gebhart/patrepeval huggingface dataset:
Resistance of CD7-deficient Mice to Lipopolysaccharide-induced Shock Syndromes (1999)

CD7 is an immunoglobulin superfamily molecule involved in T and natural killer (NK) cell activation and cytokine production. CD7-deficient animals develop normally but have antigen-specific defects in interferon (IFN)-gamma production and CD8(+) CTL generation. To determine the in vivo role of CD7 in systems dependent on IFN-gamma, the response of CD7-deficient mice to lipopolysaccharide (LPS)-induced shock syndromes was studied. In the high-dose LPS-induced shock model, 67% of CD7-deficient mice survived LPS injection, whereas 19% of control C57BL/6 mice survived LPS challenge (P < 0.001). CD7-deficient or C57BL/6 control mice were next injected with low-dose LPS (1 microgram plus 8 mg D-galactosamine [D-gal] per mouse) and monitored for survival. All CD7-deficient mice were alive 72 h after injection of LPS compared with 20% of C57BL/6 control mice (P < 0.001). After injection of LPS and D-gal, CD7-deficient mice had decreased serum IFN-gamma and tumor necrosis factor (TNF)-alpha levels compared with control C57BL/6 mice (P < 0.001). Steady-state mRNA levels for IFN-gamma and TNF-alpha in liver tissue were also significantly decreased in CD7-deficient mice compared with controls (P < 0.05). In contrast, CD7-deficient animals had normal liver interleukin (IL)-12, IL-18, and interleukin 1 converting enzyme (ICE) mRNA levels, and CD7-deficient splenocytes had normal IFN-gamma responses when stimulated with IL-12 and IL-18 in vitro. NK1.1(+)/ CD3(+) T cells are known to be key effector cells in the pathogenesis of toxic shock. Phenotypic analysis of liver mononuclear cells revealed that CD7-deficient mice had fewer numbers of liver NK1.1(+)/CD3(+) T cells (1.5 +/- 0.3 x 10(5)) versus C57BL/6 control mice (3.7 +/- 0.8 x 10(5); P < 0.05), whereas numbers of liver NK1.1(+)/CD3(-) NK cells were not different from controls. Thus, targeted disruption of CD7 leads to a selective deficiency of liver NK1.1(+)/ CD3(+) T cells, and is associated with resistance to LPS shock. These data suggest that CD7 is a key molecule in the inflammatory response leading to LPS-induced shock.
Nogo-A regulates vascular network architecture in the postnatal brain (2016)

Recently, we discovered a new role for the well-known axonal growth inhibitory molecule Nogo-A as a negative regulator of angiogenesis in the developing central nervous system. However, how Nogo-A affected the three-dimensional (3D) central nervous system (CNS) vascular network architecture remained unknown. Here, using vascular corrosion casting, hierarchical, synchrotron radiation μCT-based network imaging and computer-aided network analysis, we found that genetic ablation of Nogo-A significantly increased the three-dimensional vascular volume fraction in the postnatal day 10 (P10) mouse brain. More detailed analysis of the cerebral cortex revealed that this effect was mainly due to an increased number of capillaries and capillary branchpoints. Interestingly, other vascular parameters such as vessel diameter, -length, -tortuosity, and -volume were comparable between both genotypes for non-capillary vessels and capillaries. Taken together, our three-dimensional data showing more vessel segments and branchpoints at unchanged vessel morphology suggest that stimulated angiogenesis upon Nogo-A gene deletion results in the insertion of complete capillary micro-networks and not just single vessels into existing vascular networks. These findings significantly enhance our understanding of how angiogenesis, vascular remodeling, and three-dimensional vessel network architecture are regulated during central nervous system development. Nogo-A may therefore be a potential novel target for angiogenesis-dependent central nervous system pathologies such as brain tumors or stroke.
Kinetic Resolution of 1,2‐Diols through Highly Site‐ and Enantioselective Catalytic Silylation (2007)

Ein chiraler Silylierungskatalysator wird für die kinetische Racematspaltung von drei Klassen acyclischer 1,2-Diole genutzt. Der Katalysator unterscheidet mit sehr hoher Genauigkeit zwischen den beiden Hydroxygruppen eines Substrats. Die hohe Enantiomerenreinheit der meisten Diole wird mit katalytischen asymmetrischen Dihydroxylierungen nicht erreicht. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z703650_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Modified Mandibular Inferior Border Sagittal Split Osteotomy Reduces Postoperative Risk for Developing Inferior Border Defects (2016)

This study confirms the findings previously reported by our research group that the modified inferior border osteotomy technique in SSO results in a substantial lower frequency of persisting inferior border defects. Surgeons are advised to ensure that the lingual cortex of the inferior border is not included in the split during mandibular advancements, and in cases in which the advancement is more than 10 mm and/or the patient is older than 30 years, surgeons might want to consider using a bone graft or a bone graft substitute.
New Techniques for Path Planning in Image Space (2009)

We propose two new methods for performing local path search directly in the image space of a camera sensor. The first technique utilizes a high-resolution local image space subsystem to determine the farthest point along a global Cartesian path that can be reached along an unobstructed heading, thereby short-cutting as much of the global path as possible. To the best of our knowledge, this is the first image space planning technique that is both suitable for navigation in unstructured environments and does not use a graph-search algorithm in the image space subsystem. The second technique that we propose improves the local image space subsystem of a hierarchical image/Cartesian space planner by determining when it is safe to translate at full speed. Both techniques are implemented on an autonomous robot and experimentally evaluated against a hierarchical top-down Cartesian planner and a previously proposed hierarchical image/Cartesian space planner. Each system is tested three times on three different course layouts. The first proposed method performs comparably to existing systems when evaluated on the criteria of path length and total runtime. The second technique consistently outperforms the other three systems with respect to total runtime. 1
A Practical Entry to the Crambescidin Family of Guanidine Alkaloids. Enantioselective Total Syntheses of Ptilomycalin A, Crambescidin 657 and Its Methyl Ester (Neofolitispates 2), and Crambescidin 800 (2000)

Among the most structurally remarkable guanidine natural products are the crambescidin/ptilomycalin A family of marine alkaloids. The evolution of a practical strategy for preparing pharmacologically significant crambescidin/ptilomycalin A alkaloids that lack oxidation at C13 is described. The first total syntheses of crambescidin 800 (2), crambescidin 657 (6), and neofolitispate 2 (7) are reported in full detail. The central strategic step in these convergent total syntheses is tethered Biginelli condensation of β-keto ester 24 with ureido aminal 61 to combine all carbons of the guanidine nucleus and set the pivotal C10−C13 stereorelationship. The total synthesis of crambescidin 800 (2) was accomplished in 3% overall yield from commercially available 3-butyn-1-ol by way of 16 isolated and purified intermediates. Full details of our earlier total synthesis of ptilomycalin A (1) are also presented. The total syntheses described in this disclosure confirm the stereochemical assignments of 1, 2, 6, and 7 and rigorously establish that the absolute configuration of the hydroxyspermidine side chain of crambescidin 800 (2) is S.
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy (2023)

Computational cell type deconvolution on bulk transcriptomics data can reveal cell type proportion heterogeneity across samples. One critical factor for accurate deconvolution is the reference signature matrix for different cell types. Compared with inferring reference signature matrices from cell lines, rapidly accumulating single-cell RNA-sequencing (scRNA-seq) data provide a richer and less biased resource. However, deriving cell type signature from scRNA-seq data is challenging due to high biological and technical noises. In this article, we introduce a novel Bayesian framework, tranSig, to improve signature matrix inference from scRNA-seq by leveraging shared cell type-specific expression patterns across different tissues and studies. Our simulations show that tranSig is robust to the number of signature genes and tissues specified in the model. Applications of tranSig to bulk RNA sequencing data from peripheral blood, bronchoalveolar lavage and aorta demonstrate its accuracy and power to characterize biological heterogeneity across groups. In summary, tranSig offers an accurate and robust approach to defining gene expression signatures of different cell types, facilitating improved in silico cell type deconvolutions.
Influence of a fat layer on the near infrared spectra of human muscle: quantitative analysis based on two-layered Monte Carlo simulations and phantom experiments (2005)

The influence of fat thickness on the diffuse reflectance spectra of muscle in the near infrared (NIR) region is studied by Monte Carlo simulations of a two-layer structure and with phantom experiments. A polynomial relationship was established between the fat thickness and the detected diffuse reflectance. The influence of a range of optical coefficients (absorption and reduced scattering) for fat and muscle over the known range of human physiological values was also investigated. Subject-to-subject variation in the fat optical coefficients and thickness can be ignored if the fat thickness is less than 5 mm. A method was proposed to correct the fat thickness influence.
Resampling-based Multiple Testing: Asymptotic Control of Type I Error and Applications to Gene Expression Data (2003)

We define a general statistical framework for multiple hypothesis testing and show that the correct null distribution for the test statistics is obtained by projecting the true distribution of the test statistics onto the space of mean zero distributions. For common choices of test statistics (based on an asymptotically linear parameter estimator), this distribution is asymptotically multivariate normal with mean zero and the covariance of the vector influence curve for the parameter estimator. This test statistic null distribution can be estimated by applying the non-parametric or parametric bootstrap to correctly centered test statistics. We prove that this bootstrap estimated null distribution provides asymptotic control of most type I error rates. We show that obtaining a test statistic null distribution from a data null distribution, e.g. projecting the data generating distribution onto the space of all distributions satisfying the complete null), only provides the correct test statistic null distribution if the covariance of the vector influence curve is the same under the data null distribution as under the true data distribution. This condition is a weak version of the subset pivotality condition. We show that our multiple testing methodology controlling type I error is equivalent to constructing an error-specific confidence region for the true parameter and checking if it contains the hypothesized value. We also study the two sample problem and show that the permutation distribution produces an asymptotically correct null distribution if (i) the sample sizes are equal or (ii) the populations have the same covariance structure. We include a discussion of the application of multiple testing to gene expression data, where the dimension typically far exceeds the sample size. An analysis of a cancer gene expression data set illustrates the methodology.
Supplementary Figures S1-S2 from HOP/OB1/NECC1 Promoter DNA Is Frequently Hypermethylated and Involved in Tumorigenic Ability in Esophageal Squamous Cell Carcinoma (2023)

Supplementary Figures S1-S2 from HOP/OB1/NECC1 Promoter DNA Is Frequently Hypermethylated and Involved in Tumorigenic Ability in Esophageal Squamous Cell Carcinoma
Automated Production of Human Induced Pluripotent Stem Cell-Derived Cortical and Dopaminergic Neurons with Integrated Live-Cell Monitoring (2020)

Manual culture and differentiation protocols for human induced pluripotent stem cells (hiPSC) are difficult to standardize, show high variability and are prone to spontaneous differentiation into unwanted cell types. The methods are labor-intensive and are not easily amenable to large-scale experiments. To overcome these limitations, we developed an automated cell culture system coupled to a high-throughput imaging system and implemented protocols for maintaining multiple hiPSC lines in parallel and neuronal differentiation. We describe the automation of a short-term differentiation protocol using Neurogenin-2 (NGN2) over-expression to produce hiPSC-derived cortical neurons within 6‒8 days, and the implementation of a long-term differentiation protocol to generate hiPSC-derived midbrain dopaminergic (mDA) neurons within 65 days. Also, we applied the NGN2 approach to a small molecule-derived neural precursor cells (smNPC) transduced with GFP lentivirus and established a live-cell automated neurite outgrowth assay. We present an automated system with protocols suitable for routine hiPSC culture and differentiation into cortical and dopaminergic neurons. Our platform is suitable for long term hands-free culture and high-content/high-throughput hiPSC-based compound, RNAi and CRISPR/Cas9 screenings to identify novel disease mechanisms and drug targets.
Two-dimensional hybrid model of inductively coupled plasma sources for etching (1993)

Inductively coupled plasmas (ICPs) are currently being investigated as high density (≳1011–1012 cm−3), low pressure (&amp;lt;1–20 mTorr) sources for semiconductor etching and deposition. We have developed a two-dimensional (r,z) hybrid model for ICP sources and have used the model to investigate Ar/CF4/O2 mixtures for etching applications. The simulation consists of electromagnetic, electron Monte Carlo, and hydrodynamic modules with an ‘‘off-line’’ plasma chemistry Monte Carlo simulation. The model produces the temporally and spatially dependent magnetic and electric fields (both inductively and capacitively coupled), plasma densities, and the energy resolved flux of ions and radicals to the substrate. We discuss results for densities, power deposition, and ion energies to the substrate as a function of position.
Analysis of Lamellar Structure in Semicrystalline Polymers by Studying the Absorption of Water and Ethylene Glycol in Nylons Using Small-Angle Neutron Scattering (1998)

Preferential diffusion of deuterated solvents into the amorphous regions of a semicrystalline polymer enhances the contrast between the crystalline and amorphous regions measurable by small-angle neutron scattering. This scattering in nylons from the diffusion of D2O and deuterated ethylene glycol (d-EG) is analyzed by identifying the distinct contribution to scattering from the two amorphous regions, one in the interlamellar spaces and the other outside the lamellar stacks. The central diffuse scattering (Id) is the non-Bragg, liquidlike, or independent scattering, and is attributed to the solvents (D2O/d-EG) in the amorphous domains outside the lamellar stacks. The lamellar scattering (Il) is the interference peak from the lamellae in the stacks and is used to evaluate the distance between the lamellae, the thickness of the interlamellar spaces, and the coherence length of the lamellar stacks. The invariant calculations show that 70%−80% of the lamellar stack is crystalline. About one-third of the amorphous material in a highly crystalline nylon is in the interlamellar space, and two-thirds is outside the lamellar stacks. The thickness of the interlamellar amorphous regions into which solvent molecules diffuse varies from 10 to 60 Å depending on the thermal history and is a major contributor to the observed increase in lamellae spacing. Structural changes in nylon 6 immersed in water are accelerated at 125 °C, and this temperature could be the hydrated-equivalent of the Brill transition observed at 160 °C in dry nylon 6. Water or EG diffuses into the fold surfaces of nylon lamellae at elevated temperatures, and subsequent structural changes are accompanied by hydrolysis of the nylon chains. EG being a stronger solvent reduces the lamellar thickness at elevated temperatures.
An Overview of Innovative Techniques to Improve Cervical Cancer Screening (2006)

Although current cytomorphology-based cervical cancer screening has reduced the incidence of cervical cancer, Pap-smears are associated with high false positive and false negative rates. This has spurred the search for new technologies to improve current screening. New methodologies are automation of Pap-smear analysis, addition of new biological or molecular markers to traditional cytology or using these new markers to replace the current screening method. In this overview we will summarize data on cervical cancer epidemiology and etiology and the current cervical cancer screening approach. Available data on new screening approaches, such as quantitative cytochemistry, detection of loss of heterozygosity (LOH) and hypermethylation analysis will be reviewed. We discuss the potential of these approaches to replace or augment current screening. When available, data on cost-effectiveness of certain approaches will be provided. In short, Human Papillomavirus (HPV) DNA detection stands closest to implementation in nation-wide screening programs of all markers reviewed. However, specificity is low in women aged <35 years and the psychological effects of knowledge of HPV positivity in absence of cervical (pre) malignant disease are important drawbacks. In our opinion the results of large clinical trials should be awaited before proceeding to implement HPV DNA detection. New technologies based on molecular changes associated with cervical carcinogenesis might result in comparable sensitivity, but improved specificity. Hypermethylation analysis is likely to be more objective to identify patients with high grade squamous intra-epithelial lesions (HSIL) or invasive cancer with a higher specificity than current cytomorphology based screening.
Nanoengineered Carbon Scaffolds for Hydrogen Storage (2008)

Single-walled carbon nanotube (SWCNT) fibers were engineered to become a scaffold for the storage of hydrogen. Carbon nanotube fibers were swollen in oleum (fuming sulfuric acid), and organic spacer groups were covalently linked between the nanotubes using diazonium functionalization chemistry to provide 3-dimensional (3-D) frameworks for the adsorption of hydrogen molecules. These 3-D nanoengineered fibers physisorb twice as much hydrogen per unit surface area as do typical macroporous carbon materials. These fiber-based systems can have high density, and combined with the outstanding thermal conductivity of carbon nanotubes, this points a way toward solving the volumetric and heat-transfer constraints that limit some other hydrogen-storage supports.
Sub-40nm pattern fabrication in 157nm interferometric immersion lithography (2006)

We previously succeeded in fabricating 60-nm line-and-space (L/S) patterns with fluorine-containing silsesquioxane-type (F-SSQ) resist, BARRIERTA<sup>®</sup> J25V immersion fluid, and Novec<sup>TM</sup> HFE-7200 rinse liquid using our two-beam interferometer. In the study reported here, we tried to fabricate a finer resist pattern with this immersion fluid, but 40-nm L/S could not be resolved because of the T-top shapes produced under the same conditions. The cause of the T-top shape was photo-acid generator (PAG) leaching into HFE-7200, which in effect caused the resist layer to swell. When Fluorinert<sup>TM</sup> FC-84 with the CF<sub>3</sub> functional group, which has the lowest reactivity, was used as a rinse liquid, the resolution of 40- and 32-nm L/S without T-top shape was achieved. Next, to fabricate finer patterns, we considered improving the molecular structure to raise the refractive index. As a result of an examination based on perfluoroalkane, which has high transparency, we found that it is effective to reduce the fluorine atom concentration, transform the molecular structure to a steric structure without reducing molar refractivity, and attach a functional group such as a cyclohexyl or chloro group. Finally, with the high-refractive index immersion fluid, we attempted to fabricate 28-nm L/S. Although we tried pattern fabrication with two immersion fluid candidates, transfer of the interference patterns to the resist has not been confirmed at this time. However, since we checked that the light did reach the resist, we speculate that it will be possible to fabricate 28-nm L/S by making a minor change.
Cardiac steatosis is associated with excess body weight in otherwise healthy adults (2011)

significant correlation of lipid content with cardiac mass (r = 0.50, p = 0.01).
Biomechanical analysis of the sliding characteristics of compression hip screws. (1980)

Understanding the conditions that facilitate sliding of hip screws aids in ensuring their proper use. The higher the nail-plate angle, the easier it is to impact the hip-fixation device and thus allow bone impaction and stability at the fracture site. The potential for jamming a sliding hip screw is decreased by maximum engagement of the screw in the barrel. Differences in the material and design of sliding hip-fixation devices have relatively little effect on the sliding characteristics compared with the nail-plate angle and the engagement of the screw in the barrel.
Adolescent and parent perspectives on genomic sequencing to inform cancer care (2022)

Next-generation sequencing offers opportunities for targeted cancer therapies and may identify pathogenic germline variants. Adolescents' perception of testing is not well understood. We surveyed 16 adolescents and 59 parents regarding motivations, attitudes, and knowledge related to paired tumor/germline sequencing. Participants generally had a good objective understanding of germline genetics and cancer risk, with parents scoring higher than adolescents. Nearly all participants were motivated by a desire to help other patients and to treat their child/themselves. Most adolescents reported involvement in the decision to enroll in the study. Study findings suggest important similarities and differences between parent and adolescent views.
Effect of Lanthanum Addition on Thermal Stability and Benzene Removal Activity of Iron Oxide/Alumina Composite Powders (2012)

We investigated the effect of La addition on thermal stability and benzene removal activity of iron oxide/alumina composite powder catalyst. La addition to alumina support improved the surface area stability and the total catalytic removal conversion of benzene after heat treatment. The solid state reaction in La-added catalyst was complicated: γ-Al2O3, LaFeAl11O19, LaAlO3 and α-Al2O3 appeared in this system. It was found that Fe/La/Al2O3 with high surface area was better catalyst for benzene removal at moderate temperature even when heated at 1000-1100°C. Also we discussed that La modification increased surface active sites as well as oxygen storage capacity.