gebhart/patrepeval huggingface dataset:
Generation of Transmitted/Founder HIV-1 Infectious Molecular Clones and Characterization of Their Replication Capacity in CD4 T Lymphocytes and Monocyte-Derived Macrophages (2011)

Genome sequences of transmitted/founder (T/F) HIV-1 have been inferred by analyzing single genome amplicons of acute infection plasma viral RNA in the context of a mathematical model of random virus evolution; however, few of these T/F sequences have been molecularly cloned and biologically characterized. Here, we describe the derivation and biological analysis of ten infectious molecular clones, each representing a T/F genome responsible for productive HIV-1 clade B clinical infection. Each of the T/F viruses primarily utilized the CCR5 coreceptor for entry and replicated efficiently in primary human CD4(+) T lymphocytes. This result supports the conclusion that single genome amplification-derived sequences from acute infection allow for the inference of T/F viral genomes that are consistently replication competent. Studies with monocyte-derived macrophages (MDM) demonstrated various levels of replication among the T/F viruses. Although all T/F viruses replicated in MDM, the overall replication efficiency was significantly lower compared to prototypic "highly macrophage-tropic" virus strains. This phenotype was transferable by expressing the env genes in an isogenic proviral DNA backbone, indicating that T/F virus macrophage tropism mapped to Env. Furthermore, significantly higher concentrations of soluble CD4 were required to inhibit T/F virus infection compared to prototypic macrophage-tropic virus strains. Our findings suggest that the acquisition of clinical HIV-1 subtype B infection occurs by mucosal exposure to virus that is not highly macrophage tropic and that the generation and initial biological characterization of 10 clade B T/F infectious molecular clones provides new opportunities to probe virus-host interactions involved in HIV-1 transmission.
Rose-Colored Answers: Neuropsychological Deficits and Patient-Reported Outcomes after Stroke (2010)

Patient-reported, subjective outcomes are promoted as a standard for ethical, valid studies in many neurological disorders. Such outcomes are considered potentially more sensitive and specific to important therapeutic effects, and may be more linked to disability and disease-related life losses than conventional assessments of impairment (e.g. ability to walk, performance on language tests, serological or radiological indices). Self-report is invaluable to identify social and emotional consequences of brain injury: depression, changes in intimate and family relationships, social role and community participation losses. However, common stroke-related neuropsychological deficits are likely to confound subjective stroke outcome measures. The scientific community focused on stroke-related health outcomes may arrive at significantly underestimated patient reports of stroke-related disability, caused by a failure to adjust for the effect on self-report of spatial neglect, deficits of magnitude estimation, pathologic alteration of self-awareness, and alteration in distributed cortical systems supporting emotional semantics and abstraction.
An investigation of Rubens flame tube resonances (2009)

The Rubens flame tube is a century-old teaching demonstration that allows observers to visualize acoustic standing wave behavior [H. Rubens and O. Krigar-Menzel, (1905). Ann. Phys. 17, 149-164]. Flammable gas inside the tube flows through holes drilled along the top, and flames are then lit above. The tube is closed at one end and driven with a loudspeaker at the other end. When the tube is driven at one of its resonance frequencies, flames form a visual standing wave pattern as they vary in height according to the pressure amplitude in the tube. Although the basic performance of the tube has been explained [G. Ficken and C. Stephenson, (1979). Phys. Teach. 17, 306-310], this paper discusses a previously unreported characteristic of the tube: a shift of the tube's resonance frequencies away from those predicted by simple introductory physics. Results from an equivalent circuit model of the tube and agreement between experiments and the model suggest that the shift is caused by the presence of the holes. For teachers and educators seeking to better understand and explain the tube to students, this article serves as a resource regarding the basic phenomena affecting the behavior of the tube.
Outstanding questions in transplantation: B cells, alloantibodies, and humoral rejection (2019)

Over the past three decades, improved immunosuppression has significantly reduced T cell-mediated acute rejection rates, but long-term graft survival rates have seen only marginal improvement. The cause of late graft loss has been under intense investigation, and chronic antibody-mediated rejection (AMR) has been identified as one of the leading causes, thus providing a strong rationale for basic science investigation into donor-specific B cells and antibodies in transplantation and ways to mitigate their pathogenicity. In 2018, the American Society of Transplantation launched a community-wide online discussion of Outstanding Questions in Transplantation, and the topic of B cell biology and donor-specific antibody prevention emerged as a major area of interest to the community, leading to a highly engaged dialogue, with comments from basic and translational scientists as well as physicians (http://community.myast.org/communities/community-home/digestviewer). We have summarized this discussion from a bedside to bench perspective and have organized this review into outstanding questions within the paradigm that AMR is a leading cause of graft loss in the clinic, and points of view that challenge aspects of this paradigm. We also highlight opportunities for basic and translational scientists to contribute to the resolution of these questions, mapping important future directions for the transplant research field.
Functional timing analysis using ATPG (1995)

Paths that are never exercised are referred to as false paths and timing analysis that ignores the delay contribution of these paths is referred to as functional timing analysis. Such timing analysis provides a more accurate estimate of circuit delay compared to conventional static timing analysis. We show how unmodified conventional Automatic Test Pattern Generators (ATPG) for stuck-at faults can be used for functional timing analysis without sacrificing computational efficiency in comparison with existing approaches to the same problem. This is a significant result since it enables us to use the entire body of work in ATPG for this problem and relieves us from re-inventing new solutions for this problem. The basic algorithm can be used under an arbitrary delay model. We provide delay computation results for all the ISCAS benchmark examples under the unit-delay and the mapped-delay models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
“President Vows to Cut <Taxes> Hair”: Dataset and Analysis of Creative Text Editing for Humorous Headlines (2019)

Nabil Hossain, John Krumm, Michael Gamon. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers). 2019.
A Model-Based Approach to Synthetic Data Set Generation for Patient-Ventilator Waveforms for Machine Learning and Educational Use (2021)

Although mechanical ventilation is a lifesaving intervention in the ICU, it has harmful side-effects, such as barotrauma and volutrauma. These harms can occur due to asynchronies. Asynchronies are defined as a mismatch between the ventilator timing and patient respiratory effort. Automatic detection of these asynchronies, and subsequent feedback, would improve lung ventilation and reduce the probability of lung damage. Neural networks to detect asynchronies provide a promising new approach but require large annotated data sets, which are difficult to obtain and require complex monitoring of inspiratory effort. In this work, we propose a model-based approach to generate a synthetic data set for machine learning and educational use by extending an existing lung model with a first-order ventilator model. The physiological nature of the derived lung model allows adaptation to various disease archetypes, resulting in a diverse data set. We generated a synthetic data set using 9 different patient archetypes, which are derived from measurements in the literature. The model and synthetic data quality have been verified by comparison with clinical data, review by a clinical expert, and an artificial intelligence model that was trained on experimental data. The evaluation showed it was possible to generate patient-ventilator waveforms including asynchronies that have the most important features of experimental patient-ventilator waveforms.
Wireless backhaul node placement for small cell networks (2014)

Small cells have been proposed as a vehicle for wireless networks to keep up with surging demand. Small cells come with a significant challenge of providing backhaul to transport data to(from) a gateway node in the core network. Fiber based backhaul offers the high rates needed to meet this requirement, but is costly and time-consuming to deploy, when not readily available. Wireless backhaul is an attractive option for small cells as it provides a less expensive and easy-to-deploy alternative to fiber. However, there are multitude of bands and features (e.g. LOS/NLOS, spatial multiplexing etc.) associated with wireless backhaul that need to be used intelligently for small cells. Candidate bands include: sub-6 GHz band that is useful in non-line-of-sight (NLOS) scenarios, microwave band (6-42 GHz) that is useful in point-to-point line-of-sight (LOS) scenarios, and millimeter wave bands (e.g. 60, 70 and 80 GHz) that are recently being commercially used in LOS scenarios. In many deployment topologies, it is advantageous to use aggregator nodes, located at the roof tops of tall buildings near small cells. These nodes can provide high data rate to multiple small cells in NLOS paths, sustain the same data rate to gateway nodes using LOS paths and take advantage of all available bands. This work performs the joint cost optimal aggregator node placement, power allocation, channel scheduling and routing to optimize the wireless backhaul network. We formulate mixed integer nonlinear programs (MINLP) to capture the different interference and multiplexing patterns at sub-6 GHz and microwave band. We solve the MINLP through linear relaxation and branch-and-bound algorithm and apply our algorithm in an example wireless backhaul network of downtown Manhattan.
Reduction of Carbonyl Compounds by Cross-Linked Poly(4-vinylpyridine)-Borane in Acidic Media (1985)

Abstract Cross-linked poly(4-vinylpyridine)-borane was successfully used for the reduction of aldehydes and ketones to the corresponding alcohols. Reduction was carried out in protic and aprotic acidic media at room temperature. Polymer reactivity depends on solution pH. Due to the relative high hydrolytic stability of the borane-bound polymer, reduction can be carried out in pH 1 buffer solution and in acetic acid. A low degree of cross-linking did not affect the polymer reactivity. Complete reduction of carbonyl compounds can be reached in the presence of excess of borane-bound polymer at a 1:1 reactants molar ratio. Only two of the borane hydrides are available for reduction; the third one is consumed by hydrolysis of the partially reacted borane derivatives formed during and after reduction. The chemoselectivity in the competitive reduction of cyclohexanone and other ketones as well as acetophenone and benzaldehyde with cross-linked poly(4-vinylpyridine)-borane was investigated. The cross-linked polymer borane was found to be a much better chemoselective reduction agent than its low molecular weight analog pyridine-borane. Chemoselectivity of this polymer is as good as that of available low molecular weight chemoselective reduction agents.
Dynamic maximum power point tracker for photovoltaic applications (2002)

A dynamic process for reaching the maximum power point of a variable power source such as a solar cell is introduced. The process tracks maximum power nearly cycle-by-cycle during transients. Information from the natural switching ripple instead of external perturbation is used to support the maximizing process. The method is globally stable for DC-DC power converters, provided that a switching action is present. A prototype boost power converter that uses this method for control can follow power transients on time scales of a few milliseconds. This performance can be achieved with a simple analog control structure, which supports power processing with minimum loss.
Innovations Update (2019)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTInnovations UpdateStevan W. DjuricStevan W. DjuricMore by Stevan W. DjuricCite this: ACS Med. Chem. Lett. 2019, 10, 6, 835Publication Date (Web):June 13, 2019Publication History Published online13 June 2019Published inissue 13 June 2019https://pubs.acs.org/doi/10.1021/acsmedchemlett.9b00223https://doi.org/10.1021/acsmedchemlett.9b00223editorialACS PublicationsCopyright © 2019 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views820Altmetric-Citations-LEARN 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 PDF (180 KB) Get e-AlertscloseSUBJECTS:Medicinal chemistry Get e-Alerts
Application value of three dimensional CT reconstruction in laparoscopic partial nephrectomy (2014)

【Objective】 To evaluate the application value of three dimensional(3D) computed tomography(CT) reconstruction in laparoscopic partial nephrectomy for renal tumor. 【Methods】From May 2010 to May 2013, a retrospective cohort study was conducted on the clinical data of 23 patients with renal tumor treated by laparoscopic partial nephrectomy. After unenhanced CT of the abdomen,a high-resolution contrast-enhanced scan was taken through the kidneys, data were analyzed by using muhiplanar reconstruction and three-dimensional reformatting. The mean diameter of renal tumor was 3.2 cm.【Results】 Renal tumors were identified in the 23 patients evaluated with reconstructed images. 22 procedures were performed through retroperitonea1 approach and successful. The mean operative time was 118 min, ranging from 80 min to 159 min. No intraoperative or postoperative complication occurred. Postoperative pathological results included T1 renal cell carcinoma(RCC) in 16 patients and angiomyolipoma in 7, a patient had a positive surgical margin. During the follow up ranging from 3 to 38 months(median 16 months), neither local recurrence nor metastasis was observed. 【Conclusion】 CT with 3D reconstruction can provided a good map of renal tumor and vascular, which should become an imaging method for planning laparoscopic partial nephrectomy in patients with renal tumor.
A Front-End ASIC With Receive Sub-array Beamforming Integrated With a $32 \times 32$ PZT Matrix Transducer for 3-D Transesophageal Echocardiography (2017)

This paper presents a power- and area-efficient front-end application-specific integrated circuit (ASIC) that is directly integrated with an array of 32 × 32 piezoelectric transducer elements to enable next-generation miniature ultrasound probes for real-time 3-D transesophageal echocardiography. The 6.1 × 6.1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ASIC, implemented in a low-voltage 0.18-μm CMOS process, effectively reduces the number of receive (RX) cables required in the probe's narrow shaft by ninefold with the aid of 96 delay-and-sum beamformers, each of which locally combines the signals received by a sub-array of 3 × 3 elements. These beamformers are based on pipeline-operated analog sample-and-hold stages and employ a mismatch-scrambling technique to prevent the ripple signal associated with the mismatch between these stages from limiting the dynamic range. In addition, an ultralow-power low-noise amplifier architecture is proposed to increase the power efficiency of the RX circuitry. The ASIC has a compact element matched layout and consumes only 0.27 mW/channel while receiving, which is lower than the state-of-the-art circuit. Its functionality has been successfully demonstrated in 3-D imaging experiments.
Abstract 68: Methotrexate prevents primary immune responses against recombinant immunotoxin in murine models (2017)

Abstract Recombinant immunotoxins (rITs) are composed of a tumor antigen-targeting antibody fragment fused to a portion of Pseudomonas exotoxin A. rITs have been effective in clinical trials for patients with hematologic malignancies. The CD22 targeting rIT Moxetumomab Pasudotox has achieved overall response rates of 86% and complete remission rates of 46% in patients with relapsed-refractory Hairy Cell Leukemia. However, the therapeutic efficacy of rITs against solid tumors is limited by their immunogenicity in immune-competent patients. In clinical trials to treat mesothelioma patients with SS1P, a rIT targeting mesothelin, 90% of patients developed neutralizing antibodies against SS1P after one cycle of treatment. When immunosuppressive chemotherapy and SS1P were combined, more cycles of rIT could be given and several patients with advanced chemo-refractory mesothelioma had striking tumor regressions. This implicates high therapeutic potential for rITs against solid tumors once immunogenicity is surmounted. Methotrexate (MTX) is a folate antagonist which interferes with purine biosynthesis, and is used to treat osteosarcomas and other cancers. MTX also interferes with T cell responses and is used to treat autoimmune diseases. Based on its immunosuppressive properties, Joly et al. demonstrated that low-dose MTX prevented the formation of ADAs against recombinant human alglucosidase alfa in mice in an antigen-specific manner. We hypothesized that MTX would similarly prevent the formation of ADAs against rITs in an antigen-specific manner. To test our hypotheses, mice were treated with the mesothelin-targeting rIT RG7787 with or without MTX given 0, 24, and 48 hours after RG7787 treatment. Serum was collected and anti-RG7787 ADAs were measured by direct ELISA. We found that six doses of RG7787 combined with low dose MTX (1 mg/kg) inhibited the formation of ADAs against RG7787. This inhibition was sustained through six challenges with RG7787 without additional MTX. Further, we found that immunization with RG7787 plus MTX induced RG7787-specific tolerance, and had no effect on the ADA response against a second protein, ovalbumin. We conclude that combination of MTX and RG7787 is effective at preventing primary immune responses in a durable, antigen-specific manner. We propose to combine this agent in immune-competent cancer patients receiving rIT therapy to prevent rIT immunogenicity. Citation Format: Emily M. King, Ronit Mazor, Ira Pastan. Methotrexate prevents primary immune responses against recombinant immunotoxin in murine models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 68. doi:10.1158/1538-7445.AM2017-68
What makes a liquid crystal? The effect of free volume on soft matter (2015)

In this article, we probe the formation of liquid crystal and soft crystal phases as a consequence of minimising the free volume of the system either through design engineering of molecular shape o...
Local short- and medium-range order in amorphous transparent oxide thin films (2012)

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Comparing automatic and human evaluation of NLG systems (2006)

We consider the evaluation problem in Natural Language Generation (NLG) and present results for evaluating several NLG systems with similar functionality, including a knowledge-based generator and several statistical systems. We compare evaluation results for these systems by human domain experts, human non-experts, and several automatic evaluation metrics, including NIST, BLEU, and ROUGE. We find that NIST scores correlate best (&amp;gt; 0.8) with human judgments, but that all automatic metrics we examined are biased in favour of generators that select on the basis of frequency alone. We conclude that automatic evaluation of NLG systems has considerable potential, in particular where high-quality reference texts and only a small number of human evaluators are available. However, in general it is probably best for automatic evaluations to be supported by human-based evaluations, or at least by studies that demonstrate that a particular metric correlates well with human judgments in a given domain. 1
Ultrawideband Bandpass Filter Using Composite Right- and Left-Handedness Line Metamaterial Unit-Cell (2010)

The design of a new UWB bandpass filter is proposed, which is based upon the microstrip Composite Right-and Left-Handed Transmission-line(CRLH-TL). In order to bring the remarkable improvement in an attempt to reduce the size, taking the features of the conventional periodic CRLH-TL, only one unit of the structure is chosen. So the component less than a quarter-wavelength is realized to achieve the ultra wide band filtering without the loss of the original advantage of the CRLH-TL. Guaranteeing the compactness in size, the interdigitated coupled lines are used to realize the strong coupling for the design that will be shown to have the size of 'guided wavelength/9.4', the fractional bandwidth over 100%, the insertion loss much less than 1 dB, and the flat group-delay with an acceptable return loss performance in the predicted and measured results. 20 www.intechopen.com
The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants (2021)

<ns4:p>The SARS-CoV-2 variant B.1.1.7 reportedly exhibits substantially higher transmission than the ancestral strain and may generate a major surge of cases before vaccines become widely available, while the P.1 and B.1.351 variants may be equally transmissible and also resist vaccines. All three variants can be sensitively detected by RT-PCR due to an otherwise rare del11288-11296 mutation in orf1ab; B.1.1.7 can also be detected using the common TaqPath kit. Testing, contact tracing, and isolation programs overwhelmed by SARS-CoV-2 could slow the spread of the new variants, which are still outnumbered by tracers in most countries. However, past failures and high rates of mistrust may lead health agencies to conclude that tracing is futile, dissuading them from redirecting existing tracers to focus on the new variants. Here we apply a branching-process model to estimate the effectiveness of implementing a variant-focused testing, contact tracing, and isolation strategy with realistic levels of performance. Our model indicates that bidirectional contact tracing can substantially slow the spread of SARS-CoV-2 variants even in regions where a large fraction of the population refuses to cooperate with contact tracers or to abide by quarantine and isolation requests.</ns4:p>