gebhart/patrepeval huggingface dataset:
2‐Nitroveratryl as a Photocleavable Thiol‐Protecting Group for Directed Disulfide Bond Formation in the Chemical Synthesis of Insulin (2014)

Chemical synthesis of peptides can allow the option of sequential formation of multiple cysteines through exploitation of judiciously chosen regioselective thiol-protecting groups. We report the use of 2-nitroveratryl (oNv) as a new orthogonal group that can be cleaved by photolysis under ambient conditions. In combination with complementary S-pyridinesulfenyl activation, disulfide bonds are formed rapidly in situ. The preparation of Fmoc-Cys(oNv)-OH is described together with its use for the solid-phase synthesis of complex cystine-rich peptides, such as insulin.
Computational Color Technology (2006)

Three-Dimensional Lookup Table with InterpolationColor space transformation using a 3D lookup table (LUT) with interpolation is used to correlate the source and destination color values in the lattice points of a 3D table, where nonlattice points are interpolated by using the nearest lattice points.This method has been used in many applications with quite satisfactory results, and incorporated into the ICC profile standard. 1 In this chapter, the structure of the 3D-LUT approach is discussed and the mathematical formulations of interpolation methods are given.These methods are tested using several sets of data points.The similarities and differences of these interpolation methods are discussed.
The Preservation of Leptospires by Drying from the Liquid State (1962)

SUMMARY: Four strains of Leptospira were preserved by drying, in vacuo, small volumes (0.04 ml.) of suspension of the organism from the liquid state. The leptospires were suspended and dried in a mixture of equal parts of Korthof’s medium and 20% (w/v) glucose. Recoveries of the organisms after storage for one year were appreciably higher from desiccates stored at 4° than from those stored at about 20°.
Discovery of Genuine Functional Dependencies from Relational Data with Missing Values [Abstract for INFORSID 2019] (2019)

International audience
Regiocontrolled Intramolecular Cyclizations of Carboxylic Acids to Carbon−Carbon Triple Bonds Promoted by Acid or Base Catalyst (2006)

We systematically investigated, for the first time, the relationship between regioselectivity and acid/base effects in the cyclization reactions between carboxylic acids and carbon-carbon triple bonds. We found novel acid- and base-promoted cyclizations to selectively give isocoumarin or pyran-2(2H)-one and phthalide or furan-2(5H)-one skeletons, respectively, and established a catalytic version of regioselective heterocyclic ring synthesis. Density functional theory calculations and application to a short route to thunberginol A were also described. [reaction: see text].
Diverse Beam Search: Decoding Diverse Solutions from Neural Sequence Models (2016)

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.
Observation of β-Sheet Aggregation in a Gas-Phase Tau-Peptide Dimer (2009)

In Alzheimer's disease, the tau protein forms intracellular amyloid fibrils in which the (306)VQIVYK(311) sequence adopts parallel beta-sheets, enabling fibril formation via cross-beta "steric zippers". We investigated aggregation of the protected segment (Ac-VQIVYK-NHMe) using IR/UV hole-burning spectroscopy in the NH stretch region in a cold molecular beam combined with DFT calculations in order to characterize its structure and identify the noncovalent interactions generally responsible for aggregation and stabilization in amyloid peptides. The computed and experimental IR spectra suggest that the tau-protein fragments form extended beta-strands that are combined in a beta-sheet through characteristic backbone hydrogen bonds, indicating that this secondary structure is energetically most attractive and readily forms in the gas phase, without any "guiding" interactions from a solvent or protein environment.
Analysis of TSDC spectra for polyimide aged in a simulated space environment (2000)

Samples of polyimide have been aged under a simulated space environment for periods of up to 48 months. Changes in the polymer have been monitored using TSDC measurements. The behaviour of activation energies derived from the TSDC spectra as a function of polarisation voltage and ageing conditions are discussed and a model to explain their behaviour is presented.
The nonpathogenic commensal Neisseria: friends and foes in infectious disease (2019)

Clinicians should have increased awareness of nonpathogenic Neisseria. First, as new immunomodulating therapies become licenced, the interactions that maintain balance between commensals and their human hosts may be altered. Second, these bacteria are showing promise in their capacity to exclude pathogenic Neisseria species from their anatomical niches.
Code complete: a practical handbook of software construction (1993)

Code complete is the phrase used by programmers to announce the completion of a software program. Drawing its examples from a variety of computer languages, this book focuses on programming technique rather than the requirements of a specific programming language or environment. Steve McConnell developed True Type and Windows for the Microsoft Corporation. Topics include: front-end planning, applying good design techniques to construction, using data effectively, using common and advanced control structures, secrets of self-documenting code, testing and debugging techniques, improving performance with code tuning, managing construction activities, and relating personal character to the development of superior software.
Abstract LB-100: Development of novel selective tumor-associated carbonic anhydrase inhibitors as promising anticancer agents (2015)

Abstract The molecular complexity of cancers and therapy-related side effects often limit efficacy of numerous anti-tumor therapies, and warrant development of new drugs that are specific for certain molecular targets while minimizing the off-target effects. We previously have synthesized a series of benzene-sulfonamides incorporating cyanoacrylamide moieties (tyrphostine analogues), and investigated such new compounds as inhibitors of the metalloenzyme carbonic anhydrase (CA). Specifically, we determined the inhibitory activity of such novel compounds against the cytosolic, house-keeping human (h) isoforms hCA I and II, as well as the transmembrane, tumor-associated ones CA IX and XII. Four compounds, namely CS2, CS6, CS8 and CS13, were very potent CA IX/XII inhibitors whereas they were much less effective as inhibitors of CA I and II. To determine whether these selective tumor-associated CA inhibitors exert antitumor activity, we examined their antiproliferative activity against the human medulloblastoma Daoy cell line, human hepatoma HepG2 cell line and the human epithelial cervical cancer Hela cell line. Compounds CS6 and CS13 showed significant antiproliferative activity against the three cancer cell lines. Daoy was the most sensitive cell line, and compound CS6 was the most potent one. Remarkably, compound CS6 was more potent against Daoy cells than the multi-targeted kinase inhibitor of BCR-ABL and SRC family kinases, dasatinib, since the former exerted smaller IC50 than that exerted by the latter (4.14 versus 7.28 μg/mL). In addition, flow cytometric Annexin-V/propidium iodide assay results showed that cell death induced by compounds CS6 is mediated, at least in part, by apoptosis. Moreover, CS6 significantly inhibited tyrosine kinase activity in Daoy cells, compared to DMSO-treated (control) cells. Taken together, these data indicate that compound CS6 is a novel multiple cancer pathways inhibitor, and warrants further investigation of its antitumor activity in medulloblastoma and other brain tumors. Currently, compounds CS6 and CS13 are being tested for their inhibitory activity against dihydrofolate reductase and thymidylate synthase. Citation Format: Ahmed Mahmoud Alafeefy, Sabry Atia, Sheikh Ahmad, Khairy Zoheir, Abdelkader Ashour, Ashok Kumar. Development of novel selective tumor-associated carbonic anhydrase inhibitors as promising anticancer agents. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-100. doi:10.1158/1538-7445.AM2015-LB-100
Rescuing uncorrectable fault patterns in on-chip memories through error pattern transformation (2016)

Voltage scaling can effectively reduce processor power, but also reduces the reliability of the SRAM cells in on-chip memories. Therefore, it is often accompanied by the use of an error correcting code (ECC). To enable reliable and efficient memory operation at low voltages, ECCs for on-chip memories must provide both high error coverage and low correction latency. In this paper, we propose error pattern transformation, a novel low-latency error correction technique that allows on-chip memories to be scaled to voltages lower than what has been previously possible. Our technique relies on the observation that the number of on-chip memory errors that many ECCs can correct differs widely depending on the error patterns in the logical words they protect. We propose adaptively rearranging the logical bit to physical bit mapping per word according to the BIST-detectable fault pattern in the physical word. The adaptive logical bit to physical bit mapping transforms many uncorrectable error patterns in the logical words into correctable error patterns and, therefore, improving on-chip memory reliability. This reduces the minimum voltage at which on-chip memory can run by 70mV over the best low-latency ECC baseline, leading to a 25.7% core-wide power reduction for an ARM Cortex-A7-like core. Energy per instruction is reduced by 15.7% compared to the best baseline.
Early Clinical Experience With Orthofix External Fixation of Complex Distal Radius Fractures (1990)

Twelve patients with complex fractures of the distal radius were treated with the Orthofix external fixation system (EBI Medical Systems, Fairfield, NJ). On follow up physical examination, the average wrist dorsiflexion was 46 degrees, and the average volar flexion was 55 degrees. The average grip strength in the involved hand was 38 lb force. The average final radial angle was 18 degrees, and the average residual radial height was 12 mm. Average volar tilt was 3 degrees. The complication rate was 42%. Very rigid axial stability is afforded by the fixator, but the large 3.5 mm tapered bone screw diameter precludes redrilling for screw adjustment. The apparatus needs frequent monitoring to reconfirm the security of the locking nuts and cam mechanisms, and the Orthofix system can be reused only four times.
Interferometric optical tomography for 3-Dimensional investigation of liquids (2000)

Paper nr 428
ChemInform Abstract: New [4 + 2] Heterocycloaddition of Alkynyl Fischer Carbene Complexes. A Facile Access to Pyrimidyl Carbene Complexes. (1999)

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.
An experimental study of the temperature, relative humidity and flow rate effects on the performances of a single PEMFC (2008)

International audience
Deriving cursor control device expectations for the Orion Crew Exploration Vehicle (2010)

A unique challenge for the Orion Crew Exploration Vehicle is the need for a novel cursor control device (CCD) that allows the crew to interact with display formats while seated and restrained.Display formats will contain "controllable elements" that will be used for input by astronauts, and will most likely not be laid out in a rectilinear grid.A four-way "caged" castle switch on the CCD was designed to travel only to controllable elements toward decreasing erroneous cursor movements.The ability of the four-way castle to intuitively navigate the cursor from a user perspective is a vital consideration.A cursor expectations study was conducted to understand dominant user expectations for CCD movements when controllable elements are not arranged on a rectilinear grid.Algorithms were developed that governed cursor movement in such a way as to match the dominant user expectations, to support the development of user mental models for cursor behavior, and to guide designers when laying out display formats.
Masquerade: a novel secreted serine protease-like molecule is required for somatic muscle attachment in the Drosophila embryo. (1995)

Diverse developmental processes, such as neuronal growth cone migration and cell shape changes, are mediated by the interactions of cells with the extracellular matrix. We describe here a secreted molecule encoded by the Drosophila masquerade (mas) gene. Total loss of mas function causes defective muscle attachment. This mutant phenotype suggests that mas normally acts to stabilize cell-matrix interaction and represents a novel functional and limiting component in the adhesion process. mas encodes a 1047-amino-acid preproprotein that is further processed by proteolytic cleavage to generate two polypeptides. The carboxy-terminal polypeptide is highly similar to serine proteases and has an extracellular localization; however, it is unlikely to possess proteolytic activity, because the catalytic site serine has been substituted by a glycine residue. During embryonic development, the mas amino- and carboxy-terminal polypeptides are differentially localized. The mas carboxy-terminal polypeptide accumulates at all somatic muscle attachment sites, which corresponds well with the morphological defect seen in the mas mutants. Our findings demonstrate the involvement of an extracellular component in somatic muscle attachment. We propose that mas acts via its modified serine protease motif, either as a novel adhesion molecule and/or as a competitive antagonist of serine proteases, to stabilize muscle attachment.
An Interval-Scaled Scoring Algorithm for Visual Function Questionnaires (2007)

A simple scoring algorithm based on an inverse hyperbolic tangent transformation of average functional reserve produces highly reliable approximations of visual ability estimated from Rasch analysis for the ADVS, NEI VFQ, VAQ, and VF-14. All four instruments measure the same visual ability variable in units that can be calibrated to a common measurement scale.
‘When you hear hooves, think zebras, not horses’; two challenging cases of interstitial lung disease (ILD) (2019)

Our case series describes two siblings with complex fibrosing lung diseases. The first patient was initially given a diagnosis of sarcoidosis based on imaging and exclusion of alternative diagnoses. A number of years after diagnosis, he had rapid deterioration of his disease and following surgical lung biopsy, his lung fibrosis was re-classified as chronic hypersensitivity pneumonitis (cHP) with a usual interstitial pneumonia pattern. He subsequently underwent successful lung transplantation. The second patient presented with rapidly progressing exertional dyspnoea. His bloods, imaging, bronchoalveolar lavage and histology were discussed at our multidisciplinary team meeting. His histology was most in keeping with subacute on cHP with overlapping imaging features between the two siblings. He was treated accordingly but unfortunately succumbed to his illness shortly after diagnosis. These cases highlight the difficulties differentiating between the various interstitial lung disease (ILD) subtypes and the challenges in management while also increasing awareness of familial ILD.
Data from Prognostic Significance of Growth Kinetics in Newly Diagnosed Glioblastomas Revealed by Combining Serial Imaging with a Novel Biomathematical Model (2023)

&lt;div&gt;Abstract&lt;p&gt;Glioblastomas are the most aggressive primary brain tumors, characterized by their rapid proliferation and diffuse infiltration of the brain tissue. Survival patterns in patients with glioblastoma have been associated with a number of clinicopathologic factors including age and neurologic status, yet a significant quantitative link to &lt;i&gt;in vivo&lt;/i&gt; growth kinetics of each glioma has remained elusive. Exploiting a recently developed tool for quantifying glioma net proliferation and invasion rates in individual patients using routinely available magnetic resonance images (MRI), we propose to link these patient-specific kinetic rates of biological aggressiveness to prognostic significance. Using our biologically based mathematical model for glioma growth and invasion, examination of serial pretreatment MRIs of 32 glioblastoma patients allowed quantification of these rates for each patient's tumor. Survival analyses revealed that even when controlling for standard clinical parameters (e.g., age and Karnofsky performance status), these model-defined parameters quantifying biological aggressiveness (net proliferation and invasion rates) were significantly associated with prognosis. One hypothesis generated was that the ratio of the actual survival time after whatever therapies were used to the duration of survival predicted (by the model) without any therapy would provide a therapeutic response index (TRI) of the overall effectiveness of the therapies. The TRI may provide important information, not otherwise available, about the effectiveness of the treatments in individual patients. To our knowledge, this is the first report indicating that dynamic insight from routinely obtained pretreatment imaging may be quantitatively useful in characterizing the survival of individual patients with glioblastoma. Such a hybrid tool bridging mathematical modeling and clinical imaging may allow for stratifying patients for clinical studies relative to their pretreatment biological aggressiveness. [Cancer Res 2009;69(23):9133–40]&lt;/p&gt;&lt;/div&gt;
Network Reconstruction under Compressive Sensing (2013)

Abstract—Many real-world systems and applications such as World Wide Web, and social interactions can be modeled as networks of interacting nodes. However, in many cases, one encounters the situation where the pattern of the node-to-node interactions (i.e., edges) or the structure of a network is unknown. We address this issue by studying the Network Reconstruction Problem: Given a network with missing edges, how is it possible to uncover the network structure based on certain observable quantities extracted from partial measurements? We propose a novel framework called CS-NetRec based on a newly emerged paradigm in sparse signal recovery called Compressive Sensing (CS). The results demonstrate that our framework can perform accurately even on low number of cascades (e.g. when the number of cascades is around half of the number of existing edges in the desired network). Furthermore, our framework is capable of near-perfect reconstruction of the desired network in presence of 95 % sparsity. In addition, we compared the performance of our framework with NetInf; one of the state-of-the-art methods in inferring the networks of diffusion. The results suggest that the proposed method outperforms NetInf by an average of 10% improvement based on the F-measure. I.
Femoral Nerve Palsy in Pavlik Harness Treatment for Developmental Dysplasia of the Hip (2011)

Femoral nerve palsy is an uncommon yet clinically important complication of Pavlik harness treatment for developmental dysplasia of the hip. This complication is strongly predictive of failure of treatment, and its impact is greatest when the developmental dysplasia of the hip is higher in severity. Early recognition and management of femoral nerve palsies may improve the success of treatment.
Mathematical modelling of high velocity oxygen fuel thermal spraying of nanocrystalline materials: an overview (2002)

An emerging application of nanocrystalline materials involves the deposition of nanocrystalline coatings using high velocity oxygen fuel (HVOF) thermal spraying. Since the physical, mechanical, and chemical characteristics of a nanocrystalline coating are critically influenced by the HVOF operating parameter, mathematical modelling is increasingly being used to establish a fundamental understanding of the process, to maximize coating performance, and to minimize the amount of experimentation required. In this paper, the modelling of HVOF thermal-spray processes, including combustion, gas dynamics, momentum, and thermal transfer between the particle and gas phase, as well as the impact of particles onto a substrate is reviewed. Particular attention is paid to topics that are particularly relevant to the thermal spraying of nanocrystalline coatings.
Variations in the Density of Bone Cement After Centrifugation (1986)

Barium sulfate added to bone cement to provide radiopacity has a density about four times greater than that of polymerized radiolucent bone cement. Because centrifugation might make a clinically significant change in the distribution of barium sulfate, this process was studied. Radiolucent and radiopaque Simplex-P bone cement (Howmedica, Inc., Rutherford, New Jersey) were mixed with and without cooling and centrifuged for two or four minutes at 2,000 g or 1,000 g (gravity acceleration). The density of sections of the hardened bone cement was measured using the Archimedes principle. Erythromycin and colistin were added to cement batches to test whether or not centrifugation affected the distribution of antibiotics. Direct and radiographic observation and density measurements (cooled specimens, 2,000 g, p less than 0.01) verified that barium sulfate does accumulate at the bottom of the centrifugation tubes. Thin sections of the bone cement revealed that only larger particles (20-100 micron) of barium sulfate were deposited at the bottom. No evidence of redistribution of antibiotics after centrifugation was seen. It is recommended that Simplex-P bone cement be reformulated to eliminate concern about inhomogeneities that arise from centrifugation. Further, it is recommended that cooled, centrifuged antibiotic cement be used for long-stem revision hip surgery, where longer setting times are necessary, and room temperature cement for "fresh" hip surgery. A total centrifuge time of two minutes with a 2,000 g maximum force is recommended.