gebhart/patrepeval huggingface dataset:
Adaptation of Fluctuating Magnetoacoustic System to External Signals (2021)

The adaptation of systems to external influences is of broad interest. We study the influence of microwave signals of different shapes on the magnetoacoustic wave system with a giant nonlinearity in canted antiferromagnet FeBO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> at room temperature, which is close to its phase transition to the paramagnetic state. The classical nonlinear system obeys external deterministic signals; the modulation response describes the shape of these signals. In response to a noisy spectrum, the system shows self-organization, and mode competition selects one excited mode while suppressing others. With an increase in the power of the external signal, another self-organization is observed in the form of a narrow peak at the frequency of the fundamental minimum. This represents the first observation of the macroscopic quantum statistical phenomenon, Bose-Einstein condensation of magnetoacoustic wave quanta in a wave system with a high level of thermal fluctuations. The resulting picture of adaptation can analogously be transferred to many other adaptive wave systems, including large scale adaptive wave systems in the natural environment.
MT1-MMP Plays a Critical Role In the Modulation of Hematopoiesis. (2010)

Abstract Abstract 3851 Specific niches, in which hematopoietic stem cells (HSCs) reside control the balance between HSC quiescence and self-renewal, yet little is known about the extrinsic signals provided by the niche and how these niche signals regulate such a balance. In the recent study, activation of the fibrinolytic pathway via matrix metalloproteinases (MMPs) including MMP-9 resulted in the release of kit ligand (KitL) in the BM niche. Membrane type 1-MMP (MT1-MMP) can activate MMP-9 in the process of mutual activation of MMP. It has already known that BM myeloablation with irradiation or anti-cancer drug induces MT1-MMP expression, but the role of MT1-MMP in hematopoiesis is not well-understood. We examined MT1-MMP deficient mice (MT1-MMP-/-) 12 days after birth. MT1-MMP-/- were suffering from pancytopenia, and are reduced numbers of bone marrow mononuclear cells (BMMCs), splenocytes and number of hematopoietic progenitor cells in the BM although the number of HSCs in BM showed no significant difference. BM cytospins from MT1-MMP-/- mice showed mild erythropoietic disturbance and severer impairment of myelopoiesis. Interestingly, a powerful hematopoietic factor, Kit-ligand (KitL) levels were significantly lower in MT1-MMP-/- mice than wild type. MT1-MMP knockdown by shRNA or/and siRNA impaired KitL expression and secretion in transfected stroma cells compared to Mock controls, demonstrating that reduced KitL plasma levels were due to impaired release/production and not due to reduced numbers of stromal cells in MT1-MMP-/-. Similarly, impaired proliferation and differentiation of MT1-MMP-/- BMMCs in vitro could be restored by exogenous sKitL. Others and we reported that BM ablation induces the production of stromal cell-derived factor-1 (SDF-1; CXCL12), which plays a key role in stem cell homing and B-cell lymphopoiesis. Reduced SDF-1 expression was observed in BMMCs of MT1-MMP-/- mice and genetic knockdown of MT1-MMP resulted in lower SDF-1 expression both on a transcriptional and protein level. BMMCs of MT1-MMP-/- showed a decrease in the percentage of mature B cells compare to controls. Knocking down of MT1-MMP in stromal cell reduced the number of adherent hematopoietic cells, but addition of rec. SDF-1 could reverse the phenotype. These results suggested stromal-derived MT1-MMP was functionally important to maintain HSC function in long-term cultures of WT HSCs. Thus, MT1-MMP is a critical modulator of hematopoiesis, as it alters the growth factor output of niche cells. Disclosures: No relevant conflicts of interest to declare.
MODERN CERAMIC-ON-CERAMIC BEARINGS IN TOTAL HIP ARTHROPLASTY – MINIMUM FIVE-YEAR FOLLOW-UP (2005)

Introduction and Aims: Third generation alumina ceramic-on-ceramic bearings are being increasingly used in hip replacement surgery as an alternative to polyethylene because of the unacceptably high wear of polyethylene bearings and associated osteolysis leading to failure of hip replacement. Follow-up time with these modern ceramic bearings is still short. Method: We report the minimum five-year follow-up of our first 300 hip replacements with these bearings in 283 patients, done between June 1997 and February 1999. Three hundred ceramic-on-ceramic Osteonics Securfit or Securfit Plus stems were used with the Osteonics Securfit cup in all cases – these are cement-free and hydroxyapatite coated. The bearings were third generation alumina ceramic femoral heads and cup inserts manufactured by CeramTec. The average age was 58 years and there were 52% females. Osteoarthritis was the diagnosis in 93% and inflammatory arthritis in four percent. We used 92% 32mm bearings and eight percent 28mm bearings. Results: Mean Harris hip score improved from 56 pre-operatively to 94 at five years. Complications included: three non-fatal and no fatal pulmonary emboli, one deep and four superficial infections. There were four revisions for periprosthetic femoral fracture, one for cup malposition and one for sciatic nerve palsy in a patient with proximal focal femoral deficiency. There were a further four re-operations for psoas tendonitis where the psoas tendon was released. There were no re-operations for bearing failure and none of the ceramic components failed catastrophically, although a small number of acetabular inserts chipped around the rim during insert and were discarded. Of particular interest is the fact that there was no osteolysis seen in any of these hips, either around the acetabulum or around the femur. The usual small lytic areas noted around the calcar and the trochanteric regions of the femur that are commonly seen with polyethylene bearings were completely absent in this group. Three of the hips squeak intermittently with vigorous activity. Conclusion: Third generation ceramic-on-ceramic bearings have only been available for seven or eight years. Early results using these new bearings are encouraging, in that osteolysis to date has not been seen in this series. No hip in this series has been revised for failure of these ceramic implants. It will be a further five to 10 years before we can be certain how these newer bearings will perform in the long term, but the five-year results are encouraging.
Achieving Multicolor Long-Lived Luminescence in Dye-Encapsulated Metal–Organic Frameworks and Its Application to Anticounterfeiting Stamps (2017)

Long-lived luminescent metal-organic frameworks (MOFs) have attracted much attention due to their structural tunability and potential applications in sensing, biological imaging, security systems, and logical gates. Currently, the long-lived luminescence emission of such inorganic-organic hybrids is dominantly confined to short-wavelength regions. The long-wavelength long-lived luminescence emission, however, has been rarely reported for MOFs. In this work, a series of structurally stable long-wavelength long-lived luminescent MOFs have been successfully synthesized by encapsulating different dyes into the green phosphorescent MOFs Cd(m-BDC)(BIM). The multicolor long-wavelength long-lived luminescence emissions (ranging from green to red) in dye-encapsulated MOFs are achieved by the MOF-to-dye phosphorescence energy transfer. Furthermore, the promising optical properties of these novel long-lived luminescent MOFs allow them to be used as ink pads for advanced anticounterfeiting stamps. Therefore, this work not only offers a facile way to develop new types of multicolor long-lived luminescent materials but also provides a reference for the development of advanced long-lived luminescent anticounterfeiting materials.
Studies on fractionated hyperthermia in L1A2 tumour cellsin vitro: Response to multiple equal heat fractions (1985)

The development of thermotolerance in L1A2 cells in vitro was investigated after fractionated hyperthermia at 42 degrees C. A single pretreatment of 90 min at 42 degrees C resulted in maximal thermotolerance at a 10 h fractionation interval with a thermotolerance ratio (TTR) of approximately 4.5. Thermotolerance was maintained at this level if the cells were exposed to 1-3 additional 90 min pretreatments separated by 10 h intervals. At a 6 h fractionation interval, where thermotolerance was still developing, additional 90 min pretreatments raised the level of thermotolerance to the level induced by the 10 h interval; the TTR increased from 2.1 to 4.5. Intervals of 20 and 24 h, at which there was decay but not complete disappearance of thermotolerance, did not induce such a build-up, and the TTR remained constant at 2.5 and 1.6, respectively. With 2 h fractionation intervals, where a single pretreatment did not induce thermotolerance, no thermotolerance was induced by additional pretreatments. With a shorter preheating time (e.g. 45 min at 42 degrees C) administration of a single pretreatment induced maximal thermotolerance after 6 h with a TTR of 3.0; additional 45 min pretreatments separated by 6 h intervals maintained this level. The thermotolerance induced by multifractioned hyperthermia as described above decayed in a similar way to that of cells exposed to a single pretreatment.
A Yeast Three Hybrid Assay for Metabolic Engineering of Tetracycline Derivatives (2018)

Metabolic engineering stands to transform the discovery and production of a wide range of chemicals, but metabolic engineering currently demands considerable resource investments that restrict commercial application. To facilitate the applicability of metabolic engineering, general high-throughput and readily implemented technologies are needed to assay vast libraries of strains producing desirable chemicals. Toward this end, we describe here the development of a yeast three hybrid (Y3H) assay as a general, high-throughput, versatile and readily implemented approach for the detection of target molecule biosynthesis. Our system detects target molecule biosynthesis through a change in reporter gene transcription that results from the binding of the target molecule to a modular protein receptor. We demonstrate the use of the Y3H assay for detecting the biosynthesis of tetracyclines, a major class of antibiotics, based on the interaction between tetracyclines and the tetracycline repressor protein (TetR). Various tetracycline derivatives can be detected using our assay, whose versatility enables its use both as a screen and a selection to match the needs and instrumentation of a wide range of end users. We demonstrate the applicability of the Y3H assay to metabolic engineering by differentiating between producer and nonproducer strains of the natural product tetracycline TAN-1612. The Y3H assay is superior to state-of-the-art HPLC-MS methods in throughput and limit of detection of tetracycline derivatives. Finally, our establishment of the Y3H assay for detecting the biosynthesis of a tetracycline supports the generality of the Y3H assay for detecting the biosynthesis of many other target molecules.
Graphene Oxide Interlayers for Robust, High-Efficiency Organic Photovoltaics (2011)

Organic photovoltaic (OPV) materials have recently garnered significant attention as enablers of high power conversion efficiency (PCE), low-cost, mechanically flexible solar cells. Nevertheless, further understanding-based materials developments will be required to achieve full commercial viability. In particular, the performance and durability of many current generation OPVs are limited by poorly understood interfacial phenomena. Careful analysis of typical OPV architectures reveals that the standard electron-blocking layer, poly-3,4-ethylenedioxy-thiophene:poly(styrene sulfonate) (PEDOT:PSS), is likely a major factor limiting the device durability and possibly performance. Here we report that a single layer of electronically tuned graphene oxide is an effective replacement for PEDOT:PSS and that it significantly enhances device durability while concurrently templating a performance-optimal active layer π-stacked face-on microstructure. Such OPVs based on graphene oxide exhibit PCEs as high as 7.5% while providing a 5× enhancement in thermal aging lifetime and a 20× enhancement in humid ambient lifetime versus analogous PEDOT:PSS-based devices.
Carbohydrate-Binding Protein from Stinging Nettle as Fusion Inhibitor for SARS-CoV-2 Variants of Concern (2022)

Abstract Urtica dioica agglutinin (UDA) is a carbohydrate-binding small monomeric protein isolated from stinging nettle rhizomes. It inhibits replication of a broad range of viruses, including coronaviruses, in multiple cell types, with appealing selectivity. In this work, we investigated the potential of UDA as a broad-spectrum antiviral agent against SARS-CoV-2. UDA potently blocks entry of pseudotyped SARS-CoV-2 in A549.ACE2 + -TMPRSS2 cells, with IC 50 values ranging from 0.32 to 1.22 µM. Furthermore, UDA prevents viral replication of the early Wuhan-Hu-1 strain in Vero E6 cells (IC 50 = 225 nM), but also the replication of SARS-CoV-2 variants of concern, including Alpha, Beta and Gamma (IC 50 ranging from 115 to 171 nM). In addition, UDA exerts antiviral activity against the latest circulating Delta and Omicron variant in U87.ACE2 + cells (IC 50 values are 1.6 and 0.9 µM, respectively). Importantly, when tested in Air-Liquid Interface (ALI) primary lung epithelial cell cultures, UDA preserves antiviral activity against SARS-CoV-2 (20A.EU2 variant) in the nanomolar range. Surface plasmon resonance (SPR) studies demonstrated a concentration-dependent binding of UDA to the viral spike protein of SARS-CoV-2, suggesting interference of UDA with cell attachment or subsequent virus entry. Moreover, in additional mechanistic studies with cell-cell fusion assays, UDA inhibited SARS-CoV-2 spike protein-mediated membrane fusion. Finally, pseudotyped SARS-CoV-2 mutants with N-glycosylation deletions in the S2 subunit of the spike protein remained sensitive to the antiviral activity of UDA. In conclusion, our data establish UDA as a potent and broad-spectrum fusion inhibitor for SARS-CoV-2.
A Time-Dependent Transport-Kinetics Model for Additive Interactions in Copper Interconnect Metallization (2004)

Electrodeposition of copper in the presence of additives mixture that is typically used in "bottom-up" fill of sub-micrometer vias and trenches on semiconductor wafers is analyzed. The time-dependent additives interactions, accounting for their transport and adsorption kinetics, are incorporated in a via-fill model. Transient polarization measurements provide the adsorption time constants for polyethylene glycol (PEG) and bis(3-sulfopropyl) disulfide (SPS). Experiments indicate that the fast PEG adsorption on the electrode is diffusion controlled, while the slow SPS adsorption is controlled by the adsorption kinetics. The results are applied to a transport-kinetics model that provides the additives distribution inside a via. It is noted that the PEG diffusion to the via bottom is extremely slow due to the PEG adsorption on the sidewalls. The role of SPS in the bottom-up fill is characterized by simulating the transport within the via through analogous transport to a flat rotating disk electrode. It is observed that SPS is essential for maintaining fast deposition at the via bottom by preventing PEG adsorption. The critical necessity for a three-additive system comprised of chloride ions, PEG, and SPS is explained, and process parameters essential for bottom-up fill are identified. © 2004 The Electrochemical Society. All rights reserved.
Semantic annotation of medical images (2010)

Diagnosis and treatment planning for patients can be significantly improved by comparing with clinical images of other patients with similar anatomical and pathological characteristics. This requires the images to be annotated using common vocabulary from clinical ontologies. Current approaches to such annotation are typically manual, consuming extensive clinician time, and cannot be scaled to large amounts of imaging data in hospitals. On the other hand, automated image analysis while being very scalable do not leverage standardized semantics and thus cannot be used across specific applications. In our work, we describe an automated and context-sensitive workflow based on an image parsing system complemented by an ontology-based context-sensitive annotation tool. An unique characteristic of our framework is that it brings together the diverse paradigms of machine learning based image analysis and ontology based modeling for accurate and scalable semantic image annotation.
Polarization sign inversion and smectic-A-smectic-C surface transitions in freely suspended films of fluorinated and nonfluorinated compounds (1998)

Abstract We report ellipsometric measurements on freely suspended films of chiral liquid-crystal compounds near their smectic-A-smectic-C transition. The temperature difference between the surface and the bulk transition is found to vary considerably within a homologous series. In two compounds possessing a fluorinated alkyl chain an unexpected sign inversion of the spontaneous polarization in the ferroelectric smectic-C phase is observed which occurs only in thin but not in thick films. Key Words: ferroelectric liquid crystalsfreely suspended films
Essentials of Fuzzy Modeling and Control (1994)

From the Publisher:
At last, here is a thorough introduction that offers complete coverage of all relevant theory and applications to the rapidly evolving field of fuzzy logic. While most other books on the subject tend to be loose collections of papers reporting on the state of this or that fuzzy area, Essentials of Fuzzy Modeling and Control follows a logical, pedagogically consistent format designed to fully acquaint readers with the entire range of fuzzy concepts, tools, and modeling techniques. While it is an excellent general introduction for students, the authors' ultimate goal is to give researchers an opportunity to acquire everything they need to build the kinds of fuzzy rule-based models used in the development of the controllers now being constructed for the next generation of intelligent systems.
Abstract 38. Atypical Proliferative Lesions after Reduction Mammaplasty: Incidence and Implications in 993 Reductions (2017)

Purpose: Reduction mammoplasty occasionally reveals unsuspected proliferative lesions or carcinoma. Few studies examine incidence, risk factors, and outcomes in this population. Methods: Retrospective review was performed between 2000 and 2012. Pathology was categorized as benign, proliferative, or cancer (DCIS or invasive). Results: Five hundred seventy-three patients had 993 reduction mammaplasties (85% bilateral, 15% unilateral). Cancer was detected in 23 (2.3%) specimens and proliferative lesions in 148 (14.9%). Compared to patients with benign pathology, patients with proliferative lesions or cancer were older (p<0.001), with larger BMI (p=0.001), increased unilateral procedures (p<0.001) and more had a history of cancer (p<0.001). On multivariate regression analysis, age and prior breast cancer were independent risk factors for proliferative lesions (OR 1.057, CI 1.039–1.075, p<0.001 and OR 2.201, CI 1.291–3.752, p=0.004) and age significantly predicted cancer (OR 1.050, CI 1.009–1.093, p=0.015). There was no association with resection weight (p>0.5). Fifty-four percent of patients with proliferative lesions and no history of cancer had a change in management with increased surveillance, hormones, radiation, chemotherapy, or surgery. If there was a history of cancer, 31% had a change in management. Of patients with DCIS or cancer, all required treatment. Conclusion: Proliferative lesions of the breast may be more common that previously reported. Age and a history of breast cancer increase risk for proliferative lesions. All should be referred to oncology.
Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity (2014)

PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed.
Structural and biophysical analysis of interactions between cod and human uracil-DNAN-glycosylase (UNG) and UNG inhibitor (Ugi) (2014)

Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme-substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG-Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG-Ugi complex with previously determined structures of UNG-Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (Kb) which is one order of magnitude larger than that for hUNG-Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein-Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.
Heavy Metal Effects on β-Glucosidase Activity Influenced by pH and Buffer Systems (1999)

Inhibition of beta-glucosidase activity by Cu(II), Zn(II) and Ni(II) was investigated as a function of pH and buffer type. Both factors were found to exert a strong effect on the activity of the enzyme. All three of the investigated heavy metals inhibited the enzyme activity in acetate buffer. At metal concentrations of 0.6 mM, Zn and Ni reduced the enzyme activity by 25-30% under optimal pH conditions (pH 5-5.2). Under the same conditions, Cu showed an even more pronounced inhibitory effect than Zn and Ni. In presence of 0.6 mM Cu, the enzyme activity was lowered by more than 90% in comparison to metal free systems. In contrast to these results, no enzyme inhibition was observed in citrate buffer, even in the presence of 1 mM Cu. The inhibition of beta-glucosidase activity by Cu increased with increasing pH. Inhibition by Zn and Ni was less pH-dependent in the observed pH range (pH 4-5.5). Copper caused a distinct shift in the pH optimum of enzyme activity, whereas this was not the case for Zn or Ni. The effects of buffer and pH on enzyme inhibition by Cu, Zn and Ni were successfully described using a chemical speciation model, based on the assumption that enzyme activity depends on the protonation of the amino acids at the reactive site and that enzyme activity is inhibited by complexation of the reactive sites by the heavy metal cations. The results show the importance of taking chemical conditions and speciation into account when investigating the effect of heavy metal cations on biological systems.