gebhart/patrepeval huggingface dataset:
Optical Interference Coatings Design Contest 2013: angle-independent color mirror and shortwave infrared/midwave infrared dichroic beam splitter (2014)

An angle-independent color mirror and an infrared dichroic beam splitter were the subjects of a design contest held in conjunction with the 2013 Optical Interference Coatings topical meeting of the Optical Society of America. A total of 17 designers submitted 63 designs, 22 for Problem A and 41 for Problem B. The submissions were created through a wide spectrum of design approaches and optimization strategies. Michael Trubetskov and Weidong Shen won the first contest by submitting color mirror designs with a zero color difference (ΔE00) between normal incidence and all other incidence angles up to 60° as well as the thinnest design. Michael Trubetskov also won the second contest by submitting beam-splitter designs that met the required transmission while having the lowest mechanical coating stress and thinnest design. Fabien Lemarchand received the second-place finish for the beam-splitter design. The submitted designs are described and evaluated.
AI-assisted Code Authoring at Scale: Fine-tuning, deploying, and mixed methods evaluation (2023)

Generative LLMs have been shown to effectively power AI-based code authoring tools that can suggest entire statements or blocks of code during code authoring. In this paper we present CodeCompose, an AI-assisted code authoring tool developed and deployed at Meta internally. CodeCompose is based on the InCoder LLM that merges generative capabilities with bi-directionality. We have scaled up CodeCompose to serve tens of thousands of developers at Meta, across 9 programming languages and several coding surfaces. We present our experience in making design decisions about the model and system architecture for CodeCompose that addresses these challenges. To release a LLM model at this scale, we needed to first ensure that it is sufficiently accurate. In a random sample of 20K source code files, depending on the language, we are able to reproduce hidden lines between 40% and 58% of the time, an improvement of 1.4x and 4.1x over a model trained only on public data. We gradually rolled CodeCompose out to developers. At the time of this writing, 16K developers have used it with 8% of their code coming directly from CodeCompose. To triangulate our numerical findings, we conduct a thematic analysis on the feedback from 70 developers. We find that 91.5% of the feedback is positive, with the most common themes being discovering APIs, dealing with boilerplate code, and accelerating coding. Meta continues to integrate this feedback into CodeCompose.
Simulation of two‐phase flow with sub‐scale droplet and bubble effects (2009)

Abstract We present a new Eulerian‐Lagrangian method for physics‐based simulation of fluid flow, which includes automatic generation of sub‐scale spray and bubbles. The Marker Level Set method is used to provide a simple geometric criterion for free marker generation. A filtering method, inspired from Weber number thresholding, further controls the free marker generation (in a physics‐based manner). Two separate models are used, one for sub‐scale droplets, the other for sub‐scale bubbles. Droplets are evolved in a Newtonian manner, using a density‐extension drag force field, while bubbles are evolved using a model based on Stokes' Law. We show that our model for sub‐scale droplet and bubble dynamics is simple to couple with a full (macro‐scale) Navier‐Stokes two‐phase flow model and is quite powerful in its applications. Our animations include coarse grained multiphase features interacting with fine scale multiphase features.
Fully compliant double tensural tristable micromechanisms (DTTM) (2009)

Numerous possible micromechanism applications (e.g. three-way switches, mechanical memory and multiplex optical switches) could benefit from a device with three stable equilibrium positions. In this paper, we present a new class of tristable mechanisms called double tensural tristable mechanisms (DTTMs) which are fully compliant (i.e. they are monolithic and get their motion from the deflection of elastic components) and can be fabricated at the micro scale. A pseudo-rigid-body model (PRBM) for the DTTM has been developed. DTTMs were fabricated in polysilicon using the SUMMiT V process and tested for tristability and force–deflection characteristics. The results successfully demonstrate tristable behavior and show that the PRBM can be used to identify tristable configurations and predict their performance.
Integration of information in synthetic vision displays: why, to what extent, and how? (2004)

Current experimental synthetic vision systems present a spatially integrated presentation of physical constraints such as terrain and obstacles. This paper presents a number of assumptions regarding anticipated procedures and the use of a synthetic vision system, and addresses the desirability of integrating temporary constraints related to the airspace, the airport, and standard procedures. Following this, a number of examples are presented that illustrate a potential approach to integrate such information into a synthetic vision display. The paper ends with an overview of the results from an experiment in which the influence of an integration of temporary constraint information on pilot decision-making was examined.
Supplementary Table 3 from Human Melanoma Metastases Demonstrate Nonstochastic Site-Specific Antigen Heterogeneity That Correlates with T-cell Infiltration (2023)

&lt;p&gt;PDF file - 50K, Dendrogram distance matrix for all melanoma differentiation antigens. Dendrogram distant matrix calculated from DendroUPGMA.&lt;/p&gt;
In vivo laser-based imaging of the human fallopian tube for future cancer detection (2015)

Inherited mutations in <i>BRCA1</i> and <i>BRCA2</i> lead to 20-50% lifetime risk of ovarian, tubal, or peritoneal carcinoma. Clinical recommendations for women with these genetic mutations include the prophylactic removal of ovaries and fallopian tubes by age 40 after child-bearing. Recent findings suggest that many presumed ovarian or peritoneal carcinomas arise in fallopian tube epithelium. Although survival rate is &lt;90% when ovarian cancer is detected early (Stage_I), 70% of women have advanced disease (Stage_III/IV) at presentation when survival is less than 30%. Over the years, effective early detection of ovarian cancer has remained elusive, possibly because screening techniques have mistakenly focused on the ovary as origin of ovarian carcinoma. Unlike ovaries, the fallopian tubes are amenable to direct visual imaging without invasive surgery, using access through the cervix. To develop future screening protocols, we investigated using our 1.2- mm diameter, forward-viewing, scanning fiber endoscope (SFE) to image luminal surfaces of the fallopian tube before laparoscopic surgical removal. Three anesthetized human subjects participated in our protocol development which eventually led to 70-80% of the length of fallopian tubes being imaged in scanning reflectance, using red (632nm), green (532nm), and blue (442nm) laser light. A hysteroscope with saline uterine distention was used to locate the tubal ostia. To facilitate passage of the SFE through the interstitial portion of the fallopian tube, an introducer catheter was inserted 1- cm through each ostia. During insertion, saline was flushed to reduce friction and provide clearer viewing. This is likely the first high-resolution intraluminal visualization of fallopian tubes.
Tissue-specific expression of cell-surface Qa-2 antigen from a transfected Q7b gene of C57BL/10 mice. (1987)

We screened a cDNA library prepared from a BALB.B10 CTL clone that expresses Qa-2 antigen, and isolated four clones derived from Q7b, a Qa region gene of C57BL/10. One of these Q7b cDNAs and the Q7b chromosomal gene were subcloned into expression vectors and transfected into L cells and R1.1 thymoma cells. We found that the chromosomal Q7b gene expresses Qa-2 on the surface of R1.1 cells, but not on L cells while the Q7b cDNA expresses protein on the surface of both cell types. The levels of Qa-2 expression do not correlate with the total levels of Q7b mRNA in these transfectants. Our results suggest that the tissue-specific expression of Qa-2 may be controlled, in part, by mechanisms of alternate RNA splicing. By using hybrid gene constructs, we have mapped the tissue-specific element to the 3' part of the gene, downstream of a site near the middle of exon 4. The hybrid polypeptides differ significantly in their transmembrane and cytoplasmic regions. These portions of the protein also may play a role in the tissue-specific expression of Qa-2.
FIFOs - Innovation Through Architecture (1991)

Performance in SRAM based designs usually depends on applying a given process technology to a well known architecture. This is so because the key word in SRAM is random - the memory must meet its specifications for any pattern of accesses. FIFOs are a class of SRAM specialty memories with predictable patterns of address accesses. FIFO architectures which take advantage of this predictability permit faster parts, or parts with better speed/power trade-off in any given process than standard FIFO designs.
Neural Network-Derived Potts Models for Structure-Based Protein Design using Backbone Atomic Coordinates and Tertiary Motifs (2022)

A bstract Designing novel proteins to perform desired functions, such as binding or catalysis, is a major goal in synthetic biology. A variety of computational approaches can aid in this task. An energy-based framework rooted in the sequence-structure statistics of tertiary motifs (TERMs) can be used for sequence design on pre-defined backbones. Neural network models that use backbone coordinate-derived features provide another way to design new proteins. In this work, we combine the two methods to make neural structure-based models more suitable for protein design. Specifically, we supplement backbone-coordinate features with TERM-derived data, as inputs, and we generate energy functions as outputs. We present two architectures that generate Potts models over the sequence space: TERMinator, which uses both TERM-based and coordinate-based information, and COORDinator, which uses only coordinate-based information. Using these two models, we demonstrate that TERMs can be utilized to improve native sequence recovery performance of neural models. Furthermore, we demonstrate that sequences designed by TERMinator are predicted to fold to their target structures by AlphaFold. Finally, we show that both TERMinator and COORDinator learn notions of energetics, and these methods can be fine-tuned on experimental data to improve predictions. Our results suggest that using TERM-based and coordinate-based features together may be beneficial for protein design and that structure-based neural models that produce Potts energy tables have utility for flexible applications in protein science. Code Code will be made publically available at https://github.com/alexjli/terminator_public
Data Supplement from High Expression of <i>CAI2</i>, a <i>9p21</i>-Embedded Long Noncoding RNA, Contributes to Advanced-Stage Neuroblastoma (2023)

&lt;p&gt;CAI2 sequence and features (Supp Table S1); CAI2, ARF and p16 expression in various tumor cell lines and normal cells (Supp Table S2); Morphological assessment of low and high passage NMB7 cells after treatment by serum starvation or RA (Supp Table S3).&lt;/p&gt;
Optical characterization of Si1−xGex nanodots grown on Si substrates via ultrathin SiO2 buffer layers (2007)

Growth of Si1−xGex nanodots with x=0, 0.33, 0.67, and 1.0 was accomplished on ultrathin SiO2 buffer layers of 1–2 ML on Si(001) and Si(111) substrates using single-source gaseous precursors at 550°C. The Si1−xGex dots have diameters of ∼10nm and an areal density of ∼1011cm−2. Raman spectroscopy conducted on the nanodots shows that they are relaxed and their compositions correlate closely with the molecular ratios in the precursors used in their fabrication. Photoluminescence (PL) spectra were taken with reduced laser power density which enhanced the PL contribution from the nanodots while suppressing the PL contribution from the Si substrate. Two groups of PL peaks were observed, in the ranges of 0.8–1.0 and 1.0–1.1eV. The first group in the 0.8–1.0eV range shows peaks similar to those observed in Si with dislocations. The second group of peaks at the 1.0–1.1eV range shows an increase in intensity with increasing Ge concentration in the dots. However, both groups of peaks appear to be reproducible in Si substrates after conventional flash cleaning at 1150°C with no nanodots present. Since there is no evidence that the defect density in Si has increased after flash cleaning, the reason for their appearance is as yet undetermined.
Guidelines for aerosol devices in infants, children and adults: which to choose, why and how to achieve effective aerosol therapy (2011)

Multiple types of aerosol devices are commonly used for the administration of medical aerosol therapy to patients with pulmonary diseases. All of these devices have been shown to be effective in trials where they are used correctly. However, failure to operate any of these devices properly has been associated with poor clinical response and limited patient adherence to therapy. Therefore, the selection of the best aerosol device for the individual patient is very important for optimizing the results of medical aerosol therapy. This article presents the rationale for selecting the most appropriate aerosol device to administer inhaled drugs in specific patient populations, with emphasis on patient-, drug-, device- and environment-related factors and with a comparison between the available devices. The following recommendations for the selection of the 'best' aerosol device for each patient population are intended to help clinicians gain a clear understanding of the specific issues and challenges so that they can optimize aerosol drug delivery and its therapeutic outcomes in patients.
Real-time shading-based refinement for consumer depth cameras (2014)

We present the first real-time method for refinement of depth data using shape-from-shading in general uncontrolled scenes. Per frame, our real-time algorithm takes raw noisy depth data and an aligned RGB image as input, and approximates the time-varying incident lighting, which is then used for geometry refinement. This leads to dramatically enhanced depth maps at 30Hz. Our algorithm makes few scene assumptions, handling arbitrary scene objects even under motion. To enable this type of real-time depth map enhancement, we contribute a new highly parallel algorithm that reformulates the inverse rendering optimization problem in prior work, allowing us to estimate lighting and shape in a temporally coherent way at video frame-rates. Our optimization problem is minimized using a new regular grid Gauss-Newton solver implemented fully on the GPU. We demonstrate results showing enhanced depth maps, which are comparable to offline methods but are computed orders of magnitude faster, as well as baseline comparisons with online filtering-based methods. We conclude with applications of our higher quality depth maps for improved real-time surface reconstruction and performance capture.
ChemInform Abstract: SYNTHESIS OF (.+‐.)‐6β‐PROSTAGLANDIN I1 AND (.+‐.)‐6β‐DECARBOXYPROSTAGLANDIN I1 (1981)

Abstract Verfahren zur Darstellung von (i)‐6ß‐Decarboxyprostaglandin I, (VIa) und (i)‐6ß‐Prostaglandin I, (VIc) werden beschrieben.
The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare (2022)

The Torsion Library is a collection of torsion motifs associated with angle distributions, derived from crystallographic databases. It is used in strain assessment, conformer generation, and geometry optimization. A hierarchical structure of expert curated SMARTS defines the chemical environments of rotatable bonds and associates these with preferred angles. SMARTS can be very complex and full of implications, which make them difficult to maintain manually. Recent developments in automatically comparing SMARTS patterns can be applied to the Torsion Library to ensure its correctness. We specifically discuss the implementation and the limits of such a procedure in the context of torsion motifs and show several examples of how the Torsion Library benefits from this. All automated changes are validated manually and then shown to have an effect on the angle distributions by correcting matching behavior. The corrected Torsion Library itself is available including both PDB as well as CSD histograms in the Supporting Information and can be used to evaluate rotatable bonds at https://torsions.zbh.uni-hamburg.de.
Scalable Fiber-Array-to-Chip Interconnections with Sub-Micron Alignment Accuracy (2023)

Experimental demonstration of optical fiber array-to-chip assembly is realized with a passive self-alignment mechanism and 3D-printed ferrules. The approach explored in this paper allows an array of fibers to be interconnected to chip-level grating couplers (GCs) with sub-micron level placement accuracy. The mechanical alignment (verified to be stable over one year) enables high relative coupling efficiency (>75%) at 1550 nm. It is shown that the proposed fiber interconnection technology is compatible with 2.5D heterogeneous integration technologies.
The effect of negative pressure wound therapy with periodic instillation using antimicrobial solutions on Pseudomonas aeruginosa biofilm on porcine skin explants (2013)

Negative pressure wound therapy with instillation (NPWTi) is increasingly used as an adjunct therapy for a wide variety of infected wounds. However, the effect of NPWTi on mature biofilm in wounds has not been determined. This study assessed the effects of NPWTi using saline or various antimicrobial solutions on mature Pseudomonas aeruginosa biofilm using an ex vivo porcine skin explant biofilm model. Treatment consisted of six cycles with 10-minute exposure to instillation solution followed by 4 hours of negative pressure at -125 mm Hg over a 24-hour period. NPWTi using saline reduced bacterial levels by 1-log (logarithmic) of 7-log total colony-forming units (CFUs). In contrast, instillation of 1% povidone iodine (2-log), L-solution (3-log), 0·05% chlorhexidine gluconate (3-log), 0·1% polyhexamethylene biguanide (4-log), 0·2% polydiallyldimethylammonium chloride (4-log) and 10% povidone iodine (5-log), all significantly reduced (P < 0·001) total CFUs. Scanning electron micrographs showed disrupted exopolymeric matrix of biofilms and damaged bacterial cells that correlated with CFU levels. Compared with previous studies assessing microbicidal effects of topical antimicrobial dressings on biofilms cultured on porcine skin explants, these ex vivo model data suggest that NPWTi with delivery of active antimicrobial agents enhances the reduction of CFUs by increasing destruction and removal of biofilm bacteria. These results must be confirmed in human studies.
ChemInform Abstract: Recent Progress in the Synthesis of Naturally Occurring Triterpenoid Saponins (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Room-temperature fabrication of light-emitting thin films based on amorphous oxide semiconductor (2016)

We propose a light-emitting thin film using an amorphous oxide semiconductor (AOS) because AOS has low defect density even fabricated at room temperature. Eu-doped amorphous In-Ga-Zn-O thin films fabricated at room temperature emitted intense red emission at 614 nm. It is achieved by precise control of oxygen pressure so as to suppress oxygen-deficiency/excess-related defects and free carriers. An electronic structure model is proposed, suggesting that non-radiative process is enhanced mainly by defects near the excited states. AOS would be a promising host for a thin film phosphor applicable to flexible displays as well as to light-emitting transistors.
Asymmetric Thio-Michael/Nucleophilic Addition Domino Reaction with Chiral N-Sulfinimines (2007)

Optically active N-sulfinimines underwent stereoselective Michael/nucleophilic addition domino reaction triggered by magnesium thiolate to give alpha-phenylthiomethyl-beta-(N-sulfinylamino) esters in high diastereomeric excess. The adducts were readily converted into optically active alpha-methylene-beta-(N-sulfinylamino)esters so that this reaction provides a useful asymmetric aza-Baylis-Hillman-equivalent method.
Glutamatergic effects of dynorphin peptides on cultured oligodendrocytes (2002)

Our previous work has shown that oligodendrocytes (OLs), in addition to neurons, can synthesize the endogenous opioid dynorphin A (dyn A). Opioid effects of dynorphin are preferentially mediated through kappa opioid receptors (KORs). Signalling through KORs appears to promote OL survival in culture since blockade of KORs with the specific antagonist nor‐binaltorphamine significantly reduces OL survival and exacerbates glutamate toxicity. Structure‐activity studies have shown that kappa ligand activity resides in the N‐terminus of dyn A derived‐peptides, while C‐terminal fragments exhibit glutamatergic effects on neurons through NMDA and/or AMPA/kainate receptors. The present study was undertaken to determine whether dynorphin peptides also have glutamatergic effects on OLs. Since OLs grown in vitro are thought to have an AMPA/kainate phenotype, OLs were treated with dyn A (1–17) or dyn A (2–17) in the presence or absence of CNQX. Survival of mature and immature OLs was assessed over 72 h using a sensitive repeated measures assay. Dyn A (1–17) had no effect on OL survival. Dyn A (2–17), a dyn A‐derived peptide with nominal opioid activity, significantly reduced the survival of both immature and mature OLs. The effect was completely reversible in mature OLs by addition of CNQX at 2 h prior to dyn A (2–17), but not by simultaneous addition of CNQX. Of great interest, CNQX was unable to reverse the toxicity of dyn A (2–17) on immature OLs, suggesting that dynorphin toxicity in this population is mediated via an alternate glutamate receptor type. CNQX alone had no effect on OL viability. Results suggest that elevated dynorphin levels in CNS disease and trauma may contribute to demyelinating pathologies. Acknowledgements: Supported by Natl. MS Soc. (PEK) &amp; NIH DA 13559 (KFH).
Fourier-Domain Beamforming and Structure-Based Reconstruction for Plane-Wave Imaging (2018)

Ultrafast imaging based on coherent plane-wave compounding is one of the most important recent developments in medical ultrasound. It significantly improves the image quality and allows for much faster image acquisition. This technique, however, requires large computational load motivating methods for sampling and processing rate reduction. In this work, we extend the recently proposed frequency-domain beamforming (FDBF) framework to plane-wave imaging. Beamforming in frequency yields the same image quality while using fewer samples. It achieves at least fourfold sampling and processing rate reduction by avoiding oversampling required by standard processing. To further reduce the rate, we exploit the structure of the beamformed signal and use compressed sensing methods to recover the beamformed signal from its partial frequency data obtained at a sub-Nyquist rate. Our approach obtains tenfold rate reduction compared with standard time-domain processing. We verify performance in terms of spatial resolution and contrast based on the scans of a tissue mimicking the phantom obtained by a commercial Aixplorer system. In addition, in vivo carotid and thyroid scans processed using standard beamforming and FDBF are presented for qualitative evaluation and visual comparison. Finally, we demonstrate the use of FDBF for shear-wave elastography by generating velocity maps from the beamformed data processed at sub-Nyquist rates.