gebhart/patrepeval huggingface dataset:
Determination of Intrinsic Magnetic Response from Local Measurements of Fringing Fields (2014)

Micron-sized Hall bars and micro-SQUIDs are now used routinely to measure the local static and dynamic magnetic response with micron-scale spatial resolution. While this provides a powerful new tool, determining the intrinsic magnetization presents new challenges, as it requires correcting for demagnetization fields that vary widely with position on a sample. In this paper we develop a method to correct for the demagnetization effect at local points of a rectangular prism shaped sample using a finite element analysis of Maxwell's equation applied to local Hall sensor measurements calibrated by bulk measurements of the magnetization. This method can be generalized to other geometric shapes to analyze data obtained with local magnetic probes.
Ability of different chemically modified heparins to potentiate the biological activity of heparin-binding growth factor 1. Lack of correlation with growth factor binding (1992)

A range of chemically modified heparins was examined for their ability to bind heparin-binding growth factor 1 (HBGF-1; acidic fibroblast growth factor) and potentiate the in vitro mitogenic and neurotrophic activity of HBGF-1. It was found that carboxyl-reduced heparin bound HBGF-1 as effectively as the native heparin molecule. Totally desulfated heparin and N-desulfated heparin lack HBGF-1-binding capacity, and substitution of the exposed amino group with acetyl or acetoacetyl groups only partially restored binding capacity, indicating that N-sulfates only play a limited role in growth factor binding. However, the failure of totally desulfated, N-resulfated heparin to interact with HBGF-1 demonstrated that N-sulfates alone are insufficient and ester sulfates are absolutely essential for HBGF-1 binding. In contrast, the ability of the modified heparins to potentiate the mitogenic activity of HBGF-1 correlated only to a limited extent with their affinity for HBGF-1. Thus, the carboxyl-reduced molecule which displayed similar affinity for HBGF-1 as native heparin was consistently less potent in augmenting mitogenesis. Similarly, the N-acetylated and the N-acetoacetylated species, which had much lower affinity for HBGF-1 than the carboxyl-reduced molecule, conferred similar biological activity to HBGF-1 whereas N-desulfated heparin, which was unable to bind growth factor, potentiated the mitogenic activity of HBGF-1 for both 3T3 and HUVE cells. In contrast, the neurotrophic activity of HBGF-1 was potentiated by modified heparin species which failed to bind HBGF-1 and were without activity in the mitogenic assays.(ABSTRACT TRUNCATED AT 250 WORDS)
Investigation of Compression and Buckling Properties of a Novel Surface-Based Lattice Structure Manufactured Using Multi Jet Fusion Technology (2021)

Lattice structures possess many superior properties over solid materials and conventional structures. Application-oriented lattice structure designs have become a choice in many industries, such as aerospace, automotive applications, construction, biomedical applications, and footwear. However, numerical and empirical analyses are required to predict mechanical behavior under different boundary conditions. In this article, a novel surface-based structure named O-surface structure is designed and inspired by existing Triply Periodic Minimal Surface morphologies in a particular sea urchin structure. For comparison, both structures were designed with two different height configurations and investigated for mechanical performance in terms of compression, local buckling, global buckling, and post-buckling behavior. Both simulation and experimental methods were carried out to reveal these aforementioned properties of samples fabricated by multi jet fusion technology. The sea urchin structure exhibited better mechanical strength than its counterpart, with the same relative density almost two-folds higher in the compressive response. However, the O-surface structure recorded more excellent energy absorption and flexible behavior under compression. Additionally, the compression behavior of the O-surface structure was progressive from top to bottom. In contrast, the sea urchin structure was collapsed randomly due to originated cracks from unit cells' centers with local buckling effects. Moreover, the buckling direction of structures in long columns was also affected by keeping the relative density constant. Finally, based on specific strength, the O-surface structure exhibited 16-folds higher specific strength than the sea urchin structure.
Stretching deep architectures for text recognition (2015)

In recent years, many deep architectures have been proposed for handwritten text recognition. However, most of the previous deep models need large scale training data and a long training time to obtain good results. In this paper, we propose a novel deep learning method based on “stretching” the projection matrices of stacked feature learning models. We call the proposed method “stretching deep architectures” (or SDA). In the implementation of SDA, stacked feature learning models are first learned layer by layer, and then the stretching technique is applied on the weight matrices between successive layers. As the feature learning models can be efficiently optimized and the stretching results can be easily computed, the training of SDA is very fast and no back propagation is needed. We have tested SDA on handwritten digits recognition, Arabic subword recognition and English letter recognition tasks. Extensive experiments demonstrate that SDA performs not only better than shallow feature learning models, but also state-of-the-art deep learning models.
RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 Special Issue, Preface (2011)

Over the past ten years, the study of cell regulatory processes and their integration within complex “systems-level” models of cell physiology and cell pathology has flourished, with geometric increases in scientific publications and impact on biology. Within the broad spectrum of molecular biology disciplines, systems biology and regulatory genomics are perhaps the ones that have been most characterized by seamless and unique integration of computational and experimental sciences, allowing rapid transformation of high-throughput data into complex computational models, of models into testable hypotheses, and finally of hypotheses into knowledge via experimental validation. Today, these disciplines are achieving maturity, as demonstrated by the creation of several university departments, centers, and institutes dedicated to their study and by the popularity and growth of meetings such as the RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges. This event, which is currently in its third edition as a joint meeting, is particularly relevant as it combines unique computational and experimental perspectives, while also establishing a unique frame of reference—via the DREAM challenges—to objectively gauge the progress of our ability to dissect regulatory networks and to model biological processes.After two highly successful previous meetings at the Broad Institute, the 3rd edition of the Joint RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges was held at Columbia University, November 16–20, 2010. The conference brought together computational and experimental scientists to discuss current research directions, latest findings, and establish new collaborations towards a systems-level understanding of gene regulation and modeling of biological systems. The conference included oral presentations from accepted full-length manuscripts and high-quality abstracts, as well as 14 invited presentations from leaders in the field. Accepted full-length manuscripts that constitute significant theoretical advances to the fields of systems biology and regulatory genomics have been combined in a collection that is presented in the current issue of the Journal of Computational Biology.
Proteomics of Aspergillus fumigatus Conidia-containing Phagolysosomes Identifies Processes Governing Immune Evasion (2018)

Invasive infections by the human pathogenic fungus <i>Aspergillus fumigatus</i> start with the outgrowth of asexual, airborne spores (conidia) into the lung tissue of immunocompromised patients. The resident alveolar macrophages phagocytose conidia, which end up in phagolysosomes. However, <i>A. fumigatus</i> conidia resist phagocytic degradation to a certain degree. This is mainly attributable to the pigment 1,8-dihydroxynaphthalene (DHN) melanin located in the cell wall of conidia, which manipulates the phagolysosomal maturation and prevents their intracellular killing. To get insight in the underlying molecular mechanisms, we comparatively analyzed proteins of mouse macrophage phagolysosomes containing melanized wild-type (wt) or nonmelanized <i>pksP</i> mutant conidia. For this purpose, a protocol to isolate conidia-containing phagolysosomes was established and a reference protein map of phagolysosomes was generated. We identified 637 host and 22 <i>A. fumigatus</i> proteins that were differentially abundant in the phagolysosome. 472 of the host proteins were overrepresented in the <i>pksP</i> mutant and 165 in the wt conidia-containing phagolysosome. Eight of the fungal proteins were produced only in <i>pksP</i> mutant and 14 proteins in wt conidia-containing phagolysosomes. Bioinformatical analysis compiled a regulatory module, which indicates host processes affected by the fungus. These processes include vATPase-driven phagolysosomal acidification, Rab5 and Vamp8-dependent endocytic trafficking, signaling pathways, as well as recruitment of the Lamp1 phagolysosomal maturation marker and the lysosomal cysteine protease cathepsin Z. Western blotting and immunofluorescence analyses confirmed the proteome data and moreover showed differential abundance of the major metabolic regulator mTOR. Taken together, with the help of a protocol optimized to isolate <i>A. fumigatus</i> conidia-containing phagolysosomes and a potent bioinformatics algorithm, we were able to confirm <i>A. fumigatus</i> conidia-dependent modification of phagolysosomal processes that have been described before and beyond that, identify pathways that have not been implicated in <i>A. fumigatus</i> evasion strategy, yet.Mass spectrometry proteomics data are available <i>via</i> ProteomeXchange with identifiers PXD005724 and PXD006134.
Pronounced muscle deoxygenation during supramaximal exercise under simulated hypoxia in sprint athletes. (2008)

The purpose of this study was to determine whether acute hypoxia alters the deoxygenation level in vastus lateralis muscle during a 30 s Wingate test, and to compare the muscle deoxygenation level between sprint athletes and untrained men. Nine male track sprinters (athletic group, VO2max 62.5 ± 4.1 ml/kg/min) and 9 healthy untrained men (untrained group, VO2max 49.9 ± 5.2 ml·kg(-1)·min(-1)) performed a 30 s Wingate test under simulated hypoxic (FIO2 = 0.164 and PIO2 = 114 mmHg) and normoxic conditions. During the exercise, changes in oxygenated hemoglobin (OxyHb) in the vastus lateralis were measured using near infrared continuous wave spectroscopy. Decline in OxyHb, that is muscle deoxygenation, was expressed as percent change from baseline. Percutaneous arterial oxygen saturation (SpO2), oxygen uptake (VO2), and ventilation (VE) were measured continuously. In both groups, there was significantly greater muscle deoxygenation, lower SpO2, lower peakVO2, and higher peakVE during supramaximal exercise under hypoxia than under normoxia, but no differences in peak and mean power output during the exercise. Under hypoxia, the athletic group experienced significantly greater muscle deoxygenation, lower SpO2, greater decrement in peakVO2 and increment in peakVE during the exercise than the untrained group. When the athletic and untrained groups were pooled, the increment of muscle deoxygenation was strongly correlated with lowest SpO2 in the 30 s Wingate test under hypoxia. These results suggest that acute exposure to hypoxia causes a greater degree of peripheral muscle deoxygenation during supramaximal exercise, especially in sprint athletes, and this physiological response would be explained mainly by lower arterial oxygen saturation. Key pointsThe deoxygenation trends in the vastus lateralis muscle during 30 s Wingate test in track sprinters and untrained men under simulated hypoxic and normoxic conditions was investigated using near infrared spectroscopy.Acute hypoxia caused a greater degree of peripheral muscle deoxygenation than normoxia, whereas there were no changes in performance such as power output during 30 s Wingate test.Sprint athletes show a greater degree of peripheral muscle deoxygenation during 30 s Wingate test in hypoxia when compared with untrained subjects.A larger difference in muscle deoxygenation between hypoxia and normoxia is accompanied by lowest SpO2 at the 30 s Wingate test in hypoxia.
Dyads and dyadics (2014)

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CT myelography for outpatients. An inpatient/outpatient pilot study to assess methodology. (1985)

The diagnostic usefulness, limitations, and adverse reactions associated with computed tomographic myelography using metrizamide were assessed for broad outpatient application. The initial approach was to examine inpatients (n = 38) with low-dose metrizamide (100 mgI/ml). This low dose was believed less likely to be associated with side effects. They were then treated as if they were outpatients, with the liberties this entailed. The consequences of needle puncture were minimized by using a 25-gauge disposable needle. Thirty-four (89%) patients remained free of side effects after the procedure. Subsequently, this technique was extended to 42 outpatients, 38 (90.5%) of whom remained asymptomatic. For comparison, 170 mgI/ml was used in another 25 outpatients, who evidenced more symptoms. The potential medical, economic, and therapeutic benefits of obviating hospitalization by safer outpatient CT myelography seem clear.
Exploring the Type 2 Diabetes Mellitus Experience from the Patient Perspective (2018)

Introduction: Type 2 diabetes mellitus (T2DM) exacts tremendous burdens on the patient and patient-focused qualitative research can yield data to deepen our understanding of the individual disease experience. Methods: Research was conducted to illustrate the T2DM patient experience ranging from its proximal signs/symptoms to its distal impacts (e.g., the disease’s impact on physical, social, or emotional functioning). A targeted literature review, meetings with therapeutic experts, and qualitative concept elicitation interviews with T2DM patients were conducted, and results were thematically analyzed and then harmonized into a conceptual model to organize the sign, symptom, and disease-related impact experiences most relevant to T2DM. Results: A total of 38 unique sign/symptom and 62 impact concepts of T2DM were identified across the reviewed literature (N=26 publications), expert advice meetings (N=13), and patient interviews (N=20, mean age=60.5±9.5 years, 45% female). The signs/symptoms most frequently reported by patients were tiredness (n=16), dizziness (n=10), and neuropathy-related (n=10), while experts reported excessive thirst (n=12), frequent urination (n=11), and vision problems (n=11) most frequently. For disease impacts, the concepts most frequently reported by both experts and patients were the need to modify diet (n=11 and n=20, respectively), implement an exercise regimen (n=13 and n=17, respectively), and monitor glucose more frequently (n=10 and n=16, respectively). The most bothersome signs/symptoms reported by patients were neuropathy-related (n=8), tiredness (n=5), and vision disorders (n=4). Conclusions: Patients with T2DM experience many signs, symptoms, and impacts that if improved could give meaningful treatment benefit. Data generated from this research could be used by researchers and healthcare providers to identify treatment outcomes and inform the target concepts of T2DM questionnaires to reliably assess those outcomes. Disclosure K. Yu-Isenberg: Employee; Self; Intarcia Therapeutics, Inc. G.D. Gray: Employee; Self; Servier Global Medical Affairs. C. Foley: Consultant; Self; Intarcia Therapeutics, Inc., Servier. J.T. Stokes: None. A. Shields: Consultant; Self; Intarcia Therapeutics, Inc. G. Dickie: Consultant; Self; Intarcia Therapeutics, Inc. R. Lamoureux: Research Support; Self; Intarcia Therapeutics, Inc.. C.V. Jackson: None. B. Padilla: None. W. Polonsky: Consultant; Self; Abbott, AstraZeneca, Dexcom, Inc., Sanofi, Novo Nordisk Inc., Eli Lilly and Company, Intarcia Therapeutics, Inc., Servier, Ascensia Diabetes Care, Merck &amp; Co., Inc., MannKind Corporation, Glooko, Inc., Roche Diabetes Care Health and Digital Solutions.
Thin-film Growth and Device Fabrication of Iron-based Superconductors (2017)

Iron-based superconductors have been receiving much attention as a new family of high-critical temperature superconductors since 2008 owing to their unique properties and distinct difference from cuprates and conventional superconductors. This paper reviews our research on iron-based superconductors' thin-film with an emphasis on growth, critical current properties, and device fabrication.
Dynamic noise-feedback and mode-coupling mechanism silences the VCXOS phase noise (2008)

Frequency reference standards are essential to achieving frequency accuracy and phase stability in electronic systems. Such reference standards require the chief characteristics of low phase noise and good frequency stability. The best oscillator performance can be expensive. The novel approach (noise-feedback and mode-coupling mechanism) reported in this paper optimizes the performance of voltage-controlled crystal oscillators (VCXOs), even those with relative low <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> resonators, for low phase noise and good frequency stability. The typical measured phase noise for 120 MHz VCXO is typically -138 dBc/Hz at 100 Hz offset from the carrier, and to author knowledge, this is the best phase noise performance for this class of VCXO so far reported.
Synthesis of (−)‐DAPD (2004)

A new synthesis of (-)-DAPD, suitable for large scale development, is described.
The Role of Metal Nanoparticles in Remote Release of Encapsulated Materials (2005)

Laser mediated remote release of encapsulated fluorescently labeled polymers from nanoengineered polyelectrolyte multilayer capsules containing gold sulfide core/gold shell nanoparticles in their walls is observed in real time on a single capsule level. We have developed a method for measuring the temperature increase and have quantitatively investigated the influence of absorption, size, and surface density of metal nanoparticles using an analytical model. Experimental measurements and numerical simulations agree with the model. The treatment presented in this work is of general nature, and it is applicable to any system where nanoparticles are used as absorbing centers. Potential biomedical applications are highlighted.
Near Infrared Folate-Targeted, Intraoperative Visualization of Pituitary Adenoma (2017)

Introduction: Pituitary adenomas account for ~10% of intracranial tumors and have an estimated prevalence of 15–20% in the general US population. Surgical resection is the primary treatment for pituitary adenomas and the trans-sphenoidal approach remains the most common route. However, recurrence of tumor is seen in up to 20% of surgical cases and intraoperative magnetic resonance imaging is expensive and not readily available. Because some pituitary adenomas are known to overexpress folate receptor α (FRα), we hypothesized that a folate analog conjugated to a near infrared (NIR) fluorescent dye could provide increased optical contrast for margin detection. We present preliminary results of this novel clinical trial.
Structure and antitumor activity of a .BETA.-1,3-glucan isolated from the culture filtrate of Sclerotinia sclerotiorum IFO 9395. (1986)

An antitumor glucan (SSG) was isolated from the culture filtrate of Sclerotinia sclerotiorum IFO 9395 by sequential use of ethanol precipitation, ion exchange chromatography on diethyl-aminoethyl-Sephadex A-25, and precipitation with ammonium sulfate. From the results of methylation analysis and carbon-13 nuclear magnetic resonance spectroscopy, SSG was concluded to be a β-1, 3-D-glucan branched at position 6 of every two 3-substituted β-glucosyl units. SSG formed a complex with congo red in dilute alkali solution, and showed potent antitumor activity against the solid form of sarcoma 180 in ICR mice.
ChemInform Abstract: An Effective Method for the Preparation of Chiral Polyoxy 8‐Membered Ring Enone Corresponding to the B Ring of Taxol. (2001)

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.
Graph-CoVis: GNN-based Multi-view Panorama Global Pose Estimation (2023)

In this paper, we address the problem of wide-baseline camera pose estimation from a group of 360° panoramas under upright-camera assumption. Recent work has demonstrated the merit of deep-learning for end-to-end direct relative pose regression in 360° panorama pairs [11]. To exploit the benefits of multi-view logic in a learning-based framework, we introduce Graph-CoVis, which non-trivially extends CoVisPose [11] from relative two-view to global multi-view spherical camera pose estimation. Graph-CoVis is a novel Graph Neural Network based architecture that jointly learns the co-visible structure and global motion in an end-to-end and fully-supervised approach. Using the ZInD [4] dataset, which features real homes presenting wide-baselines, occlusion, and limited visual overlap, we show that our model performs competitively to state-of-the-art approaches.
Towards multivalent CD1d ligands: synthesis and biological activity of homodimeric α-galactosyl ceramide analogues (2012)

A library of dimeric CD1d ligands, containing two α-galactosyl ceramide (α-GalCer) units linked by spacers of varying lengths has been synthesised. The key dimerisation reactions were carried out via copper-catalysed click reactions between a 6"-azido-6"-deoxy-α-galactosyl ceramide derivative and various diynes. Each α-GalCer dimer was tested for its ability to stimulate iNKT cells.