gebhart/patrepeval huggingface dataset:
Structural Energies of A1 Deposited on the GaAs(110) Surface (1981)

Major controversies over the structure of A1 atoms deposited on the GaAs(110) surface have been resolved by using a first-principles energy-minimization method. The most stable configuration is that of A1 atoms replacing the second layer Ga atoms beneath the surface. At temperatures where this reaction cannot be activated, two important processes are found to exist. In the low-coverage limit, A1 atoms favor twofold sites to form strong bonds with the substrate atoms. At higher coverages, A1 atoms tend to cluster and make new bonds among themselves.
Crucial points at diagnosis. Type 2 diabetes or slow type 1 diabetes. (1999)

Two major types of diabetes have been recognized since the late 1930s. However, in recent times there have been major changes in classification and understanding of these types, including improved knowledge of maturity-onset diabetes in the young, with the identification of mutations relating to impaired insulin secretion and the recognition of slow-onset type 1 diabetes in adults now designated as latent autoimmune diabetes in adults (LADA). A major problem area in diabetes classification concerns cases of slowly progressive forms of type 1 and type 2 diabetes, particularly in adults aged 25-50 years. This is a more contemporary problem because cases of type 2 diabetes are presenting at an increasingly younger age. In the landmark U.K. Prospective Diabetes Study of type 2 diabetes, islet cell antibodies (ICAs) and antibodies to glutamic acid decarboxylase (anti-GAD) were measured at diagnosis in 3,672 patients. The overall proportion with ICAs was 6%, and anti-GADs was 10%. These subjects clearly had type 1 diabetes or LADA by both phenotypic and genotypic features. The presence of auto antibodies correlated particularly with a younger age and phenotypic features consistent with type 1 diabetes (e.g., early age at diagnosis, lower BMI, and reduced beta-cell function). Overall, of patients requiring insulin by 6 years, 38% were anti-GAD+ at baseline compared with 5.3% of those not on insulin at 6 years. Antibodies to GAD indicate an underlying autoimmune process and have a high positive predictive value for type 1 diabetes and future insulin dependency in adults.
A New Approach to β-Fluoropyrroles Based on the Michael Addition of Isocyanomethylide Anions to α-Fluoroalkenyl Sulfones and Sulfoxides (1994)

Abstract The reactions of 2-aryl-1-fluorovinyl phenyl sulfones with carbanions derived from isocyanoacetates gave mixtures of 3-aryl-4-fluoro-2-pyrrolecarboxylates and 3-aryl-4-fluoro-4-phenylsulfonyl-2-isocyanobutanoates, simple Michael addition products, in variable ratios depending upon the conditions employed. On the other hand, the reaction of 1-fluoro-1-propenyl phenyl sulfone afforded mainly the simple Michael addition products in moderate yields as well as a small amount of 4-phenylsulfonyl-3-methyl-2-pyrrolecarboxylates and a trace amount of 4-fluoro-3-methyl-2-pyrrolecarboxylates. 1-Fluoropropenyl phenyl sulfoxide underwent mainly the simple Michael addition to give butenoates and a small amount of 4-fluoro-2-pyrrolecarboxylates.
847 Modeling basal cell carcinoma in 3D organotypic raft cultures (2022)

Basal cell carcinoma (BCC) is the most-commonly diagnosed cancer worldwide with limited availability for non-surgical treatments. The Hedgehog signaling cascade drives tumorigenesis, but efforts to develop effective chemotherapeutics have been thwarted by chemoresistant tumor recurrence. A contributing factor to this is an overall lack of human-based preclinical models. We endeavored to develop 3D organotypic raft models that mimic characteristics of human BCC by combining primary normal human epidermal keratinocytes (NHEK) with established murine BCC cells. . We hypothesize that the co-culture of BCC cells with NHEK will elicit pro-tumorigenic, pre-cancerous changes in the NHEK. NHEK and the ASZ BCC cell line were mixed at ratios of 90:10, 75:25, and 50:50 NHEK to ASZ with 100% NHEK and 100% ASZ controls and were seeded onto dermis mimics. Samples were harvested after 12 days of culture and analyzed by hemotoxylin and eosin (H&E) staining, qPCR, western blot, and immunostaining. H&E staining supports successful incorporation of cancer cells with phenotypes that display features of early-stage BCCs. Species-specific immunostaining and qPCR analyses of the human cell populations revealed abnormal development of cytoskeletal structure, cell adhesion, and barrier function that mimic the pathology of patient BCC. Specifically, keratin 10, desmoglein, desmocollin, and filaggrin proteins and transcripts are down-regulated specifically in human cells in the ASZ-containing cultures. As the percent of BCC cells incorporation increased in the 3D cultures, these components decrease. These results suggest that BCC cells can influence neighboring non-cancerous keratinocytes and prevent their proper differentiation. These results are promising for evaluating pre-existing and new chemotherapeutics designed for treating BCC.
Enhanced Low-Order Model with Radiation for Total Temperature Probe Analysis and Design (2018)

&lt;div&gt;Analysis and design of total temperature probes for accurate measurements in hot, high-speed flows remains a topic of great interest in aerospace propulsion and a number of other engineering areas. One can apply detailed computational methods for simultaneous convection, conduction and radiation heat transfer, but such approaches are not suitable for rapid, routine analysis and design studies. For these studies, there is still a place for low-order approximate methods, and that is the subject of this article. Here, an enhanced, low-order model is presented that includes conduction with variable thermal conductivity, convection with varying convection coefficient, varying diameter (and thus area) along the length of the sensor and radiation, all implemented in a convenient &lt;i&gt;MATLAB&lt;/i&gt; code. We have also developed a new novel procedure to integrate the enhanced low-order model with computational fluid dynamics/conjugate heat transfer (CHT/CFD) simulations to accurately predict the important influences of radiation under different conditions in a very efficient manner.&lt;/div&gt;
Efficacy, dose–response, and aerosol delivery of dry powder synthetic lung surfactant treatment in surfactant-deficient rabbits and premature lambs (2022)

These studies confirm the clinical potential of DP synthetic lung surfactant with B-YL peptide as a SP-B mimic to alleviate surfactant deficiency when delivered as a liquid bolus or as an aerosol.
EWS/ATF1 expression induces sarcomas from neural crest–derived cells in mice (2013)

Clear cell sarcoma (CCS) is an aggressive soft tissue malignant tumor characterized by a unique t(12;22) translocation that leads to the expression of a chimeric EWS/ATF1 fusion gene. However, little is known about the mechanisms underlying the involvement of EWS/ATF1 in CCS development. In addition, the cellular origins of CCS have not been determined. Here, we generated EWS/ATF1-inducible mice and examined the effects of EWS/ATF1 expression in adult somatic cells. We found that forced expression of EWS/ATF1 resulted in the development of EWS/ATF1-dependent sarcomas in mice. The histology of EWS/ATF1-induced sarcomas resembled that of CCS, and EWS/ATF1-induced tumor cells expressed CCS markers, including S100, SOX10, and MITF. Lineage-tracing experiments indicated that neural crest-derived cells were subject to EWS/ATF1-driven transformation. EWS/ATF1 directly induced Fos in an ERK-independent manner. Treatment of human and EWS/ATF1-induced CCS tumor cells with FOS-targeted siRNA attenuated proliferation. These findings demonstrated that FOS mediates the growth of EWS/ATF1-associated sarcomas and suggest that FOS is a potential therapeutic target in human CCS.
3D mouse embryo model: EMA148, Stage TS24, Age E16.0 (est) (2017)

The eMouseAtlas team have generated a series of 3D images to capture mouse embryo development and to use as a spatial framework for gene-expression and other spatially organised data. The resource is published and available on the Web at http://www.emouseatlas.org/emap/ema/.
Gene transfer of CFTR to airway epithelia: low levels of expression are sufficient to correct Cl − transport and overexpression can generate basolateral CFTR (2005)

Gene transfer of CFTR cDNA to airway epithelia is a promising approach to treat cystic fibrosis (CF). Most gene transfer vectors use strong viral promoters even though the endogenous CFTR promoter is very weak. To learn whether expressing CFTR at a low level in a fraction of cells would correct Cl(-) transport, we mixed freshly isolated wild-type and CF airway epithelial cells in varying proportions and generated differentiated epithelia. Epithelia with approximately 20% wild-type cells generated approximately 70% the transepithelial Cl(-) current of epithelia containing 100% wild-type cells. These data were nearly identical to those previously obtained with CFTR expressed under control of a strong promoter in a CF epithelial cell line. We also tested high level CFTR expression using the very strong cytomegalovirus (CMV) promoter as well as the cytokeratin-18 (K18) promoter. In differentiated airway epithelia, the CMV promoter generated 50-fold more transgene expression than the K18 promoter, but the K18 promoter generated more transepithelial Cl(-) current at high vector doses. Using functional studies, we found that with marked overexpression, some CFTR channels were present in the basolateral membrane where they shunted Cl(-) flow, thereby reducing net transepithelial Cl(-) transport. These results suggest that very little CFTR is required in a fraction of CF epithelial cells to complement Cl(-) transport because transepithelial Cl(-) flow is limited at the basolateral membrane. Thus they suggest a broad leeway in promoter strength for correcting the CF gene transfer, although at very high expression levels CFTR may be mislocalized to the basolateral membrane.
Ultra‐short echo‐time 2D time‐of‐flight MR angiography using a half‐pulse excitation (1999)

Flow-related artifacts remain a significant concern for magnetic resonance (MR) angiography because their appearance in angiograms adversely impacts accuracy in evaluation of arterial stenoses. In this paper, a half-pulse excitation scheme for improved two-dimensional time-of-flight (2D TOF) angiography is described. The proposed method eliminates the need for gradient moment nulling (of all orders), providing significant reductions in spin dephasing and consequent artifactual signal loss. Furthermore, because the post-excitation refocusing and flow compensation gradients are obviated, the achievable echo time is dramatically shortened. The half-pulse excitation is employed in conjunction with a fast radial-line acquisition, allowing ultra-short echo times on the order of 250–300 μsec. Radial-line acquisition methods also provide additional benefits for flow imaging: effective mitigation of pulsatile flow artifacts, full k-space coverage, and decreased scan times. The half-pulse excitation/radial-line sequence demonstrated improved performance in initial clinical evaluations of the carotid bifurcation when compared with a conventional 2D TOF sequence. Magn Reson Med 41:591–599, 1999. © 1999 Wiley-Liss, Inc.
Load side state estimation in robot with joint elasticity (2012)

For robots with joint elasticity, discrepancies exist between the motor side and the load side. Thus the load side (end-effector) performance can hardly be guaranteed with motor side measurements alone. In this paper, a computationally easy load side state estimation scheme is proposed for the robots with joint elasticity, which is equipped with motor encoders and a low-cost end-effector MEMS sensor such as 3-axial accelerometer. An optimization based inverse differential kinematics algorithm is developed to obtain the load side joint acceleration estimate. Then the joint position and velocity estimation problem is decoupled into simple 2-order kinematic Kalman filters for each joint. Maximum likelihood principle is utilized to estimate the fictitious noise covariances. Both offline and online solutions are derived. The extension to other sensor configurations is discussed as well. The effectiveness of the developed method is validated through simulation and experimental study on a 6-DOF industrial robot.
RNA targeting, trafficking, and translation in dendrites (2007)

It is well established that a subset of proteins can be translated in dendrites independently of the cell soma. Recent studies have begun to elucidate the dynamic regulation and functional consequences of this local protein synthesis. In addition to more detailed analyses of mRNA localization, translation, and trafficking in dendrites, new research highlights possible roles of local translation in synaptic plasticity, suggesting a critical role for local translation in neuronal activity.
Performance evaluation of automated white matter hyperintensity segmentation algorithms in a multicenter cohort on cognitive impairment and dementia (2023)

To conclude, the deep learning algorithm, when retrained, performed well in the multicenter context. Nevertheless, the performance was close to traditional methods. We provide methodological recommendations for future studies using automated WMH segmentation to quantify and assess WMH along the continuum of cognitive impairment and AD dementia.
Controlled Humidity Levels for Fine Spatial Detail Information in Enzyme-Assisted N-Glycan MALDI MSI (2022)

Investigation of the spatial distribution of <i>N</i>-glycans in tissue specimens has emerged as a powerful tool in clinical research, in part, because altered <i>N</i>-glycans are often a hallmark of disease progression. Mass spectrometry imaging of <i>N</i>-glycans relies on peptide <i>N</i>-glycanase spraying and tissue incubation for efficient <i>in situ</i> release of <i>N</i>-glycans from their carrier proteins. Unstandardized and uncontrolled incubation steps often cause significant delocalization of released <i>N</i>-glycans, resulting in the inability to link given <i>N</i>-glycan composition to a specific microanatomical region in the tissue. Herein, we optimized the incubation step to provide accurate and sensitive MALDI-MSI of <i>N</i>-glycans. Specifically, we tested saturated solutions of various salts that maintain constant relative humidity in the incubation chamber. We showed that the best performance was achieved using a saturated solution of KNO<sub>3</sub> that maintains an 89% RH. Under these conditions, near maximal sensitivity was achieved with the minutest ion delocalization, which we demonstrated at a 35 μm spatial resolution, where we observed six distinct spatial patterns that colocalize to distinct microanatomical compartments in a kidney nephrectomy tissue section.
22 GB optical disc system for high definition digital video recording (2002)

We report the 22 GB and 35 Mbps rewritable disk system for HD digital video recording. We apply a high numerical aperture (NA) objective and a blue laser diode (LD) on optical pickup, using the land/groove recording technique. We show some new technologies with which we can ensure playability.
Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding (2006)

Methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to human health, particularly through hospital acquired infection. The spread of MRSA means that novel targets are required to develop potential inhibitors to combat infections caused by such drug-resistant bacteria. Thymidylate kinase (TMK) is attractive as an antibacterial target as it is essential for providing components for DNA synthesis. Here, we report crystal structures of unliganded and thymidylate-bound forms of S. aureus thymidylate kinase (SaTMK). His-tagged and untagged SaTMK crystallize with differing lattice packing and show variations in conformational states for unliganded and thymidylate (TMP) bound forms. In addition to open and closed forms of SaTMK, an intermediate conformation in TMP binding is observed, in which the site is partially closed. Analysis of these structures indicates a sequence of events upon TMP binding, with helix alpha3 shifting position initially, followed by movement of alpha2 to close the substrate site. In addition, we observe significant conformational differences in the TMP-binding site in SaTMK as compared to available TMK structures from other bacterial species, Escherichia coli and Mycobacterium tuberculosis as well as human TMK. In SaTMK, Arg 48 is situated at the base of the TMP-binding site, close to the thymine ring, whereas a cis-proline occupies the equivalent position in other TMKs. The observed TMK structural differences mean that design of compounds highly specific for the S. aureus enzyme looks possible; such inhibitors could minimize the transfer of drug resistance between different bacterial species.
Intracellular Growth of Bacterial Pathogens: The Role of Secreted Effector Proteins in the Control of Phagocytosed Microorganisms (2015)

The ability of intracellular pathogens to subvert the host response, to facilitate invasion and subsequent infection, is the hallmark of microbial pathogenesis. Bacterial pathogens produce and secrete a variety of effector proteins, which are the primary means by which they exert control over the host cell. Secreted effectors work independently, yet in concert with each other, to facilitate microbial invasion, replication, and intracellular survival in host cells. In this review we focus on defined host cell processes targeted by bacterial pathogens. These include phagosome maturation and its subprocesses: phagosome-endosome and phagosome-lysosome fusion events, as well as phagosomal acidification, cytoskeleton remodeling, and lysis of the phagosomal membrane. We further describe the mode of action for selected effectors from six pathogens: the Gram-negative Legionella, Salmonella, Shigella, and Yersinia, the Gram-positive Listeria, and the acid-fast actinomycete Mycobacterium.
The Power of Temporal Features for Classifying News Articles (2019)

Temporal information extracted from texts and normalized to some standard format has been exploited in a variety of tasks such as information retrieval and question answering. Classifying documents into categories using temporal features has not yet been tried. Such a method might be particularly valuable when classifying sensitive texts such as patient records, i.e., whenever the pure content of the documents should not be used for the classification. In this paper, we describe, as a proof-of-concept, our work on classifying news articles exploiting only features defined over extracted and normalized temporal expressions. Our evaluation of two classification models on large German and English news archives shows promising results and demonstrates the discriminative power of temporal features for topically classifying text documents.
2416 Three Dimensional Flow Mechanism of Rotating Stall in an Axial Flow Compressor (2006)

Recently, it has been clarified that unsteady vortical flow field at rotating stall in an axial flow compressor rotor is subject to tornado-type separation vortex linking from the rotor blade suction surface to the casing wall by experimental fluid dynamics and computational fluid dynamics. With the growth of rotating stall, the tornado-type separation vortex rolls up to ahead of the rotor and the vortex leg moves to the midspan from the tip on the blade. Based on these features, the flow mechanism of rotating stall is explained by the three-dimensional separation vortex structure and its interaction with the casing wall and the blade surface.
Spindle-to-Cortex Communication in Cleaving Frog Eggs (2017)

During cytokinesis, the mitotic spindle communicates with the cell cortex to position a cleavage furrow that will cut through the cell in the plane defined by the metaphase plate. We investigated the molecular basis of this communication in <i>Xenopus laevis</i> eggs, where the signal has to travel ∼400 µm in ∼30 min to reach the cortex from the first anaphase spindle. At anaphase onset, huge microtubule asters grow out from the poles of the spindle and meet at the plane previously defined by the metaphase plate. This disc-shaped boundary plane recruits the chromosome passenger complex (CPC) and centralspindlin to antiparallel microtubule bundles. It grows out to the cell cortex as the asters expand, where it induces the furrow. CPC and centralspindlin were not recruited to boundaries between asters from different spindles, suggesting a role of chromatin in triggering the CPC-positive state. Recruitment of CPC to aster boundaries was reconstituted in an extract system, and we observed that recruitment was stimulated by proximity to chromatin. Finally, we discuss models for molecular processes involved in initiation and growth of the CPC-positive disc that communicates the position of the metaphase plate to the cortex over hundreds of micrometers in frog eggs.
Image Encryption Method Based on the B-Transform for the Improvement of the DCT Compression Efficiency (2013)

This paper presents the encryption method followed by compression with image.It encrypts the image using the B-transform and then compresses by the DCT (Discrete Cosine Transform) based the standard image compression method (e.g.JPEG).The output of B-transform is the partially sorted string and the additional position information from the original permutation string.The additional position information generates the B-code.This code used by the encryption key whose space is 10 19500 enough to avoid to brute-force attack.Also, when the compression ratio of the reconstructed image is same, the PSNR of our method is about 1.5 times better than the conventional scheme.So, the proposed algorithm provides the secure encryption and the improvement of compression efficiency.
Radiated Noise Properties from Inverter Unit Considering Antenna Height Dependency and Reflection Effects in Semi-Anechoic Chamber (2022)

Switching operation of semiconductor devices used in power electronics equipment generates electromagnetic (EM) noise, which may cause a malfunction in around equipment. In addition, power electronics equipment must meet electromagnetic compatibility (EMC) requirements. However, it is difficult to design power electronics equipment with suppressing EM noise due to its complex structure. In order to clarify the radiated EM noise properties from power electronics equipment, this paper presents the polarization and reflection effects of the radiated EM noise and the directivities of an inverter unit based on the 10 m far-field measurements in the semi-anechoic chamber.