gebhart/patrepeval huggingface dataset:
B-CELL EPITOPE SPECIFICITY OF CARBOXY TERMINUS OF<i>MYCOBACTERIUM PARATUBERCULOSIS</i>ModD (2010)

Epitope mapping of ModD of Mycobacterium paratuberculosis was performed using overlapping peptides. In total, 80 overlapping peptides, covering the entire mature ModD, were commercially synthesized. Each peptide spanned 14 amino acids with an offset of 4 amino acids, i.e., with an overlap of 10 amino acids. Synthetic peptide antigenicity was evaluated by enzyme-linked immunosorbent assay (ELISA) using rabbit antisera to culture filtrate (CF) of M. avium or M. paratuberculosis or recombinant ModD (rModD). The peptides o f ModD reacting most strongly (ELISA OD > 1.0) were clustered near the N- and C-terminal ends. The peptides around the C-terminal end only showed the greatest specificity for M. paratuberculosis, yielding high ELISA OD values with rabbit anti-M. paratuberculosis CF serum and low ELISA OD values with rabbit anti-M. avium CF serum. Sera from naturally M. paratuberculosis-infected cattle, however, bound poorly to the short, 14-amino-acid peptides. Thus, two longer peptides covering amino acids 100 to 125 and 328 to 353 were synthesized based on their broad reactivity to rabbit serum against M. paratuberculosis CF. The peptide covering amino acids 328 to 353 showed the highest level of specific bovine antibody binding.
TINTI: A System for Retrieval in Text Tables TITLE2: (1997)

TINTIN: A System for Retrieval in Text Tables Pallavi Pyreddy and W. Bruce Croft Center for Intelligent Information Retrieval Dept. of Computer Science University of Massachusetts Amherst, MA 01003 {pyreddy,croft}@cs.umass.edu} Tables form an important kind of data element in text retrieval. Often, the gist of an entire news article or other exposition can be concisely captured in tabular form. In this paper, we examine the utility of exploiting information other than the key words in a digital document to provide the users with more flexible and powerful query capabilities. More specifically, we exploit the structural information in a document to identify tables and their component fields and let the users query based on these fields. Our empirical results have demonstrated that heuristic method based table extraction and component tagging can be performed effectively and efficiently. Moreover, our experiments in retrieval using the TINTIN system have strongly indicated that such structural decomposition can facilitate better representation of user''s information needs and hence more effective retrieval of tables.
Human papillomavirus type 48 (1989)

The cloning and partial characterization of the genome of human papillomavirus (HPV) type 48 is presented. Hybridization and short DNA sequence analyses permitted the alignment of the genome to the HPV genetic map.
Synthesis and photophysical properties of fluorescent 2,5‐dibenzoxazolylphenols and related compounds with excited state proton‐transfer (1993)

Abstract A series of new 2,5‐dibenzoxazolylphenols and related compounds was prepared by condensation of hydroxy‐ and methanesulfonamidoterephthalic acids with 2‐aminophenols. These displayed excited state intramolecular proton‐transfer fluorescence at room temperature and above with quantum yields as high as 0.48 and emission peaks of 492‐517 nm. The methanesulfonamido group was found about as effective a proton donor as the phenolic hydroxyl group. Incorporation of substituents onto the benzoxazole moieties increased solubility of the fluors in hydrocarbon solvents in some cases, but reduced quantum yields. These fluors are of interest as wavelength shifters in a scintillating detecting medium for ionizing radiation.
Dynamic changes in circulating tumor cell levels as a prognostic marker in stage IV non-small cell lung cancer. (2013)

8109 Background: We have previously reported the performance of our immuno-enrichment free HighEDefinition CTC (HDECTC) assay in the enumeration and characterization of circulating tumor cells (CTCs) in lung cancer patients. In the HD-CTC assay, nucleated cells are fluorescently labeled and imaged using automated microscopy. CTCs are defined as morphologically distinct, cytokeratin positive, CD45 negative cells. Here, we investigate further how CTCs numbers and physical properties relate to prognosis in NSCLC patients. Methods: The HD-CTC assay was applied for CTC enumeration in 362 blood samples collected longitudinally from 81 Stage IV NSCLC patients. Blood was collected at time 0, 3 weeks, and every 3 months thereafter. The collection protocol was restarted at disease progression, resulting in a sample number ranging between one and 12 samples per patient. Results: Eighty-one patients were enrolled, with 41 patients in 1 st line therapy, 11 in 2 nd , 17 in 3 rd , 7 in 4 th , 3 in 5 th and 2 in 6 th line therapy. Average age was 63, range 33 to 90; male to female ratio was 1:1.19. Eighty-six percent of patients had CTCs in at least one blood sample; CTC counts ranged from 0 to 885 CTCs/ml with a mean of 23.5 CTCs/ml across all samples. While no correlation was found between the absolute CTC concentration and survival, it was observed that for the 26 patients that had samples collected both at the start and during firstEline chemotherapy, an increase in CTC level between the two time points was significantly associated with longer survival (p < 0.001). Conclusions: As detected with our assay, it is the change in CTC level upon entering 1 st line chemotherapy and not the absolute CTC concentration that carries prognostic information. This observation highlights not only the importance of CTCs as prognostic biomarkers, but also that of access to serially collected specimens. The latter is here made possible only by the fact that the HDECTC assay samples tumor cells from peripheral blood.
Synergistic incorporation of hybrid heterobimetal–nitrogen atoms into carbon structures for superior oxygen electroreduction performance (2016)

A hybrid heterobimetal–nitrogen-doped carbon structure exhibits good electrochemical properties in ORR.
Discrete ray tracing (1992)

Discrete ray tracing, or 3-D raster ray tracing (RRT), which, unlike existing ray tracing methods that use geometric representation for the 3-D scene employs a 3-D discrete raster of voxels for representing the 3-D scene in the same way a 2-D raster of pixels represents a 2-D image, is discussed. Each voxel is a small quantum unit of volume that has numeric values associated with it representing some measurable properties or attributes of the real object or phenomenon at that voxel. It is shown that RRT operates in two phases: preprocessing voxel and discrete ray tracing. In the voxel phase, the geometric model is digitized using 3-D scan-conversion algorithms that convert the continuous representation of the model into a discrete representation within the 3-D raster. In the second phase, RRT employs a discrete variation of the conventional recursive ray tracer in which 3-D discrete rays are traversed through the 3-D raster to find the first surface voxel. Encountering a nontransparent voxel indicates a ray-surface hit. Results obtained by running the RRT software one one 20-MIPS (25-GHz) processor of a Silicon Graphics 4D/240GTX are presented in terms of CPU time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Wireless Mesh Infrastructure for Ubiquitous Voice and Video (2008)

Here is to propose a demonstration of opportunistic wireless mesh networks for broadband wireless Internet access, supporting real-time services, e.g., of voice and video. The enabling technology is of the large-scale cognitive networking, which opportunistically utilizes network resources including both spectrum bandwidth and mesh radio (station) availability. We further demonstrate that: (1) vast saving in the deployment/planning costs of wireless mesh networks can be achieved by establishing fluid networks without predetermined topology; (2) Better (opportunistic) network resource utilization can be achieved to establish reliable communications over multiple wireless hops. The network performance therefore reaches its instantaneous maximum.
Figure Captioning with Reasoning and Sequence-Level Training (2019)

Figures, such as bar charts, pie charts, and line plots, are widely used to convey important information in a concise format. They are usually human-friendly but difficult for computers to process automatically. In this work, we investigate the problem of figure captioning where the goal is to automatically generate a natural language description of the figure. While natural image captioning has been studied extensively, figure captioning has received relatively little attention and remains a challenging problem. First, we introduce a new dataset for figure captioning, FigCAP, based on FigureQA. Second, we propose two novel attention mechanisms. To achieve accurate generation of labels in figures, we propose Label Maps Attention. To model the relations between figure labels, we propose Relation Maps Attention. Third, we use sequence-level training with reinforcement learning in order to directly optimizes evaluation metrics, which alleviates the exposure bias issue and further improves the models in generating long captions. Extensive experiments show that the proposed method outperforms the baselines, thus demonstrating a significant potential for the automatic captioning of vast repositories of figures.
Growth and Transfer of Monolithic Horizontal ZnO Nanowire Superstructures onto Flexible Substrates (2010)

Abstract A method of fabricating horizontally aligned ZnO nanowire (NW) arrays with full control over the width and length is demonstrated. A cross‐sectional view of the NWs by transmission electron microscopy shows a “mushroom‐like” structure. Novel monolithic multisegment superstructures are fabricated by making use of the lateral overgrowth. Ultralong horizontal ZnO NWs of an aspect ratio on the order of ten thousand are also demonstrated. These horizontal NWs are lifted off and transferred onto a flexible polymer substrate, which may have many great applications in horizontal ZnO NW‐based nanosensor arrays, light‐emitting diodes, optical gratings, integrated circuit interconnects, and high‐output‐power alternating‐current nanogenerators.
Diffraction pattern based optimization of lithographic targets for improved printability (2013)

Conventional resolution enhancement techniques (RET) are becoming increasingly inadequate at addressing the challenges of sub-wavelength lithography. In particular, features show high sensitivity to process variation in low-k<sub>1</sub> lithography. While advanced mask optimization techniques such as process window optical proximity correction (PWOPC) exist to address this, they modify electrical properties of shapes in a way that is incommunicable to the designer. A more design-aware approach for improving printability is to perform retargeting, which is a modification of target layout shapes to improve their process window. Retargeting can be performed rule-based or model-based. The former has fast runtime but is not a scalable technique since rules cannot cover the entire search space of two-dimensional shape configurations, especially with technology scaling. The latter provides more coverage of complex 2-D optical interactions compared to rules, but suffers from high runtime and inability to communicate modified design intent back to the designer. In this paper, we explore an alternative approach to retargeting which overcomes the drawbacks of both these methods. We develop a target optimization method based on knowledge of source and the diffraction pattern of the layout. We demonstrate that target optimization can be performed at fast runtime using just the Fourier transform of the layout. This approach is more scalable than rule-based retargeting, but also allows communication of modified design intent by integration into extraction tools.
Intelligent Radiation Sensor System (IRSS) Advanced Technology Demonstration (ATD) (2010)

In response to the Domestic Nuclear Detection Office's (DNDO) BAA 09-102 Passport Systems, Inc. of Billerica, MA has carried out a system-level trade space study and started development of a networked system of Intelligent Personal Radiation Locators (IRPLs) and Human Portable Radiation Detection Systems (HPRDSs) designed to improve the detection, localization, and identification of potential radiological threats. A system of this nature is targeted to situations where it is not feasible to direct traffic through portal radiation detection systems, e.g. large events, search team objectives, etc. The capability to intelligently network individual portable detectors using advanced algorithms and COTS hardware has been shown within this program to significantly increase the effectiveness of an assortment of portable radiation detectors, including those devices currently available to first responders and search teams, in a variety of NORM (naturally occurring radioactive material) backgrounds. An overview of current work will be provided in two parts: 1) Results of our system analysis will highlight important drivers in the trade space of network protocols, detection efficiencies, computational requirements, and human interfaces; and 2) Development status of both the prototype hardware and the advanced suite of detection, localization, and identification algorithms will be shown. Conclusions are derived from a combination of simulation and actual data collection efforts.
Computer Generated Hologram Reconstruction using Liquid Crystal Spatial Light Modulators (1993)

Liquid Crystal Devices (LCDs) have been widely used for Spatial Light modulators (SLMs) because of its easy operating characteristics.
Three‐Dimensional Database Mining Identifies a Unique Chemotype that Unites Structurally Diverse Botulinum Neurotoxin Serotype A Inhibitors in a Three‐Zone Pharmacophore (2008)

A search query consisting of two aromatic centers and two cationic centers was defined based on previously identified small molecule inhibitors of the botulinum neurotoxin serotype A light chain (BoNT/A LC) and used to mine the National Cancer Institute Open Repository. Ten small molecule hits were identified, and upon testing, three demonstrated inhibitory activity. Of these, one was structurally unique, possessing a rigid diazachrysene scaffold. The steric limitations of the diazachrysene imposed a separation between the overlaps of previously identified inhibitors, revealing an extended binding mode. As a result, the pharmacophore for BoNT/A LC inhibition has been modified to encompass three zones. To demonstrate the utility of this model, a novel three-zone inhibitor was mined and its activity was confirmed.
Automating camera management for lecture room environments (2001)

Given rapid improvements in network infrastructure and streaming-media technologies, a large number of corporations and universities are recording lectures and making them available online for anytime, anywhere access. However, producing high-quality lecture videos is still labor intensive and expensive. Fortunately, recent technology advances are making it feasible to build automated camera management systems to capture lectures. In this paper we report on our design, implementation and study of such a system. Compared to previous work-which has tended to be technology centric-we started with interviews with professional video producers and used their knowledge and expertise to create video production rules. We then targeted technology components that allowed us to implement a substantial portion of these rules, including the design of a virtual video director. The system's performance was compared to that of a human operator via a user study. Results suggest that our system's quality in close to that of a human-controlled system. In fact most remote audience members could not tell if the video was produced by a computer or a person.
The role of interleukin-9 and the interleukin-9 receptor gene candidates in asthma (2002)

It is now generally well accepted that atopic asthma is a complex heritable disorder of the airways in which symptoms depend on environmental exposure [1]. This lung disorder is associated with clinical signs and symptoms of airway hyperresponsiveness (AHR), an exaggerated narrowing of the airways to provocative stimuli, and eosinophilic inflammation associated with reversible airway obstruction. Significant biologic variability in airway responsiveness occurs in humans, and baseline bronchial hyperresponsiveness is recognized as a heritable risk factor for asthma [2-5]. While significant biologic variability in airway responsiveness in rodents and humans has been observed, little is understood about the genetic regulation of AHR [5]. Moreover, it remains unclear whether or how AHR is associated with an underlying predisposition to eosinophilic airway inflammation. Recently, genetic linkage studies and functional genomics in humans and mice have implicated interleukin-9 (IL-9) and its receptor in the genetics of AHR and asthma [6-15]. In this chapter, we will review evidence supporting a central role for IL-9 as a regulator of AHR and a critical mediator of allergic asthma and mucosal Th2 immunity.
Chapter 6. Immunotherapeutic Strategies Towards Treatment of Alzheimer's Disease (2010)

Treatment of Alzheimer's disease (AD) by recruiting an immune response against beta-amyloid (Aβ) was suggested by findings that monoclonal antibodies against synthetic Aβ peptide can keep the peptides from aggregating into neurotoxic fibrils and can dissolve already formed amyloid. Active and passive immunization studies in transgenic mice models of AD show that antibodies against Aβ peptide are effective in reducing Aβ levels and plaque pathology, as well as attenuating cognitive deficits in animal models of AD sometimes associated with adverse reactions. Although the causative role of Aβ peptide in AD pathogenesis is well-established, it is less clear whether Aβ, deposited as amyloid or some other less well-characterized Aβ soluble assembly, initiates the cascade eventually leading to neuronal death and dysfunction. In view of this debate, decreasing Aβ production from its precursor protein APP is a logical step to intervene. Here we describe a new approach to reduce Aβ peptide formation, based on blocking the β-secretase cleavage site of APP using antibodies which interfere with APP-BACE interaction. It is not yet clear if the various strategies for mobilizing the immune system will end up being a treatment to prevent or to treat AD. However, immunotherapy has clearly strengthened the hypothesis that Aβ peptide plays a central role in AD and has stimulated a new area for development of Alzheimer's therapeutics and for their further evaluation in renewed human phase clinical trials.
Dynamic Parity Grouping for Improving Write Performance of RAID-5 Disk Arrays (1994)

One major drawback of a RAIDS disk array system is that an update to a data block may involve four disk accesses. Such a high overhead is especially undesirable for workloads with a high update rate. In this paper, we present a dynamic parity grouping (DPG) scheme for efficient parity buffering to reduce the write overhead of a RAID-5 system. In DPG, special parity groups are dynamically created for data blocks with high write activity, referred to as the hot data blocks, in addition to default parity groups for the remaining cold data blocks. The parity blocks of the special parity groups are then buffered in the disk controller cache. As a result, the number of disk accesses on a write to a hot data block is reduced to two.
Live Measles Vaccine Expressing the Secreted Form of the West Nile Virus Envelope Glycoprotein Protects against West Nile Virus Encephalitis (2004)

The Schwarz strain of measles virus (MV), a live attenuated RNA virus, is one of the safest and most effective human vaccines available. Immunization with MV vaccine expressing heterologous antigen is an attractive strategy to prevent emerging viral diseases. West Nile virus (WNV), which recently emerged in North America, is an important mosquito-borne flavivirus that causes numerous cases of human encephalitis, thus urging the development of a vaccine. To evaluate the efficacy of recombinant MV for the prevention of WNV encephalitis, we constructed a live attenuated Schwarz MV (MVSchw-sE(WNV)) expressing the secreted form of the envelope glycoprotein from the virulent IS-98-ST1 strain of WNV. Inoculation of MV-susceptible mice with MVSchw-sE(WNV) induced both high levels of specific anti-WNV neutralizing antibodies and protection from a lethal challenge with WNV. Passive administration with antisera to MVSchw-sE(WNV) prevented WNV encephalitis in BALB/c mice challenged with a high dose of WNV. The present study is the first to report that a recombinant live attenuated vector based on an approved and widely used MV vaccine can protect against a heterologous, medically important pathogen.
Utilization of Biomass Residues for the Remediation of Metal-Polluted Soils (1998)

The utilization of biomass residues as sources for natural chelates is a new approach to improve the ecological and economical balance of leaching techniques for the remediation of metal-polluted soils. Residues, such as molasses, blood meal, and silage effluents, containing various aliphatic carboxylic acids, sugar acids, and amino acids or their precursor compounds were selected, hydrolyzed and oxidized, if required, and analyzed for their organic constituents. Soils that were contaminated with metals via sewage sludge amendment were extracted in batch and column experiments at various pH values. Grass silage effluent removed ∼75% of Cd and >50% of Cu and Zn at pH 4.4. The neutralized effluent was less effective except for Cu (69% leached). The neutral blood meal hydrolysate extracted primarily Cu (55−66%) and Ni (38−67%). Metal bonds attacked by this extractant were identified using a sequential leaching procedure. Hydrolysates containing sugar acids mobilized Cu and Pb under alkaline conditions. The actual results support the conclusion that biomass residues have a potential to serve as extractants in remediation techniques.
Ultrahigh Resolution Ion Beam Processes (1976)

Abstract : This is the first semiannual progress report on the program 'Ultra- high Resolution Ion Beam Processes.' The overall goal of the program is to establish the technical and economic feasibility of applying submicrometer diameter focused ion beams to microcircuit fabrication without the use of masks. The progress for this reporting period consists of obtaining and operating two high brightness ion sources, analyzing focusing lenses and columns, and designing and fabricating a focusing column for each ion source. These columns are now about 80% complete and it is expected that one will be put into operation during the next quarter. Keywords include: Ion Beam, Sputtering, Focusing Column, and Einzel Lens.
Optimal training for block transmissions over doubly-selective fading channels (2002)

High data rates give rise to frequency-selective propagation, while carrier frequency-offsets and mobility-induced Doppler shifts introduce time-selectivity in wireless links. To mitigate the resulting time- and frequency-selective (or doubly-selective) channels, an optimal training strategy is designed in this paper for block transmissions over doubly-selective channels, relying on a basis expansion channel model. The optimality in designing our PSAM parameters consists of maximizing a tight lower bound on the average channel capacity, that is also shown to be equivalent to the minimization of the minimum mean-square channel estimation error. Numerical results corroborate our theoretical designs.