translation. This technique was used to correct images of a volunteer's moving wrist. For all slices of the motion corrupted data volumes, artifacts were dramatically reduced. Though the algorithm only accounts for interview translational motion, it is robust enough to correct real in vivo images that may also be corrupted by small amounts of rotational or out-of-plane motion. Experiments underway show the algorithm can tolerate bulk rotation of several degrees between orthogonal image pairs and that corrections using fractional NEX scans are possible. The current results and such ongoing advancements should make this correction technique practical for certain clinical scenarios vulnerable to in-plane translation.
Zero magnetostrictive amorphous alloys with high permeability and high magnetic induction (1981)

The rapidly quenched zero magnetostrictive Co-Fe-Si-B amorphous alloys having high magnetic induction and high permeability have been studied. The magnetic annealing under the vertical magnetic field H⊥ and under the rotating magnetic field Hφ has been investigated to obtain high permeability even though the alloys have the Curie temperature Tc higher than the crystallization temperature Tx. A zero magnetostrictive amorphous alloy with saturation magnetization σs = 115 e.m.u./gr and with initial permeability μi = 8,000 at 1 kHz has been obtained using the new method of magnetic annealing.
The Electro-Adsorption Chiller: Performance Rating of a Novel Miniaturized Cooling Cycle for Electronics Cooling (2006)

The paper describes the successful amalgamation of the thermoelectric and the adsorption cycles into a combined electro-adsorption chiller (EAC). The symbiotic union produces an efficiency or COP (coefficient of performance) more than threefold when compared with their individual cycles. The experiments conducted on the bench-scale prototype show that it can meet high cooling loads, typically 120W with an evaporator foot print of 25cm2, that is 5W∕cm2 at the heated surface temperature of 22°C, which is well below that of the room temperature. The COPs of the EAC chiller vary from 0.7 to 0.8, which is comparable to the theoretical maximum of about 1.1 at the same operating conditions. With a copper-foam cladded evaporator, the high cooling rates have been achieved with a low temperature difference. In addition to meeting high cooling rates, the EAC is unique as (i) it has almost no moving parts and hence has silent operation, (ii) it is environmentally friendly as it uses a nonharmful adsorbent (silica gel), and (iii) water is used as the refrigerant.
Rapid Detection of the<i>Chlamydiaceae</i>and Other Families in the Order<i>Chlamydiales</i>: Three PCR Tests (1999)

Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, family Chlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized the Chlamydiaceae: a multiplex test targeting the ompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation.
Designing High-Performance Enterprise Wi-FiNetworks. (2008)

Use of mobile computing devices such as laptops, PDAs, and Wi-Fi enabled phones is increasing in the workplace. As the usage of corporate 802.11 wireless networks (WLANs) grows, network performance is becoming a significant concern. We have built DenseAP, a novel system for improving the performance of enterprise WLANs using a dense deployment of access points (APs). In sharp contrast with wired networks, one cannot increase the capacity of a WLAN by simply deploying more equipment (APs). To increase capacity, the APs must be assigned appropriate channels and the clients must make intelligent decisions about which AP to associate with. Furthermore, the decisions about channel assignment, and associations must be based on a global view of the entire WLAN, rather than the local viewpoint of an individual client or AP. Given the diversity of Wi-Fi devices in use today, another constraint on the design of DenseAP is that it must not require any modification to Wi-Fi clients. In this paper, we show how the DenseAP system addresses these challenges, and provides significant improvements in performance over existing WLANs.
<i>GSTP1</i> CpG island hypermethylation as a molecular biomarker for prostate cancer (2003)

Somatic hypermethylation of CpG island sequences at GSTP1, the gene encoding the pi-class glutathione S-transferase, appears to be characteristic of human prostatic carcinogenesis. To consider the potential utility of this epigenetic alteration as a biomarker for prostate cancer, we present here a comprehensive review of the literature describing somatic GSTP1 changes in DNA from prostate cells and tissues. GSTP1 CpG island hypermethylation has been detected in prostate cancer DNA using a variety of assay techniques, including (i) Southern blot analysis (SB), after treatment with (5-m)C-sensitive restriction endonucleases, (ii) the polymerase chain reaction, following treatment with (5-m)C-sensitive restriction endonucleases (RE-PCR), (iii) bisulfite genomic sequencing (BGS), and (iv) bisulfite modification followed by the polymerase chain reaction, using primers selective for target sequences containing (5-m)C (MSP). In the majority of the case series so far reported, GSTP1 CpG island hypermethylation was present in DNA from at least 90% of prostate cancer cases. When analyses have been carefully conducted, GSTP1 CpG island hypermethylation has not been found in DNA from normal prostate tissues, or from benign prostatic hyperplasia (BPH) tissues, though GSTP1 CpG island hypermethylation changes have been detected in DNA from candidate prostate cancer precursor lesions proliferative inflammatory atrophy (PIA) and prostatic intraepithelial neoplasia (PIN). Using PCR methods, GSTP1 CpG island hypermethylation has also been detected in urine, ejaculate, and plasma from men with prostate cancer. GSTP1 CpG island hypermethylation, a somatic epigenetic alteration, appears poised to serve as a molecular biomarker useful for prostate cancer screening, detection, and diagnosis.
Durability of LDPE nanocomposites with clay, silica, and zinc oxide II. weatherability of the nanocomposites (2013)

Three LDPE nanocomposites based on the nanoscale fillers, montmorillonite clay, silica, and zinc oxide were studied to determine if the reinforcement they imparted was accompanied by any change in the weatherability of the nanocomposite. Changes in weathering behavior were monitored in samples exposed to natural weathering outdoors over a period of 24 months of exposure. Because of superior light‐shielding afforded by the high specific surface area of nanofillers a stabilization effect might be anticipated. Alternatively chemical effects may enhance weatherability. In all three nanocomposites studied, the weatherability compared to unfilled LDPE did not significantly change due to the presence of 5 wt% of the nanofillers. The efficient reinforcement afforded by the nanofillers is not accompanied by a loss or enhancement in durability of the material. POLYM. COMPOS., 34:1878–1883, 2013. © 2013 Society of Plastics Engineers
Expressnet: A High-Performance Integrated-Services Local Area Network (1983)

Expressnet is a local area communication network comprising an inbound channel and an outbound channel to which the stations are connected. Stations transmit on the outbound channel and receive on the inbound channel. The inbound channel is connected to the outbound channel so that all signals transmitted on the outbound channel are duplicated on the inbound channel, thus achieving broadcast communication among the stations. In order to transmit on the bus, the stations utilize a distributed access protocol which achieves a conflict-free round-robin scheduling. This protocol is more efficient than existing round-robin Schemes as the time required to switch control from one active user to the next in a round is minimized (on the order of a carrier detection time), and is independent of the end-to-end network propagation delay. This improvement is particularly significant when the channel data rate is so high, or the end-to-end propagation delay is so large, Or the packet size is so small as to render the end-to-end propagation delay a significant fraction of, or larger than, the transmission time of a packet. Moreover, some features of Expressnet make it particularly suitable for voice applications. In view of integrating voice and data, a simple access protocol is described which meets the bandwidth requirement and maximum packet delay constraint for voice communication at all times, while guaranteeing a minimum bandwidth requirement for data traffic. Finally, it is noted that the voice/data access protocol constitutes a highly adaptive allocation scheme of channel bandwidth, which allows data users to recover the bandwidth unused by the voice application. It can be easily extended to accommodate any number of applications, each with its specific requirements.
Coral-automating the design of systems-on-chip using cores (2002)

The reuse of pre-designed and pre-verified IP blocks or cores has been touted as the enabler of large systems-on-chip designs. However, the lack of appropriate tools and the increasing complexity of such cores makes them inherently difficult and error-prone to use. This paper presents a new tool, "Coral", for the design of systems using cores. Coral is based on a new synthesizable virtual design representation which is automatically synthesized to a real design. Novel algorithms are presented to interconnect cores automatically as well as configure system parameters, such as interrupt maps, DMA channel assignments, etc. Coral significantly reduces the time, complexity and potential for errors associated with SoC integration.