gebhart/patrepeval huggingface dataset:
Genome-wide Enrichment of TERT Rare Variants in Idiopathic Pulmonary Fibrosis Patients of Latino Ancestry (2022)

Genome-wide rare variant studies of IPF patients of non-European ancestry have been understudied. Here, we evaluate the enrichment of rare genetic variants of 241 unrelated non-European cases, representing individuals of Latino, African, South Asian, East Asian, and Other Admixed ancestry. Gene burden analysis of deleterious rare (protein-truncating and missense) variants demonstrate an excess of TERT rare damaging variants (OR 67.1, 95% CI [23.1, 195.0], P = 9.4 x 10-14) in non-European subjects. Analysis by ancestry demonstrated an excess of rare, damaging TERT variants in the Latino subgroup (OR 80.9, 95% CI [17.3, 383.8], P = 2.6 x 10-8). Although the non-European group did not show enrichment of PARN, RTEL1, and KIF15 rare deleterious variants, these groups all showed a trend in the same direction as the European ancestry group. For TERT and KIF15, the inclusion of IPF patients of non-European ancestry led to a higher odds ratios and increased evidence in favor of rare deleterious variant contributions, thus demonstrating the increased power of multi-ethnic studies over single-ethnicity studies. To our knowledge, this is the first study that confirms the involvement of rare deleterious TERT variants for IPF patients of Latino and non-European ancestry. To better understand the genetic underpinnings of IPF patients of all ancestries, additional work will be needed to broaden patient recruitment to normalize imbalances.
Unifying Charge Generation, Recombination, and Extraction in Low‐Offset Non‐Fullerene Acceptor Organic Solar Cells (2020)

Abstract Even though significant breakthroughs with over 18% power conversion efficiencies (PCEs) in polymer:non‐fullerene acceptor (NFA) bulk heterojunction organic solar cells (OSCs) have been achieved, not many studies have focused on acquiring a comprehensive understanding of the underlying mechanisms governing these systems. This is because it can be challenging to delineate device photophysics in polymer:NFA blends comprehensively, and even more complicated to trace the origins of the differences in device photophysics to the subtle differences in energetics and morphology. Here, a systematic study of a series of polymer:NFA blends is conducted to unify and correlate the cumulative effects of i) voltage losses, ii) charge generation efficiencies, iii) non‐geminate recombination and extraction dynamics, and iv) nuanced morphological differences with device performances. Most importantly, a deconvolution of the major loss processes in polymer:NFA blends and their connections to the complex BHJ morphology and energetics are established. An extension to advanced morphological techniques, such as solid‐state NMR (for atomic level insights on the local ordering and donor:acceptor ππ interactions) and resonant soft X‐ray scattering (for donor and acceptor interfacial area and domain spacings), provide detailed insights on how efficient charge generation, transport, and extraction processes can outweigh increased voltage losses to yield high PCEs.
A phase II trial of rapid androgen cycling and docetaxel (Doc) in prostate cancer patients with a rising prostate-specific antigen (PSA) in the noncastrate state (2007)

5004 Introduction: Prostate cancer patients in the noncastrate state with a rapidly rising PSA are at high-risk for cancer-specific mortality. Since hormonal therapy alone is not curative, we have explored the use of rapid androgen cycling with Doc to recruit proliferating cells into successive waves of apoptosis, thereby shifting the treatment outcome for these patients from palliation to cure. Methods: Patients with noncastrate levels of testosterone (T), a rising PSA ± metastases, and = 6 months of prior hormones were eligible. Cohort 1: Six 4- week cycles of monthly leuprolide and Doc (75 mg/m2), with 7 days of topical T repletion (AndroGel 1% 5G) prior to each treatment. Cohort 2: Nine 3-week cycles of Doc (70 mg/m2), with 3 days of T repletion per cycle and 3-month depot leuprolide on day 1 of cycles 1, 5, and 9. The primary endpoint was the proportion of patients with a treatment-specific undetectable PSA at 6 and 18 months defined as: = 0.05 after surgery, = 0.5 after radiation, or = 2.0ng/ml with untreated disease. This is based on the premise that an undetectable PSA is a prerequisite to, but no guarantee of cure. Results: There were no increases in sequential PSA peaks or troughs and 100 out of 102 patients completed the planned 6 months of chemohormonal treatment. Twenty three of 62 (37%) patients in cohort 1, and 25 of 38 (66%) patients in cohort 2 achieved the primary endpoint of a treatment-specific undetectable PSA at 6 months. At 12 months, no patient in cohort 1 had maintained an undetectable PSA in the setting of a noncastrate T level; whereas, 8 of 15 (53%) patients in cohort 2 have achieved the endpoint at 12 months. Toxicities were similar to those observed with Doc and hormonal therapy administered separately. Conclusions: Rapid androgen cycling with docetaxel is feasible, and can induce successive declines in PSA peaks and troughs. The more dose-dense cohort 2 schedule of 21-day Doc administration for 9 cycles, along with reduced exposure to androgen repletion from 7 to 3 days, has resulted in a higher proportion of undetectable PSA outcomes at both 6 (66% vs. 37%) and 12 (53% vs. 0%) months. Complete PSA outcomes for cohort 2 at 12 and 18 months are still pending. Supported by Sanofi-Aventis, CA-05816, and PepsiCo. No significant financial relationships to disclose.
Recognition and prediction in a network music performance system for Indian percussion (2007)

Playing music over the Internet, whether for real-time jamming, network performance or distance education, is constrained by the speed of light which introduces, over long distances, time delays unsuitable for musical applications. Current musical collaboration systems generally transmit compressed audio streams over low-latency and high-bandwidth networks to optimize musician synchronization. This paper proposes an alternative approach based on pattern recognition and music prediction. Trained for a particular type of music, here the Indian tabla drum, the system called TablaNet identifies rhythmic patterns by recognizing individual strokes played by a musician and mapping them dynamically to known musical constructs. Symbols representing these musical structures are sent over the network to a corresponding computer system. The computer at the receiving end anticipates incoming events by analyzing previous phrases and synthesizes an estimated audio output. Although such a system may introduce variants due to prediction approximations, resulting in a slightly different musical experience at both ends, we find that it demonstrates a high level of playability with an immediacy not present in other systems, and functions well as an educational tool.
Level of HER-2/neu protein expression in primary breast cancer may impact the development of HER-2/neu-specific endogenous immunity (2005)

3450 Tolerance to self tumor antigens is circumvented when those antigens are overexpressed. We questioned whether the magnitude or incidence of humoral or cellular immune response to self-antigen HER-2/neu (HER2) is influenced by the level of HER2 overexpression as defined by immunohistochemical (IHC) assessment of tumors in breast cancer patients. We obtained IHC results on 90 women with Stage II, II and IV breast cancer. Patients were categorized with 1+, 2+ or 3+ HER2 overexpression. Circulating antibodies to HER2 were measured in 90 patients using ELISA, and HER2-specific T cell responses were measured in 48 patients using a modified limiting dilution assay. In order to assess general immunity, we measured antibody and T cell response to tetanus toxoid (tt). There were no significant differences in the mean tt responses in each IHC group (p= 0.771). There were no significant differences in magnitude of HER2-specific antibodies or T cells between IHC groups (p= 0.110 and 0.500 respectively). There was a trend toward an increased prevalence of HER2-specific antibody (p=0.073) and T cell (p=0.088) immunity as HER2 overexpression increased. In addition, we found that tumor overexpresssion was not associated with the increased ability of patients to mount a HER2-specific humoral or cellular immune response to vaccination with HER2 peptide-based vaccine.
Hybridcoherentandfrequency-shifted-referenceultrawidebandradio I (2009)

DepartmentofElectricalEngineering,UniversityofSouthernCalifornia,LosAngeles,CA,UnitedStates c DepartmentofElectricalandComputerEngineering,UniversityofMassachusetts,Amherst,MA,UnitedStates d MitsubishiElectricResearchLab,Cambridge,MA,UnitedStates a r t i c l e i n f o
Simple synthesis of 32P-labelled inositol hexakisphosphates for study of phosphate transformations (2017)

We developed enzymic approaches that allow the synthesis of labeled <i>myo</i>-inositol 1,[<sup>32</sup>P]2,3,4,5,6-hexakisphosphate; <i>neo</i>-inositol 1,[<sup>32</sup>P]2,3,4,[<sup>32</sup>P]5,6 - hexakisphosphate and 1D-<i>chiro</i>-inositol [<sup>32</sup>P]1,2,3,4,5,[<sup>32</sup>P]6-hexakisphosphate. Additionally, we describe HPLC separations of all inositol hexakisphosphates yet identified in soils, using a collection of soil inositol phosphates described in the seminal historic studies of Cosgrove, Tate and coworkers. Our study will enable others to perform radiotracer experiments to analyze fluxes of phosphate to/from inositol hexakisphosphates in different soils.
Virtual-channel flow control (2002)

Network throughput can be increased by dividing the buffer storage associated with each network channel into several virtual channels. Each physical channel is associated with several small queues, virtual channels, rather than a single deep queue. The virtual channels associated with one physical channel are allocated independently but compete with each other for physical bandwidth. Virtual channels decouple buffer resources from transmission resources. This decoupling allows active messages to pass blocked messages using network bandwidth that would otherwise be left idle. Simulation studies show that, given a fixed amount of buffer storage per link, virtual-channel flow control increases throughput by a factor of 3.5, approaching the capacity of the network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Developing System Head Curves for Water Distribution Pumping: A 500‐gpm pump puts out 500 gpm. Right? Wrong? Well, maybe. It depends on the system head curve. (1989)

This article discusses cases in which water use near pump stations needs to be taken into consideration and illustrates how to use a pipe network model to determine a system head curve for those conditions. System head curves can be improved by consolidating water users at a single node, or, for more complex distribution systems, by using a water distribution model to determine system heads.
Subcellular localization of S-adenosyl-L-methionine:tRNA methyltransferases with aminoacyl-tRNA synthetases in human and mouse: normal and leukemic leukocytes. (1976)

The subcellular distributions of S-adenosyl-L-methionine:tRNA methyltransferases and aminoacyl-tRNA synthetases were investigated with the use of human and mouse normal and leukemic leukocyte cell lines. Differential centrifugation of homogenized cell suspensions produced three pelleted subcellular fractions (nuclear and membrane, microsomal, and postribosomal) and a supernatant fraction. Each fraction was assayed for both methyltransferase activity and synthetase activity. The largest amounts, 40-50%, of total methyltransferase and synthetase activities were localized in either the microsomal or the postribosomal fractions, depending on cell type. In addition, the highest specific activities of these two enzyme systems were found to be present in the microsomal and postribosomal fractions. The psotribosomal fraction from leukemic leukocytes had a methyltransferase specific activity higher than that of the microsomal fraction, while the same two fractions of normal leukocytes had approximately equal activities. Specific activities of aminoacyl-tRNA synthetases were found to be approximately equal for these two fractions, whether they were from normal or leukemic leukocytes. The activity of tRNA methyltransferases and synthetases within the postribosomal fraction of the cytoplasm suggests the existence of high-molecular-weight enzyme complexes for the modification as well as the aminoacylation of tRNA.
Selective detection of plasma low molecular weight heparin concentration with ultraviolet emission spectroscopy (2006)

Objectives: An increasing number of patients undergoing cardiac surgery are pre-treated with low molecular-weight (2–6kDa) heparins (LMWH) with a longer half-life time than unfractioned (10–15kDa) heparins (UFH). In contrast to UFH, LMWH cannot be detected by routine methods and neutralized by protamine. In addition, regular UFH in use contain a considerable amount of LMWH. In this study, a new method for selective determination of UFH, LMWH and heparin-protamine complexes in plasma using ultraviolet (UV)-fluorescence spectroscopy is presented.
Coordinated Multi-Point Massive MIMO Cellular Systems with Sectorized Antennas (2018)

Non-cooperative cellular Massive MIMO, combined with max-min power control, is known to give substantial improvements in per-user throughput compared with conventional 4G technology. We investigate further refinements to Massive MIMO, first, in the form of three-fold sectorization, which can be viewed as an effective reduction in cell size, and second, three-fold sectorization combined with coordinated multi-point operation, in which the three sectors cooperate in the joint service of their users. We analyze the downlink performance of the system for zero-forcing precoding and propose centralized and decentralized power control schemes. The simulation results reveal that sectorization, and multi-point coordinated sectorization lead to 2.36× and 8.56× improvements in the 95%-likely per-user throughput, respectively.
Ly-6C high Monocytes Depend on Nr4a1 to Balance Both Inflammatory and Reparative Phases in the Infarcted Myocardium (2014)

Ly-6C(high) monocytes orchestrate both inflammatory and reparative phases during myocardial infarction and depend on Nr4a1 to limit their influx and inflammatory cytokine expression.
Thermal nonlinearities in gold nanostructures (2012)

The plasmon resonance is found to broaden and red-shift under strong femtosecond/picosecond irradiation. Using a standard two-temperature model we find a correlation mapping the electron gas and lattice temperatures to the Drude damping coefficient.
Sequence of an epidermal growth factor-binding protein. (1984)

A cDNA clone has been isolated that corresponds to the entire translated region of the mRNA coding for the epidermal growth factor-binding protein type B. The complete nucleotide sequence and the predicted amino acid sequence of the protein were elucidated. The protein sequence was compared to some related serine proteases. This comparison supports the notion that several serine proteases suggested to be involved in the processing of precursors to polypeptide hormones and growth factors are closely related to each other. It appears that these proteases are descendants of a common ancestral gene and thus form a distinct subfamily among the serine proteases.
Nacelle-to-Tower Multilevel IPT System for Small-Scale Wind Turbines (2020)

The use of small-scale wind turbines (SSWTs) in private households not only allows for increased renewable energy generation but also improved grid stability and resilience of individual regions. However, there are strict requirements regarding the efficiency, reliability, and electrical safety of SSWTs because of their low power levels, long payback period, and the fact that they are installed nearby residential areas. This article proposes a novel yaw inductive power transfer system based on a multilevel converter, which mitigates the main disadvantages of SSWTs-slip rings, low-voltage energy generation, etc. The system utilizes low-voltage mosfets in multilevel boost-series resonant topology combined with zero-voltage switching techniques to maximize efficiency. The operating principle, switching waveforms, and behavior of the converter are described and analyzed. The cell voltage balancing algorithms are presented as well. Two different control techniques for power flow regulation have been introduced and compared. The effectiveness of the proposed solution has been verified by building a 3.3-kW prototype system and a comprehensive measuring of its performance. The experimental results show that the peak power transfer efficiency reaches 92.5% while converting generator voltage from 60 V dc to grid compatible 400 V dc.
Variation Tolerance in a Multichannel Carbon-Nanotube Transistor for High-Speed Digital Circuits (2009)

This paper introduces the theory of a carbon-nanotube multichannel transistor and shows that, due to statistical averaging in such a structure, a lot of variations in growth and processing can be tolerated. A model of such a structure has been presented, and Monte Carlo simulations have been performed to identify which of the imperfections and sources of variation are more critical than others. We use this theoretical framework to study short and multichannel carbon-nanotube FET structures for high-performance VLSI.
Fragment Screening in Complex Systems (2016)

As the field of fragment-based drug discovery (FBDD) continues to evolve, attention is starting to turn to protein targets that are less straightforward to work with. This chapter examines FBDD in situations where the protein targets are challenging to work with particularly from the perspective of generating X-ray structural information. It assesses when fragment screening is likely to be useful, focusing on tractability and its relationship to the screening paradigms available, giving examples of the various types of biophysical and biochemical screens across a range of targets. The chapter also outlines a number of strategies for validating and optimizing fragment hits. The growing body of literature reviewed in the chapter appears to support the notion that fragment screening and optimization should be considered for complex targets, particularly where the druggability (to small molecules) of the targets is good.
A Self‐Assembling Dendritic Reactor: Versatile Formation of Characteristic Patterns with Nanoscale Dimension (2015)

Spherical dendrimers with phenylazomethine backbones are modified onto atomically flat mica or graphite substrates with a simple solvent based spin-coating method, and the resulting surfaces are observed by atomic force microscopy. Especially on the mica substrate, dendrimers form very fine and highly regular patterns with aligned nano-dot arrays and lines. An important observation is that the interval of each dot or line is ≈400 nm whereas previously reported self-assembling patterns exhibit longer intervals than 5 μm. It is revealed that spherical dendrimers with relatively low intermolecular interactions without any terminal modifications are suitable for the fine self-assembling pattern formation. This fact suggests that the regular pattern arises from a physical dissipative structure formation due to a fingering instability induced by Marangoni convection but not by anisotropic intermolecular interactions.
Figure S1 from SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells (2023)

&lt;p&gt;Representative SMAD4 IHC, FaDu negative control, SCC25/SCC61 positive control.&lt;/p&gt;
Stem Cell Transplantation for Cardiac Repair is Improved by Mechanical Preconditioning (2009)

We have previously shown that muscle‐derived stem cells (MDSCs) are significantly better than myoblasts at maintaining cardiac function after a myocardial infarction, which is likely due to higher survival and vascular endothelial growth factor secretion (VEGF) after transplantation. VEGF has been shown to be critical for cardiac repair, and mechanically stimulated MDSCs have increased VEGF secretion. We hypothesized that transplanting mechanically preconditioned MDSCs would result in increased repair of a myocardial infarction. After injection with mechanically stretched MDSCs, cardiac function at all time points is improved above unstimulated cells and saline. The improvement is likely due to an increase in angiogenesis and a small decrease in scar tissue formation in the mechanically preconditioned group. To clarify the mechanisms we explored cell behavior in vitro, where we saw increased VEGF secretion. Results from our VEGF secretion study also demonstrate that the effect of mechanical stimulation is time‐dependent, indicating that loading history control may be important to achieve ideal regeneration. The tight regulation and timing demonstrated by these results suggest that the mechanical loading history can predispose the MSDCs toward specific responses that are advantageous for cell transplantation.
Supplementary Methods from A Meta-analysis of Lung Cancer Gene Expression Identifies <i>PTK7</i> as a Survival Gene in Lung Adenocarcinoma (2023)

&lt;p&gt;PDF file - 60KB&lt;/p&gt;
Determination of the absolute configuration of [16O,17O,18O]phosphate monoesters by using phosphorus-31 NMR (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the absolute configuration of [16O,17O,18O]phosphate monoesters by using phosphorus-31 NMRStephen L. Buchwald and Jeremy R. KnowlesCite this: J. Am. Chem. Soc. 1980, 102, 21, 6601–6602Publication Date (Print):October 8, 1980Publication History Published online1 May 2002Published inissue 8 October 1980https://pubs.acs.org/doi/10.1021/ja00541a056https://doi.org/10.1021/ja00541a056research-articleACS PublicationsRequest reuse permissionsArticle Views440Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts