gebhart/patrepeval huggingface dataset:
Improved giant magnetostrictive materials: New and improved Terfenol-D (1997)

The giant magnetostrictive terbium-iron alloy material, Terfenol-D, offers the highest strain of any magnetostrictive material at room temperature using practical drive fields. The increasing use of Terfenol-D in a wide variety of production devices and systems has driven the development of new, advanced manufacturing techniques in material production to provide greater strain performance, uniformity, rod size, and production capacity. As more applications for this smart material are developed, the demand for reliable design data to enable applications engineers to take advantage of Terfenol-D’s superior properties has also grown. Recent developments in production techniques have made strides to fulfill needs in both areas. The ETREMA crystal growth (ECG) system, based on the modified Bridgman process, is capable of producing larger rod sizes (65-mm diameter and 175-mm length) with greater quality control, performance, material homogeneity, and uniformity. These improvements are quantified with material property data. Terfenol-D samples are characterized in a transducer under a wide variety of real-world operating conditions. Results show greatly improved consistency of material performance, in terms of material properties, from test to test.
Bandelettes et représentation géométrique des images (2002)

The results show that gamma GCS is strongly expressed in NSCLCs and probably takes part in the defense of the tumor cells against oxidative damage. This is reflected by the lower extent of apoptosis in tumors with a high gamma GCS expression. Because expression of gamma GCS has been connected with chemoresistance, downregulation of its activity by inhibitors in NSCLC might have putative therapeutic potential in the treatment of lung carcinoma.
Transcribed ultraconserved noncoding RNAs (T-UCR) are involved in Barrett's esophagus carcinogenesis (2014)

Barrett's esophagus (BE) involves a metaplastic replacement of native esophageal squamous epithelium (Sq) by columnar-intestinalized mucosa, and it is the main risk factor for Barrett-related adenocarcinoma (BAc). Ultra-conserved regions (UCRs) are a class non-coding sequences that are conserved in humans, mice and rats. More than 90% of UCRs are transcribed (T-UCRs) in normal tissues, and are altered at transcriptional level in tumorigenesis. To identify the T-UCR profiles that are dysregulated in Barrett's mucosa transformation, microarray analysis was performed on a discovery set of 51 macro-dissected samples obtained from 14 long-segment BE patients. Results were validated in an independent series of esophageal biopsy/surgery specimens and in two murine models of Barrett's esophagus (i.e. esophagogastric-duodenal anastomosis). Progression from normal to BE to adenocarcinoma was each associated with specific and mutually exclusive T-UCR signatures that included up-regulation of uc.58-, uc.202-, uc.207-, and uc.223- and down-regulation of uc.214+. A 9 T-UCR signature characterized BE versus Sq (with the down-regulation of uc.161-, uc.165-, and uc.327-, and the up-regulation of uc.153-, uc.158-, uc.206-, uc.274-, uc.472-, and uc.473-). Analogous BE-specific T-UCR profiles were shared by human and murine lesions. This study is the first demonstration of a role for T-UCRs in the transformation of Barrett's mucosa.
Association between textural and morphological tumor indices on baseline PET‐CT and early metabolic response on interim PET‐CT in bulky malignant lymphomas (2017)

The combination of usual prognostic factors with appropriately chosen textural and shape parameters evaluated on baseline PET-CT improves the prediction of early metabolic response in bulky lymphoma.
The Discovery and Preclinical Development of ASG-5ME, an Antibody–Drug Conjugate Targeting SLC44A4-Positive Epithelial Tumors Including Pancreatic and Prostate Cancer (2016)

Here, we report the development of an antibody-drug conjugate, ASG-5ME, which targets the solute carrier receptor SLC44A4. SLC44A4 is a member of a family of putative choline transporters that we show to be markedly upregulated in a variety of epithelial tumors, most notably prostate and pancreatic cancer. SLC44A4 is normally expressed on the apical surface of secretory epithelial cells, but in cancer we show expression is not restricted to the luminal surface in advanced and undifferentiated tumors. ASG-5ME consists of a human IgG2 anti-SLC44A4 antibody conjugated through a cleavable linker to the microtubule-disrupting agent monomethylauristatin E. It has potent antitumor activity in both cell line - and patient-derived xenograft models of pancreatic and prostate cancers. Combination studies with ASG-5ME and nab-paclitaxel demonstrated combination effect in both pancreatic and prostate tumor models. Altogether, the data presented here suggest that ASG-5ME may have the potential to offer a new therapeutic option for the treatment of pancreatic and prostate cancers. Mol Cancer Ther; 15(11); 2679-87. ©2016 AACR.
Adrenal vein sampling: External validation of multinomial regression modelling and left adrenal vein‐to‐peripheral vein ratio to predict lateralization index without right adrenal vein sampling (2020)

Minimal changes in specificity from development to validation cohorts validate the use of MRM and LAV/PV to predict the lateralization index when the right AVS is missing. Both methods had better accuracy for right than left lateralization detection.
Stimulation of DNA repair by the spermatidal TP1 protein (2001)

The chromatin remodeling process that takes place during spermiogenesis in mammals is characterized by a transient increase in DNA single-strand breaks (SSB). The mammalian transition proteins (TPs) are expressed at a high level at mid-spermiogenesis steps coincident with chromatin remodeling and could be involved in the repair of these lesions since SSB are no longer detected in terminally differentiated spermatids. We report that TP1 can stimulate the repair of SSB in vitro and demonstrate that in vivo repair of UV-induced DNA lesions is enhanced in mammalian cells stably expressing TP1. These results suggest that, aside from its role in DNA compaction, this major transition protein may contribute to the yet unidentified enzymatic activity responsible for the repair of SSB at mid-spermiogenesis steps. These results also suggest that the TP1 proteins have the potential to participate in the repair process following genotoxic insults and therefore may play an active role in the maintenance of the integrity of the male haploid genome during spermiogenesis.
Evolutionary Potential of (β/α)8-Barrels:  Functional Promiscuity Produced by Single Substitutions in the Enolase Superfamily (2003)

The members of the mechanistically diverse, (beta/alpha)(8)-barrel fold-containing enolase superfamily evolved from a common progenitor but catalyze different reactions using a conserved partial reaction. The molecular pathway for natural divergent evolution of function in the superfamily is unknown. We have identified single-site mutants of the (beta/alpha)(8)-barrel domains in both the l-Ala-d/l-Glu epimerase from Escherichia coli (AEE) and the muconate lactonizing enzyme II from Pseudomonas sp. P51 (MLE II) that catalyze the o-succinylbenzoate synthase (OSBS) reaction as well as the wild-type reaction. These enzymes are members of the MLE subgroup of the superfamily, share conserved lysines on opposite sides of their active sites, but catalyze acid- and base-mediated reactions with different mechanisms. A comparison of the structures of AEE and the OSBS from E. coli was used to design the D297G mutant of AEE; the E323G mutant of MLE II was isolated from directed evolution experiments. Although neither wild-type enzyme catalyzes the OSBS reaction, both mutants complement an E. coli OSBS auxotroph and have measurable levels of OSBS activity. The analogous mutations in the D297G mutant of AEE and the E323G mutant of MLE II are each located at the end of the eighth beta-strand of the (beta/alpha)(8)-barrel and alter the ability of AEE and MLE II to bind the substrate of the OSBS reaction. The substitutions relax the substrate specificity, thereby allowing catalysis of the mechanistically diverse OSBS reaction with the assistance of the active site lysines. The generation of functionally promiscuous and mechanistically diverse enzymes via single-amino acid substitutions likely mimics the natural divergent evolution of enzymatic activities and also highlights the utility of the (beta/alpha)(8)-barrel as a scaffold for new function.
One-pot synthesis of a ceria–graphene oxide composite for the efficient removal of arsenic species (2016)

Arsenic contamination has posed a health risk to millions of people around the world. In this study, we describe a simple and facile one-step hydrothermal synthesis of a ceria-graphene oxide (ceria-GO) composite for the efficient removal of arsenic species. The prepared ceria-GO composite materials exhibited almost complete (over 99.99%) and quick removal of both arsenic species within 0.1 mg L<sup>-1</sup> of the initial concentration. The calculated adsorption capacities were 185 mg g<sup>-1</sup> for As(iii) and 212 mg g<sup>-1</sup> for As(v). It was found that Ce<sup>3+</sup> is an active site and continuously adsorbs arsenic species; there is a concomitant change from Ce<sup>4+</sup> to Ce<sup>3+</sup> due to the solution redox environment. This increase in the Ce<sup>3+</sup> concentration further facilitates the complete removal of arsenic species in solution. Thus our approach offers a promising potential for the treatment of arsenic-contaminated drinking water.
Data-driven taxonomy forest for fine-grained image categorization (2015)

Fine-grained image categorization must handle huge cross-class ambiguities and a large number of classes. Inspired by the success of rigid hierarchical classification, we propose a new flexible hierarchical classification method, called a data-driven taxonomy forest. It constructs a multitude of taxonomies, each of which converts a complex multi-class problem to a more easily tractable path-finding problem. We demonstrate how a stochastic representation of local classification hypotheses incorporated in multiple taxonomies deals skillfully with error propagation and over-fitting. Various strategies for instance space decomposition are investigated from the viewpoint of taxonomy complexity. We comprehensively evaluate our data-driven taxonomy forest using Oxford Flower 102 and Oxford Pet benchmarks and show its superiority in effectiveness and generality to rigid hierarchical classification in fine-grained image categorization tasks.
Modeling of Needle Steering via Duty-Cycled Spinning (2007)

As flexible bevel tip needles are inserted into tissue, a deflection force causes the needle to bend with a curvature dependent on relative stiffness and bevel angle. By constantly spinning the needle during insertion, the bevel angle is essentially negated and a straight trajectory can be achieved. Incorporating duty-cycled spinning during needle insertion provides proportional control of the curvature of the needle trajectory through tissue. This paper proposes a kinematic model for needle steering via duty-cycled spinning. Validation using experimental results is also presented.
5-Endo Cyclizations of NHC-Boraallyl Radicals Bearing Ester Substituents: Characterization of Derived 1,2-Oxaborole Radicals and Boralactones (2018)

EPR studies of radical hydrogen abstraction reactions of N-heterocyclic carbene (NHC) complexes of alkenylboranes bearing two ester substituents revealed not the expected boraallyl radicals but instead isomeric 1,2-oaxborole radicals. Such radicals are new, and DFT calculations show that they arise from the initially formed boraallyl radicals by a rapid, exothermic 5- endo cyclization. These spectroscopic and computational discoveries prompted a series of preparative experiments that provided access to a novel family of robust NHC-boralactones. A one-pot procedure was developed to access the boralactones directly from an NHC-borane (NHC-BH<sub>3</sub>) and dimethyl acetylenedicarboxylate.
Dietary Modification of Yolk Lipid with Menhaden Oil (1991)

Due to the numerous proposed cardiovascular benefits associated with consumption of omega-3 fatty acids, marketing of an egg enriched by omega-3 fatty acid may benefit the egg producer. Effects on yolk composition of a standard laying hen diet enriched with 3% menhaden oil (test diet), versus an isocaloric (control) diet containing no added fat, were evaluated for 18 wk. Dietary menhaden oil did not alter egg production, egg weight, total yolk fat, or yolk cholesterol. However, yolk contents of omega-6 and omega-3 fatty acids were influenced by diet. Arachidonic acid decreased and eicosapentaenoic acid increased in eggs from hens fed the test diet following 1 wk of dietary treatment. Docosahexaenoic acid and linolenate increased in eggs from hens fed the test diet at 2 and 3 wk of the trial, respectively. These alterations in yolk composition resulted in a decrease in the ratio of omega-6 to omega-3 fatty acids from 18 for eggs from hens fed the control diet to 3 for eggs from hens fed the test diet. At Weeks 14 and 18, hens (n = 10 per diet) were killed and necropsied. No change in gross scoring of hepatic lipidosis was observed. Histologically, significantly greater scores for hepatocellular lipid infiltration were recorded for liver sections from hens fed menhaden oil than for control hens. Increased microscopic hepatic lipid infiltration observed with dietary omega-3 administration may have significance for flocks predisposed to fatty liver syndrome and may also provide a unique system in which to study the effects of dietary omega-3 fatty acids on liver lipid metabolism.
Front Matter: Volume 10927 (2019)

00, 01, 02,
Staphylococcal Protein A Induces Leukocyte Necrosis by Complexing with Human Immunoglobulins (2021)

One of the defining features of Staphylococcus aureus is its ability to evade and impair the human immune response through expression of staphylococcal protein A (SpA). Herein, we describe a previously unknown mechanism by which SpA can form toxic immune complexes when in the presence of human serum, which leads to the loss of human leukocytes. Further, we demonstrate that these toxic complexes are formed specifically through SpA's interaction with intact human IgG and that, in the presence of purified IgG Fab and Fc fragments, SpA shows no such toxicity. The mechanism of action of this toxicity appears to be one mediated by necrosis and not by apoptosis, as previously hypothesized, with up to 90% of human B cells rapidly becoming necrotic following stimulation with SpA-IgG complexes. This phenomenon depends on the immunoglobulin binding capacity of SpA, as a nonbinding mutant of SpA did not induce necrosis. Importantly, immune sera raised against SpA had the capacity to significantly reduce the observed toxicity. An unprecedented toxic effect of SpA-IgG complexes on monocytes was also observed, suggesting the existence of a novel mechanism independent from the interaction of SpA with the B cell receptor. Together, these data implicate SpA in inducing indiscriminate leukocyte toxicity upon formation of complexes with IgG and highlight the requirement for vaccination strategies to inhibit this mechanism. <b>IMPORTANCE</b> Staphylococcus aureus is one of the largest health care threats faced by humankind, with a reported mortality rate within the United States greater than that of HIV/AIDS, tuberculosis, and viral hepatitis combined. One of the defining features of S. aureus as a human pathogen is its ability to evade and impair the human immune response through expression of staphylococcal protein A. Herein, we show that SpA induces necrosis in various immune cells by complexing with human immunoglobulins. Vaccination of mice with a nontoxigenic SpA mutant induced sera capable of inhibiting this mechanism. These observations shed new light on the toxic mechanisms of this key staphylococcal virulence factor and on protective modalities of SpA-based vaccination.
An n-well CMOS dynamic RAM (1982)

A new n-well CMOS dynamic RAM is proposed. Experimental results with a 4K RAM, fabricated with advanced 2-µm lithography, are presented. For the design of RAM's greater than 256K, two major problems need to be solved: the increase in substrate current, and alpha-particle-induced soft errors. The new n-well CMOS RAM technology provides a solution to these problems. Use of PMOS transistors as load elements in peripheral circuits of the n-well CMOS RAM reduces the substrate current by at least two orders of magnitude. In addition, the potential barrier between the n-type, well and the p-type substrate rejects holes generated in the substrate, resulting in the reduction of soft error rates.
Targeting a Novel RNA-Protein Interaction for Therapeutic Intervention of Hantavirus Disease (2016)

An evolutionarily conserved sequence at the 5' terminus of hantaviral genomic RNA plays an important role in viral transcription initiation and packaging of the viral genome into viral nucleocapsids. Interaction of viral nucleocapsid protein (N) with this conserved sequence facilitates mRNA translation by a unique N-mediated translation strategy. Whereas this evolutionarily conserved sequence facilitates virus replication with the assistance of N in eukaryotic hosts having multifaceted antiviral defense, we demonstrate its interaction with N presents a novel target for therapeutic intervention of hantavirus disease. Using a high throughput screening approach, we identified three lead inhibitors that bind and induce structural perturbations in N. The inhibitors interrupt N-RNA interaction and abrogate both viral genomic RNA synthesis and N-mediated translation strategy without affecting the canonical translation machinery of the host cell. The inhibitors are well tolerated by cells and inhibit hantavirus replication with the same potency as ribavarin, a commercially available antiviral. We report the identification of a unique chemical scaffold that disrupts a critical RNA-protein interaction in hantaviruses and holds promise for the development of the first anti-hantaviral therapeutic with broad spectrum antiviral activity.
Evaluation of Membrane Bioreactor Process Capabilities to Meet Stringent Effluent Nutrient Discharge Requirements (2005)

A six-stage membrane bioreactor (MBR) pilot plant was operated to determine and demonstrate the capability of this process to produce a low-nutrient effluent, consistent with the nutrient reduction goals for the Chesapeake Bay. Biological nitrogen removal was accomplished using a multistage configuration with an initial anoxic zone (using the carbon in the influent wastewater), an aerobic zone (where nitrification occurred), a downstream anoxic zone (where methanol was added as a carbon source), and the aerated submerged membrane zone. The capability to reliably reduce effluent total nitrogen to less than 3 mg/L as nitrogen (N) was demonstrated. A combination of biological (using an initial anaerobic zone) and chemical (using alum) phosphorus removal was used to achieve effluent total phosphate concentrations reliably less than 0.1 mg/L as phosphorus (P) and as low as 0.03 mg/L as P. Alum addition also appeared to enhance the filtration characteristics of the MBR sludge and to reduce membrane fouling. Aeration of the submerged membranes results in thickened sludge with a high dissolved oxygen concentration (approaching saturation), which can be recycled to the main aeration zone rather than to an anoxic or anaerobic zone to optimize biological nutrient removal. Biological nutrient removal was characterized using the International Water Association Activated Sludge Model No. 2d. The stoichiometry of chemical phosphorus removal was also consistent with conventional theory and experience. The characteristics of the solids produced in the MBR were compared with those of a parallel full-scale conventional biological nitrogen removal process and were generally found to be similar. These results provide valuable insight to the design and operating characteristics of MBRs intended to produce effluents with very low nutrient concentrations.
Noninvasive vasectomy using a focused ultrasound clip: thermal measurements and simulations (2001)

Both simulations and experiments suggest that a therapeutic window exists in which thermal occlusion of the vas may be achieved without the formation of skin burns in the canine model (power = 5-7 W, surface intensity = 1.4-1.9 W/cm2, time = 20-50 s). This range of ablation parameters will help guide future experiments to refine incisionless vasectomy using focused ultrasound.
High-efficiency metal-semiconductor-metal photodetectors on heteroepitaxially grown Ge on Si (2006)

We demonstrate extremely efficient germanium-on-silicon metal-semiconductor-metal photodetectors with responsivities (R) as high as 0.85 A/W at 1.55 microm and 2V reverse bias. Ge was directly grown on Si by using a novel heteroepitaxial growth technique, which uses multisteps of growth and hydrogen annealing to reduce surface roughness and threading dislocations that form due to the 4.2% lattice mismatch. Photodiodes on such layers exhibit reverse dark currents of 100 mA/cm2 and external quantum efficiency up to 68%. This technology is promising to realize monolithically integrated optoelectronics.
Commercial 4-Dimensional Echocardiography for Murine Heart Volumetric Evaluation after Myocardial Infarction (2020)

Abstract Background Traditional preclinical echocardiography (ECHO) modalities, including 1-dimensional motion-mode (M-Mode) and 2-dimensional long axis (2D-US), rely on geometric and temporal assumptions about the heart for volumetric measurements. Surgical animal models, such as the mouse coronary artery ligation (CAL) model of myocardial infarction, result in morphologic changes that do not fit these geometric assumptions. New ECHO technology, including 4-dimensional ultrasound (4D-US), improves on these traditional models. This paper aims to compare commercially available 4D-US to M-mode and 2D-US in a mouse model of CAL. Methods 37 mice underwent CAL surgery, of which 32 survived to a 4 week post-operative time point. ECHO was completed at baseline, 1 week, and 4 weeks after CAL. M-mode, 2D-US, and 4D-US were taken at each time point and evaluated by two separate echocardiographers. At 4 weeks, a subset (n=12) of mice underwent cardiac magnetic resonance (CMR) imaging to serve as a reference standard. End systolic volume (ESV), end diastolic volume (EDV), and ejection fraction (EF) were compared among imaging modalities. Hearts were also collected for histologic evaluation of scar size (n=16) and compared to ECHO-derived wall motion severity index (WMSI) and global longitudinal strain as well as gadolinium-enhanced CMR to compare scar assessment modalities. Results 4D-US provides close agreement of ESV (Bias: -2.55%, LOA: -61.55 to 66.66) and EF (US Bias: 11.23%, LOA -43.10 to 102.8) 4 weeks after CAL when compared to CMR, outperforming 2D-US and M-mode estimations. 4D-US has lower inter-user variability as measured by intraclass correlation (ICC) in the evaluation of EDV (0.91) and ESV (0.93) when compared to other modalities. 4D-US also allows for rapid assessment of WMSI, which correlates strongly with infarct size by histology (r=0.77). Conclusion 4D-US outperforms M-Mode and 2D-US for volumetric analysis 4 weeks after CAL and has higher inter-user reliability. 4D-US allows for rapid calculation of WMSI, which correlates well with histologic scar size.