gebhart/patrepeval huggingface dataset:
Advancements in transformation optics-enabled gradient-index lens design (2015)

Transformation Optics (TO) provides the mathematical framework for representing the behavior of electromagnetic radiation in a given geometry by “transforming” it to an alternative, usually more desirable, geometry through an appropriate mapping of the constituent material parameters. Using a quasi-conformal mapping, the restrictions on the required material parameters can be relaxed allowing isotropic inhomogeneous all-dielectric materials to be employed. This approach has led to the development of a new and powerful design tool for gradient-index (GRIN) optical systems. Using TO, aspherical lenses can be transformed to simpler spherical and flat geometries or even rotationally-asymmetric shapes which result in true 3D GRIN profiles. TO can also potentially be extended to collapse an entire lens system into a representative GRIN profile thus reducing its physical dimensions while retaining the optical performance of the original system. However, dispersion effects of the constituent materials often limit the bandwidth of metamaterial and TO structures thus restricting their potential applicability. Nonetheless, with the proper pairing of GRIN profile and lens geometry to a given material system, chromatic aberrations can be minimized. To aid in the GRIN construction, we employ advanced multi-objective optimization algorithms which allow the designer to explicitly view the trade-offs between all design objectives such as RMS spot size, field-of-view (FOV), lens thickness, 𝛥𝑛, and focal drift due to chromatic aberrations. We present an overview of our TO-enabled GRIN lens design process and analysis techniques while demonstrating designs which minimize the presence of mono- and poly-chromatic aberrations and discuss their requisite material systems.
Tsunami, javnozdravstveni rizici i izazovi (2005)

Jaki potres, 8,9 stupnjeva po Richterovoj skali pogodio je u ranim jutarnjim satima 26. prosinca 2004. godine zapadnu obalu Sjeverne Sumatre u Indoneziji. Kao posljedica tog potresa tsunami, vodeni val, zahvatio je Južnu, Jugoistocnu Aziju i Istocnu Afriku uzrokujuci smrt velikog broja ( preko 165000) ljudi i ogromna ostecenja građevina, prometnica, usjeva, ribarske infrastrukture, elektricnih postrojenja i vodova. Zahvacene su mnoge zemlje koje granice s Indijskim oceanom: Indonezija, Sri Lanka, Maldivi, Indija, Tajland, Malezija, Banglades, Burma, Tanzanija, Sejseli, Kenija i Somalija. Vlade Indonezije i Sri Lanke proglasile su nacionalnu katastrofu a vlada u Maldivi izvanredno stanje. Sada nakon sto se takva katastrofa dogodila biti ce za to podrucje uspostavljen sustav uzbunjivanja. Kamo srece da je on vec prije postojao u Indijskom oceanu (kao sto postoji na Pacifiku), jer bi bilo dovoljno vremena za sprjecavanje ovakve  neslucene katastrofe.  Tsunami, takav kao sto je pogodio Južnu Aziju,  ima ozbiljne javno-zdravstvene posljedice.
Packet types (2000)

In writing networking code, one is often faced with the task of interpreting a raw buffer according to a standardized packet format. This is needed, for example, when monitoring network traffic for specific kinds of packets, or when unmarshaling an incoming packet for protocol processing. In such cases, a programmer typically writes C code that understands the grammar of a packet and that also performs any necessary byte-order and alignment adjustments. Because of the complexity of certain protocol formats, and because of the low-level of programming involved, writing such code is usually a cumbersome and error-prone process. Furthermore, code written in this style loses the domain-specific information, viz. the packet format, in its details, making it difficult to maintain.
Pleurotolysin, a Novel Sphingomyelin-specific Two-component Cytolysin from the Edible Mushroom Pleurotus ostreatus, Assembles into a Transmembrane Pore Complex (2004)

Self-assembling, pore-forming cytolysins are illustrative molecules for the study of the assembly and membrane insertion of transmembrane pores. Here we purified pleurotolysin, a novel sphingomyelin-specific two-component cytolysin from the basidiocarps of Pleurotus ostreatus and studied the pore-forming properties of the cytolysin. Pleurotolysin consisted of non-associated A (17 kDa) and B (59 kDa) components, which cooperatively caused leakage of potassium ions from human erythrocytes and swelling of the cells at nanomolar concentrations, leading to colloid-osmotic hemolysis. Hemolytic assays in the presence of poly(ethylene glycol)s with different hydrodynamic diameters suggested that pleurotolysin formed membrane pores with a functional diameter of 3.8-5 nm. Pleurotolysin-induced lysis of human erythrocytes was specifically inhibited by the addition of sphingomyelin-cholesterol liposomes to the extracellular space. Pleurotolysin A specifically bound to sphingomyelin-cholesterol liposomes and caused leakage of the internal carboxyfluorescein in concert with pleurotolysin B. Experiments including solubilization of pleurotolysin-treated erythrocytes with 2% (w/v) SDS at 25 degrees C and SDS-polyacrylamide gel electrophoresis/Western immunoblotting showed that pleurotolysin A and B bound to human erythrocytes in this sequence and assembled into an SDS-stable, 700-kDa complex. Ring-shaped structures with outer and inner diameters of 14 and 7 nm, respectively, were isolated from the solubilized erythrocyte membranes by a sucrose gradient centrifugation. Pleurotolysin A and B formed an SDS-stable, ring-shaped complex of the same dimensions on sphingomyelin-cholesterol liposomes as well.
Beyond ray optics: building photonics intuition for waveguide modes using digital simulations and games (2023)

Engineering students in optics and photonics need robust intuitions for the micron-scale behavior of light in dielectric materials. Educators often use textbook images of ray diagrams and static electric field profiles to introduce the behavior of light, after which undergraduate and graduate students are expected to run commercial software simulations to explore the dynamic behavior of waveguide modes. While incredibly powerful and flexible, complex commercial software tools are difficult for novices to use, preventing students from gaining nuanced conceptual insights about the behavior of optical components and devices. The Virtual Manufacturing Lab (VM-Lab) at MIT has created a series of simulations that use novel data visualizations and dynamic electric field profiles to teach the fundamentals of photonic circuit components. This work identifies key misconceptions on the topics of fiber optics, waveguides, and photonic integrated circuits which prevent students from building an accurate model for light propagating in a micron-scale dielectric waveguide. A library of interactive photonics simulations helps students learn about silicon photonics by exploring waveguide modes, mode superposition, on-chip interferometers, resonant structures, and more. In addition, interactive learning games introduce students to the application areas of photonic integrated circuits, including on-chip chemical sensing, hyperscale data centers, RF wireless communication, and LiDAR imaging.
Sequestosome-1/p62 Is the Key Intracellular Target of Innate Defense Regulator Peptide (2009)

Innate defense regulator-1 (IDR-1) is a synthetic peptide with no antimicrobial activity that enhances microbial infection control while suppressing inflammation. Previously, the effects of IDR-1 were postulated to impact several regulatory pathways including mitogen-activated protein kinase (MAPK) p38 and CCAAT-enhancer-binding protein, but how this was mediated was unknown. Using a combined stable isotope labeling by amino acids in cell culture-proteomics methodology, we identified the cytoplasmic scaffold protein p62 as the molecular target of IDR-1. Direct IDR-1 binding to p62 was confirmed by several biochemical binding experiments, and the p62 ZZ-type zinc finger domain was identified as the IDR-1 binding site. Co-immunoprecipitation analysis of p62 molecular complexes demonstrated that IDR-1 enhanced the tumor necrosis factor alpha-induced p62 receptor-interacting protein 1 (RIP1) complex formation but did not affect tumor necrosis factor alpha-induced p62-protein kinase zeta complex formation. In addition, IDR-1 induced p38 MAPK activity in a p62-dependent manner and increased CCAAT-enhancer-binding protein beta activity, whereas NF-kappaB activity was unaffected. Collectively, these results demonstrate that IDR-1 binding to p62 specifically affects protein-protein interactions and subsequent downstream events. Our results implicate p62 in the molecular mechanisms governing innate immunity and identify p62 as a potential therapeutic target in both infectious and inflammatory diseases.
The feasibility of producing aluminum-lithium structures for cryogenic tankage applications by laser beam welding (1993)

Aluminum-lithium alloys exhibit high strength, high elastic modulus, and low density as well as excellent cryogenic mechanical properties making them ideal material candidates for cryogenic tanks. NASA has proposed the use of 'built-up' structure for panels fabricated into cryogenic tanks replacing current conventional machining. Superplastically formed stiffeners would be joined to sheet (tank skin) that had been roll formed to the radius of the tank in order to produce panels. Aluminum-lithium alloys of interest for producing the built-up structure include alloy 2095-T6 stiffeners to 2095-T8 sheet and alloy 8090-T6 stiffeners to 2090-T83 sheet. Laser welding, with comparable joint properties, offers the following advantages over conventional welding: higher production rates, minimal degradation within the heat affected zones, and full process automation. This study established process parameters for laser beam welding, mechanical property determinations, metallographic characterization, and fabrication of prototype panels. Tensile tests representing partial penetration of the skin alloys provided joint efficiencies between 65 and 77 percent, depending upon alloy and degree of penetration. Results of tension shear tests of lap welds indicated that the combination of 2095-T6 to 2090-T8 exhibited significantly higher weld shear strength at the interface in comparison to welds of 8090-T6 to 2090-T83. The increased shear strength associated with 2095 is believed to be due to the alloy's ability to precipitation strengthening (naturally age) after welding.
Predictive Models for Length of Stay and Discharge Disposition in Elective Spine Surgery: Development, Validation, and Comparison to the ACS NSQIP Risk Calculator (2022)

The predictive models developed in this study can enable accurate preoperative estimation of LOS and risk of rehabilitation discharge for adult patients undergoing elective spine surgery. The demonstrated models exhibited better performance than NSQIP for prediction of LOS and equivalent performance to NSQIP for prediction of discharge location.
Cutaneous hyalohyphomycosis in a girdled lizard (Cordylus giganteus) caused by the Chrysosporium anamorph of Nannizziopsis vriesii and successful treatment with voriconazole (2010)

The Chrysosporium anamorph of Nannizziopsis vriesii was associated with dermatomycosis and high mortality in a group of captive giant girdled lizards (Cordylus giganteus). Treatment of one of the infected girdled lizards with voriconazole, which was selected on the basis of in vitro sensitivity testing of the isolate, resulted in resolution of lesions and negative fungal cultures from the skin. Three hours after oral administration of 10 mg/kg, the plasma level of voriconazole exceeded the 0.25-μg/mL minimal inhibitory concentration tenfold. In conclusion, administration of voriconazole at 10 mg/kg of body weight once daily for 10 weeks resulted in clinical cure and was well tolerated. A longer follow-up time and larger studies will be necessary to determine the long-term efficacy and safety of this treatment in giant girdled lizards.
Malicious activity detection in a memory (2023)

A method and apparatus for monitoring a volatile memory in a computer system. Samples of compressed data from locations in the volatile memory in the computer system are read. Data in the volatile memory is reconstructed using the samples of compressed data. The data is an image of the volatile memory. The image enables determining whether an undesired process is present in the volatile memory.
The Neuropsychiatric Disease-Associated Genecacna1cMediates Survival of Young Hippocampal Neurons (2016)

Genetic variations in CACNA1C, which encodes the Cav1.2 subunit of L-type calcium channels (LTCCs), are associated with multiple forms of neuropsychiatric disease that manifest high anxiety in patients. In parallel, mice harboring forebrain-specific conditional knockout of cacna1c (forebrain-Cav1.2 cKO) display unusually high anxiety-like behavior. LTCCs in general, including the Cav1.3 subunit, have been shown to mediate differentiation of neural precursor cells (NPCs). However, it has not previously been determined whether Cav1.2 affects postnatal hippocampal neurogenesis in vivo. Here, we show that forebrain-Cav1.2 cKO mice exhibit enhanced cell death of young hippocampal neurons, with no change in NPC proliferation, hippocampal size, dentate gyrus thickness, or corticosterone levels compared with wild-type littermates. These mice also exhibit deficits in brain levels of brain-derived neurotrophic factor (BDNF), and Cre recombinase-mediated knockdown of adult hippocampal Cav1.2 recapitulates the deficit in young hippocampal neurons survival. Treatment of forebrain-Cav1.2 cKO mice with the neuroprotective agent P7C3-A20 restored the net magnitude of postnatal hippocampal neurogenesis to wild-type levels without ameliorating their deficit in BDNF expression. The role of Cav1.2 in young hippocampal neurons survival may provide new approaches for understanding and treating neuropsychiatric disease associated with aberrations in CACNA1C. Visual Abstract.
Nonnegative constraint analysis of key fluorophores within human breast cancer using native fluorescence spectroscopy excited by selective wavelength of 300 nm (2015)

Native fluorescence spectroscopy offers an important role in cancer discrimination. It is widely acknowledged that the emission spectrum of tissue is a superposition of spectra of various salient fluorophores. In this study, the native fluorescence spectra of human cancerous and normal breast tissues excited by selected wavelength of 300 nm are used to investigate the key building block fluorophores: tryptophan and reduced nicotinamide adenine dinucleotide (NADH). The basis spectra of these key fluorophores' contribution to the tissue emission spectra are obtained by nonnegative constraint analysis. The emission spectra of human cancerous and normal tissue samples are projected onto the fluorophore spectral subspace. Since previous studies indicate that tryptophan and NADH are key fluorophores related with tumor evolution, it is essential to obtain their information from tissue fluorescence but discard the redundancy. To evaluate the efficacy of for cancer detection, linear discriminant analysis (LDA) classifier is used to evaluate the sensitivity, and specificity. This research demonstrates that the native fluorescence spectroscopy measurements are effective to detect changes of fluorophores' compositions in tissues due to the development of cancer.
Short and Efficient Synthesis of a Vinyl-Substituted Tricyclic Erythromycin Derivative (2005)

Tricyclic erythromycin A derivatives are known potent antibacterial agents, but the potential of substituted tricyclic erythromycin A derivatives remains largely unexplored. To study this lead, the tricyclic ring system was synthesized by an efficient three-step synthesis starting from the allylic alcohol utilizing a novel azidoisocyanate. These tricyclic analogues can be used as scaffolds to probe secondary ribosomal binding sites. [structure: see text]
Empirical evaluation of bias field correction algorithms for computer-aided detection of prostate cancer on T2w MRI (2011)

In magnetic resonance imaging (MRI), intensity inhomogeneity refers to an acquisition artifact which introduces a non-linear variation in the signal intensities within the image. Intensity inhomogeneity is known to significantly affect computerized analysis of MRI data (such as automated segmentation or classification procedures), hence requiring the application of bias field correction (BFC) algorithms to account for this artifact. Quantitative evaluation of BFC schemes is typically performed using generalized intensity-based measures (percent coefficient of variation, %CV ) or information-theoretic measures (entropy). While some investigators have previously empirically compared BFC schemes in the context of different domains (using changes in %CV and entropy to quantify improvements), no consensus has emerged as to the best BFC scheme for any given application. The motivation for this work is that the choice of a BFC scheme for a given application should be dictated by application-specific measures rather than ad hoc measures such as entropy and %CV. In this paper, we have attempted to address the problem of determining an optimal BFC algorithm in the context of a computer-aided diagnosis (CAD) scheme for prostate cancer (CaP) detection from T2-weighted (T2w) MRI. One goal of this work is to identify a BFC algorithm that will maximize the CaP classification accuracy (measured in terms of the area under the ROC curve or AUC). A secondary aim of our work is to determine whether measures such as %CV and entropy are correlated with a classifier-based objective measure (AUC). Determining the presence or absence of these correlations is important to understand whether domain independent BFC performance measures such as %CV , entropy should be used to identify the optimal BFC scheme for any given application. In order to answer these questions, we quantitatively compared 3 different popular BFC algorithms on a cohort of 10 clinical 3 Tesla prostate T2w MRI datasets (comprising 39 2D MRI slices): N3 , PABIC, and the method of Cohen et al. Results of BFC via each of the algorithms was evaluated in terms of %CV , entropy, as well as classifier AUC for CaP detection from T2w MRI. The CaP classifier was trained and evaluated on a per-pixel basis using annotations of CaP obtained via registration of T2w MRI and ex vivo whole-mount histology sections. Our results revealed that different BFC schemes resulted in a maximization of different performance measures, that is, the BFC scheme identified by minimization of %CV and entropy was not the one that maximized AUC as well. Moreover, existing BFC evaluation measures (%CV , entropy) did not correlate with AUC (application-based evaluation), but did correlate with each other, suggesting that domain-specific performance measures should be considered in making a decision regarding choice of appropriate BFC scheme. Our results also revealed that N3 provided the best correction of bias field artifacts in prostate MRI data, when the goal was to identify prostate cancer.
Dark application communities (2006)

In considering new security paradigms, it is often worthwhile to anticipate the direction and nature of future attack paradigms. We identify a class of attacks based on the idea of a "Dark" Application Community (DAC) - a collection of bots and zombie machines that actively performs binary-level supervision of applications to help an attacker automate the process of finding vulnerabilities. A collection of such hosts can observe and attempt to influence the behavior of automatic defense systems. An attacker can use the DAC as both a test platform for subverting security applications and as a reconnaissance network for exploiting commonly deployed automatic update and early warning systems.
Progression Free Survival Is Predicated by Categorical Response, and Supports the Attainment of VGPR/CR as An Objective for Long Term Disease Control in Waldenstrom's Macroglobulinemia. (2009)

Abstract Abstract 4993 The attainment of higher response rates, as well as better categorical responses has occurred with the introduction of novel biological agents, including rituximab in the treatment of WM. However, there is a paucity of knowledge as to whether the attainment of better categorical responses is associated with improved outcomes. We therefore analyzed the impact of categorical responses on progression free survival (PFS) in 159 WM patients naïve to rituximab therapy and who received a rituximab based regimen: cyclophosphamide (n=58), nucleoside analogue (n=43), immunomodulatory agent (n=35), or bortezomib (n=23). The median follow-up for all patients was 83.5 months. Baseline characteristics were as follows: median age 62 years; serum IgM 3670 mg/dL; hematocrit 31.7%. Eighty-two patients had a B2M ≥3.0 g/L, and the IPSS score was I (n=64); II (n=57) and III (n=38). One hundred eight (68%) patients were previously untreated. Categorical responses were as follows: Complete Response (CR) defined as absence of clinically evident bone marrow or extramedullary disease, normal range serum IgM and negative immunofixation study (n=14); Very Good Partial Response (VGPR) defined as ≥90% reduction in serum IgM (n=21); Partial Response (PR) defined as ≥ 50% to &lt;90% reduction in serum IgM (n=79); Minor Response (MR) defined as ≥ 25% to &lt;50% in serum IgM (n=30); No Response (NR; n=14). No association between categorical response attainment and baseline serum IgM, B2M, Hematocrit or IPSS score was observed when employing a proportional hazards model. Achievement of better categorical responses was incrementally associated with improved PFS (p&lt;0.0001 by log rank analysis), including attainment of a minor response, in both previously untreated and treated patients. No separation of curves was observed between VGPR and CR (Figure 1). Median TTP for patients achieving CR or VGPR was 71.8 months versus 38.6 months for those with PR or MR (Figure 2; p=0.008). Attainment of at least a VGPR served as an independent marker for improved PFS by univariate analysis. The results suggest that categorical responses, including MR and VGPR have prognostic value in WM, and that efforts aimed at improving categorical responses may lead to improved treatment outcomes in patients with WM. Disclosures No relevant conflicts of interest to declare.
Pericellular matrix and cell surface glycoproteins of virus-transformed mouse epithelial cells. (1982)

Mouse embryo Mus musculus castaneous epithelial cells, transformed with Moloney murine sarcoma virus (MSV) or with ecotropic murine leukemia virus (MuLV), were analyzed for production of pericellular matrix glycoproteins. The nontransformed, MSV-transformed, and MuLV-transformed cells produced fibronectin, laminin, type I collagen, and small amounts of type III collagen when studied by immunofluorescence using specific antibodies. The virus-transformed epithelial cells produced enhanced amounts of fibronectin into their growth media. Nontransformed M. musculus castaneous epithelial cells mainly produced type I collagen, as shown by metabolic labeling and polypeptide analysis. A significant increase in the glycoprotein production was seen by the MuLV-transformed cells, whereas small changes in the collagen production were apparent after MSV transformation. MuLV-transformed cells produced increased amounts of type I collagen and also some collagenous polypeptides that comigrated with procollagen type IV chains. The ratio of the procollagen type I chains deposited in the matrix was altered in transformed cells. Radioactive surface labeling of the cells revealed changes of the high-molecular-weight glycoproteins in both the MSV- and the MuLV-transformed cells. Unlike virus-transformed fibroblastic cells, these transformed epithelial cells deposited and retained connective tissue glycoproteins in their pericellular matrices. The results indicate that viral transformation modulates the pericellular matrix and surface glycoproteins of cultured mouse epithelial cels. The ability of virus-transformed epithelial cells to deposit pericellular matrices is a major difference between them and virus-transformed fibroblastic cells.