gebhart/patrepeval huggingface dataset:
Epidemiology of Thyroid Dysgenesis: The Familial Component (2010)

The pathophysiology of thyroid dysgenesis remains unclear and, until recently, this disorder was generally regarded as sporadic. However, a small but significant proportion of familial cases have been identified (2%) through the study of subjects with congenital hypothyroidism, and more recent work has revealed an even higher proportion of familial thyroid dysgenesis in both symptomatic and asymptomatic individuals. These studies strongly suggest the existence of a familial component of this disorder involving dominant genetic predisposition factors with a low penetrance.
Gata3ZsG and Gata3ZsG-fl: Novel murine Gata3 reporter alleles for identifying and studying Th2 cells and ILC2s in vivo (2022)

T helper-2 (Th2) cells and type 2 innate lymphoid cells (ILC2s) play crucial roles during type 2 immune responses; the transcription factor GATA3 is essential for the differentiation and functions of these cell types. It has been demonstrated that GATA3 is critical for maintaining Th2 and ILC2 phenotype <i>in vitro</i>; GATA3 not only positively regulates type 2 lymphocyte-associated genes, it also negatively regulates many genes associated with other lineages. However, such functions cannot be easily verified <i>in vivo</i> because the expression of the markers for identifying Th2 and ILC2s depends on GATA3. Thus, whether Th2 cells and ILC2s disappear after <i>Gata3</i> deletion or these <i>Gata3</i>-deleted "Th2 cells" or "ILC2s" acquire an alternative lineage fate is unknown. In this study, we generated novel GATA3 reporter mouse strains carrying the <i>Gata3</i> <sup>ZsG</sup> or <i>Gata3</i> <sup>ZsG-fl</sup> allele. This was achieved by inserting a ZsGreen-T2A cassette at the translation initiation site of either the wild type <i>Gata3</i> allele or the modified <i>Gata3</i> allele which carries two <i>loxP</i> sites flanking the exon 4. ZsGreen faithfully reflected the endogenous GATA3 protein expression in Th2 cells and ILC2s both <i>in vitro</i> and <i>in vivo</i>. These reporter mice also allowed us to visualize Th2 cells and ILC2s <i>in vivo</i>. An inducible <i>Gata3</i> deletion system was created by crossing <i>Gata3</i> <sup>ZsG-fl/fl</sup> mice with a tamoxifen-inducible Cre. Continuous expression of ZsGreen even after the <i>Gata3</i> exon 4 deletion was noted, which allows us to isolate and monitor GATA3-deficient "Th2" cells and "ILC2s" during <i>in vivo</i> immune responses. Our results not only indicated that functional GATA3 is dispensable for regulating its own expression in mature type 2 lymphocytes, but also revealed that GATA3-deficient "ILC2s" might be much more stable <i>in vivo</i> than <i>in vitro</i>. Overall, the generation of these novel GATA3 reporters will provide valuable research tools to the scientific community in investigating type 2 immune responses <i>in vivo</i>.
n-Channel Polymers by Design: Optimizing the Interplay of Solubilizing Substituents, Crystal Packing, and Field-Effect Transistor Characteristics in Polymeric Bithiophene-Imide Semiconductors (2008)

Electron transporting (n-channel) polymer semiconductors for field-effect transistors are rare. In this investigation, the synthesis and characterization of new electron-depleted N-alkyl-2,2'-bithiophene-3,3'-dicarboximide-based pi-conjugated homopolymers and copolymers containing the 2,2'-bithiophene unit are reported. A novel design approach is employed using computational modeling to identify favorable monomer properties such as core planarity, solubilizing substituent tailorability, and appropriate electron affinity with gratifying results. Monomeric model compounds are synthesized to confirm these properties, and a crystal structure reveals a short 3.43 A pi-pi stacking distance with favorable solubilizing substituent orientations. A family of 10 homopolymers and bithiophene copolymers is then synthesized via Yamamoto and Stille polymerizations, respectively. Two of these polymers are processable in common organic solvents: the homopolymer poly(N-(2-octyldodecyl)-2,2'-bithiophene-3,3'-dicarboximide) (P1) exhibits n-channel FET activity, and the copolymer poly(N-(2-octyldodecyl)-2,2':5',2'':5'',2'''-quaterthiophene-3,3'-dicarboximide) (P2) exhibits air-stable p-channel FET operation. After annealing, P1 films exhibit a very high degree of crystallinity and an electron mobility > 0.01 cm (2) V(-1) s(-1) with a current on-off ratio of 10 (7), which is remarkably independent of film-deposition conditions. Extraordinarily, P1 films also exhibit terracing in AFM images with a step height matching the X-ray diffraction d spacing, a rare phenomenon for polymeric organic semiconductors. Another fascinating property of these materials is the air-stable p-channel FET performance of annealed P2 films, which exhibit a hole mobility of approximately 0.01 cm(2) V(-1) s(-1) and a current on-off ratio of 10(7).
SenseWeb: Browsing the Physical World in Real Time (2006)

Geo-centric web interface such as MSN Virtual Earth (http://local.live.com) and Google Maps (http://maps.google.com) are useful to visualize spatially and geographically related data such as addresses, neighborhoods, weather, traffic, and so on. Desires to augment additional useful information to these interfaces have led people to create custom applications that overlay their own data on top of browsable maps. Examples of such applications overlay housing information (http://www.housingmaps.com) and crime-rate data (http://www.chicagocrime.org/map/) on Google maps, locations of vehicles (http://jprestonsystems.2mydns.com/ vemap.aspx?name=demoacct2) and podcasters (http://www.podlook.com/map.aspx) on MSN Virtual Earth, weather data on custom maps (http://www.wunderground.com), etc. Such applications have been possible after Google Maps and MSN Virtual Earth have published useful APIs to overlay location data on their maps. We envision publishing and querying real-time data (e.g., from sensors) over such geo-centric web interfaces. Existing solutions, although useful to write simple applications as above, have several drawbacks in achieving this vision. First, publishing even a single stream of data as a useful service is a nontrivial task. Many useful data is not being published yet because the data owners do not have enough programming expertise, or publishing it requires too much effort. Second, all the existing applications are mutually incompatible. One can’t bring up a single map that shows both the housing information and crimerates in an area. Third, existing solutions do not provide useful primitives such as querying live sensors based on keywords or location and aggregating the results in useful ways. The SenseWeb project at Microsoft Research Figure 1: SenseWeb Architecture.
The influences of stomatal size and density on rice abiotic stress resilience (2023)

A warming climate coupled with reductions in water availability and rising salinity are increasingly affecting rice (Oryza sativa) yields. Elevated temperatures combined with vapour pressure deficit (VPD) rises are causing stomatal closure, further reducing plant productivity and cooling. It is unclear what stomatal size (SS) and stomatal density (SD) will best suit all these environmental extremes. To understand how stomatal differences contribute to rice abiotic stress resilience, we screened the stomatal characteristics of 72 traditionally bred varieties. We found significant variation in SS, SD and calculated anatomical maximal stomatal conductance (g<sub>smax</sub> ) but did not identify any varieties with SD and g<sub>smax</sub> as low as transgenic OsEPF1oe plants. Traditionally bred varieties with high SD and small SS (resulting in higher g<sub>smax</sub> ) typically had lower biomasses, and these plants were more resilient to drought than low SD and large SS plants, which were physically larger. None of the varieties assessed were as resilient to drought or salinity as low SD OsEPF1oe transgenic plants. High SD and small SS rice displayed faster stomatal closure during increasing temperature and VPD, but photosynthesis and plant cooling were reduced. Compromises will be required when choosing rice SS and SD to tackle multiple future environmental stresses.
Immunogenomic determinants of tumor microenvironment correlate with superior survival in high-risk neuroblastoma (2021)

Our results indicate that tumors from children with high-risk neuroblastoma harboring a strong T cell-inflamed signature have a more favorable clinical outcome, and neoantigen load is a prognosis predictor, independent of T cell inflammation. Strategies to target SOX11 and other signaling pathways associated with non-T cell-inflamed tumors should be pursued as potential immune-potentiating interventions.
Phenomenology Based Decomposition of Sea Clutter with a Secondary Target Classifier (2023)

Sea clutter consists of three components: a mean Doppler spectrum, persistent spikes, and discrete spikes, with a random degree of relative power for each component. We propose a non-linear optimization technique designed to decompose noisy sea clutter into these three components plus a noise component using sparsity inducing norms and linear time-invariant (LTI) filtering in various domains. This novel approach is proposed for non-stationary clutter because it avoids any quasistationarity assumptions, unlike the currently proposed state-of-the-art detectors [1]. The decomposition is applied to real South African sea clutter data provided by the Council for Scientific and Industrial Research (CSIR) [2]. We additionally propose a secondary classifier stage for post-processing of potential target detections from the decomposition, and discuss some features that assist in classification between targets and persistent spikes beyond amplitude. Several such extensions are discussed in the conclusion.
Propagation of EM waves in axial symmetric structures and its implication for 3D rigorous lithography process simulation (2004)

Amid the different approaches to rigorously model the scattering of electromagnetic waves in sub-wavelength photolithography process, waveguide methods have been proven to be accurate and efficient. While totally different from the time domain methods such as FEM and TDFD, waveguide methods simultaneously compute diffraction of the incident plane waves with different incidence angles by a periodical dielectric structure. EM modes inside dielectric layers are solved for by decoupling the eigen-system and the electromagnetic field boundary conditions between each two adjacent layers are applied to stitch the modes and obtain the full scattering matrix. It is clear that the number of orders of the plane waves under consideration directly affects the accuracy of a waveguide simulator. However, in a 3-D simulation, simulation time and memory usage increase drastically with the increase of the number of orders. These limitations prevent waveguide methods from being applied to large layout patterns that require higher simulation orders. Since many cases under study in lithography process optimization and layout printability analysis are actually axial-symmetric about both x and y axes, it is possible to use this symmetry to simplify the calculation. Based on our definitions of the four fundamental groups of symmetric and anti-symmetric functions and the operations between these symmetric groups, we have made some fundamental discoveries of the waveguide propagating behaviors inside symmetric dielectric structures. In this paper, we will describe our new rigorous theory to decompose the propagating waves in a symmetric layer into four symmetric and anti-symmetric transmitting plane wave groups. Each group can be directly stitched to the next layer without losing symmetry or anti-symmetry. Furthermore, any form of incident waves can be reorganized into the above four plane wave groups, so can the reflective and refraction fields. We have shown that by using this field decomposition technique, we can compute scattering of the four smaller diffraction mode groups separately and the computational complexity will be greatly reduced as compared with the full mode simulation. We have developed a new version of the 3-D simulator, METRO, which incorporated this new method and achieved very high computational efficiency. For example, a 33 by 33-order, double precision simulation will only require 300M bytes memory and take less than 15 minutes without any loss of accuracy on a 1G processor compared with 1.7G memory usage and 10 hours simulating time on the same processor without symmetric simplification.
A Novel Germline Mutation of Multiple Endocrine Neoplasia Type 1 (MEN1) Gene in a Japanese MEN1 Patient and Her Daughter. (1999)

Familial multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant inherited disorder characterized by tumors of the parathyroid, anterior pituitary and gastro-entero-pancreatic endocrine tissues. The MEN1 gene has recently been cloned and its germline mutations have been considered to play an important role in the tumorigenesis of MEN1. We analyzed a Japanese MEN1 patient and her daughter for germline mutations of the MEN1 gene. The proband (60 y.o.) had primary hyperparathyroidism (PHP) and gastrinoma, and her daughter (30 y.o.) had prolactinoma. Clinical examinations revealed no evidence of PHP in the daughter. We identified a novel heterozygous germline mutation (712 A del) at codon 201 in exon 3 of the MEN1 gene in the proband. Restriction digestion analysis revealed the same mutation pattern in her daughter. These findings suggest that this family has familial MEN1 including a rare case of MEN1 with a single lesion of the pituitary. Genetic examinations are useful as diagnostic tools for any rare or variant case of familial MEN1.
Glial scar and immune cell involvement in tissue remodeling and repair following acute CNS injuries (2014)

Inadequate axonal regeneration is a common phenomenon occurring following acute injury to the central nervous system (CNS), and is often associated with permanent neurological deficits. The injured axons attempting to regenerate face the inhospitable environment of the CNS scar, which can hinder axonal growth and sprouting. In addition, in response to the insult, intense activation and infiltration of immune cells take place. Both the scar tissue and immune response, which have received a bad reputation in the context of CNS repair are essential for the overall recovery from CNS injuries, but are not optimally controlled. The glial scar contributes to protection of the spared neural tissues by establishing a boundary between damaged and salvageable tissue, and by educating the immune cells to promote the healing of the CNS tissue. In turn, the immune cells, and in particular the infiltrating macrophages, exert several functions at the lesion site, including resolution of the microglial response, control of scar tissue degradation, and production of growth factors; thereby, promoting neuronal survival, axonal regeneration, and tissue remodeling. As axonal regeneration and tissue remodeling are viewed as critical steps for the overall functional recovery following CNS injury, a detailed understanding of the mechanisms underlying the timely formation and degradation of the CNS scar, and its crosstalk with the inflammatory response, are of great importance, both biologically and clinically.
Quantitative Image Analysis to Predict the Neoplastic Region in Oral Squamous Cell Carcinoma using Multiple Fluorescent Contrast Agents (2010)

Three probes targeting molecular or morphologic characteristics of cancer were topically applied to freshly resected oral tissue. Optical contrast was used to predict the region of neoplasia; predicted regions agree well with histopathology maps.
Interferometric Carrier Envelope Phase Control of Few-Cycle IR Pulses (2012)

Interferometric CEP control in a white light seeded optical parametric amplifier is demonstrated by relative phase shifting between white light and pump beam prior to their difference frequency generation, resulting in CEP controlled Idler pulses.
Abstracts of Scientific Posters (1994)

Journal Article Abstracts of Scientific Posters Get access Clinical Chemistry, Volume 40, Issue 6, 1 June 1994, Pages 989–990, https://doi.org/10.1093/clinchem/40.6.989 Published: 01 June 1994
Factors Affecting the Enhancement of Oxidative Stress Tolerance in Transgenic Tobacco Overexpressing Manganese Superoxide Dismutase in the Chloroplasts (1995)

Two varieties of tobacco (Nicotiana tabacum var PBD6 and var SR1) were used to generate transgenic lines overexpressing Mn-superoxide dismutase (MnSOD) in the chloroplasts. The overexpressed MnSOD suppresses the activity of those SODs (endogenous MnSOD and chloroplastic and cytosolic Cu/ZnSOD) that are prominent in young leaves but disappear largely or completely during aging of the leaves. The transgenic and control plants were grown at different light intensities and were then assayed for oxygen radical stress tolerance in leaf disc assays and for abundance of antioxidant enzymes and substrates in leaves. Transgenic plants had an enhanced resistance to methylviologen (MV), compared with control plants, only after growth at high light intensities. In both varieties the activities of FeSOD, ascorbate peroxidase, dehydroascorbate reductase, and monodehydroascorbate reductase and the concentrations of glutathione and ascorbate (all expressed on a chlorophyll basis) increased with increasing light intensity during growth. Most of these components were correlated with MV tolerance. It is argued that SOD overexpression leads to enhancement of the tolerance to MV-dependent oxidative stress only if one or more of these components is also present at high levels. Furthermore, the results suggest that in var SR1 the overexpressed MnSOD enhances primarily the stromal antioxidant system.
SINR and Throughput Scaling in Ultradense Urban Cellular Networks (2015)

We consider a dense urban cellular network where the base stations (BSs) are stacked vertically as well as extending infinitely in the horizontal plane, resulting in a greater than two dimensional (2D) deployment. We use a dual-slope path loss model that is well supported empirically, wherein a “close-in” pathloss exponent α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> is used for distances less than a corner distance R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> , and then changes to α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> > α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> outside R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> . We extend recent 2D coverage probability and potential throughput results to d dimensions, and prove that if the close-in path loss exponent α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> <; d, then the SINR eventually decays to zero. For example, α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ≤ 3 results in an eventual SINR of 0 for all users in a 3D network, which is a troubling fact. We also show that the potential (i.e. best case) aggregate throughput decays to zero for α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> <; d/2. Both of these scaling results also hold for the more realistic case that we term 3D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , where there are no BSs below the user, as in a dense urban network with the user on or near the ground.
Unscented Kalman Filter and 3D vision to improve cable driven surgical robot joint angle estimation (2016)

Cable driven manipulators are popular in surgical robots due to compact design, low inertia, and remote actuation. In these manipulators, encoders are usually mounted on the motor, and joint angles are estimated based on transmission kinematics. However, due to non-linear properties of cables such as cable stretch, lower stiffness, and uncertainties in kinematic model parameters, the precision of joint angle estimation is limited with transmission kinematics approach. To improve the positioning of these manipulators, we use a pair of low cost stereo camera as the observation for joint angles and we input these noisy measurements into an Unscented Kalman Filter (UKF) for state estimation. We use the dual UKF to estimate cable parameters and states offline. We evaluated the effectiveness of the proposed method on a Raven-II experimental surgical research platform. Additional encoders at the joint output were employed as a reference system. From the experiments, the UKF improved the accuracy of joint angle estimation by 33- 72%. Also, we tested the reliability of state estimation under camera occlusion. We found that when the system dynamics is tuned with offline UKF parameter estimation, the camera occlusion has no effect on the online state estimation.
Effect of Ficus deltoidea Aqueous Extract on Blood Glucose Level in Normal and Mild Diabetic Rats (2007)

Ficus deltoidea, which is locally known as ‘mas cotek,’ has been traditionally believed to have hypoglycaemic activity. In this study, hypoglycaemic activity of aqueous extract of Ficus deltoidea in normal and mild diabetic rats (streptozotocin induced) was evaluated. The extract was administered orally at different doses (100, 500 and 1000 mg/kg) to both groups in fasting and post prandial state. The result shows that the aqueous extract of Ficus deltoidea did not have any hypoglycaemic activity in normal rats as well as in fasting mild diabetic group. In post prandial mild diabetic rats, aqueous extract of Ficus deltoidea at the dose of 1000 mg/kg show hypoglycaemic activity after 2 (p < 0.01), 4 (p < 0.05) and 6 (p < 0.01) hours extract administration. Metformin, 500 mg/kg also shows hypoglycaemic activity after 2 (p < 0.05), 4 (p < 0.01) and 6 (p < 0.01) hours administration. Therefore, we suggested that mechanism of action of the Ficus deltoidea aqueous extract maybe through enhancement of glucose uptake to muscle tissue and reduce hepatic gluconeogenesis.
Probabilistic Model-Based Diagnosis: An Electrical Power System Case Study (2010)

We present in this paper a case study of the probabilistic approach to model-based diagnosis. Here, the diagnosed system is a real-world electrical power system (EPS), i.e., the Advanced Diagnostic and Prognostic Testbed (ADAPT) located at the NASA Ames Research Center. Our probabilistic approach is formally well founded and based on Bayesian networks (BNs) and arithmetic circuits (ACs). We pay special attention to meeting two of the main challenges often associated with real-world application of model-based diagnosis technologies: model development and real-time reasoning. To address the challenge of model development, we develop a systematic approach to representing EPSs as BNs, supported by an easy-to-use specification language. To address the real-time reasoning challenge, we compile BNs into ACs. AC evaluation (ACE) supports real-time diagnosis by being predictable, fast, and exact. In experiments with the ADAPT BN, which contains 503 discrete nodes and 579 edges and produces accurate results, the time taken to compute the most probable explanation using ACs has a mean of 0.2625 ms and a standard deviation of 0.2028 ms. In comparative experiments, we found that, while the variable elimination and join tree propagation algorithms also perform very well in the ADAPT setting, ACE was an order of magnitude or more faster.