gebhart/patrepeval huggingface dataset:
Mammalian production of an isotopically enriched outer domain of the HIV-1 gp120 glycoprotein for NMR spectroscopy (2011)

NMR spectroscopic characterization of the structure or the dynamics of proteins generally requires the production of samples isotopically enriched in (15)N, (13)C, or (2)H. The bacterial expression systems currently in use to obtain isotopic enrichment, however, cannot produce a number of eukaryotic proteins, especially those that require post-translational modifications such as N-linked glycosylation for proper folding or activity. Here, we report the use of an adenovirus vector-based mammalian expression system to produce isotopically enriched (15)N or (15)N/(13)C samples of an outer domain variant of the HIV-1 gp120 envelope glycoprotein with 15 sites of N-linked glycosylation. Yields for the (15)N- and (15)N/(13)C-labeled gp120s after affinity chromatography were 45 and 44 mg/l, respectively, with an average of over 80% isotope incorporation. Recognition of the labeled gp120 by cognate antibodies that recognize complex epitopes showed affinities comparable to the unlabeled protein. NMR spectra, including (1)H-(15)N and (1)H-(13)C HSQCs, (15)N-edited NOESY-HSQC, and 3D HNCO, were of high quality, with signal-to-noise consistent with an efficient level of isotope incorporation, and with chemical shift dispersion indicative of a well-folded protein. The exceptional protein yields, good isotope incorporation, and ability to obtain well-folded post-translationally modified proteins make this mammalian system attractive for the production of isotopically enriched eukaryotic proteins for NMR spectroscopy.
Neutralizing Antibody Evasion Ability of Adenovirus Vector Induced by the Bioconjugation of Methoxypolyethylene Glycol Succinimidyl Propionate (MPEG-SPA) (2004)

Although adenovirus vectors (Ad) which possesses high transduction efficiency are widely used for gene therapy in animal models, clinical use is very limited. One of the main reason is that nearly 80% of human beings possess anti-Ad antibodies. In this study, we tried to modify Ad with methoxypolyethylene glycol (MPEG) activated by succinimidyl propionate, and, the neutralizing antibody evasion ability of PEGylated Ad was evaluated. The results demonstrated that PEG-Ad showed stronger protection ability against anti-Ad neutralizing antibody compared to that with unmodified-Ad. Considering there are many people carrying neutralizing antibody against Ad and readministration of Ad was necessary for treating chronic diseases, this strategy, which was also applicable to other vectors, can be used for developing improved vectors.
Facile synthesis of various 4-carboxylic acid derivatives and their amide analogues of benzopyrans (2012)

2H-Benzopyran-4-carboxylic acid derivative (III) is obtained via stepwise oxidation of the corresponding 4-methyl analogue (I).
Anisotropic orientation of the carbon fiber/liquid crystalline epoxy resin composites (2006)

Anisotropic orientation of carbon fiber (CF)/liquid crystalline epoxy (LCE) resin composite was readily induced during curing on a CF surface along a long molecular axis of CF. Orientation of LCE was confirmed with polarized optical microscope (POM) and wide angle X-ray diffractometer (WAXD). In addition, anisotropic ordering of LCE was correlated with curing rate, dynamic mechanical properties and thermal expansion behaviors of CF/LCE composite. Curing of LCE was accelerated in the presence of CF and the rubbery modulus of the CF/LCE composites cured at low temperature was enhanced by long-range, long axis orientational ordering of the LCE resin along a CF surface. Fully cured CF/LCE composite showed a negative coefficient of thermal expansion in the fiber direction. These results obtained in this study are interpreted in terms of structural changes occurring during curing.
Multigrid algorithms for optimization and inverse problems (2003)

A variety of new imaging modalities, such as optical diffusion tomography, require the inversion of a forward problem that is modeled by the solution to a three-dimensional partial differential equation. For these applications, image reconstruction can be formulated as the solution to a non-quadratic optimization problem. In this paper, we discuss the use of nonlinear multigrid methods as both tools for optimization and algorithms for the solution of difficult inverse problems. In particular, we review some existing methods for directly formulating optimization algorithm in a multigrid framework, and we introduce a new method for the solution of general inverse problems which we call multigrid inversion. These methods work by dynamically adjusting the cost functionals at different scales so that they are consistent with, and ultimately reduce, the finest scale cost functional. In this way, the multigrid optimization methods can efficiently compute the solution to a desired fine scale optimization problem. Importantly, the multigrid inversion algorithm can greatly reduce computation because both the forward and the inverse problems are more coarsely discretized at lower resolutions. An application of our method to optical diffusion tomography shows the potential for very large computational savings.
Medical Mimics of Psychiatric Conditions, Part 1 (2016)

present as behavioral or psychiatric emergencies.
Spatial Sampling for Crop Pests in Two Center Pivot Irrigated Fields (1999)

Controlling pests only where necessary may be a method to reduce pesticide use, decrease costs, and prevent environmental damage. The spatial distribution of a pest within a field must be known for site-specific management to be possible. With knowledge of the characteristic distribution of a pest, cost-effective sampling plans and management units can be designed for site-specific management. In 1997, two center pivot irrigated corn (Zea Mays L.) fields in eastern Colorado (175 and 130 ac.) were sampled and analyzed for weed seed bank and seedlings populations, triazine resistant pigweed seed bank, plant parasitic nematodes, white mold sclerotia, and western corn rootworm egg populations. Many crop and field attributes were sampled by other collaborating researchers. Research sampling plans were based on the biology of each pest, and time and cost constraints. Three research sampling plans were used: regular, random-directed, and star grids. There were a total of 682 observation sites in Field 1 and 621 observation sites in Field 2 that were used to sample pest populations. The size of each pest population varied between fields. Within a field pest populations tended to be spatially aggregated. Weed distributions and density varied among species. As average weed seedling or seed densities increased, the number of observation sites that were weed-free decreased. Spiral, stunt, and lesion nematode species were detected in both fields. The nematode species observed separately were spatially aggregated, but when the species were combined the spatial distribution was uniformly distributed. White mold sclerotia were not detected in either field. Western corn rootworm eggs were detected in 19 of 91 observation sites leaving most of Field 2 rootworm free. It may be possible to design directed pest sampling plans that are based on crop and field attributes.
Nonlinear identification of neuron models (2015)

The paper discusses when and how a nonlinear autonomous system can be uniquely identified from periodic data. This is a central problem in systems biology, where it e.g. arises when the dynamics of spiking neurons are modeled. The paper illustrates the problem by least squares identification of two autonomous neuron models, of order 4 and 2. The Hodgkin-Huxley model is well established, however it is of fourth order. As previously proved, this may not allow a unique identification from spiking neuron data. The paper illustrates this conclusion numerically, by least squares identification of a second order polynomial autonomous model, using spiking data generated by a fourth order Hodgkin-Huxley model. Further support is provided by identification of the second order FitzHugh-Nagumo model which can be exactly described by the model structure of the applied least squares algorithm. The Fitz-Hugh-Nagumo model can hence be uniquely identified from spiking neuron data. The paper also discusses computational complexity and provides results on the noise sensitivity of the applied least squares algorithm, when the sampling period is varied.
A Wide Dynamic Range CMOS Image Sensor with Improved Heat-Resistance and Image Quality at High Temperatures (2008)

A 1/4-inch VGA wide-dynamic-range complementary metal oxide semiconductor (CMOS) image sensor with resistance to high temperatures has been developed using a lateral overflow capacitor in a pixel, a very low dark-current front-end-of-line (VLDC FEOL) , and either an inorganic cap layer on an on-chip-micro-lens (OCML) or a metal hermetically sealed package to suppress the degradation of the spectra response of the OCML and color filter. The dark current level was reduced to 25e-/sec/pixel at 60°C. Sensor chips with no cap and ones with the inorganic cap layer on the OCML were assembled into either a metal hermetically sealed package or a conventional package. The chips with the inorganic cap layer and the ones with the metal hermetically sealed package showed no significant degradation of the spectra response in any of the R/G/B pixels even after a thermal stress test at 150°C. Improved image sensing performances were observed up to 85°C, and the dynamic range was extended to 94dB.
Program Synthesis (2017)

Program synthesis is the task of automatically finding a program in the underlying programming language that satisfies the user intent expressed in the form of some specification. Since the inception of artificial intelligence in the 1950s, this problem has been considered the holy grail of Computer Science. Despite inherent challenges in the problem such as ambiguity of user intent and a typically enormous search space of programs, the field of program synthesis has developed many different techniques that enable program synthesis in different real-life application domains. It is now used successfully in software engineering, biological discovery, compute-raided education, end-user programming, and data cleaning. In the last decade, several applications of synthesis in the field of programming by examples have been deployed in mass-market industrial products. This monograph is a general overview of the state-of-the-art approaches to program synthesis, its applications, and subfields. It discusses the general principles common to all modern synthesis approaches such as syntactic bias, oracle-guided inductive search, and optimization techniques. We then present a literature review covering the four most common state-of-the-art techniques in program synthesis: enumerative search, constraint solving, stochastic search, and deduction-based programming by examples. It concludes with a brief list of future horizons for the field.
Galileo High Accuracy Service (HAS) Algorithm and Receiver Development and Testing (2022)

The Galileo High Accuracy Service (HAS) will provide free of charge high accuracy corrections aiming to achieve Precise Point Positioning (PPP) in real time through the Galileo signal (E6-B) and by terrestrial means (Internet). The HAS will comprise two services levels; Service Level 1 (SL1) with global coverage providing high accuracy corrections (orbits, clocks) and biases (code and phase) for Galileo E1/E5b/E5a/E6 and E5AltBOC and GPS L1/L5/L2 signals. Service Level 2 (SL2) with regional coverage providing SL1 corrections plus atmospheric (at least ionospheric) corrections and potential additional biases. Within this context, the Galileo High Accuracy Reference Algorithm for SL1 and User Terminal (HAUT) project was awarded by the European Union Agency for the Space Programme (EUSPA) to Spaceopal GmbH and its partners ANavS GmbH, DLR IKN, IABG mbH and Iguassu Software Systems. In April 2022 and only after one-year development, the project achieved its Acceptance Review and delivered a Galileo HAS User Terminal capable to work with corrections from the Galileo HAS signal (E6-B) and terrestrial means. In this article, highlights on the User Algorithm and User Terminal are presented. Performance results using corrections and products generated by the Galileo HAS infrastructure and IGS are introduced.
Growth and Development of Mice Breathing 42% Oxygen (1981)

Chalon, J.; Dwarakanath, R.; Tang, C-K.; Ramanathan, S.; Katz, R.; Turndorf, H. Author Information
Data from Plasma KIM-1 Is Associated with Recurrence Risk after Nephrectomy for Localized Renal Cell Carcinoma: A Trial of the ECOG-ACRIN Research Group (E2805) (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;No circulating biomarkers are currently available to identify patients at highest risk of recurrence after nephrectomy for renal cell carcinoma (RCC). Kidney injury molecule-1 (KIM-1) is overexpressed in RCC and its ectodomain circulates in plasma. We investigated whether plasma KIM-1 is a prognostic biomarker in patients with localized RCC after nephrectomy.&lt;/p&gt;Experimental Design:&lt;p&gt;The ECOG-ACRIN E2805 (ASSURE) trial evaluated adjuvant sunitinib, sorafenib, or placebo in resected high-risk RCC. KIM-1 levels were measured from banked plasma at trial enrollment 4–12 weeks after nephrectomy. Lognormal accelerated failure time models were used to test for association between KIM-1 and disease-free survival (DFS) as well as overall survival (OS).&lt;/p&gt;Results:&lt;p&gt;Plasma from 418 patients was analyzed. Higher post-nephrectomy KIM-1 was associated with worse DFS across all study arms after adjustment for Fuhrman grade, T stage, N stage, and tumor histology [survival time ratio 0.56 for 75th vs. 25th percentile of KIM-1; 95% confidence interval (CI), 0.42–0.73; &lt;i&gt;P&lt;/i&gt; &lt; 0.001]. The association between KIM-1 and DFS was stronger among patients with pathologic nodal involvement (&lt;i&gt;P&lt;/i&gt;&lt;sub&gt;interaction&lt;/sub&gt; = 0.0086). The addition of post-nephrectomy KIM-1 improved the concordance of clinical prognostic models [Stage, Size, Grade, and Necrosis (SSIGN) concordance 0.57 vs. 0.43, &lt;i&gt;P&lt;/i&gt; = 0.05; UCLA International Staging System (UISS) concordance 0.60 vs. 0.40, &lt;i&gt;P&lt;/i&gt; = 0.0005]. Higher post-nephrectomy KIM-1 was also associated with worse OS after multivariable adjustment (survival time ratio 0.71 for 75th vs. 25th percentile of KIM-1; 95% CI, 0.56–0.91; &lt;i&gt;P&lt;/i&gt; &lt; 0.001).&lt;/p&gt;Conclusions:&lt;p&gt;Post-nephrectomy plasma KIM-1 is associated with DFS and OS in RCC, and may be a biomarker for microscopic residual disease.&lt;/p&gt;&lt;/div&gt;
Security architecture for wireless LANs: corporate and public environment (2002)

Wireless local area networks (WLANs) are envisaged to be used in different environments including corporate and public. This brings forward different requirements on security for WLANs. This paper studies the security requirements for WLANs in the envisaged environments and presents possible solutions for them. A qualitative comparison of the solutions are done in terms of security and practicality of implementation.
LECT2 makes the amyloid list (2014)

In this issue of Blood, Mereuta et al report that we must now add leukocyte cell–derived chemotaxin 2 (LECT2) to the list of proteins that can cause systemic amyloidosis, a fibrillar protein deposition disease that leads to end-organ damage and related symptoms and requires a tissue diagnosis demonstrating apple-green birefringence in Congo Red–stained sections viewed microscopically under polarized light. When dissected from affected tissue, digested into protein fragments of different lengths for proteomic analysis, and assessed by mass spectrometry for their original constituents, amyloid deposits reveal a unique signature of chaperones such as apolipoprotein E and serum amyloid P-component (arrows) as well as the identity of the critical main culprit: the amyloid-forming protein (red boxes).
Furfural conversion over calcined Ti and Fe metal-organic frameworks under continuous flow conditions (2023)

Furfural is an interesting bio-platform derived from lignocellulosic biomass that can be converted into chemicals and add-value products. In this work, the continuous-flow hydrogenation of furfural with 2-propanol was carried out using transition metal-based catalysts. C-MIL-101(Fe) and C-MIL-125(Ti), were successfully synthesized upon calcination of the parent MOFs obtained by the solvothermal method and their performances were compared in the hydrogenation of furfural. Interestingly, an 83% furfural conversion has been achieved over calcined C-MIL-125(Ti) with 77% of selectivity for FOL. Calcined C-MIL-101(Fe) provided lower furfural conversion and FOL selectivity, with an interesting switch towards acetal products.
Abstract P1-11-16: Her2/neu Overexpressing Breast Cancer Patients Retain an Immunological Proficiency Compromised in Her2/neu-Negative Cases (2010)

Abstract Although breast cancers overexpressing HER2/neu are associated with a worse prognosis, a high rate of complete responses is usually induced in these patients by current therapeutic strategies, such as Trastuzumab, that also directly mediates antibody-dependent cellular cytotoxicity and possesses immunomodulating properties. Moreover, other chemotherapeutics used in this setting, i.e. doxorubicin and Taxol, were shown to enhance antigen-specific immune responses. On these grounds, a thorough evaluation of the immunologic profile of breast cancer patients may be helpful to predict clinical responses to such therapies. We therefore analyzed at diagnosis different immunological parameters of patients with locally advanced HER2+ (n=18) and HER2- (n=30) breast cancer eligible for neoadjuvant chemotherapy, respectively treated with weekly Paclitaxel (80 mg/mq/ev) and Trastuzumab (4mg/kg/ev day 1 followed by 2 mg/kg/ev weekly), or Epirubicin (90 mg/mq/ev) and Docetaxel (75mg/mq/ev) every 3 weeks. Immunophenotyping of circulating immune cells disclosed several differences in HER2- cases as compared with HER2+ patients and healthy controls (n=20). In particular, HER2- patients showed a higher percentage of NK and B cells (10.2 and 10.0%, respectively) and a lower CD4/CD8 T cell ratio (1.8; with a prevalence of naïve and central memory cells in the CD8+ population) if compared to HER2+ patients (NK 5.8%, B cells 8.2%, and CD4/CD8=2.3) and healthy controls (NK 5.5%, B cells 7.7%, and CD4/CD8=2.2). In addition, HER2- cases had higher numbers of circulating CD4+ regulatory T cells (1.6% FoxP3+CD25+CD127- of CD4+ T cells) with respect to donors (0.9%). Moreover, IFN-gamma ELISPOT assay demonstrated spontaneous T cell responses to a broad spectrum of HLA-A*0201-restricted peptides derived from breast cancer-associated antigens (HER2/neu, MUC-1, mammaglobin-A, Taxol resistance-associated gene-3, survivin, and Bcl-xL) in both groups of tumour patients, although the extent of these responses was usually higher in HER2+ cases. Finally, a multiparametric evaluation of the serum levels of 9 different cytokines revealed a comparable profile in HER2+ cases and in controls, whereas HER2- patients showed significantly lower cytokine amounts compared to healthy donors (IL-2, IL-6, and IL-8) and to HER2+ breast cancers (IL-6, IL-8, and IL-10). Preliminary data revealed a pathological complete response (pCR) in 44.4% of HER2+ patients (8/18), compared to 16.7% of the HER2- arm (5/30). These results are consistent with a retained immunologic proficiency of HER2+ patients, showing an innate tumor-specific immune response. Such features may at least partly account for the clinical benefit of drugs acting through, but also promoting, immunemediated effects. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P1-11-16.
Quantifying Blood-Spinal Cord Barrier Permeability after Peripheral Nerve Injury in the Living Mouse (2014)

DCE-MRI provides a sensitive and non-invasive method to follow BSCB permeability in the same group of mice over time. Examining differences between mouse strains, we demonstrated that there is an important genetically-based control of the PNI-induced increase in BSCB permeability and that the critical genetic determinants of BSCB opening after PNI are distinct from those that determine genetic variability in PNI-induced pain hypersensitivity.
Orexin Receptor Antagonists Differ from Standard Sleep Drugs by Promoting Sleep at Doses That Do Not Disrupt Cognition (2013)

Current treatments for insomnia, such as zolpidem (Ambien) and eszopiclone (Lunesta), are γ-aminobutyric acid type A (GABAA)-positive allosteric modulators that carry a number of side effects including the potential to disrupt cognition. In an effort to develop better tolerated medicines, we have identified dual orexin 1 and 2 receptor antagonists (DORAs), which promote sleep in preclinical animal models and humans. We compare the effects of orally administered eszopiclone, zolpidem, and diazepam to the dual orexin receptor antagonist DORA-22 on sleep and the novel object recognition test in rat, and on sleep and two cognition tests (delayed match to sample and serial choice reaction time) in the rhesus monkey. Each compound's minimal dose that promoted sleep versus the minimal dose that exerted deficits in these cognitive tests was determined, and a therapeutic margin was established. We found that DORA-22 has a wider therapeutic margin for sleep versus cognitive impairment in rat and rhesus monkey compared to the other compounds tested. These data were further supported with the demonstration of a wider therapeutic margin for DORA-22 compared to the other compounds on sleep versus the expression of hippocampal activity-regulated cytoskeletal-associated protein (Arc), an immediate-early gene product involved in synaptic plasticity. These findings suggest that DORAs might provide an effective treatment for insomnia with a greater therapeutic margin for sleep versus cognitive disturbances compared to the GABAA-positive allosteric modulators currently in use.
Pedestrian Dead Reckoning With Smartglasses and Smartwatch (2016)

Wearable miniature inertial sensors have been widely used for pedestrian dead reckoning (PDR). Typical low-cost PDR systems use sensors attached to either the human trunk or feet. The recent emergence of smartglasses and smart watches provides an opportunity to use both types of wearable devices in position tracking. This paper proposes a novel method of utilizing both a smartwatch and smartglasses for PDR. The general idea is to use the relative angle between arm swing direction and head direction to detect any head-turn motion that would otherwise skew the position dead reckoning propagation. A complete PDR solution that includes step detection, step length estimation, head-rotation detection, and dead reckoning using a smartwatch and smartglasses that are currently available in the market is presented. Using the smartglasses, step detection with an error rate less than 0.4% and a cumulative distance error of less than 2.4% on 800 m walks and runs is achieved. In the dead reckoning field experiments, the proposed algorithm produces result that closely track the actual path when plotted on Google Maps, outperforming solutions that only use the smartwatch or smartglasses alone.
Purine analogues plus cyclophosphamide versus purine analogues alone for first-line therapy of patients with chronic lymphocytic leukaemia (2016)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: