gebhart/patrepeval huggingface dataset:
Separation and characterization of the troponin components from bovine cardiac muscle. (1976)

The three major components of bovine cardiac troponin were separated by successive chromatography on sulfopropyl-Sephadex and DEAE-Sephadex columns in the presence of 6 M urea. All three of the bovine cardiac troponin subunits were necessary to restore full troponin activity in both skeletal and cardiac actomyosin ATPase assay systems. The 38,000-dalton subunit bound tropomyosin, and the 20,000-dalton subunit bound calcium, like skeletal TN-T and TN-C, respectively. The 28,000 component, although presumably analogous to skeletal TN-I, gave very little inhibition of actomyosin ATPase activity. Differences between cardiac and skeletal troponin subunits were also found in the elution patterns from ion exchange columns and in amino acid composition, thus demonstrating a significant muscle-type specificity.
Relocalization using virtual keyframes for online environment map construction (2009)

The acquisition of surround-view panoramas using a single hand-held or head-worn camera relies on robust real-time camera orientation tracking. In absence of robust tracking recovery methods, the complete acquisition process has to be re-started when tracking fails. This paper presents methodology for camera orientation relocalization, using virtual keyframes for online environment map construction. Instead of relying on real keyframes from incoming video, the proposed approach enables camera orientation relocalization by employing virtual keyframes which are distributed strategically within an environment map. We discuss our insights about a suitable number and distribution of virtual keyframes, as suggested by our experiments on virtual keyframe generation and orientation relocalization. After a shading correction step, we relocalize camera orientation in real-time by comparing the current camera frame to virtual keyframes. While expanding the captured environment map, we continue to simultaneously generate virtual keyframes within the completed portion of the map, as descriptors to estimate camera orientation. We implemented our camera orientation relocalizer with the help of a GPU fragment shader for real-time application, and evaluated the speed and accuracy of the proposed approach.
The low-toxicity 9-cis UAB30 novel retinoid down-regulates the DNA methyltransferases and has anti-telomerase activity in human breast cancer cells (2007)

Retinoic acids and their derivatives potentiate anti-cancer effects in breast cancer cells. The aberrant expression of telomerase is critical to the continued proliferation of most cancer cells. Thus, telomerase is an attractive target for chemoprevention and treatment of breast cancer. 9cUAB30 is a novel synthetic retinoid X receptor-selective retinoic acid (RA) that effectively reduces the tumorigenic phenotype in mouse breast carcinoma with lower toxic effects than natural retinoid treatments. We have assessed 9cUAB30 retinoic acid treatment of human breast cancer cells to determine the potential of this drug as an effective telomerase inhibitor and its application to cancer therapy. 9cUAB30 was found to decrease DNA methyltransferase and telomerase expression in MDA-MB-361, T-47D, and MCF-7 human breast cancer cells and to inhibit the proliferation of these cells. This low-toxicity retinoid also reduced colony formation in soft agar assays in each of these cell types. Combination treatments of 9cUAB30 and all-trans RA proved to be synergistically more effective than either RA alone, further suggesting a possible general epigenetic mechanism that contributes to the anti-telomerase activity of the retinoids. Therefore, the novel retinoid, 9cUAB30, is effective in inhibiting the growth of human breast cancer cells, its anti-cancer effects appear to be related to telomerase inhibition and the mechanism for this process could be mediated through epigenetic modifications.
Observation of Optical Precursors in Water (2004)

We observe the formation of optical precursors while propagating 540 fs pulses through 700 mm of deionized water. The launched pulses were strongly chirped to give them a bandwidth of approximately 60 nm to more readily excite the precursors. The precursors attenuated nonexponentially with distance.
Graphene-SGX: a practical library OS for unmodified applications on SGX (2017)

Intel SGX hardware enables applications to protect themselves from potentially-malicious OSes or hypervisors. In cloud computing and other systems, many users and applications could benefit from SGX. Unfortunately, current applications will not work out-of-the-box on SGX. Although previous work has shown that a library OS can execute unmodified applications on SGX, a belief has developed that a library OS will be ruinous for performance and TCB size, making application code modification an implicit prerequisite to adopting SGX.

This paper demonstrates that these concerns are exaggerated, and that a fully-featured library OS can rapidly deploy unmodified applications on SGX with overheads comparable to applications modified to use shim layers. We present a port of Graphene to SGX, as well as a number of improvements to make the security benefits of SGX more usable, such as integrity support for dynamically-loaded libraries, and secure multiprocess support. Graphene-SGX supports a wide range of unmodified applications, including Apache, GCC, and the R interpreter. The performance overheads of Graphene-SGX range from matching a Linux process to less than 2× in most single-process cases; these overheads are largely attributable to current SGX hardware or missed opportunities to optimize Graphene internals, and are not necessarily fundamental to leaving the application unmodified. Graphene-SGX is open-source and has been used concurrently by other groups for SGX research.
Chimeric Antigen Receptors With Mutated IgG4 Fc Spacer Avoid Fc Receptor Binding and Improve T Cell Persistence and Antitumor Efficacy (2014)

The success of adoptive therapy using chimeric antigen receptor (CAR)-expressing T cells partly depends on optimal CAR design. CARs frequently incorporate a spacer/linker region based on the constant region of either IgG1 or IgG4 to connect extracellular ligand-binding with intracellular signaling domains. Here, we evaluated the potential for the IgG4-Fc linker to result in off-target interactions with Fc gamma receptors (FcγRs). As proof-of-principle, we focused on a CD19-specific scFv-IgG4-CD28-zeta CAR and found that, in contrast to CAR-negative cells, CAR+ T cells bound soluble FcγRs in vitro and did not engraft in NSG mice. We hypothesized that mutations to avoid FcγR binding would improve CAR+ T cell engraftment and antitumor efficacy. Thus, we generated CD19-specific CARs with IgG4-Fc spacers that had either been mutated at two sites (L235E; N297Q) within the CH2 region (CD19R(EQ)) or incorporated a CH2 deletion (CD19Rch2Δ). These mutations reduced binding to soluble FcγRs without altering the ability of the CAR to mediate antigen-specific lysis. Importantly, CD19R(EQ) and CD19Rch2Δ T cells exhibited improved persistence and more potent CD19-specific antilymphoma efficacy in NSG mice. Together, these studies suggest that optimal CAR function may require the elimination of cellular FcγR interactions to improve T cell persistence and antitumor responses.
Garment-Based Monitoring of Respiration Rate Using a Foam Pressure Sensor (2005)

Comfortable body monitoring is crucial to many wearable devices. However, many traditional sensors impede wearability by their physical structure or functional requirements. This paper presents the application of a novel garment-integrated foam-based pressure sensor used for monitoring the wearer's respiration rate. The sensor was evaluated in a torso garment during a 10-minute treadmill test. Results were accurate within one breath per minute, as compared to a standard airflow breathing test.
In Vitro Degradation of Serum Amyloid A by Cathepsin D and Other Acid Proteases: Possible Protection Against Amyloid Fibril Formation (1995)

The effects of acid proteases on degradation of serum amyloid A protein (SAA) were investigated in vitro. Human recombinant SAA1 (rSAA1), when incubated with human spleen extracts at pH 3.2, was degraded in the amino-terminal portion of the molecule. This reaction was inhibited by an acid protease inhibitor, pepstatin. The degraded SAA molecules lacking nine or more amino-terminal residues, when exposed to in vitro fibril-forming conditions, failed to form Congo red positive precipitates and did not show amyloid fibril-like structure by electron microscopy. This suggests that the amino-terminal portion of SAA is essential for fibril formation. Cathepsin D, one of the lysosomal enzymes, also initiated degradation of rSAA1 at the amino-terminus. Cathepsin D immunoreactivity was detected in marginal areas of amyloid deposits in spleens from patients with reactive amyloidosis. These findings suggest that cathepsin D or similar acid proteases may be involved in SAA catabolism and may protect against amyloid formation.
Modeling of Mechanical Properties and Structural Design of Spider Web (2004)

With a unique combination of strength and toughness among materials, spider silk is the model for engineering materials. This paper presents the stress-strain behavior of Nephila clavipes spider silk under tension, transverse compression, and torsional deformation obtained by a battery of micro testing equipment. The experimental results showed significantly higher toughness than the state-of-the-art fibers in tension and in transverse compression. Higher shear modulus was also observed for the spider silk comparing to other liquid crystalline fibers such as aramid fibers. On the basis of the experimental results finite element analysis is used to simulate static and dynamic properties of spider web and to explore the role of both material properties and architectural design in its structural integrity and mechanical performance.
Text Summarization with Pretrained Encoders (2019)

Bidirectional Encoder Representations from Transformers (BERT) represents the latest incarnation of pretrained language models which have recently advanced a wide range of natural language processing tasks. In this paper, we showcase how BERT can be usefully applied in text summarization and propose a general framework for both extractive and abstractive models. We introduce a novel document-level encoder based on BERT which is able to express the semantics of a document and obtain representations for its sentences. Our extractive model is built on top of this encoder by stacking several inter-sentence Transformer layers. For abstractive summarization, we propose a new fine-tuning schedule which adopts different optimizers for the encoder and the decoder as a means of alleviating the mismatch between the two (the former is pretrained while the latter is not). We also demonstrate that a two-staged fine-tuning approach can further boost the quality of the generated summaries. Experiments on three datasets show that our model achieves state-of-the-art results across the board in both extractive and abstractive settings. Our code is available at https://github.com/nlpyang/PreSumm
Different glycosylation of cadherins from human bladder non-malignant and cancer cell lines (2002)

These results indicate that N-glycosylation pattern of cadherin from bladder cancer cell line undergoes modification during carcinogenesis.
Differential expression of the ed sequence-containing form of cellular fibronectin in embryonic and adult human tissues (1987)

Monoclonal mouse hybridoma antibodies were obtained for secreted cellular fibronectin (cFn) from A8387 fibrosarcoma cells. One of them, 52-DH1 (DH), reacted exclusively with cFns but not with plasma Fns (pFns) in immunoblotting and solid-phase EIA. The DH antibody also recognized thermolysin cFn fragments and beta-galactosidase-Fn fusion protein which contained the ED sequence specific to at least some forms of cFns. On the other hand, the DH antibody failed to recognize a fusion protein that was otherwise identical but lacked the ED sequence. Thus, the antigenic determinant for the DH antibody was located to the ED sequence. The DH antibody was then used to study the expression of ED sequence containing cFn (EcFn). For comparisons, another monoclonal antibody, 52BF12 (BF), recognizing equally well both pFns and cFns, was used. Immunoblotting of pFn fragments indicated that this antibody had the antigenic determinant at or close to the cell-binding site of Fn. EcFn was revealed by the DH antibody in embryonic and adult fibroblasts and in a variety of other cultured normal and malignant human cells. In embryonic tissues EcFn was abundant in developing basement membranes, as shown in foetal kidney and muscle, while in adult tissues it was confined only to endothelia of larger blood vessels. Furthermore, in embryonic tissues the capillaries showed bright EcFn-positivity not found any more in adult tissues. Human plasma contained a small quantity of EcFn, which may hence have an endothelial origin. EcFn was also prominent in the stroma of malignant tumours as well as in reactive benign conditions, such as granulation tissue and decidual cells. The results suggest that EcFn is a form of the protein which may have a particular role in developing and reactive tissues in embryos and adults.
Functions of WW domains in the nucleus (2001)

The WW domain is a protein module found in a wide range of signaling proteins. It is one of the smallest protein modules that folds as a monomer without disulfide bridges or cofactors. WW domains bind proteins containing short linear peptide motifs that are proline-rich or contain at least one proline. Although the WW domain was initially considered a 'cytoplasmic module', the proteins containing WW domains have also been localized in the cell nucleus. Moreover, these proteins have been documented to participate in co-activation of transcription and modulation of RNA polymerase II activity. The carboxy-terminal domain (CTD) of RNA polymerase II acts as an assembly platform for distinct WW domain-containing proteins that affect the function of the RNA polymerase II. The formation of complexes between CTD and WW domain-containing proteins is regulated by phosphorylation of the CTD. Since the CTD sequence is highly repetitive and a target of several post-translational modifications and conformational changes, it presents a unique structure capable of enormous molecular diversity. The WW domain has been implicated in several human diseases including Alzheimer's disease. The WW domain-containing iso-prolyl isomerase named Pin1, a protein known to be essential for cell cycle progression, was shown to be active in restoration of the microtubule-binding activity of Tau, a protein of neurofibrillar tangles found in the brains of Alzheimer's patients. It is the WW domain of Pin1 that interacts directly with Tau protein. In addition, the WW domain-containing adapter protein FE65 was shown to regulate processing of Alzheimer's amyloid precursor protein. It is expected that by understanding the details of the WW domain-mediated protein-protein interactions, we will be able to illuminate numerous signaling pathways which control certain aspects of transcription and cell cycle.
FGF‐2 modulates Wnt signaling in undifferentiated hESC and iPS cells through activated PI3‐K/GSK3β signaling (2010)

Fibroblast growth factor-2 (FGF-2) is widely used to culture human embryonic stem cells (hESC) and induced pluripotent stem (iPS) cells. Despite its importance in maintaining undifferentiated hESC phenotype, a lack of understanding in the role of FGF-2 still exists. Here, we investigate the signaling events in hESC following the addition of exogenous FGF-2. In this study, we show that hESC express all forms of fibroblast growth factor receptors (FGFRs) which co-localize on Oct3/4 positive cells. Furthermore, downregulation of Oct3/4 in hESC occurs following treatment with an FGFR inhibitor, suggesting that FGF signaling may regulate Oct3/4 expression. This is also observed in iPS cells. Also, downstream of FGF signaling, both mitogen activated protein kinase (MAPK) and phosphoinositide 3-kinase pathways (PI3-K) are activated following FGF-2 stimulation. Notably, inhibition of MAPK and PI3-K signaling using specific kinase inhibitors revealed that activated PI3-K, rather than MAPK, can mediate pluripotent marker expression. To understand the importance of PI3-K activation, activation of Wnt/beta-catenin by FGF-2 was investigated. Wnt signaling had been implicated to have a role in maintaining of pluripotent hESC. We found that upon FGF-2 stimulation, GSK3beta is phosphorylated following which nuclear translocation of beta-catenin and TCF/LEF activation occurs. Interestingly, inhibition of the Wnt pathway with Dikkopf-1 (DKK-1) resulted in only partial suppression of the FGF-2 induced TCF/LEF activity. Prolonged culture of hESC with DKK-1 did not affect pluripotent marker expression. These results suggest that FGF-2 mediated PI3-K signaling may have a direct role in modulating the downstream of Wnt pathway to maintain undifferentiated hESC.
Overproduction of a functional A1 ATPase from the archaeon Methanosarcina mazei Gö1 in Escherichia coli (2001)

Single subunits of the A1 ATPase from the archaeon Methanosarcina mazei Gö1 were produced in E. coli as MalE fusions and purified, and polyclonal antibodies were raised against the fusion proteins. A DNA fragment containing the genes ahaE, ahaC, ahaF, ahaA, ahaB, ahaD, and ahaG, encoding the hydrophilic A1 domain and part of the stalk of the A1AO ATPase of M. mazei Gö1, was constructed, cloned into an expression vector and transformed into different strains of Escherichia coli. In any case, a functional, ATP-hydrolysing A1 ATPase was produced. Western blots demonstrated the production of subunits A, B, C, and F in E. coli, and minicell analyses suggested that subunits D, E, and G were produced as well. This is the first demonstration of a heterologous production of a functional ATPase from an archaeon. The A1 ATPase was sensitive to freezing but lost only about 50% of its activity within 18 days on ice. Inhibitor studies revealed that the heterologously produced A1 ATPase is insensitive to azide, dicyclohexylcarbodiimide and bafilomycin A1, but sensitive to diethylstilbestrol and its analogues dienestrol and hexestrol. The expression system described here will open new avenues towards the functional and structural analyses of this unique class of enzymes.
Automatic segmentation of speech into syllabic units (1975)

As a first step toward automatic phonetic analysis of speech, one desires to segment the signal into syllable-sized units. Experiments were conducted in automatic segmentation techniques for continuous, reading-rate speech to derive such units. A new segmentation algorithm is described that allows assessment of the significance of a loudness minimum to be a potential syllabic boundary from the difference between the convex hull of the loudness function and the loudness function itself. Tested on roughly 400 syllables of continuous text, the algorithm results in 6.9% syllables missed and 2.6% extra syllables relative to a nominal, slow-speech syllable count. It is suggested that inclusion of alternative fluent-form syllabifications for multisyllabic words and the use of phonological rules for predicting syllabic contractions can further improve agreement between predicted and experimental syllable counts. Subject Classification: 70.40, 70.60.
Design of a mimic of nonamyloidogenic and bioactive human islet amyloid polypeptide (IAPP) as nanomolar affinity inhibitor of IAPP cytotoxic fibrillogenesis (2006)

Protein aggregation into cytotoxic oligomers and fibrils in vivo is linked to cell degeneration and the pathogenesis of >25 uncurable diseases, whereas the high aggregation propensity and insolubility of several bioactive polypeptides and proteins in vitro prevent their therapeutic use. Aggregation of human islet amyloid polypeptide (IAPP) into pancreatic amyloid is strongly associated with the pathogenesis of type II diabetes. IAPP is a 37-residue polypeptide that acts as a neuroendocrine regulator of glucose homeostasis. However, IAPP misfolds and self-associates into cytotoxic aggregates and fibrils even at nanomolar concentrations. Because IAPP aggregation causes beta-cell death and prohibits therapeutic application of IAPP in diabetes, we pursued a minimalistic chemical design approach to generate a molecular mimic of a nonamyloidogenic and bioactive IAPP conformation that would still be able to associate with IAPP and thus inhibit its fibrillogenesis and cytotoxicity. We show that the double N-methylated full length IAPP analog [(N-Me)G24, (N-Me)I26]-IAPP (IAPP-GI) is a highly soluble, nonamyloidogenic, and noncytotoxic IAPP molecular mimic and an IAPP receptor agonist. Moreover, IAPP-GI binds IAPP with low nanomolar affinity and completely blocks IAPP cytotoxic self-assembly and fibrillogenesis with activity in the low nanomolar concentration range. Importantly, IAPP-GI dissociates cytotoxic IAPP oligomers and fibrils and is able to reverse their cytotoxicity. Bifunctional soluble IAPP mimics that combine bioactivity with the ability to block and reverse IAPP cytotoxic self-assembly are promising candidates for the treatment of diabetes. Moreover, our amyloid disease inhibitor design concept may be applicable to other protein aggregation diseases.
Gold Valence Transition and Phase Diagram in the Mixed-Valence Complexes, M2[AuIX2][AuIIIX4] (M = Rb, Cs; X = Cl, Br, and I) (2000)

Abstract In this paper, I review the structural and physical properties of the gold mixed-valence complexes, M2[AuIX2][AuIIIX4] (M = Rb, Cs; X = Cl, Br, and I), having perovskite-type structure. In spite of the three dimensional perovskite-type structure, the charge transfer interaction between AuI and AuIII in these complexes is two-dimensional. These complexes undergo the pressure-induced Au valence transition from the mixed valence state of AuI,III to the single valence state of AuII, which is coupled with a structural phase transition. In the pressure region below the Au valence transition, these complexes show a metallic behavior, which would be attributed to a dynamic two-electron exchange between the AuI and AuIII states (i.e. highly mobile bipolarons). The metallic cubic phase appearing commonly for these complexes under high pressure and high temperature can be obtained as a metastable phase even at ambient pressure and room temperature. Moreover, as a recent topic, I report the photo-induced Au valence transition for Cs2[AuIBr2][AuIIIBr4].