gebhart/patrepeval huggingface dataset:
Nonlinear Dark-Field Imaging of One-Dimensional Defects in Monolayer Dichalcogenides (2019)

One-dimensional defects in two-dimensional (2D) materials can be particularly damaging because they directly impede the transport of charge, spin, or heat and can introduce a metallic character into otherwise semiconducting systems. Current characterization techniques suffer from low throughput and a destructive nature or limitations in their unambiguous sensitivity at the nanoscale. Here we demonstrate that dark-field second harmonic generation (SHG) microscopy can rapidly, efficiently, and nondestructively probe grain boundaries and edges in monolayer dichalcogenides (i.e., MoSe<sub>2</sub>, MoS<sub>2</sub>, and WS<sub>2</sub>). Dark-field SHG efficiently separates the spatial components of the emitted light and exploits interference effects from crystal domains of different orientations to localize grain boundaries and edges as very bright 1D patterns through a Čerenkov-type SHG emission. The frequency dependence of this emission in MoSe<sub>2</sub> monolayers is explained in terms of plasmon-enhanced SHG related to the defect's metallic character. This new technique for nanometer-scale imaging of the grain structure, domain orientation and localized 1D plasmons in 2D different semiconductors, thus enables more rapid progress toward both applications and fundamental materials discoveries.
Table S3 from USP9X Downregulation Renders Breast Cancer Cells Resistant to Tamoxifen (2023)

&lt;p&gt;Patient and tumor characteristics of patients with ERa positive breast cancers&lt;/p&gt;
Closed-loop neural control of cursor motion using a Kalman filter (2005)

Recently, we proposed a Kalman filter method to model the probabilistic relationship between neural firing in motor cortex and hand kinematics. In this paper, we demonstrate on-line, closed-loop, neural control of cursor motion using the Kalman filter. In this task a monkey moves a cursor on a computer monitor using either a manipulandum or their neural activity recorded with a chronically implanted micro-electrode array. A number of advantages of the Kalman filter were explored during the on-line tasks and we found that the Kalman filter had superior performance to previously reported linear regression methods. While the results suggest the applicability of the Kalman filter for neural prosthesis applications, we observed the decoded cursor position was noisier under brain control as compared with manual control using the manipulandum. To smooth the cursor motion without decreasing accuracy we propose a method that smoothes the neural firing rates. This smoothing method is described and its validity is quantitatively evaluated with recorded data.
SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesis (2010)

Huntington's disease (HD), an incurable neurodegenerative disorder, has a complex pathogenesis including protein aggregation and the dysregulation of neuronal transcription and metabolism. Here, we demonstrate that inhibition of sirtuin 2 (SIRT2) achieves neuroprotection in cellular and invertebrate models of HD. Genetic or pharmacologic inhibition of SIRT2 in a striatal neuron model of HD resulted in gene expression changes including significant down-regulation of RNAs responsible for sterol biosynthesis. Whereas mutant huntingtin fragments increased sterols in neuronal cells, SIRT2 inhibition reduced sterol levels via decreased nuclear trafficking of SREBP-2. Importantly, manipulation of sterol biosynthesis at the transcriptional level mimicked SIRT2 inhibition, demonstrating that the metabolic effects of SIRT2 inhibition are sufficient to diminish mutant huntingtin toxicity. These data identify SIRT2 inhibition as a promising avenue for HD therapy and elucidate a unique mechanism of SIRT2-inhibitor-mediated neuroprotection. Furthermore, the ascertainment of SIRT2's role in regulating cellular metabolism demonstrates a central function shared with other sirtuin proteins.
Effects of Flow‐Induced Microfluidic Chip Wall Deformation on Imaging Flow Cytometry (2019)

Abstract Imaging flow cytometry is a powerful tool by virtue of its capability for high‐throughput cell analysis. The advent of high‐speed optical imaging methods on a microfluidic platform has significantly improved cell throughput and brought many degrees of freedom to instrumentation and applications over the last decade, but it also poses a predicament on microfluidic chips. Specifically, as the throughput increases, the flow speed also increases (currently reaching 10 m/s): consequently, the increased hydrodynamic pressure on the microfluidic chip deforms the wall of the microchannel and produces detrimental effects lead to defocused and blur image. Here, we present a comprehensive study of the effects of flow‐induced microfluidic chip wall deformation on imaging flow cytometry. We fabricated three types of microfluidic chips with the same geometry and different degrees of stiffness made of polydimethylsiloxane (PDMS) and glass to investigate material influence on image quality. First, we found the maximum deformation of a PDMS microchannel was &gt;60 μm at a pressure of 0.6 MPa, while no appreciable deformation was identified in a glass microchannel at the same pressure. Second, we found the deviation of lag time that indicating velocity difference of migrating microbeads due to the deformation of the microchannel was 29.3 ms in a PDMS microchannel and 14.9 ms in a glass microchannel. Third, the glass microchannel focused cells into a slightly narrower stream in the X‐Y plane and a significantly narrower stream in the Z‐axis direction (focusing percentages were increased 30%, 32%, and 5.7% in the glass channel at flow velocities of 0.5, 1.5, and 3 m/s, respectively), and the glass microchannel showed stabler equilibrium positions of focused cells regardless of flow velocity. Finally, we achieved the world's fastest imaging flow cytometry by combining a glass microfluidic device with an optofluidic time‐stretch microscopy imaging technique at a flow velocity of 25 m/s. © 2019 International Society for Advancement of Cytometry
Computational model predicts effective delivery of 188-Re-labeled melanin-binding antibody to metastatic melanoma tumors with wide range of melanin concentrations (2007)

Metastatic melanoma is almost always deadly and new methods of treatment are urgently needed. Recently, we established the feasibility of radioimmunotherapy (RIT) for experimental melanoma in mice using a 188-rhenium (188Re)-labeled monoclonal antibody (mAb) 6D2 (IgM) to melanin. Our objective was to determine the effects of varying tumor melanin concentration and of different diffusivities and lymphatic clearance rates of the normal tissue, on the absorbed dose to the tumor in simulated therapy, in preparation for a clinical trial of RIT for melanoma. Using finite element analysis (FEA), we created a pharmacokinetic model that describes melanin-targeting RIT of a melanoma micrometastasis (1.3-mm radius) imbedded in normal tissue (14.3-mm radius). Our method incorporates antibody plasma kinetics, transcapillary transport, interstitial diffusion, and lymphatic clearance. Michaelis-Menten kinetics was used to model mAb binding to tumor melanin for melanin concentrations of 76, 7.6, 0.76, 0.076, and 0.0076 micromol/l. An absorbed dose was calculated, after accounting for direct and crossfire irradiation, on the basis of a 7.4-GBq intravenous dose of 188Re-6D2. The results showed that penetration of mAb into the tumor was inversely proportional to tumor melanin concentration. Decreased diffusivity and increased lymphatic clearance of the surrounding normal tissue decreased the dose to the tumor. The formation of mAb-melanin complex was remarkably similar within a 1000-fold range of melanin concentration, resulting in total doses of 2840, 2820, 2710, and 1990 cGy being delivered to tumors with melanin concentrations of 76, 7.6, 0.76, and 0.076 micromol/l, respectively. In conclusion, RIT of metastatic melanoma can be effective over a wide range of tumor melanin concentrations. The results can be useful in the design of a clinical trial of melanin-targeting RIT in patients with metastatic melanoma.
Exemplar-Based Sparse Representation Features: From TIMIT to LVCSR (2011)

The use of exemplar-based methods, such as support vector machines (SVMs), k-nearest neighbors (kNNs) and sparse representations (SRs), in speech recognition has thus far been limited. Exemplar-based techniques utilize information about individual training examples and are computationally expensive, making it particularly difficult to investigate these methods on large-vocabulary continuous speech recognition (LVCSR) tasks. While research in LVCSR provides a good testbed to tackle real-world speech recognition problems, research in this area suffers from two main drawbacks. First, the overall complexity of an LVCSR system makes error analysis quite difficult. Second, exploring new research ideas on LVCSR tasks involves training and testing state-of-the-art LVCSR systems, which can render a large turnaround time. This makes a small vocabulary task such as TIMIT more appealing. TIMIT provides a phonetically rich and hand-labeled corpus that allows easy insight into new algorithms. However, research ideas explored for small vocabulary tasks do not always provide gains on LVCSR systems. In this paper, we combine the advantages of using both small and large vocabulary tasks by taking well-established techniques used in LVCSR systems and applying them on TIMIT to establish a new baseline. We then utilize these existing LVCSR techniques in creating a novel set of exemplar-based sparse representation (SR) features. Using these existing LVCSR techniques, we achieve a phonetic error rate (PER) of 19.4% on the TIMIT task. The additional use of SR features reduce the PER to 18.6%. We then explore applying the SR features to a large vocabulary Broadcast News task, where we achieve a 0.3% absolute reduction in word error rate (WER).
Par j 1 and Par j 2, the major allergens from Parietaria judaica pollen, have similar immunoglobulin E epitopes (2003)

Three similar IgE-epitopes of major allergens from P. judaica have been described. They could be good candidates for designing of IgE haptens as therapeutic agents with reduced anaphylactic side-effects or for developing hypoallergenic variants of these major allergens.
Combinatorial screening of chemically defined human mesenchymal stem cell culture substrates (2012)

Self-assembled monolayers (SAMs) of alkanethiolates on gold are chemically defined substrates that can be used to evaluate the effects of an immobilized biomolecule. However, the types of biomolecules that can influence stem cell behavior are numerous and inter-related, and efficient experimental formats are a critical need. Here we employed a SAM array technology to investigate the effects of multiple, distinct peptides and peptide combinations on human mesenchymal stem cell (hMSC) behavior. Specifically, we characterized the conjugation of peptide mixtures to SAM arrays and then investigated the combined effects of a bone morphogenic protein receptor-binding peptide (BR-BP), a heparin proteoglycan-binding peptide (HPG-BP), and varied densities of the integrin-binding ligand Gly-Arg-Gly-Asp-Ser-Pro (GRGDSP) on hMSC surface coverage and alkaline phosphatase activity. Results indicate that an amine reactive fluorescent probe can be used to characterize peptide composition after immobilization in SAM array spots. Furthermore, hMSC response to BR-BP and HPG-BP is dependent on GRGDSP density and at day 7, hMSC alkaline phosphatase expression is highly dependent on GRGDSP density. Taken together, we demonstrate how a SAM array approach can be used to probe the combinatorial effects of multiple peptides and motivate further investigations into potential synergies between cell adhesion and other bioactive peptides.
Performance Evaluation of Horizontal Wells (1998)

Abstract Horizontal wells have been drilled in many oil and gas reservoirs. Measuring or calculating the productivity of horizontal wells has been difficult because of their long length in the formation compared with vertical wells and because of the inadequacy of measurements during drilling and production. In this paper, we examine the performance of horizontal wells. First, we review the theoretical productivity of horizontal wells and examine the sensitivity of productivity to well and reservoir parameters. We then compare theoretical and actual productivities from horizontal wells in several oil fields to show that most horizontal wells do not produce at their full potential because of the effects of wellbore and near-wellbore formation conditions right after drilling on cleanup. Second, using field examples, we show that the new integrated production logging measurements can be used to assess horizontal well productivity by identifying productive zones, fluid entries, and determining the fluid distribution (oil, gas, and water) in the wellbore. We also show how reservoir heterogeneity affects the reservoir pressure distribution. The field examples indicate that horizontal wells have permanent water sumps, regardless of whether they produce water. In these wells, we show that when a large percentage of the wellbore cross section is filled with water, reduced oil entry occurs. To assess the effect of the water sumps, flow restrictions, and noncontributing sections along the wellbore on the well productivity, a numerical model with actual well trajectories and openhole and production log measurements is used to estimate well productivity. These horizontal well performance simulations indicate 30 to 50 percent productivity reduction when they are compared with their full potential. P. 231
Three-Dimensional Carotid Ultrasound Plaque Texture Predicts Vascular Events (2014)

Changes in both plaque texture and volume are strongly predictive of vascular events. In high-risk patients, 3D ultrasound plaque measurements should be considered for vascular event risk prediction.
Depth-Based 3D Hand Pose Estimation: From Current Achievements to Future Goals (2017)

In this paper, we strive to answer two questions: What is the current state of 3D hand pose estimation from depth images? And, what are the next challenges that need to be tackled? Following the successful Hands In the Million Challenge (HIM2017), we investigate the top 10 state-of-the-art methods on three tasks: single frame 3D pose estimation, 3D hand tracking, and hand pose estimation during object interaction. We analyze the performance of different CNN structures with regard to hand shape, joint visibility, view point and articulation distributions. Our findings include: (1) isolated 3D hand pose estimation achieves low mean errors (10 mm) in the view point range of [70, 120] degrees, but it is far from being solved for extreme view points; (2) 3D volumetric representations outperform 2D CNNs, better capturing the spatial structure of the depth data; (3) Discriminative methods still generalize poorly to unseen hand shapes; (4) While joint occlusions pose a challenge for most methods, explicit modeling of structure constraints can significantly narrow the gap between errors on visible and occluded joints.
Understanding and defending the binder attack surface in Android (2016)

In Android, communications between apps and system services are supported by a transaction-based Inter-Process Communication (IPC) mechanism. Binder, as the cornerstone of this IPC mechanism, separates two communicating parties as client and server. As with any client-server model, the server should not make any assumption on the validity (sanity) of client-side transaction. To our surprise, we find this principle has frequently been overlooked in the implementation of Android system services. In this paper, we try to answer why developers keep making this seemingly simple mistake by studying more than 100 vulnerabilities on this attack surface. We analyzed these vulnerabilities to find that most of them are rooted at a common confusion of where the actual security boundary is among system developers. We thus highlight the deficiency of testing only on client-side public APIs and argue for the necessity of testing and protection on the Binder interface --- the actual security boundary. Specifically, we design and implement BinderCracker, an automatic testing framework that supports context-aware fuzzing and actively manages the dependency between transactions. It does not require the source codes of the component under test, is compatible with services in different layers, and performs much more effectively than simple black-box fuzzing. We also call attention to the attack attribution problem for IPC-based attacks. The lack of OS-level support makes it very difficult to identify the culprit apps even for developers with adb access. We address this issue by providing an informative runtime diagnostic tool that tracks the origin, schema, content, and parsing details of each failed transaction. This brings transparency into the IPC process and provides an essential step for other in-depth analysis or forensics.
Design, Synthesis, and Biological Evaluation of 1,2,3,7-Tetrahydro-6H-purin-6-one and 3,7-Dihydro-1H-purine-2,6-dione Derivatives as Corticotropin-Releasing Factor1 Receptor Antagonists (2004)

A growing body of evidence suggests that CRF(1) receptor antagonism offers considerable therapeutic potential in the treatment of diseases resulting from elevated levels of CRF, such as anxiety and depression. A series of novel 1,2,3,7-tetrahydro-6H-purin-6-one and 3,7-dihydro-1H-purine-2,6-dione derivatives was synthesized and evaluated as corticotropin releasing factor-1 (CRF(1)) receptor antagonists. Compounds within this series, represented by compound 12d (IC(50) = 5.4 nM), were found to be highly potent CRF(1) receptor antagonists. In addition, compounds 12d and 12j were determined to be selective CRF(1) antagonists. The synthesis, structure-activity relationships and pharmacokinetic properties of compounds within this series is presented.
Characterization of well‐defined poly(ethylene glycol) hydrogels prepared by thiol‐ene chemistry (2011)

Abstract Considering the large number of applications for hydrogels, a better understanding of the relation between molecular structure and mechanical properties for well‐defined hydrogel is essential. A new library has been compiled of poly(ethylene glycol) polymers (PEG) of different length end functionalized with diallyl, dithiol, and dimethacrylate, and crosslinked with complementary trifunctional crosslinkers. In this study, the hydrogels were initially analyzed by FT‐Raman and NMR to study the conversion ratio of the functional groups. The effects of solvent type, solid content concentration, curing time and length of the PEG chains on the final leaching, swelling and tensile properties of the hydrogels were studied. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields (1998)

The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 769–780, 1998
The puzzle of a comprehensive picture of drift phen omenon in chalchogenide alloys (2013)

In a phase change memory the device resistance corresponding to the am orphous phase monotonically increases with time after the reset programming operation. This phenomenon, called drift, affects the stability of the high resistive state, namely the reset state. In this work, the prismatic picture of the experimental findings on drift oriented to have a unified int erpretation will be reported. The debate on the physical description of structural relaxation (SR) phenom ena leading to the drift of the current will be discussed.
The use of porphyrins for eradication ofStaphylococcus aureusin burn wound infections (1997)

The assessment of deuteroporphyrin-hemin complex as an agent for the treatment of burn wounds infected with a multiple-drug resistant strain of Staphylococcus aureus was performed. The effect of the porphyrin on the survival of the infectious bacteria was first assayed in culture, and later tested as well in a burned infected animal model. The addition of deuteroporphyrin and hemin, separately or together (as a complex) to a growing culture of S. aureus was monitored during 8 hours. It was found that deuteroporphyrin alone was strongly bactericidal only after photosensitization. On the other hand, hemin alone was moderately bactericidal but light independent. A combination of both deuteroporphyrin and hemin was extremely potent even in the dark and did not require illumination to eradicate the bacteria. The in vivo experiments by application of the above porphyrins in combination to infected burn wounds in guinea pigs was an effective way to reduce dramatically the contaminating S. aureus. Reduction of more than 99% of the viable bacteria was noted after the porphyrin mixture was dropped on the eschar or injected into the eschar, an effect that lasted for up to 24 hours. The deuteroporphyrin-hemin complex may be suggested as a new bactericidal treatment of S. aureus infected burns since it was found to be a potent and promising anti-Staphylococcal agent.