gebhart/patrepeval huggingface dataset:
Mediation of Host Immune Responses after Immunization of Neonatal Calves with a Heat-Killed Mycobacterium avium subsp. paratuberculosis Vaccine (2011)

A major drawback of current whole-cell vaccines for Mycobacterium avium subsp. paratuberculosis is the interference with diagnostic tests for bovine tuberculosis (TB) and paratuberculosis. The current study was designed to explore the effects of immunization with a heat-killed whole-cell vaccine (Mycopar) on diagnostic test performance and to characterize host immune responses to vaccination over a 12-month period. Neonatal dairy calves were assigned to treatment groups consisting of (i) controls, not vaccinated (n = 5), and (ii) vaccinates, vaccinated with Mycopar vaccine (n = 5). The results from this study demonstrated a rapid initiation of M. avium subsp. paratuberculosis-specific gamma interferon (IFN-γ) in vaccinated calves by 7 days, with robust responses throughout the study. Vaccinated calves also had responses to M. bovis purified protein derivative tuberculin (BoPPD) but minimal reactivity to ESAT-6/CFP-10, an M. bovis recombinant fusion protein. The levels of antigen-specific interleukin-4 (IL-4) and IL-10 were markedly decreased in vaccinated calves between days 7 and 90 of the study but thereafter were similar to the levels in controls. Vaccinated calves began to seroconvert at 4 months, with 4/5 calves having detectable M. avium subsp. paratuberculosis antibody by 6 months. The responses in test platforms for bovine TB were negligible in the vaccinate group, as only one calf had a response, which was in the suspect range of the comparative cervical skin test. Serum antibody responses to M. bovis antigens ESAT-6, CFP-10, and MPB83 were negative on the Vet TB STAT-PAK, DPP VetTB, and DPP BovidTB tests. These results suggest that the Mycopar vaccine will interfere with diagnostic tools for paratuberculosis but result in low interference with the comparative cervical skin test and emerging serologic tests for M. bovis.
Intracerebroventricular amyloid-β antibodies reduce cerebral amyloid angiopathy and associated micro-hemorrhages in aged Tg2576 mice (2009)

Although immunization against amyloid-beta (Abeta) holds promise as a disease-modifying therapy for Alzheimer disease (AD), it is associated with an undesirable accumulation of amyloid in the cerebrovasculature [i.e., cerebral amyloid angiopathy (CAA)] and a heightened risk of micro-hemorrhages. The central and peripheral mechanisms postulated to modulate amyloid with anti-Abeta immunotherapy remain largely elusive. Here, we compared the effects of prolonged intracerebroventricular (i.c.v.) versus systemic delivery of anti-Abeta antibodies on the behavioral and pathological changes in an aged Tg2576 mouse model of AD. Prolonged i.c.v. infusions of anti-Abeta antibodies dose-dependently reduced the parenchymal plaque burden, astrogliosis, and dystrophic neurites at doses 10- to 50-fold lower than used with systemic delivery of the same antibody. Both i.c.v. and systemic anti-Abeta antibodies reversed the behavioral impairment in contextual fear conditioning. More importantly, unlike systemically delivered anti-Abeta antibodies that aggravated vascular pathology, i.c.v.-infused antibodies globally reduced CAA and associated micro-hemorrhages. We present data suggesting that the divergent effects of i.c.v.-delivered anti-Abeta antibodies result from gradually engaging the local (i.e., central) mechanisms for amyloid clearance, distinct from the mechanisms engaged by high doses of anti-Abeta antibodies that circulate in the vasculature following systemic delivery. With robust efficacy in reversing AD-related pathology and an unexpected benefit in reducing CAA and associated micro-hemorrhages, i.c.v.-targeted passive immunotherapy offers a promising therapeutic approach for the long-term management of AD.
Three-dimensional lithium-ion batteries with interdigitated electrodes (2013)

Secondary lithium-ion batteries have found multiple applications in portable electronics where high charge and discharge rates are not required to improve performance. However, lithium-ion batteries are currently being sought for high power applications that require long cycle life, such as those encountered in the transportation sector. To meet these performance requirements, the shortcomings that have relegated the use of conventional lithium-ion batteries to low-power applications need to be addressed. In an attempt to fabricate batteries with high power densities, current technology is moving toward electrode materials with irregular surfaces resulting in high interfacial surface areas and short characteristic lithium-ion diffusion lengths. The use of three-dimensional (3D) architectures with interdigitated electrodes with the above described electrode characteristics have been proposed to alleviate these shortcomings because it allows a significant decoupling of the inversely proportional relationship between energy and power density. This conference proceeding manuscript is focused on the idealized calculations of both nanowire and foam 3D architectures utilizing electrode and electrolyte components that are currently being developed. A brief discussion of the use of electrodeposition as the main synthetic technique towards realizing a truly 3D solid-state lithium-ion cell is also presented.
Functional effects of amino acid substitutions within the large binding pocket of the phosphotriesterase OpdA from<i>Agrobacterium</i>sp. P230 (2006)

The phosphotriesterase OpdA from Agrobacterium sp. P230 has about 10-fold higher activity for dimethyl organophosphate (OP) insecticides, than its homologue from Flavobacterium sp. ATCC27551, organophosphate hydrolase (OPH). OpdA shows about 10% amino acid sequence divergence from OPH and also has a 20 residue C-terminal extension. Here we show that the difference in kinetics is largely explained by just two amino acid differences between the two proteins. A truncated form of OpdA demonstrated that the C-terminal extension has no effect on its preference for dimethyl organophosphate substrates. Chimeric proteins of OPH and OpdA were then analysed to show that replacement of a central region of OpdA sequence, which encodes the residues in the large subsite of the active site, with the homologous region in OPH decreased the activity of OpdA towards dimethyl OPs, to values close to those for OPH. Site-directed mutagenesis in this region identified two differences between the proteins, Y257H and F272L (with the OpdA residues first) as being responsible for this reduction. These two differences were also responsible for the increased activity of OpdA towards the diisopropyl organophosphate, diisopropyl fluorophosphate, relative to OPH. Molecular modelling of triethyl phosphate in the active site of OpdA confirmed a reduction in the size of the large subsite relative to OPH.
Effect of a Low Work Function Insert on Hollow Cathode Temperature and Operation (2013)

Current state of the art hollow cathodes use traditional thermionic emission materials, such as lanthanum hexaboride (LaB6), cerium hexaboride (CeB6), and barium-calcium aluminate impregnated porous tungsten (Ba-W). The work functions of LaB6 and CeB6 are near 2.7 eV, while the work function of Ba-W is near 2.1 eV. Recently, a C12A7 electride hollow cathode was developed and operated. C12A7 electride is a crystalline ceramic in which electrons clathrated in sub-nanometer sized cages act as a conductive medium. Due to its unique atomic structure and large size, C12A7 electride has a predicted work function of 0.6 eV. A prototype C12A7 electride hollow cathode was successfully fabricated and operated as a proof-of-concept. It has been successfully started at room temperature without the benefit of a heater. The operation is stable and reproducible, and barrel temperatures below 600°C have been observed.
A Framework for Automatic Segmentation of Lung Nodules from Low Dose Chest CT Scans (2006)

To accurately separate each pulmonary nodule from its background in a low dose computer tomography (LDCT) chest image, two new adaptive probability models of the visual appearance of small 2D and large 3D pulmonary nodules are jointly used to control the evolution of the deformable model. The appearance prior is modeled with a translation and rotation invariant Markov-Gibbs random field of voxel intensities with pairwise interaction. The model is analytically identified from a set of training nodule images with normalized intensity ranges. Both the nodules and their background in each current multi-modal chest image are also modeled with a linear combination of discrete Gaussians that closely approximate the empirical marginal probability distribution of voxel intensities. Experiments with real LDCT chest images confirm the high accuracy of the proposed approach.
4D coronary artery reconstruction based on retrospectively gated rotational angiography: first in-human results (2007)

A method is proposed that allows for a fully automated computation of a series of high-resolution volumetric reconstructions of a patient's coronary arteries based on a single rotational acquisition. During the 7.2 second acquisition the coronary arteries are injected with contrast material while the imaging system rotates around the patient to obtain a series of X-ray projection images over an angular range of 180 degrees. Based on the simultaneously recorded ECG-signal the projection images corresponding to the same cardiac cycle can be utilized to reconstruct three-dimensional (3D) high-spatial-resolution angiograms of the coronary arteries in multiple (3D+t) cardiac phases within the cardiac cycle. The proposed acquisition protocol has been applied to 22 patients and the tomograpic reconstructions depicted the main arteries as well as the main bifurcations in multiple cardiac phases in all enrolled patients. For the first time, this feasibility study shows that a three-dimensional description of the coronary arteries can be obtained intraprocedurally in a conventional interventional suite by means of tomographic reconstruction from projection images without any user interaction.
Cavity-Enhanced Direct Frequency Comb Spectroscopy: Technology and Applications (2010)

Cavity-enhanced direct frequency comb spectroscopy combines broad bandwidth, high spectral resolution, and ultrahigh detection sensitivity in one experimental platform based on an optical frequency comb efficiently coupled to a high-finesse cavity. The effective interaction length between light and matter is increased by the cavity, massively enhancing the sensitivity for measurement of optical losses. Individual comb components act as independent detection channels across a broad spectral window, providing rapid parallel processing. In this review we discuss the principles, the technology, and the first applications that demonstrate the enormous potential of this spectroscopic method. In particular, we describe various frequency comb sources, techniques for efficient coupling between comb and cavity, and detection schemes that utilize the technique's high-resolution, wide-bandwidth, and fast data-acquisition capabilities. We discuss a range of applications, including breath analysis for medical diagnosis, trace-impurity detection in specialty gases, and characterization of a supersonic jet of cold molecules.
Wireless gas detection with a smartphone via rf communication (2014)

Chemical sensing is of critical importance to human health, safety, and security, yet it is not broadly implemented because existing sensors often require trained personnel, expensive and bulky equipment, and have large power requirements. This study reports the development of a smartphone-based sensing strategy that employs chemiresponsive nanomaterials integrated into the circuitry of commercial near-field communication tags to achieve non-line-of-sight, portable, and inexpensive detection and discrimination of gas-phase chemicals (e.g., ammonia, hydrogen peroxide, cyclohexanone, and water) at part-per-thousand and part-per-million concentrations.
Amylin Receptor: A Common Pathophysiological Target in Alzheimer’s Disease and Diabetes Mellitus (2013)

Amylin (islet amyloid polypeptide) and amyloid-beta (Aβ) protein, which are deposited within pancreatic islets of diabetics and brains of Alzheimer's patients respectively, share many biophysical and physiological properties. Emerging evidence indicates that the amylin receptor is a putative target receptor for the actions of human amylin and Aβ in the brain. The amylin receptor consists of the calcitonin receptor dimerized with a receptor activity-modifying protein and is widely distributed within central nervous system. Both amylin and Aβ directly activate this G protein-coupled receptor and trigger multiple common intracellular signal transduction pathways that can culminate in apoptotic cell death. Moreover, amylin receptor antagonists can block both the biological and neurotoxic effects of human amylin and Aβ. Amylin receptors thus appear to be involved in the pathophysiology of Alzheimer's disease and diabetes, and could serve as a molecular link between the two conditions that are associated epidemiologically.
Controlled removal of hydrogen atoms from H-terminated silicon surfaces (2020)

The controlled formation of dangling bond structures on a H-terminated silicon surface is the first step in an atomically precise method of fabrication of silicon quantum electronic devices. An ultrahigh vacuum scanning tunneling microscope (STM) tip is used to selectively desorb hydrogen atoms from a Si(100)-2×1:H surface by injecting electrons with the sample held at a positive bias voltage. The authors propose a lithography method that allows the STM to operate under negative bias imaging conditions and simultaneously desorb H atoms as required. A high frequency signal is added to the negative bias voltage to deliver the required energy for hydrogen removal. The resulting current at this frequency and its harmonics are filtered to minimize their effect on the operation of the STM’s feedback control loop. The authors show that the chance of tip-sample crash during the lithography process is reduced by employing this method. They also demonstrate that this approach offers a significant potential for controlled and precise removal of H atoms from a H-terminated silicon surface and thus may be used for the fabrication of practical silicon-based atomic-scale devices.
STAT5 programs a distinct subset of GM-CSF-producing T helper cells that is essential for autoimmune neuroinflammation (2014)

T helper (TH)-cell subsets, such as TH1 and TH17, mediate inflammation in both peripheral tissues and central nervous system. Here we show that STAT5 is required for T helper-cell pathogenicity in autoimmune neuroinflammation but not in experimental colitis. Although STAT5 promotes regulatory T cell generation and immune suppression, loss of STAT5 in CD4+ T cells resulted in diminished development of experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis. Our results showed that loss of encephalitogenic activity of STAT5-deficient autoreactive CD4+ T cells was independent of IFN-γ or interleukin 17 (IL-17) production, but was due to the impaired expression of granulocyte-macrophage colony-stimulating factor (GM-CSF), a crucial mediator of T-cell pathogenicity. We further showed that IL-7-activated STAT5 promotes the generation of GM-CSF-producing CD4+ T cells, which were preferentially able to induce more severe EAE than TH17 or TH1 cells. Consistent with GM-CSF-producing cells being a distinct subset of TH cells, the differentiation program of these cells was distinct from that of TH17 or TH1 cells. We further found that IL-3 was secreted in a similar pattern as GM-CSF in this subset of TH cells. In conclusion, the IL-7-STAT5 axis promotes the generation of GM-CSF/IL-3-producing TH cells. These cells display a distinct transcriptional profile and may represent a novel subset of T helper cells which we designate as TH-GM.
A Tikhonov Regularization Scheme for Focus Rotations With Focused Ultrasound-Phased Arrays (2016)

Phased arrays have a wide range of applications in focused ultrasound therapy. By using an array of individually driven transducer elements, it is possible to steer a focus through space electronically and compensate for acoustically heterogeneous media with phase delays. In this paper, the concept of focusing an ultrasound-phased array is expanded to include a method to control the orientation of the focus using a Tikhonov regularization scheme. It is then shown that the Tikhonov regularization parameter used to solve the ill-posed focus rotation problem plays an important role in the balance between quality focusing and array efficiency. Finally, the technique is applied to the synthesis of multiple foci, showing that this method allows for multiple independent spatial rotations.
Identification of a MADS‐box gene, <i>FLOWERING LOCUS M</i>, that represses flowering (2001)

The timing of flowering is important for the reproductive success of plants. Here we describe the identification and characterization of a new MADS-box gene, FLOWERING LOCUS M (FLM), which is involved in the transition from vegetative to reproductive development. FLM is similar in amino-acid sequence to FLC, another MADS-box gene involved in flowering-time control. flm mutants are early flowering in both inductive and non-inductive photoperiods, and flowering time is sensitive to FLM dosage. FLM overexpression produces late-flowering plants. Thus FLM acts as an inhibitor of flowering. FLM is expressed in areas of cell division such as root and shoot apical regions and leaf primordia.
Implementation of hexagonal micromirror arrays as phase-mostly spatial light modulators (1995)

Hexagonal micromirror arrays and associated test structures have been fabricated using a commercial surface-micromachining process. The hexagonal micromirrors are 50 micrometers across and are arranged in a hexagonal array of 127 mirrors with 75 micrometers center-to-center spacing between nearest micromirrors. Each micromirror is supported by three flexure hinges, each of which surrounds one third of the micromirror perimeter. Each micromirror in the array can be displaced independently through a vertical distance of over 1 micrometers by a voltage applied to an underlying address electrode. The flexures and other highly diffracting or poorly reflecting areas can be covered by a statinary reflecting plate with holes that expose the moving micromirrors. These micromirror arrays function as efficient phase-mostly spatial light modulators. Applications for these micro-opto-electro-mechanical systems include optical processing, coherent beam shaping, and adaptive optics. This design has several important advantages. First, the hexagonal micromirror and array geometries maximize the active surface area of the array. Second, the use of three flexures instead of four, as is typical for square phase-mostly micromirrors, lowers the required drive voltage. Third, the reflecting cover plate ensures that light efficiency is maximized and that a substantial stationary coherent reference plane is provided. Design considerations for fabricating the arrays in commercial surface mciromachining processes are discussed. The deflection versus voltage behavior of the hexagonal micromirror is determined analytically and experimentally. Test results are used to design the next generation array.
Antigen-Independent Differentiation and Maintenance of Effector-like Resident Memory T Cells in Tissues (2012)

Differentiation and maintenance of recirculating effector memory CD8 T cells (T(EM)) depends on prolonged cognate Ag stimulation. Whether similar pathways of differentiation exist for recently identified tissue-resident effector memory T cells (T(RM)), which contribute to rapid local protection upon pathogen re-exposure, is unknown. Memory CD8αβ(+) T cells within small intestine epithelium are well-characterized examples of T(RM), and they maintain a long-lived effector-like phenotype that is highly suggestive of persistent Ag stimulation. This study sought to define the sources and requirements for prolonged Ag stimulation in programming this differentiation state, including local stimulation via cognate or cross-reactive Ags derived from pathogens, microbial flora, or dietary proteins. Contrary to expectations, we found that prolonged cognate Ag stimulation was dispensable for intestinal T(RM) ontogeny. In fact, chronic antigenic stimulation skewed differentiation away from the canonical intestinal T cell phenotype. Resident memory signatures, CD69 and CD103, were expressed in many nonlymphoid tissues including intestine, stomach, kidney, reproductive tract, pancreas, brain, heart, and salivary gland and could be driven by cytokines. Moreover, TGF-β-driven CD103 expression was required for T(RM) maintenance within intestinal epithelium in vivo. Thus, induction and maintenance of long-lived effector-like intestinal T(RM) differed from classic models of T(EM) ontogeny and were programmed through a novel location-dependent pathway that was required for the persistence of local immunological memory.
Privacy and Regression Model Preserved Learning (2014)

Sensitive data such as medical records and business reports usually contains valuable information that can be used to build prediction models. However, designing learning models by directly using sensitive data might result in severe privacy and copyright issues. In this paper, we propose a novel matrix completion based framework that aims to tackle two challenging issues simultaneously: i) handling missing and noisy sensitive data, and ii) preserving the privacy of the sensitive data during the learning process. In particular, the proposed framework is able to mask the sensitive data while ensuring that the transformed data are still usable for training regression models. We show that two key properties, namely model preserving and privacy preserving, are satisfied by the transformed data obtained from the proposed framework. In model preserving, we guarantee that the linear regression model built from the masked data approximates the regression model learned from the original data in a perfect way. In privacy preserving, we ensure that the original sensitive data cannot be recovered since the transformation procedure is irreversible. Given these two characteristics, the transformed data can be safely released to any learners for designing prediction models without revealing any private content. Our empirical studies with a synthesized dataset and multiple sensitive benchmark datasets verify our theoretical claim as well as the effectiveness of the proposed framework.
Malolactic Fermentation in Wine by Direct Inoculation with Freeze-Dried<i>Leuconostoc oenos</i>Cultures (1996)

The identification of 850 bacterial isolates collected from French, Portuguese, Italian, and Spanish wines undergoing malolactic fermentation showed that 77% belonged to the species <i>Leuconostoc oenos</i>. Hybridization of total bacterial DNA using phage DNA as probe indicated that 80% of the <i>L. oenos</i> isolates were lysogenic. <i>L. oenos</i> strains were selected for growth in wine with low pH and high ethanol concentration by use of a turbidostat and further screened for their ability to maintain the adaptation to the wine environment during propagation, freezing, and freeze-drying. Several of the selected freeze-dried strains survived 100% the direct inoculation into commercial wines where they started to grow without a lag phase. The immediate survival and the lag phase of the inoculated bacteria strongly influenced the total duration of the malolactic fermentation. Cultures for direct inoculation may substantially improve the management of malolactic fermentation in winemaking.