gebhart/patrepeval huggingface dataset:
Increased Expression of BCMA on Systemic Lupus Erythematosus B Cells is Associated with Enhanced Response to CpG (99.43) (2009)

Abstract BLyS and APRIL are members of the TNF superfamily that regulate B cell survival and autoreactivity, and can exist as homotrimers or BLyS/APRIL heterotrimers (HT). To further understand BLyS and APRIL function in SLE, we examined the expression profiles of their receptors (BAFF-R, TACI and BCMA) and their functional effects on B cell subsets. Whereas BAFF-R expression on SLE B cells was significantly lower compared to its levels on healthy control B cells (MFI of control vs SLE, naïve=1387 vs 929, p=0.002; memory=1290 vs 840, p=0.003), BCMA expression was substantially higher on SLE B cells (MFI of control vs SLE: 18 vs 28, p=0.038). This was most pronounced in the memory B cell subset (MFI of control vs SLE=19 vs 29, p=0.008) but was also evident on certain subsets of CD27- B cells. BCMA+ cells were mostly IgD+ and tended to be larger than BCMA-negative cells, and had higher CD19 and CD86 expression, indicating a greater degree of activation. FACS sorted BCMA+ B cells proliferated and differentiated much more potently than BCMA- B cells following CpG stimulation. CpG mainly induced the proliferation of BCMA+ B cells and increased BCMA expression on total B cells. These findings may help to explain the observed expansion of DNA-reactive SLE B cells in the presence of BLyS, APRIL or HT.
Tilt-Responsive Techniques for Digital Drawing Boards (UIST 2020 Paper) (2020)

Drawing boards offer a self-stable work surface that is continuously adjustable. On digital displays, such as the Microsoft Surface Studio, these properties open up a class of techniques that sense and respond to tilt adjustments. Each display posture—whether angled high, low, or somewhere in-between—affords some activities, but not others. Because what is appropriate also depends on the application and task, we explore a range of app-specific transitions between reading vs. writing (annotation), public vs. personal, shared person-space vs. task-space, and other nuances of input and feedback, contingent on display angle. Continuous responses provide interactive transitions tailored to each use-case. We show how a variety of knowledge work scenarios can use sensed display adjustments to drive context-appropriate transitions, as well as technical software details of how to best realize these concepts. A preliminary remote user study suggests that techniques must balance effort required to adjust tilt, versus the potential benefits of a sensed transition. Video embedded below, or watch on YouTube
A new human gene from the Down syndrome critical region encodes a proline-rich protein highly expressed in fetal brain and heart (1995)

Down syndrome is a major cause of mental retardation and congenital heart defects. While most of the affected individuals have three copies of chromosome 21, patients with partial trisomy 21 have also been described. These rare cases define a minimal region for the Down syndrome phenotype encompassing about 3 Mb around D21S55. By using a new method for the identification of coding sequences (Alu-splice PCR) we have identified a new gene, DSCR1, from region 21q22.1-q22.2. DSCR1 encodes a novel protein which has an acidic domain, a serine-proline motif, a putative DNA binding domain and a proline-rich region with the characteristics of a SH3 domain ligand. These features suggest that DSCR1 could be involved in transcriptional regulation and/or signal transduction. DSCR1 is highly expressed in human brain and heart, and increased expression in the brains of young rats compared with adults suggests a role for DSCR1 during central nervous system development. Structural characteristics, together with its particular expression in brain and heart, encourage us to suggest that the overexpression of DSCR1 may be involved in the pathogenesis of Down syndrome, in particular mental retardation and/or cardiac defects.
&#x201C;Green&#x201D; micro-architecture and circuit co-design for ternary content addressable memory (2008)

In this paper, an energy-efficient and high performance ternary content addressable memory (TCAM) are presented. It employs the concept of "green" microarchitecture and circuit co-design. For achieving energy-efficient TCAM architecture, hierarchy search-line scheme and butterfly match-line scheme are proposed. Moreover, the match-lines are also implemented by noise-tolerant XOR-based conditional keeper and don't-care based power gating scheme to reduce not only search time but power consumption. In order to reduce increasing leakage power with advanced technologies, furthermore, the proposed TCAM design employs super cut-off power gating technique and multi-mode data-retention power gating technique to reduce leakage currents without reducing search time and destroying noise margin. An energy-efficient 256times144 TCAM array is implemented in TSMC 0.13 um and designed in 65 nm Berkeley Predictive Technology Model, respectively. The simulation results show the leakage power reduction is 70.7% and energy metric of TCAM macro is 0.047 fJ/bit/search.
Repositioning of static analysis alarms (2018)

The large number of alarms reported by static analysis tools is often recognized as one of the major obstacles to industrial adoption of such tools.
Design of a Novel In-Pipe Reliable Leak Detector (2014)

Leakage is the major factor for unaccounted losses in every pipe network around the world (oil, gas, or water). In most cases, the deleterious effects associated with the occurrence of leaks may present serious economical and health problems. Therefore, leaks must be quickly detected, located, and repaired. Unfortunately, most state-of-the-art leak detection systems have limited applicability, are neither reliable nor robust, while others depend on the user experience. In this paper, we present a new in-pipe leak detection system. It performs autonomous leak detection in pipes and, thus, eliminates the need for the user experience. This paper focuses on the detection module and its main characteristics. Detection in based on the presence of a pressure gradient in the neighborhood of the leak. Moreover, the proposed detector can sense leaks at any angle around the circumference of the pipe with only two sensors. We validate the concepts by building a prototype and evaluate the system's performance under real conditions in an experimental laboratory setup.
Modeling of Power/Ground Planes Using Triangular Elements (2013)

As the operating frequency of electronic devices increases and system miniaturization continues, designing power delivery networks (PDNs) that supply quality power throughout the system becomes very challenging. To guarantee successful performance of the PDN, an accurate and time-efficient simulation method that computes the PDN impedance is required. In this paper, we propose a computationally efficient PDN modeling method that analyzes multilayer power/ground planes. The proposed method solves the differential form of Maxwell's equation applied on the circuit representation of a plane pair. To use the analogy between the equations of the electromagnetic field and the equivalent circuit, a dual mesh is created on the metal surface. The use of a nonuniform triangular mesh enables effective discretization of multidimensional and irregular geometries. Moreover, the differential equation generates a sparse system matrix, which requires small computer resources. The proposed model is extended to multiple plane pairs, and the modeling of apertures located on any layer is also included. Simulation results show that the proposed method can solve complex structures with less computational effort than other modeling methods, while maintaining accuracy. In addition, the application of the absorbing boundary condition (ABC) to the proposed method is presented. Applying ABC to the plane boundaries prevents outgoing waves from reflecting back into the plane pair, hence removing plane resonances. The use of the first-order ABC results in a simple implementation and the results show good correlation with the results from a full-wave solver using higher order ABC.
Development of an Aerosol Dose Collection Apparatus for In Vitro Dissolution Measurements of Orally Inhaled Drug Products (2020)

The aim of the study was to develop a robust and standardized in vitro dissolution methodology for orally inhaled drug products (OIDPs). An aerosol dose collection (ADC) system was designed to uniformly deposit the whole impactor stage mass (ISM) over a large filter area for dissolution testing. All dissolution tests were performed under sink conditions in a sodium phosphate buffered saline solution containing 0.2%w/w sodium dodecyl sulphate. An adapted USP Apparatus V, Paddle over Disk (POD), was used throughout the study. The dissolution characteristics of the ISM dose of a commercial metered-dose inhaler (MDI) and a range of dry powder inhaler (DPI) formulations containing inhaled corticosteroids were tested. The uniform distribution of the validated ISM dose considerably reduced drug loading effects on the dissolution profiles for both MDI and DPI formulations. The improvement in the robustness and discriminatory capability of the technique enabled characterization of dissolution rate differences between inhaler platforms and between different DPI product strengths containing fluticasone propionate. A good correlation between in vivo mean absorption time and in vitro dissolution half-life was found for a range of the inhaled corticosteroids. The ADC system and the reproducible in vitro POD dissolution measurements provided a quantitative-based approach for measuring the relationship between the influence of device and the dispersion characteristics on the aerosol dissolution of low solubility compounds. The in vitro dissolution method could potentially be applied as a dissolution methodology for compendial, quality control release testing, and during development of both branded orally inhaled drug products and their generic counterparts.
Optimizing Wafer Polishing Through Phenomenological Modeling (1995)

Key issues involved in implementing Warnock's phenomenological erosion model for chemical‐mechanical polishing (CMP) optimization are addressed. Mathematical details of the model are examined through an enhanced and generalized development. The improved development gives rise to a version of the model that allows for closer fits to experimental data and nonuniform discretization of the wafer features. The model's suitability for use in wafer polishing optimization is determined by examining the model's dependence on its adjustable parameters and by addressing its computational efficiency. Lastly, the minimization of adequate objective functions representing the optimal CMP process is described.
Voltage-gated sodium channels (2002)

It is known that the neuron-specific pattern of transcription of some voltage-gated sodium channels (VGSCs) is regulated by a specific sequence, the NRSE/RE1 (neuron-restricted silencing element) and its cognate binding protein. In addition, a role for accessory subunits in high-level channel expression and channel anchoring with respect to extracellular signals is also now established. More recently, signals ranging from growth factors such as GDNF to nerve damage or demyelinating diseases have been shown to alter the cohort of sodium (Na) channels expressed in neurons and may also alter their spatial pattern of expression. This chapter focuses on the possible regulatory role of accessory subunits that have been found to associate with Na channel α subunits, and factors that alter channel expression.
Regression of Some High-risk Features of Age-related Macular Degeneration (AMD) in Patients Receiving Intensive Statin Treatment (2016)

High-dose statins may result in resolution of drusenoid pigment epithelial detachments (PEDs) and improvement in VA, without atrophy or neovascularization in a high-risk subgroup of AMD patients. Confirmation from larger studies is warranted.
Effect of Foot-and-Mouth Disease Virus 2B Viroporin on Expression and Extraction of Mammalian Cell Culture Produced Foot-and-Mouth Disease Virus-like Particles (2022)

To improve the production of foot-and-mouth disease (FMD) molecular vaccines, we sought to understand the effects of the FMD virus (FMDV) 2B viroporin in an experimental, plasmid-based, virus-like particle (VLP) vaccine. Inclusion of the FMDV viroporin 2B into the human Adenovirus 5 vectored FMD vaccine enhanced transgene expression despite independent 2B expression negatively affecting cell viability. Evaluating both wildtype 2B and mutants with disrupted viroporin activity, we confirmed that viroporin activity is detrimental to overall transgene expression when expressed independently. However, the incorporation of 2B into an FMD molecular vaccine construct containing a wildtype FMDV 3C protease, a viral encoded protease responsible for processing structural proteins, resulted in enhancement of transgene expression, validating previous observations. This benefit to transgene expression was negated when using the FMDV 3C<sup>L127P</sup> mutant, which has reduced processing of host cellular proteins, a reversion resulting from 2B viroporin activity. Inclusion of 2B into VLP production constructs also adversely impacted antigen extraction, a possible side effect of 2B-dependent rearrangement of cellular membranes. These results demonstrate that inclusion of 2B enhanced transgene expression when a wildtype 3C protease is present but was detrimental to transgene expression with the 3C<sup>L127P</sup> mutant. This has implications for future molecular FMD vaccine constructs, which may utilize mutant FMDV 3C proteases.
Self-Repairing SRAM for Reducing Parametric Failures in Nanoscaled Memory (2006)

We present a self-repairing SRAM to reduce parametric failures using an on-chip leakage sensor and application of proper body bias. Simulations in a predictive 70nm technology show 5-40% (depending on inter-die Vt variation) improvement in SRAM yield. A test-chip is fabricated and measured in 0.13 mum CMOS to demonstrate operation of the self-repair system
Non-Coherent Angle and Angle-Rate Estimator for a Slewing Monopulse Antenna (2019)

We introduce a novel angle and angle-rate estimation algorithm for a mechanically slewing monopulse radar. The algorithm non-coherently combines monopulse measurements from several target echoes that were received as the radar was slewing. The non-coherent sums incorporate the antenna motion and are used for parameter estimation. The algorithm is broadly applicable to many radars that employ monopulse feeds and slew while searching for a target. It is also applicable to scanning receivers, such as beacon trackers, that use a monopulse feed or a direction finding array for estimating the angle to the target.
Gellan Gum-Hyaluronic Acid Spongy-like Hydrogels and Cells from Adipose Tissue Synergize Promoting Neoskin Vascularization (2014)

Currently available substitutes for skin wound healing often result in the formation of nonfunctional neotissue. Thus, urgent care is still needed to promote an effective and complete regeneration. To meet this need, we proposed the assembling of a construct that takes advantage of cell-adhesive gellan gum-hyaluronic acid (GG-HA) spongy-like hydrogels and a powerful cell-machinery obtained from adipose tissue, human adipose stem cells (hASCs), and microvascular endothelial cells (hAMECs). In addition to a cell-adhesive character, GG-HA spongy-like hydrogels overpass limitations of traditional hydrogels, such as reduced physical stability and limited manipulation, due to improved microstructural arrangement characterized by pore wall thickening and increased mean pore size. The proposed constructs combining cellular mediators of the healing process within the spongy-like hydrogels that intend to recapitulate skin matrix aim to promote neoskin vascularization. Stable and off-the-shelf dried GG-HA polymeric networks, rapidly rehydrated at the time of cell seeding then depicting features of both sponges and hydrogels, enabled the natural cell entrapment/encapsulation and attachment supported by cell-polymer interactions. Upon transplantation into mice full-thickness excisional wounds, GG-HA spongy-like hydrogels absorbed the early inflammatory cell infiltrate and led to the formation of a dense granulation tissue. Consequently, spongy-like hydrogel degradation was observed, and progressive wound closure, re-epithelialization, and matrix remodelling was improved in relation to the control condition. More importantly, GG-HA spongy-like hydrogels promoted a superior neovascularization, which was enhanced in the presence of human hAMECs, also found in the formed neovessels. These observations highlight the successful integration of a valuable matrix and prevascularization cues to target angiogenesis/neovascularization in skin full-thickness excisional wounds.
Learning protein sequence embeddings using information from structure. (2019)

Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for understanding function. Existing approaches for detecting structural similarity between proteins from sequence are unable to recognize and exploit structural patterns when sequences have diverged too far, limiting our ability to transfer knowledge between structurally related proteins. We newly approach this problem through the lens of representation learning. We introduce a framework that maps any protein sequence to a sequence of vector embeddings - one per amino acid position - that encode structural information. We train bidirectional long short-term memory (LSTM) models on protein sequences with a two-part feedback mechanism that incorporates information from (i) global structural similarity between proteins and (ii) pairwise residue contact maps for individual proteins. To enable learning from structural similarity information, we define a novel similarity measure between arbitrary-length sequences of vector embeddings based on a soft symmetric alignment (SSA) between them. Our method is able to learn useful position-specific embeddings despite lacking direct observations of position-level correspondence between sequences. We show empirically that our multi-task framework outperforms other sequence-based methods and even a top-performing structure-based alignment method when predicting structural similarity, our goal. Finally, we demonstrate that our learned embeddings can be transferred to other protein sequence problems, improving the state-of-the-art in transmembrane domain prediction.
Optimization of sulphur production in a biotechnological sulphide‐removing reactor (1990)

A new biotechnological process for sulphide removal is proposed. The principle of this process is that sulphide is converted into elemental sulphur, which can be removed by sedimentation. In this article, investigations on the optimization of the sulphur production are reported. It seems that less than 10% sulphate is produced at low oxygen concentration, when the sulphide concentration in the reactor exceeds 10 mg/L. At sulphide concentrations higher than 20 mg/L only 5% of the incoming sulphide is converted to sulphate even at high oxygen concentrations. An immobilized biomass on recticulated polyurethane produced more sulphate than a free cell suspension at the same oxygen and sulphide concentration.
Image description and 3-D reconstruction from image trajectories of rotational motion (1993)

A new technique for reconstructing the 3-D structure and motion of a scene undergoing relative rotational motion with respect to the camera is discussed. Given image correspondences of point features tracked over many frames, a two-stage technique for reconstruction is presented. A grouping algorithm that exploits spatio-temporal constraints of the common motion to achieve a reliable description of discrete point correspondences as curved trajectories in the image plane is developed. In contrast, trajectories fitted to points independent of each other lead to arbitrary image descriptions and very inaccurate 3-D parameters. A new closed-form solution, under perspective projection, for the 3-D motion and location of points from the computed image trajectories is also presented. Both stages are applied to real image sequences with good results. This approach represents a first step in a longer-term research effort examining the role of explicit spatio-temporal organization in the interpretation of scenes from dynamic images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Phosphodiesterase 3B Regulates cAMP Levels in Human Erythrocytes (2007)

It was reported that cAMP participates in a signaling pathway that couples activation of Gs with ATP release from erythrocytes (RBCs). cAMP levels are the product of adenylyl cyclase (AC) activity and degradation by phosphodiesterases (PDEs). RBCs possess AC activity, however, their PDE activity is poorly characterized. Insulin, a PDE3 activator, decreases cAMP levels in RBCs. Here, we investigate the hypothesis that PDE3B is present and active in RBCs. PDE3B was identified in RBC membranes by Western analysis. RBCs (50% HCT) were incubated with the PGI2 analog, iloprost (ILO, 1 μM), in the absence and presence of selective PDE3 inhibitors. ILO alone produced a 90.3±20.6% increase in cAMP (P<0.05). In the presence of cilostazol (CILO, 30 or 100 μM) or its parent compound, cilostamide (CMDE, 30 μM), basal cAMP levels were unchanged. However, in the presence of 30 and 100 μM CILO, ILO–induced cAMP levels increased from 3.0±0.5 to 5.4±1.1 (n=6, P<0.05) and 3.9±0.6 to 10.2±2.7 (n=7, P<0.05) pmole/1010 RBCs, respectively. In addition, CMDE also potentiated ILO-induced cAMP levels from 3.0±0.7 to 5.1±1.4 pmole/1010 RBCs (n=4, P<0.05). Here we demonstrate that PDE3 is present in RBC membranes and is important in the regulation of ILO-induced increases in cAMP. Inhibition of PDE3B could facilitate ATP release from RBCs in response to physiological stimuli. Funded by NIH grant HL-64180 and ADA grant RA-133.
Further purification and characterization of macromomycin. (1976)

The antitumor polypeptide, macromomycin (MCR) produced by Streptomyces macromomyceticus, was purified by ammonium sulfate precipitation, ultrafiltration and chromatographic techniques using Amberlite IRA-410, DEAE Sephadex A-25 (CI- and OH-type) and Sephadex G-50. Purified MCR was obtained as a white powder by lyophilization. MCR, thus purified, exhibited a single peak on Sephadex G-50 chromatography with no detectable contaminant by ultracentrifugation and polyacrylamide gel electrophoresis. MCR is an acidic polypeptide having an isoelectric point of pH 5.4. It contains no arginine and methionine. The molecular weight was 11,700, 12,500 and 11,400 by amino acid composition, gel filtration and analytical ultracentrifugation, respectively. MCR is labile as a lyophilized powder but is successfully stabilized by the addition of maltose.