gebhart/patrepeval huggingface dataset:
Extended adjuvant endocrine therapy in a longitudinal cohort of young breast cancer survivors (2023)

Extended adjuvant endocrine therapy (eET) improves outcomes in breast cancer survivors. Most studies however have been limited to postmenopausal women, and optimal eET for young survivors is uncertain. We report eET use among participants in the Young Women's Breast Cancer Study (YWS), a multicenter prospective cohort of women age ≤40 newly diagnosed with breast cancer enrolled between 2006-2016. Women with stage I-III hormone receptor-positive breast cancer, ≥6 years from diagnosis without recurrence were considered eET candidates. Use of eET was elicited from annual surveys sent years 6-8 after diagnosis, censoring for recurrence/death. 663 women were identified as eET candidates with 73.9% (490/663) having surveys eligible for analysis. Among eligible participants, mean age was 35.5 (±3.9), 85.9% were non-Hispanic white, and 59.6% reported eET use. Tamoxifen monotherapy was the most reported eET (77.4%), followed by aromatase inhibitor (AI) monotherapy (21.9%), AI-ovarian function suppression (AI-OFS) (6.8%) and tamoxifen-OFS (3.1%). In multivariable analysis, increasing age (per year odds ratio [OR]: 1.10, 95% confidence interval [CI]: 1.04-1.16), stage (II v. I: OR: 2.86, 95% CI: 1.81-4.51; III v. I: OR: 3.73, 95%CI: 1.87-7.44) and receipt of chemotherapy (OR: 3.66, 95% CI: 2.16-6.21) were significantly associated with eET use. Many young breast cancer survivors receive eET despite limited data regarding utility in this population. While some factors associated with eET use reflect appropriate risk-based care, potential sociodemographic disparities in uptake warrants further investigation in more diverse populations.
Analysis of the PROCEED registry by baseline prostate-specific antigen (PSA) quartiles: Preliminary analysis of real-world sipuleucel-T (sip-T) use. (2016)

193 Background: Sip-T is an FDA-approved, autologous cellular immunotherapy for asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC). Post-hoc analysis of the phase 3 IMPACT study revealed that compared with the highest baseline PSA quartile, patients (pts) in the lowest quartile treated with sip-T had a larger overall survival (OS) benefit, suggesting sip-T is most beneficial if administered earlier in the treatment of mCRPC (Schellhammer et al., Urology. 2013.). This analysis evaluated pt characteristics by PSA quartiles in PROCEED (NCT01306890). Methods: Pts enrolled in PROCEED with baseline PSA and ≥ 1 sip-T infusion were included in this analysis. PSA values were divided into quartiles, and trends in baseline pt characteristics were evaluated as well as time to first anticancer intervention (tACI) with approved mCRPC therapies (docetaxel [D], cabazitaxel, abiraterone [abi], or enzalutamide [enz]) following sip-T treatment. Radium-223 was approved too late in the conduct of PROCEED to be included in the tACI analysis. Results: PSA quartiles from 1880 eligible PROCEED pts were lower than those of IMPACT (Table). Pts in the highest PROCEED quartile were older, more likely to have ECOG performance status ≥ 1, &gt; 10 bone metastases, visceral metastases, and higher ALP and LDH, and lower hemoglobin compared with the lowest PROCEED quartile. More African American men and greater prior systemic therapy use were observed in the highest PSA quartile. Following sip-T, the median tACI (11.0, 8.2, 7.6, and 6.6 mos) was inversely proportional to PSA quartile. Conclusions: Lower baseline PSA values in PROCEED relative to IMPACT suggest that in a real-world setting, clinicians are using sip-T earlier in the treatment of mCRPC. Pts in the lowest PSA quartile had the best prognostic features and longest tACI. Additional patient follow-up is ongoing to evaluate OS and survival by quartile from PROCEED. Clinical trial information: NCT01306890. [Table: see text]
Too cool for school?: The effects of gamification in an advanced interdisciplinary course (2014)

Gamification is a subject of a great deal of conversations and advocates believe that the familiarity of gaming to the current student population gives it considerable potential to transform teaching and learning. The research literature presents a more ambiguous view and it remains to be seen whether or not gamifying instruction can significantly strengthen student learning outcomes. This question forms the basis of the current study, which focuses on an extensive gamification exercise applied in an upper-division interdisciplinary course. To phrase it colloquially, this research asks whether or not gamification is too cool for school.
Interaction of a soliton with an impurity in the sine-Gordon model of a commensurate charge-density-wave system (1988)

Adiabatic and radiative effects accompanying interactions of a kink with a point-like impurity are studied by means of the perturbation theory within the framework of a model of a damped DC-driven charge-density-wave system based on a perturbed sine-Gordon equation. A threshold (maximum) value of the DC voltage (external drive applied to the system) admitting capture of a kink (charged soliton) by an impurity is found. The maximum voltage allowing the existence of pinned states of the kink is also found, and the corresponding dependence of the density of released kinks on the voltage is evaluated, provided that the coordinate of an individual impurity relative to an underlying lattice is a uniformly distributed random quantity. It is demonstrated that this dependence gives rise to an additional peculiar branch of the current-voltage characteristic (CVC) of the system. The energy emitted by a moving kink during its collision with the impurity is calculated. It is shown that, provided that the level of direct dissipative losses is sufficiently low, the radiative losses render the CVC hysteretic.
2005 Donor Eligibility Requirements: Unintended Consequences for Stem Cell Development (2015)

Regulatory ambiguity concerning donor eligibility screening and testing requirements for human embryonic stem cell lines, in particular those lines created before 2005, are causing significant concern for drug developers. Technically, most of these lines fail to meet eligibility under U.S. Food and Drug Administration (FDA) rules for product licensure, and many developers are unaware that FDA approval to begin trials under an exemption is not an assurance that the FDA will grant licensure of the product. This Perspective outlines the ambiguity and the problem it has caused and proposes a workable solution. The intent is to generate stakeholder and FDA discussion on this issue.
Operation of the Collaborative Composite Manufacturing (CCM) System (2019)

The automated tape placement and the automated fiber placement (AFP) machines provide a safer working environment and reduce the labor intensity of workers than the traditional manual fiber placement does. Thus, the production accuracy, repeatability and efficiency of composite manufacturing are significantly improved. However, the current AFP systems can only produce the composite components with large open surface or simple revolution parts, which cannot meet the growing interest in small complex or closed structures from industry. In this research, by employing a 1-degree of freedom (DoF) rotational stage, a 6-RSS parallel robot, and a 6-DoF serial robot, the dexterity of the AFP system can be significantly improved for manufacturing complex composite parts. The rotational stage mounted on the parallel robot is utilized to hold the mandrel and the serial robot carries the placement head to mimic two human hands that have enough dexterity to lay the fiber to the mandrel with complex contour. Although the CCM system increases the flexibility of composite manufacturing, it is quite time-consuming or even impossible to generate the feasible off-line path, which ensures uniform lay-up of subsequent fibers considering the constraints like singularities, collisions between the fiber placement head and mandrel, smooth fiber direction change and keeping the fiber placement head along the norm of the part's surface, etc. Moreover, due to the existing positioning error of the robots, the on-line path correction is needed. Therefore, the on-line pose correction algorithm is proposed to correct the paths of both parallel and serial robots, and to keep the relative path between the two robots unchanged through the visual feedback when the constraint or singularity problems in the off-line path planning occur. The experimental results demonstrate the designed CCM system can fulfill the movement needed for manufacturing a composite structure with Y-shape.
Solubility in non-ionic detergents distinguishes between slowly and rapidly degraded plasma membrane proteins. (1994)

Four cell surface-exposed, integral membrane proteins from H4-II-E-3 hepatoma monolayer cultures, derivatized by the membrane-impermeant reagent sulfosuccinimidyl 2-(biotin-amido)ethyl-1,3-dithioproprionate, were resistant to extraction with Triton X-100 at 0 degrees C. Thirty-three other similarly derivatized proteins were solubilized under these same conditions. Antisera were prepared that reacted only with Triton X-100-insoluble proteins. All four Triton X-100-insoluble proteins precipitated with the antibody were slowly degraded (t1/2 > 100 h). By contrast, all but four Triton X-100-soluble proteins were rapidly degraded (t1/2 = 24 h). The detergent-insoluble proteins did not possess glycosylphosphatidylinositol anchors nor were they solubilized by Triton X-100 after disruption of the cytoskeleton. In addition, they were insoluble in Triton X-100 in isolated membrane preparations but soluble when isolated on streptavidin-agarose and removed from other membrane proteins. We conclude that protein-protein interactions within the membrane itself result in insolubility in non-ionic detergents for a small cohort of plasma membrane proteins and that this may be directly related to the increased metabolic stability for this class of proteins.
The induction of aneuploidy by 3-nitrobenzo[a]pyrene in Chinese hamster ovary cells (1990)

Nitrobenzo[a]pyrenes are found in urban air particulates and particulates from diesel exhaust, gasoline engines and wood burning stoves. Following exposure of Chinese hamster ovary cells (CHO-K1-BH4) to 3-nitrobenzo[a]pyrene (3-NB[a]P), cells with multiple nuclei and/or nuclei with multiple lobes were observed. When CHO cells were treated with 5 micrograms/ml 3-NB[a]P for 5 or 20 h, aneuploidy was noted in these cells at 24-96 h post-exposure. The addition of N6, O2'-dibutyryl adenosine 3':5'-cyclic monophosphate to 3-NB[a]P-exposed CHO cell cultures appeared to reduce the amount of aneuploidy in treated cultures. Structure--activity studies showed that 1-NB[a]P was a much less effective inducer of aneuploidy than 3-NB[a]P and 6-NB[a]P was ineffective. 1-, 3- and 6-nitrosobenzo[a]pyrenes were not effective inducers of aneuploidy in CHO cells, and aneuploidy was not observed in cultures treated with 3-NB[a]P in the presence of S9 activation. It appears that the parent 3-NB[a]P is responsible for producing aneuploidy in CHO cells.
Clinically significant incidental findings on the unenhanced CT portion of PET/CT studies: frequency in 250 patients. (2005)

Clinically significant findings from the unenhanced CT portion of PET/CT are relatively infrequent (3%) but could be serious enough to warrant major alterations in clinical management. Thus, we believe it is most appropriate for the CT portion to be interpreted by a physician skilled in CT interpretation with special attention to the lesions that PET alone can fail to detect.
Tissue engineering of heart valves by recellularization of glutaraldehyde-fixed porcine valves using bone marrow-derived cells (2006)

To increase the biocompatibility and durability of glutaraldehyde (GA)-fixed valves, a biological coating with viable endothelial cells (ECs) has been proposed. However, stable EC layers have not been formed successfully on GA-fixed valves due to their inability to repopulate. In this study, to improve cellular adhesion and proliferation, the GA-fixed prostheses were detoxified by treatment with citric acid to remove free aldehyde groups. Canine bone marrow mononuclear cells (MNCs) were differentiated into EC-like cells and myofibroblast-like cells in vitro. Detoxified prostheses were seeded and recellularized with differentiated bone marrow- derived cells (BMCs) for seven days. Untreated GA-fixed prostheses were used as controls. Cell attachment, proliferation, metabolic activity, and viability were investigated and cell-seeded leaflets were histologically analyzed. On detoxified GA-fixed prostheses, BMC seeding resulted in uninhibited cell proliferation after seven days. In contrast, on untreated GA-fixed prostheses, cell attachment was poor and no viable cells were observed. Positive staining for smooth muscle a-actin, CD31, and proliferating cell nuclear antigen was observed on the luminal side of the detoxified valve leaflets, indicating differentiation and proliferation of the seeded BMCs. These results demonstrate that the treatment of GA-fixed valves with citric acid established a surface more suitable for cellular attachment and proliferation. Engineering heart valves by seeding detoxified GA-fixed biological valve prostheses with BMCs may increase biocompatibility and durability of the prostheses. This method could be utilized as a new approach for the restoration of heart valve structure and function in the treatment of end-stage heart valve disease.
Dominant Effects of Tubulin Overexpression in Saccharomyces cerevisiae (1989)

The consequences of altering the levels of alpha- and beta-tubulin in Saccharomyces cerevisiae were examined by constructing fusions of the structural genes encoding the tubulins to strong galactose-inducible promoters. Overexpression of beta-tubulin (TUB2) was lethal: cells arrested in the G2 stage of the cell cycle exhibited an increased frequency of chromosome loss, were devoid of microtubules, and accumulated beta-tubulin in a novel structure. Overexpression of the major alpha-tubulin gene (TUB1) was not lethal and did not affect chromosome segregation. The rate of alpha-tubulin mRNA and protein synthesis was increased, but the protein did not accumulate. Overexpression of both alpha- and beta-tubulin together resulted in arrested cell division, and cells accumulated excess tubules that contained both alpha- and beta-tubulin. Transient overexpression of both tubulins resulted in a high frequency of chromosome loss. These data suggest that strong selective pressure exists to prevent excess accumulation of microtubules or beta-tubulin and suggest a model by which this goal may be achieved by selective degradation of unassembled alpha-tubulin. Furthermore, the phenotype of beta-tubulin overexpression is similar to the phenotype of a beta-tubulin deficiency. These results add to a number of recent studies demonstrating that mutant phenotypes generated by overexpression can be informative about the function of the gene product.
Deep Learning with Convolutional Neural Network for Proportional Control of Finger Movements from surface EMG Recordings (2021)

The control of robotic prosthetic hands (RPHs) for upper limb amputees is far from optimal. Simultaneous and proportional finger control of a RPH based on EMG signals is still challenging. Based on EMG and kinematics recordings of subjects following a pre-defined sequence of single and multi-fingers movements, we aimed at predicting finger flexion and thumb opposition angles. We compared two deep learning (DL) based approaches, the first one using the raw EMG signals and the second one using the spectrogram of the signal as input, with the standard state of the art decoding technique (STD) for finger angle regression. Using a genetic algorithm for hyper-parameter optimization, we obtained an optimized model architecture (and set of features in the case of STD) for each condition on one recording session. Then, we evaluated the best model of each condition on the eleven EMG and finger kinematics recordings available from four subjects. The two DL approaches based on convolutional neural networks predicted finger angles with a similar mean squared error loss but both of them outperformed the standard approach for the regression of simultaneous single-finger angles. This proposed decoding strategy and hyperparameter optimization framework provides a basis to further improve single finger proportional control for RPHs.
Modulation of therapy-induced senescence by reactive lipid aldehydes (2016)

Current understanding points to unrepairable chromosomal damage as the critical determinant of accelerated senescence in cancer cells treated with radiation or chemotherapy. Nonetheless, the potent senescence inducer etoposide not only targets topoisomerase II to induce DNA damage but also produces abundant free radicals, increasing cellular reactive oxygen species (ROS). Toward examining roles for DNA damage and oxidative stress in therapy-induced senescence, we developed a quantitative flow cytometric senescence assay and screened 36 redox-active agents as enhancers of an otherwise ineffective dose of radiation. While senescence failed to correlate with total ROS, the radiation enhancers, etoposide and the other effective topoisomerase inhibitors each produced high levels of lipid peroxidation. The reactive aldehyde 4-hydroxy-2-nonenal, a lipid peroxidation end product, was sufficient to induce senescence in irradiated cells. In turn, sequestering aldehydes with hydralazine blocked effects of etoposide and other senescence inducers. These results suggest that lipid peroxidation potentiates DNA damage from radiation and chemotherapy to drive therapy-induced senescence.
Cardioprotection by combination of three compounds from ShengMai preparations in mice with myocardial ischemia/reperfusion injury through AMPK activation-mediated mitochondrial fission (2016)

GRS is a drug combination of three active components including ginsenoside Rb1, ruscogenin and schisandrin. It derived from the well-known TCM formula ShengMai preparations, a widely used traditional Chinese medicine for the treatment of cardiovascular diseases in clinic. The present study explores the cardioprotective effects of GRS on myocardial ischemia/reperfusion (MI/R) injury compared with ShengMai preparations and investigates the underlying mechanisms. GRS treatment significantly attenuated MI/R injury and exhibited similar efficacy as Shengmai preparations, as evidenced by decreased myocardium infarct size, ameliorated histological features, the decrease of LDH production and improved cardiac function, and also produced a significant decrease of apoptotic index. Mechanistically, GRS alleviated myocardial apoptosis by inhibiting the mitochondrial mediated apoptosis pathway as reflected by inhibition of caspase-3 activity, normalization of Bcl-2/Bax levels and improved mitochondrial function. Moreover, GRS prevented cardiomyocytes mitochondrial fission and upregulated AMPKα phosphorylation. Interestingly, AMPK activation prevented hypoxia and reoxygenation induced mitochondrial fission in cardiomyocytes and GRS actions were significantly attenuated by knockdown of AMPKα. Collectively, these data show that GRS is effective in mitigating MI/R injury by suppressing mitochondrial mediated apoptosis and modulating AMPK activation-mediated mitochondrial fission, thereby providing a rationale for future clinical applications and potential therapeutic strategy for MI/R injury.
Precise interference analysis of OFDMA time-asynchronous wireless ad-hoc networks (2010)

This paper presents a unified mathematical performance analysis of the physical layer in orthogonal frequency division multiple access (OFDMA) wireless ad hoc networks, where several independent transmitter-receiver pairs share a common wideband channel in a local area environment. Multiuser interference (MUI) occurs when the signals from different users arrive at a given receiver with arbitrary timing misalignments, leading to the destruction of the orthogonality between subcarriers. Precise interference analysis in white Gaussian noise and Rayleigh multipath fading is developed in a partially loaded OFDMA network. New exact expressions of symbol and bit error rates are given in the case of interleaved subcarrier assignment schemes. On the other hand, tight upper bounds and accurate improved Gaussian approximations are developed for arbitrary subcarrier assignment schemes. Furthermore, expressions of the cutoff rates are derived and employed to estimate the spectral efficiency in bits/sec./Hz. These are used to quantify the improvement in the spectral efficiency that can be achieved by a common MUI mitigating technique based on the extension of guard intervals and dynamic positioning of FFT windows.
Heterogeneity of Signal Transducer and Activator of Transcription Binding Sites in the Long-Terminal Repeats of Distinct HIV-1 Subtypes (2007)

HIV-1 can be subdivided into distinct subtypes; the consequences of such a genomic variability remain largely speculative. The long terminal repeats (LTR) control HIV transcription and reflect the major differences of distinct viral subtypes. Three regions in the HIV-1 subtype B LTR are close matches to the Signal Transducer and Activator of Transcription (STAT) consensus sequence. Here, we show heterogeneity in these putative STAT binding sites among HIV-1 LTR subtypes A through G. Transfection of constitutively activated STAT5 lead to transcriptional activation of HIV-1 expression in 293T cells transfected with a reporter assay driven by HIV-1 LTR subtype B. Constitutively activated STAT5 transactivated the LTR of various subtypes in U937 cells with different potency. These findings support and expand the potential relevance of STAT5 activation in HIV infection and may bear relevance for a differential regulation of latency and expression of different subtypes of HIV-1.
Extremely stretchable and conductive water-repellent coatings for low-cost ultra-flexible electronics (2015)

Rapid advances in modern electronics place ever-accelerating demands on innovation towards more robust and versatile functional components. In the flexible electronics domain, novel material solutions often involve creative uses of common materials to reduce cost, while maintaining uncompromised performance. Here we combine a commercially available paraffin wax-polyolefin thermoplastic blend (elastomer matrix binder) with bulk-produced carbon nanofibres (charge percolation network for electron transport, and for imparting nanoscale roughness) to fabricate adherent thin-film composite electrodes. The simple wet-based process produces composite films capable of sustained ultra-high strain (500%) with resilient electrical performance (resistances of the order of 10(1)-10(2) Ω sq(-1)). The composites are also designed to be superhydrophobic for long-term corrosion protection, even maintaining extreme liquid repellency at severe strain. Comprised of inexpensive common materials applied in a single step, the present scalable approach eliminates manufacturing obstacles for commercially viable wearable electronics, flexible power storage devices and corrosion-resistant circuits.