gebhart/patrepeval huggingface dataset:
Segmented shape memory alloy actuators using hysteresis loop control (2006)

A new approach to the design and control of shape memory alloy (SMA) actuators is presented. SMA wires are divided into many segments and their thermal states are controlled individually as a group of finite state machines. Instead of driving a current to the entire SMA wire and controlling the wire length based on the analog strain–temperature characteristics, the new method controls the binary state (hot or cold) of individual segments and thereby the total displacement is proportional to the length of the heated segments, i.e. austenite phase. Although the thermomechanical properties of SMA are highly nonlinear and uncertain with a prominent hysteresis, segmented binary control is robust and stable, providing characteristics similar to a stepping motor. However, the heating and cooling of each segment to its bi-stable states entail longer time and larger energy for transition. In this paper, an efficient method for improving the speed of response and power consumption is developed by exploiting the inherent hysteresis of SMA. Instead of keeping the extreme temperatures continuously, the temperatures return to intermediate 'hold' temperatures closer to room temperature but sufficient to keep constant phase. Coordination of the multitude of segments having independent thermal states allows for faster response with little latency time even for thick SMA wires. Based on stress dependent thermomechanical characteristics, the hold temperature satisfying a given stress margin is obtained. The new control method is implemented using the Peltier effect thermoelectric devices for selective segment-by-segment heating and cooling. Experiments demonstrate the effectiveness of the proposed method.
Transcutaneous Glucose Sensing by Surface-Enhanced Spatially Offset Raman Spectroscopy in a Rat Model (2010)

This letter presents the first quantitative, in vivo, transcutaneous glucose measurements using surface enhanced Raman spectroscopy (SERS). Silver film over nanosphere (AgFON) surfaces were functionalized with a mixed self-assembled monolayer (SAM) and implanted subcutaneously in a Sprague-Dawley rat. The glucose concentration was monitored in the interstitial fluid. SER spectra were collected from the sensor chip through the skin using spatially offset Raman spectroscopy (SORS). The combination of SERS and SORS is a powerful new approach to the challenging problem of in vivo metabolite and drug sensing.
Abstract NG01: SPOP mutation is associated with genomic instability in prostate cancer (2015)

Abstract Background: Genomic instability is a fundamental feature of human cancer, and DNA repair defects resulting in impaired genome maintenance promote pathogenesis of many types of cancers. In prostate cancer, structural genomic rearrangements, including translocations and copy number aberrations, are a key mechanism driving tumorigenesis. Recently, whole genome sequencing revealed a striking abundance, complexity, and heterogeneity of genomic rearrangements, potentially suggesting distinct mechanisms of instability in different molecular classes of prostate cancer. However, the somatic alterations underlying these phenomena remain largely undefined. Recurrent mutations in SPOP, the substrate-recognition component of an E3-ubiquitin ligase, represent the most common point mutations in primary prostate cancer, occurring in about 10% of tumors. SPOP mutations define a distinct molecular class of prostate cancer; they are mutually exclusive with TMPRSS2-ERG fusions, but harbor distinct patterns of copy number aberrations. Here, we report that SPOP mutant prostate cancers also harbor increased numbers of genomic rearrangements, and functional data suggest that SPOP mutation alters repair of DNA double strand breaks (DSB). Methods: We systematically investigated somatic alterations associated with genomic rearrangements, using a composite data set of 402 clinically localized prostate cancers. Functional analyses in vitro and in vivo were used to define pathways affected, and interrogate DNA repair phenotypes. Results: In human prostate cancers, SPOP mutation is an early event specifically associated with increased intrachromosomal genomic rearrangements. Using a zebrafish model, SPOP mutation results in a transcriptional response consistent with BRCA1 inactivation, implicating altered repair of DSB. In vitro data suggest that SPOP participates in repair of DSB, and SPOP mutation impairs homology-directed repair (HDR), instead promoting error-prone non-homologous end joining (NHEJ). Finally, SPOP mutation sensitizes prostate cancer cells to DNA damaging therapeutic agents such as PARP inhibitors. Conclusions: These results implicate SPOP as a novel participant in DSB repair, suggest that SPOP mutation drives prostate tumorigenesis in part through genomic instability, and indicate that SPOP mutant prostate cancer may be selectively responsive to DNA damaging therapeutics. Citation Format: Christopher E. Barbieri, Gunther Boysen, Davide Prandi, Sung-Suk Chae, Arun Dahiya, Srilakshmi Nataraj, Mirjam Blattner, Clarisse Marotz, Limei Xu, Julie Huang, Paola Lecca, Sagar Chhangawala, Pengbo Zhou, Andrea Sboner, Francesca Demichelis, Yariv Houvras, Mark A. Rubin. SPOP mutation is associated with genomic instability in prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr NG01. doi:10.1158/1538-7445.AM2015-NG01
Terpolymers from lactide and bisphenol a derivatives: Scale‐up, properties, and blends (2011)

Abstract Terpolymerization of L‐lactide (LA) and bisphenol A derivatives was performed on few hundred gram scale, and the resultant terpolymer (TP) was characterized by gel permeation chromatography, infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), and thermogravimetric analysis. Moderate molecular weight ( M n ∼ 12 kg/mol) TP was achieved with glass transition temperatures about 100°C (DSC and DMA). The TP exhibited improved thermal stability compared with polylactide (PLA), with a thermal degradation temperature of about 80°C higher than PLA. Although the TP exhibited distinctly different surface morphology compared with that of PLA, both showed similar contact angle and surface energy (ca. 40 mN/m) properties. Blends of PLA and TP showed enhanced glass transition (∼ 5°C change in T g ) temperatures compared with PLA homopolymer. This is due to the compatibility of PLA and TP. Thus, TP could be used as an additive for PLA‐based blends to enhance compatibility with phenolic‐based resins. TP electrospun fiber morphology is also reported. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Genome-scale antibody responses in TB (2010)

High-throughput methods have made it possible to generate microarrays carrying all ~4,000 proteins of MMycobacterium tuberculosis (M.tb). With this platform, large numbers of individual sera from infected humans and animals can be tested for antibody detection. Preliminary results of probing M.tb proteome microarrays with sera collected under a uniform study protocol at various sites worldwide from > 500 pulmonary TB suspects who received a final diagnosis of active TB or non-TB-disease (NTBD) showed that approximately 500 M.tb proteins reacted with at least one serum, while the rest of the proteome reacted to none. Thus the immunoproteome of M.tb is approximately one-tenth the size of the total proteome. It was also found that, among the ~500 reactive proteins, only a fraction reacted differentially to active TB sera versus NTBD sera. It is intuitive that serodiagnostic antigens belong to this antigen subset. Additionally, no obvious pattern of reactivity was observed among active TB sera. This result indicates that, within the pool of seroreactive antigens, target recognition greatly varies from individual to individual. We also explored the association between proteome-scale antibody responses and clinical and demographic covariates, such as patients’ age and gender, country of origin, bacillary burden (expressed as sputum smear grade), HIV status, etc. In particular, we found that the antibody response to some antigens positively correlated with sputum smear grade, while the response to others was independent of smear grade. The previously reported positive correlation between reactivity to the 38 kDa antigen and bacillary burden supports the proteome-wide results. We also observed that, while antibody profiles varied among sera, antigens exhibiting the highest differential ability were recognized across geographical sites. Thus, it should be possible to identify serodiagnostic antigens that can be utilized worldwide. As previously reported, HIV co-infection dampened the antibody response. Moreover, results of protein class analysis showed that reactivity to the glyoxylate bypass proteins was associated with active TB. This metabolic pathway is essential for M.tb growth and survival in mice, and is up-regulated in tubercle bacilli found in human sputa. Thus, the analysis of antibody responses at the proteome scale can be informative of the biology of tubercle bacilli in the human host. In addition, proteome microarray probing with sera from experimentally infected macaques showed that antibody responses vary with progression to disease, supporting the possibility that disease progression can be monitored by serology.
88 °C, continuous-wave operation of apertured, intracavity contacted, 1.55 μm vertical-cavity surface-emitting lasers (2001)

We demonstrate a lattice-matched 1.55 μm vertical-cavity surface-emitting laser operating continuous wave up to 88 °C. The laser employs AlAsSb-based mirrors, which provide high reflectivity and lattice matching to InP. The poor electrical and thermal conductivity of these mirrors is circumvented by utilizing an InP double-intracavity contacted structure. Benefits of the intracavity contacts are addressed by comparing the characteristics with the alternative contact scheme where current is injected through the Sb-based mirrors. Current and optical confinement is provided by an undercut aperture. The device shows a threshold current of 800 μA, a differential efficiency of 23%, and a maximum output power of over 1 mW at 20 °C.
Nitroaliphatic difluoroformals and process of manufacture (1975)

Some new nitroaliphatic difluoroformal compounds are described. The compounds are intended for use in formulating PBX compositions and as energetic plasticizers or fluidic dispersant materials for plastic explosive compositions. Methods of preparation and several examples are given. (PMA)
Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies (2019)

The CD4 binding site (CD4bs) of the HIV-1 envelope glycoprotein is susceptible to multiple lineages of broadly neutralizing antibodies (bnAbs) that are attractive to elicit with vaccines. The CH235 lineage (VH1-46) of CD4bs bnAbs is particularly attractive because the most mature members neutralize 90% of circulating strains, do not possess long HCDR3 regions, and do not contain insertions and deletions that may be difficult to induce. We used virus neutralization to measure the interaction of CH235 unmutated common ancestor (CH235 UCA) with functional Env trimers on infectious virions to guide immunogen design for this bnAb lineage. Two Env mutations were identified, one in loop D (N279K) and another in V5 (G458Y), that acted synergistically to render autologous CH505 transmitted/founder virus susceptible to neutralization by CH235 UCA. Man5-enriched N-glycans provided additional synergy for neutralization. CH235 UCA bound with nanomolar affinity to corresponding soluble native-like Env trimers as candidate immunogens. A cryo-EM structure of CH235 UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 revealed interactions of the antibody light chain complementarity determining region 3 (CDR L3) with the engineered Env loops D and V5. These results demonstrate that virus neutralization can directly inform vaccine design and suggest a germline targeting and reverse engineering strategy to initiate and mature the CH235 bnAb lineage.
A Frequency Demodulation Approach to Induction Motor Speed Detection (2011)

Rotor slot harmonics are found in the stator current waveforms for most squirrel-cage induction motors. These harmonics are caused by the finite number of rotor slots in a motor, and their frequencies are inherently correlated with the motor's rotational speed. A frequency demodulation approach is proposed in this paper to continuously and accurately track the rotational speed for induction motors that are operated at either dynamic or steady-state conditions from fixed-frequency power supplies. First, a complex current vector is synthesized from polyphase electrical current measurements. Second, a local oscillator and a mixer are cascaded with a digital filter to heterodyne a specific rotor slot harmonic and suppress adjacent interferences. A finite impulse response differentiator is then employed as a frequency demodulator to approximate the time derivative of the phase of this specific rotor slot harmonic and to resolve its instantaneous frequency. Finally, the induction motor speed is calculated from this resolved instantaneous rotor slot harmonic frequency. Experimental results demonstrate that the proposed scheme is capable of interleaving data acquisition with real-time computation, iteratively estimating motor speed on a sample-by-sample basis.
Synthesis and properties of an oligomeric divinyl-terminated aromatic ether containing resin (2009)

The synthesis of a novel oligomeric divinyl-terminated aromatic ether containing resin and polymerization with silane containing compounds utilizing a hydrosilylation reaction is demonstrated. The transparent, clear polymers exhibit high thermal and oxidative stability while exhibiting elastomeric and plastic properties depending on the curing temperature and curing agent.
When Regression Meets Manifold Learning for Object Recognition and Pose Estimation (2018)

In this work, we propose a method for object recognition and pose estimation from depth images using convolutional neural networks. Previous methods addressing this problem rely on manifold learning to learn low dimensional viewpoint descriptors and employ them in a nearest neighbor search on an estimated descriptor space. In comparison we create an efficient multi-task learning framework combining manifold descriptor learning and pose regression. By combining the strengths of manifold learning using triplet loss and pose regression, we could either estimate the pose directly reducing the complexity compared to NN search, or use the learned descriptor for the NN descriptor matching. By in depth experimental evaluation of the novel loss function we observed that the view descriptors learned by the network are much more discriminative resulting in almost 30% increase regarding relative pose accuracy compared to related works. On the other hand, regarding directly regressed poses we obtained important improvement compared to simple pose regression. By leveraging the advantages of both manifold learning and regression tasks, we are able to improve the current state-of-the-art for object recognition and pose retrieval.
Simultaneous Luminescence Pressure and Temperature Mapping System (1995)

A simultaneous luminescence pressure and temperature mapping system is developed including improved dye application techniques for surface temperature and pressure measurements from 5 torr to 1000 torr with possible upgrade to from 0.5 torr to several atmospheres with improved camera resolution. Adsorbed perylene dye on slip-cast silica is pressure (oxygen) sensitive and reusable to relatively high temperatures (approximately 150 C). Adsorbed luminescence has an approximately linear color shift with temperature, which can be used for independent temperature mapping and brightness pressure calibration with temperature.
Flattening of central corneal curvature with Intrastromal Corneal Rings of increasing thickness: An eye-bank eye study (1993)

Intrastromal Corneal Rings (ICRs) have been demonstrated to flatten human corneas when implanted into peripheral intrastromal corneal channels. To study the flattening effect, ICRs of increasing thickness, 0.26, 0.31, 0.36, 0.41, and 0.46 mm, were placed into oversized (approximately 70% depth) intrastromal channels in 38 eye-bank eyes. Each of 33 eyes received one ICR; the mean change in dioptric data was obtained for four meridians using an intraoperative photokeratoscope. Intrastromal corneal rings of increasing thickness resulted in corneal flattening of 3.8 +/- 1.1, 4.9 +/- 0.6, 5.2 +/- 1.1, 5.3 +/- 1.9, and 7.3 +/- 1.6 diopters, respectively, for keratoscope mire 2. One of each size ICR was placed into one of five additional eye-bank eyes; the degree of flattening measured by laser holographic interferometry was 1.8, 2.9, 5.5, 4.7, and 10.1 diopters, respectively, for the central 6 mm corneal zone. These results indicate that the ICR provides a fairly linear flattening relationship over the range of thicknesses tested. Additionally, laser holographic interferometry wave unit maps of preoperative and postoperative corneas demonstrated that the ICR tends to preserve positive corneal asphericity if present preoperatively.
Enhancement of Peptidoglutaminase Deamidation of Soy Protein by Heat Treatment and/or Proteolysis (1988)

ABSTRACT The limited deamidating ability of B. circulans peptidoglutaminase towards soy protein was increased 27‐fold by protein hydrolysis and altering soy protein conformation by moist heat. Adding disulfide bond reducing agents such as cysteine or sodium sulfite or salts such as NaCl or KC1 to the reaction mixture had little or no effect on deamidation. However, heat treatment at 100°C for 15 min, both before and after Alcalase proteolysis, rendered soy protein very susceptible to amide hydrolysis by peptidoglutaminase.
Supplementary Figure 3 from Inhibition of Soluble Tumor Necrosis Factor Prevents Chemically Induced Carcinogenesis in Mice (2023)

<p>MCA and TNF-exclusion don't affect Tregs. Splenocytes were simultaneously stained with anti-CD4-FITC and anti-CD25-PE mAb, fixed, permeabilized, stained with anti-FoxP3-APC mAb, and examined by flow cytometry. (A) Gating strategies: Gate 1, single cells; Gate 2, mononuclear cells; Gate 3A, two-color analyses of CD4+and CD25+ mononuclear cells; Gate 3B, two-color analyses of CD4+ and FoxP3+ mononuclear cells; and Gate 4, three-color analysis of CD4+CD25+FoxP3+ mononuclear cells. (B) Bar-graph presents individual data of three separate experiments (one day 14, and two day 84 after MCA injection) showing percentages of CD4+CD25+ (blue bars), CD4+FoxP3+ (green bars) and CD4+CD25+FoxP3+ (red bars) Tregs.</p>
Plasma levels of <i>JAK2</i> mRNA in patients with chronic myeloproliferative diseases with and without V617F mutation: implications for prognosis and disease biology (2009)

The association of V617F JAK2 expression levels with disease behavior has not been studied in patients with nonchronic myelogenous leukemia (CML) myeloproliferative disease (MPD). We found plasma levels of total JAK2 mRNA to be higher in patients with non-CML MPD (n=175) than in CML patients (n=45) and normal controls (n=58) (each P<0.001). Overall survival was studied in 68 patients and showed positive correlation with levels of total and mutant JAK2 mRNA in patients with the V617F mutation, but not those without the mutation. These findings suggest that total JAK2 expression levels play a role in the biology of the disease in V617F-positive patients, and a therapy aiming at downmodulating the expression of the total JAK2 mRNA should be considered. In conclusion, we studied JAK2 total and V6217F mutant mRNA levels in plasma. We show high levels of JAK2 expression in MPD patients and these levels correlate with survival.
Digital watermarking by geometric warping (2002)

A new method is presented for watermarking digital images and video streams. This technique embeds information in an image by changing the geometric features of the image. The method is essentially different from existing techniques in which a pseudo-noise pattern is added to the image. The new method has the advantage that the detection is computationally faster than existing methods. Furthermore, it is easier to detect the watermark in images that have been rotated, scaled, or distorted by a geometric transformation. The watermark is formed by a predefined dense pixel pattern, such as a collection of lines. Salient points in an image are warped into the vicinity of the line pattern in such a way that the changes to the image are imperceptible.
Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor (2014)

Vitamin D receptor (VDR) ligands are therapeutic agents that are used for the treatment of psoriasis, osteoporosis, and secondary hyperparathyroidism and have immense potential as therapeutic agents for autoimmune diseases, cancers, and cardiovascular diseases. However, the major side effect of VDR ligands, the development of hypercalcemia, limits their expanded use. To develop tissue-selective VDR modulators, we have designed vitamin D analogues with an adamantane ring at the side chain terminal, which would interfere with helix 12, the activation function 2, and modulate the VDR potency. Here we report 25- or 26-adamantyl-23,23,24,24-tetradehydro-19-norvitamin D derivatives (ADTK1-4, 4b,a and 5a,b). These compounds showed high VDR affinities (90% at maximum), partial agonistic activities (EC50 10(-9)-10(-8) M with 40-80% efficacy) in transactivation, and tissue-selective activity in target gene expressions. We investigate the structure-activity relationships of these compounds on the basis of their X-ray crystal structures.
CHOMP: A Framework and Instruction Set for Latency Tolerant, Massively Multithreaded Processors (2012)

Given the recent advent of the multicore era [1], we find that parallel application performance is no longer solely gated by an architecture's core arithmetic unit performance. Memory bandwidth has failed to grow at the same rate as effective core density. This paper presents a framework for constructing tightly coupled, chip-multithreading [CMT] processors that contain specific features well-suited to hiding latency to main memory and executing highly concurrent applications. This framework, deemed the “Convey Hybrid OpenMP” or CHOMP architecture, is built around a RISC instruction set that permits the hardware and software runtime mechanisms to participate in efficient scheduling of concurrent application workloads regardless of the distribution and type of instructions utilized. In this manner, all instructions in CHOMP have the ability to participate in the concurrency algorithms present in the hardware scheduler that drive context switch events. This, coupled with a set of hardware supported extended memory semantic instructions, means that the CHOMP architecture is well suited to executing applications that access memory using non-unit stride or irregular access patterns. Furthermore, the CHOMP architecture and framework contains specific logic and instruction set support that allows application-level, dynamic power gating of individual register files and function pipes.