gebhart/patrepeval huggingface dataset:
Pathogenesis of medication-related osteonecrosis of the jaw: a comparative study of in vivo and in vitro trials (2018)

Objective This study was performed to determine whether the results of prevailing in vivo and in vitro studies offer a reliable model for investigation of medication-related osteonecrosis of the jaw (MRONJ). Methods Embase, Medline, and the Cochrane Library were searched for articles published from September 2003 to June 2017 involving experimental approaches to the pathogenesis of MRONJ. In vivo and in vitro trials were analyzed with respect to the scientific question, study design, methodology, and results. Results Of 139 studies, 87, 46, and 6 conducted in vivo, in vitro, and both in vivo and in vitro experiments, respectively. Rats, mice, dogs, minipigs, sheep, and rabbits were the preferred animal models used. Osteoblasts, osteoclasts, fibroblasts, keratinocytes, macrophages, and human umbilical vein endothelial cells were the preferred cell types. Zoledronate, alendronate, ibandronate, and risedronate were the most frequent bisphosphonates used. MRONJ was most reliably induced in minipigs because of the close relationship with human bone physiology. In vitro studies showed that reduced viability, growth, and migration of cells in the bone and soft tissues were causative for MRONJ. Other than exposed jawbone after tooth extraction, no reliable cofactors were found. Conclusion The minipig is the most suitable animal model for MRONJ.
Conformational Changes in HIV-1 Env Trimer Induced by a Single CD4 as Revealed by Cryo-EM (2017)

The HIV-1 Envelope (Env), a heterotrimeric glycoprotein on the virus surface, mediates attachment and entry into host cells, and is also the sole target for neutralizing antibodies. HIV-1 Env has a number of defenses that protect its most vulnerable regions from antibody recognition, which include glycan shielding, variable loops, and conformational masking. These defenses pose a challenge to both vaccine and therapeutics development The functional requirement of entry, however, necessitates conservation of receptor binding sites, as well as their exposure at specific points on the entry pathway (Figure An understanding of the interactions of HIV-1 with cellular receptors, and of its mechanism of entry, is therefore, intricately tied with efforts to develop an effective vaccine or therapeutic.
Bone Structure and Function (2009)

This chapter discusses the normal structure and function of the skeleton and the various ways it is regulated. The skeleton is both an organ and a type of connective tissue. Knowledge of its various identifiable parts greatly facilitates an understanding of skeletal function and also the disease processes that can occur. Normally, the major skeletal processes of resorption and formation are tightly coupled. This feature plays a role in the normal function of skeletal renewal. Disturbances of the remodeling cycle can be seen in a number of generalized skeletal disorders including metabolic bone disease and conditions such as Paget disease. This chapter discusses the macroscopic and microscopic anatomy of the skeleton as well as its biochemical makeup. It introduces the emerging information about the molecular control of bone cells and the skeletal processes.
Rare Examples of Transition-Metal−Main-Group Metal Heterometallic Metal−Organic Frameworks from Gallium and Indium Dipyrrinato Complexes and Silver Salts:  Synthesis and Framework Variability (2007)

New main-group metal dipyrrinato complexes [M(4-pyrdpm)3], where M = Ga3+ or In3+ and 4-pyrdpm is the anion of 5-(4-pyridyl)dipyrrin (4-pyrdpmH), have been synthesized and incorporated into metal-organic frameworks (MOFs) by reacting the dipyrrinato complexes with silver(I) salts. MOFs formed with AgOTf (OTf = O3SCF3) and AgSbF6 gave frameworks with three-dimensional (10,3) and two-dimensional (6,3) topologies, respectively. In contrast, AgPF6 produced both (10,3) and (6,3) network topologies, suggesting that the PF6 anion has little preference for templating (10,3) versus (6,3) frameworks within this system. These findings update an earlier MOF study that examined the role of these anions in templating related heterometallic MOFs which used [Fe(4-pyrdpm)3] and [Co(4-pyrdpm)3] metalloligands. All of the dipyrrin compounds reported here have been characterized by single-crystal X-ray crystallography, including the first crystallographically characterized example of a 1,2,3-unsubstituted free-base dipyrrin, 4-pyrdpmH.
High-temperature single-molecule kinetic analysis of thermophilic archaeal MCM helicases (2016)

The minichromosome maintenance (MCM) complex is the replicative helicase responsible for unwinding DNA during archaeal and eukaryal genome replication. To mimic long helicase events in the cell, a high-temperature single-molecule assay was designed to quantitatively measure long-range DNA unwinding of individual DNA helicases from the archaeons Methanothermobacter thermautotrophicus (Mth) and Thermococcus sp. 9°N (9°N). Mth encodes a single MCM homolog while 9°N encodes three helicases. 9°N MCM3, the proposed replicative helicase, unwinds DNA at a faster rate compared to 9°N MCM2 and to Mth MCM. However, all three MCM proteins have similar processivities. The implications of these observations for DNA replication in archaea and the differences and similarities among helicases from different microorganisms are discussed. Development of the high-temperature single-molecule assay establishes a system to comprehensively study thermophilic replisomes and evolutionary links between archaeal, eukaryal, and bacterial replication systems.
Al-2.96 Photomask (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Baseline Telomere Length and Effects of a Multidomain Lifestyle Intervention on Cognition: The FINGER Randomized Controlled Trial (2017)

Leukocyte telomere length (LTL) is a biomarker of aging, and it is associated with lifestyle. It is currently unknown whether LTL is associated with the response to lifestyle interventions. The goal is to assess whether baseline LTL modified the cognitive benefits of a 2-year multidomain lifestyle intervention (exploratory analyses). The Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) was a 2-year randomized controlled trial including 1,260 people at risk of cognitive decline, aged 60-77 years identified from the general population. Participants were randomly assigned to the lifestyle intervention (diet, exercise, cognitive training, and vascular risk management) and control (general health advice) groups. Primary outcome was change in cognition (comprehensive neuropsychological test battery). Secondary outcomes were changes in cognitive domains: memory, executive functioning, and processing speed. 775 participants (392 control, 383 intervention) had baseline LTL (peripheral blood DNA). Mixed effects regression models with maximum likelihood estimation were used to analyze change in cognition as a function of randomization group, time, baseline LTL, and their interaction. Intervention and control groups did not significantly differ at baseline. Shorter LTL was related to less healthy baseline lifestyle. Intervention benefits on executive functioning were more pronounced among those with shorter baseline LTL (p-value for interaction was 0.010 adjusted for age and sex, and 0.007 additionally adjusted for baseline lifestyle factors). The FINGER intervention cognitive benefits were more pronounced with shorter baseline LTL, particularly for executive functioning, indicating that the multidomain lifestyle intervention was especially beneficial among higher-risk individuals.
Molecularly Engineered “Janus GroEL”: Application to Supramolecular Copolymerization with a Higher Level of Sequence Control (2020)

Herein we report the synthesis and isolation of a shape-persistent Janus protein nanoparticle derived from the biomolecular machine chaperonin GroEL (<sup><b>A</b></sup><b>GroEL</b><sup><b>B</b></sup>) and its application to DNA-mediated ternary supramolecular copolymerization. To synthesize <sup><b>A</b></sup><b>GroEL</b><sup><b>B</b></sup> with two different DNA strands <b>A</b> and <b>B</b> at its opposite apical domains, we utilized the unique biological property of GroEL, i.e., Mg<sup>2+</sup>/ATP-mediated ring exchange between <sup><b>A</b></sup><b>GroEL</b><sup><b>A</b></sup> and <sup><b>B</b></sup><b>GroEL</b><sup><b>B</b></sup> with their hollow cylindrical double-decker architectures. This exchange event was reported more than 24 years ago but has never been utilized for molecular engineering of GroEL. We leveraged DNA nanotechnology to purely isolate Janus <sup><b>A</b></sup><b>GroEL</b><sup><b>B</b></sup> and succeeded in its precision ternary supramolecular copolymerization with two DNA comonomers, <b>A**</b> and <b>B*</b>, that are partially complementary to <b>A</b> and <b>B</b> in <sup><b>A</b></sup><b>GroEL</b><sup><b>B</b></sup>, respectively, and programmed to self-dimerize on the other side. Transmission electron microscopy allowed us to confirm the formation of the expected dual-periodic copolymer sequence -(<sup><b>B*/B</b></sup><b>GroEL</b><sup><b>A/A**/A**/A</b></sup><b>GroEL</b><sup><b>B/B*</b></sup>)- in the form of a laterally connected lamellar assembly rather than a single-chain copolymer.
A 0.25W fully integrated class-D audio power amplifier in 0.35&#x03BC;m CMOS (2007)

A fully integrated class-D audio power amplifier using Pulse Width Modulation (PWM) technique is presented. The output stage is an H-bridge with 5.75 mm wide nMOS transistors and 15 mm wide pMOS transistors, which can deliver up to 0.25 W <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</inf> to an 16 Ω load. The chip measuring 1.2×2.4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , including pads, was fabricated in a 0.35 μm CMOS process. It uses a single 3.3 V supply and a PWM carrier frequency of 2.5 MHz. The chip was designed and simulated with Cadence IC design tools as a student project in the course IC-project and verification at Lund University. The chip was verified and works well with a measured THD+N of 0.5% and efficiency of 76% at 0.25 W <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</inf> output power into 16 Ω.
Production of Narrow‐Size‐Distribution Polymer‐Pigment‐Nanoparticle Composites via Electrohydrodynamic Atomization (2007)

Abstract Near‐monodisperse, size‐controllable, poly(methyl methacrylate)‐pigment nanoparticle composites were produced using electrohydrodynamic atomization (EHDA). The geometric mean diameters of the composite particles were in the 0.91 to 1.90 µm‐diameter range with geometric standard deviations of approximately 1.05 to 1.12. Increasing the polymer volume fraction and liquid flow‐rate resulted in an increase in the diameter of the composite particles, which agreed well with droplet scaling relations for EHDA. The results here demonstrate that EHDA can be used for polymer‐nanoparticle‐composite production and as an alternative to conventional inkjet printing. magnified image
Effect of Ageing Atmosphere on Three-way Catalytic Performance of Supported Rh Catalysts (2021)

Deactivation of a mixture of Rh/Al2O3 and CeO2–ZrO2 (CZ) by high-temperature ageing was clearly observed in three-way catalytic reactions under lean/rich perturbation conditions. The light-off temperature at which 50 % conversion was achieved was increased in the order of fresh < stoichi. ≈ rich < rich/lean < lean ageing conditions. Rh dispersion and presence of isolated Rh sites, revealed from in-situ FT-IR spectroscopy following CO adsorption, were responsible for the high light-off activity. NO conversion in higher temperature regions under lean/rich perturbation conditions was influenced by the ageing atmosphere. H2-TPR measurements suggested the formation of Rh–CZ interactions with different strengths depending on the atmosphere during high-temperature ageing. The strength of the Rh–CZ interaction was suspected to be important to achieve high NO conversion in higher temperature regions.
Measuring foam model shapes with a contact digitizer (2011)

Accurate model measurements can assist clinical service providers in the identification of problems and the repair of carving equipment. This facilitates the delivery of high quality sockets to practitioners and patients.
CMOS photo-transistor array detection system for visual light identification (ID) (2008)

Visible light communication is a wireless communication method modulating the light of visible LED. In this study, high sensitive photo-transistor array has been developed for the visible light identification (ID) using CMOS 0.35 mum process. The response sensitivity of photo-transistor is over 0.8 A/W. The photo-transistor is selected by the outer signal in order to separate the signals from multiple light sources. The image of light sources is scanned by CCD module, and the brightest position is determined by C++ software.
Permanent magnet DC linear machine model for real time simulation (2006)

One of the challenges in real time modeling of electrical machines is obtaining the electrical parameters of the machine, especially with non-standard geometries as is the case at this level of developments in permanent magnet DC linear motors (PMDCLMs). In this paper, finite element analysis method is used to evaluate the inductances of the machine as a function of mover, in this case permanent magnet, position. These inductances are then tabulated and directly used in the simulation of the motor on a real time digital simulator. The developed model has the advantage of allowing dynamic characteristics of the machine, with available switching converter models, to be evaluated before its construction
Interactive transformation of java programs in eclipse (2006)

Implementing large and sweeping changes to software source code can be tedious and error-prone. A conceptually simple change may require a significant code editing effort. Integrating scriptable source-to-source program transformations into development environments can assist developers with this task. We present a developer-oriented interactive source code transformation tool for Java that addresses this need.
Methylphenidate Treatment in ADHD/borderline Personality Disorder Adolescent Girls and Smoking Behavior (2009)

Background: Cigarette smoking and nicotine dependence is prevalent among the attention deficit/hyperactivity disorder (ADHD) pediatric population. We assessed the influence of methylphenidate treatment on the smoking behavior of adolescent girls with ADHD/ borderline personality disorder (BPD). Method: Twelve ADHD/BPD female adolescent smokers aged 14-19 years were treated with MPH for an 8 week period. The severity of ADHD was assessed by the ADHD Rating Scale (ADHD-RS) and the smoking behavior was rated by Fagerstorm Test for Nicotine Dependence (FTND). Results: Significant improvement was detected in ADHD symptomathology, (Baseline vs. endpoint: ADHD-RS : 33.1±6.8 vs. 19.9±6.8, t=6.875, df=11, p=0.0001). A decline in the severity of nicotine dependence, as assessed by FTND (baseline vs. endpoint: 4.1±2.6 vs. 2.0±1.9, t = 4.056, df=11, p= 0.0019), was observed. No significant correlation was found between changes in the ADHD-RS and the FTND following methylphenidate treatment (r=0.09935, p=0.7587). Conclusion: Methylphenidate may attenuate smoking behavior in ADHD/BPD female adolescent smokers.
Verifiable Hypotheses for Thymosin β4-Dependent and -Independent Angiogenic Induction of Trichinella spiralis-Triggered Nurse Cell Formation (2013)

Trichinella spiralis has been reported to induce angiogenesis for nutrient supply and waste disposal by the induction of the angiogenic molecule vascular endothelial cell growth factor (VEGF) during nurse cell formation. However, the action mechanism to induce VEGF in nurse cells by T. spiralis is not known. Hypoxia in nurse cells was suggested as a possible mechanism; however, the presence of hypoxic conditions in infected muscle or nurse cells and whether hypoxia indeed induces the expression of VEGF and subsequent angiogenesis in the infected muscle are both a matter of debate. Our recent studies have shown that thymosin β4, a potent VEGF inducing protein, is expressed in the very early stages of T. spiralis muscle infection suggesting the induction of VEGF in early stage nurse cells. Nevertheless, we now show that hypoxic conditions were not detected in any nurse cell stage but were detected only in the accumulated inflammatory cells. These studies propose that induction of angiogenesis by VEGF in T. spiralis-infected nurse cells was mediated by thymosin β4 and is unrelated to hypoxic conditions.
Paraffin-Based 6-Gene Model Predicts Outcome of Diffuse Large B-Cell Lymphoma Patients Treated with R-CHOP. (2007)

Abstract Background: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease characterized by highly variable clinical outcomes. It is therefore of paramount importance to be able to predict the outcome of patients at the time of diagnosis. Previously, we constructed a 6 gene model for outcome prediction of DLBCL patients treated with anthracycline-based chemotherapies (Lossos et al NEJM 2004, 350:1829). However, the standard therapy has evolved to rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone (R-CHOP). Subset analyses of clinical trials have suggested that some of the prognostic factors lose their predictive power in R-CHOP treated patients. Consequently, the molecular gold standard for survival prediction in R-CHOP treated patients has not been established. Herein, we evaluated the predictive power of the 6-gene model in R-CHOP treated DLBCL patients. We have employed new methodology that allows quantitation of gene expression from paraffin embedded, fixed tissues. Methods: RNA was extracted from 100 paraffin-embedded specimens (Chen et al Diagn Mol Pathol 2007, 16:61), from patients with DLBCL treated with R-CHOP in British Columbia (73) and at the University of Miami (27). Expression of the 6 genes comprising the model was measured in these samples and the mortality-prediction score was calculated for each patient, as reported previously. Results: The study group consisted of 100 patients with a median age of 58 y (range, 16–92y) that were followed for a median of 2.1 years (range, 0.1–5.6). Distribution according to IPI: 0–1 factor, 42; 2 factors, 24; 3 factors, 19; and ≥4 factors, 14. RNA of sufficient quality and quantity was successfully extracted from all the 100 paraffin embedded specimens tested, some of which had been stored for up to 6 years. The mortality-prediction score derived from the model divided patients into low-risk (50%) and high-risk (50%) subgroups with significantly different overall survival (OS) (p=0.02) and progression free survival (PFS) (p=0.02). Notably the OS was similar between the groups during the 1st year, due to the inclusion of patients with advanced age and poor performance status, but it was markedly different beyond the first 2 years, with the 3 year OS of 80% and 50% in the low risk and high risk groups, respectively. The predictive power of the 6-gene model was independent of the IPI prognostic factors for prediction of OS (P=0.06) and PFS (p=0.01) in these patients. Conclusions: The prognostic value of the 6-gene model remains significant in the era of R-CHOP treatment. Further, using the new RNA extraction methodology, we demonstrate that the model can be applied to routinely available formalin-fixed paraffin blocks from initial diagnostic biopsies, even after long term storage. Following validation in an independent cohort of patients, the six gene model may be practically applied in routine clinical practice.
Management of Intratemporal Facial Nerve Schwannoma (2003)

In cases with good facial nerve function, it would be better to consider an alternative method for preserving the facial nerve. Furthermore, when facial nerve paralysis has developed to more than House-Brackmann grade III, an immediate operation is recommended to obtain a good postoperative facial functional recovery.
Evaluation of transducer configurations for ultrasound cross-correlation flowmeters (2014)

Ultrasound cross-correlation flowmeters are utilized to measure the flow velocity of liquids or gases in pipes. The basic concept is to measure the time interval needed by the flow for travelling a given distance between two measurement channels, each consisting of a pair of ultrasound transducers. At each channel, ultrasound waves are emitted in a direction perpendicularly to the flow, and phase and amplitude modulations, which are caused by turbulences and naturally occurring speed of sound variations inside the flowing medium, are assessed. In this paper, different configurations of circular and linear ultrasound transducers have been evaluated for flow velocity measurement in small pipes. The specific problem is that the apertures of the utilized ultrasound transducers are relatively large compared to the diameter of the pipe. The crosstalk between the two channels is another problem, especially for ultrasound beams with large opening angles. Experiments have been performed using different setups consisting of an acrylic glass pipe with 8 mm inner diameter and two measurement channels at a distance of 12 mm from each other. Measurements have been performed using circular (8 mm diameter, 2 MHz frequency) and, alternatively, linear transducers (8 mm length, 1 mm width, 1.4 MHz frequency), and a turbine flowmeter has been used as a reference. It will be shown that the normalized covariance function can be used as a measure to assess the performance of the cross-correlation flowmeter and the reliability of flow velocity estimates. Results of measurements obtained with degassed water have shown that in the case of highly homogeneous liquids the best performance of the flowmeter is achieved by using the phase modulation signals for the cross-correlation.