gebhart/patrepeval huggingface dataset:
Processing of human cytomegalovirus envelope glycoproteins in and egress of cytomegalovirus from human astrocytoma cells (1992)

The synthesis of human cytomegalovirus (HCMV) envelope glycoproteins and the production of infectious HCMV in human astrocytoma and skin fibroblast (SF) cells were analysed. HCMV envelope glycoproteins synthesized in astrocytoma cells had lower Mrs than the same glycoproteins synthesized in SF cells regardless of the strain of HCMV used, showing that the differences observed were due to differences in processing by the host cell and not the strain of HCMV used. HCMV envelope glycoproteins synthesized in astrocytoma cells were found to contain less galactosamine. Moreover, when synthesized in SF cells some HCMV glycoproteins contained a protease-resistant fragment owing to the presence of a cluster of O-linked oligosaccharides on the polypeptide. This fragment was not present when these HCMV glycoproteins were synthesized in astrocytoma cells. These data suggested that HCMV glycoproteins synthesized in astrocytoma cells contain fewer O-linked oligosaccharides. In contrast, other post-translational events such as proteolytic cleavage of the HCMV gB glycoprotein and the formation of disulphide-linked complexes did occur. The virus produced in astrocytoma cells was capable of infecting SF cells, suggesting that complete O-glycosylation is not needed to produce infectious HCMV. However, astrocytoma cells were slow to release virus into the culture medium, suggesting that a fully functional Golgi network is needed for efficient egress of HCMV from the host cell.
Computer-aided Detection System for Breast Masses on Digital Tomosynthesis Mammograms: Preliminary Experience (2005)

The purpose of the study was to design a computer-aided detection (CAD) system for breast mass detection on digital breast tomosynthesis (DBT) mammograms and to perform a preliminary evaluation of the performance of this system. Twenty-six patients were imaged with a prototype DBT system. Institutional review board approval and written informed patient consent were obtained. Use of the data set in this study was HIPAA compliant. The CAD system first screened the three-dimensional volume of the mass candidates by means of gradient-field analysis. Each mass candidate was segmented from the structured background, and its image features were extracted. A feature classifier was designed to differentiate true masses from normal tissues. The CAD system was trained and tested by using a leave-one-case-out method. The classifier calculated a mean area under the test receiver operating characteristic curve of 0.91 +/- 0.03 (standard error of mean). The CAD system achieved a sensitivity of 85%, with 2.2 false-positive objects per case. The results demonstrate the feasibility of the authors' approach to the development of a CAD system for DBT mammography.
Adenovirus vector library: an approach to the discovery of gene and protein function (2003)

A method was developed to generate a complex cDNA expression library within an adenovirus type 5 (Ad5)-based vector backbone, termed AdLibrary. Construction of the AdLibrary entailed the conversion of an Ad5 genome-containing cosmid to infectious virus particles. The Ad5 genome was modified by replacing the E1A and E1B genes with a Rous sarcoma virus-driven expression cassette. Conversion was accomplished by liberating the viral genome by restriction enzyme digestion and transfection in HEK 293 cells, which support the growth of E1A/E1B-deficient virus. A test AdLibrary demonstrated the possibility of converting and identifying a marker gene present at a frequency of 1/10(5) in the cosmid library. To demonstrate the utility of this technology, an AdLibrary was used to isolate a viral gene by its biological function. Virus growth was selected for with an AdLibrary on A549 cells, which do not complement for E1A/E1B function. The AdLibrary was generated with cDNAs derived from HeLa cells productively infected with Ad5. A cDNA corresponding to Ad5 E1A 13S was selected and isolated from the AdLibrary using this strategy. Since multiple genes are assayed simultaneously, this technology should expedite the discovery of genes affecting defined biological activities. This AdLibrary approach provides an opportunity to exploit the efficient gene delivery capabilities of adenovirus vectors for the rapid discovery of gene and protein function.
Spin glass behaviour of amorphous Ge–Mn alloy thin films (2007)

Magnetic measurements are performed under ac and dc conditions on well characterized Ge100−xMnx (x in at.%) amorphous thin films prepared by thermal co-evaporation onto oxidized Si or glass substrates at room temperature. M–H hysteresis loops at 5 K show that saturation does not occur even at a high applied field of 30 or 50 kOe. The temperature dependence of the dc and ac susceptibility shows a cusp with a position and magnitude that vary with the frequency during the ac susceptibility measurements. These results suggest a spin glass behaviour at low temperatures. Two competing magnetic interactions between Mn ions, which are responsible for the spin glass behaviour, are considered to be the direct antiferromagnetic coupling and the indirect ferromagnetic coupling through conduction electrons or holes. Scaling analysis indicates that the indirect ferromagnetic interactions are long range.
HMM adaptation using a phase-sensitive acoustic distortion model for environment-robust speech recognition (2008)

In this paper, we present a new approach to HMM adaptation that jointly compensates for additive and convolutive acoustic distortion in environment-robust speech recognition. The hallmark of our new approach is the use of a nonlinear, phase-sensitive model of acoustic distortion that captures phase asynchrony between clean speech and the mixing noise. In the first step of the developed algorithm, both the static and dynamic portions of the noise and channel parameters are estimated in the cepstral domain, using the speech recognizer’s “feedback” information and the vector-Taylor-series linearization technique on the nonlinear phase-sensitive model. In the second step, the estimated noise and channel parameters are used to effectively adapt the static and dynamic portions of the HMM means and variances also using the linearized phase-sensitive acoustic distortion model. In the experimental evaluation using the standard Aurora 2 task, the proposed new algorithm achieves 93.3% accuracy using the clean-trained complex HMM backend as the baseline system for unsupervised HMM adaptation. This reaches the highest performance number in the literature on this task with clean-trained HMM model. The experimental results show that the phase term, which was missing in all previous HMM-adaptation work, contributes significantly to the achieved high recognition accuracy.
Animated, Dynamic Voronoi Treemaps (2010)

The Voronoi Treemap is a space-filling treemap technique that relaxes the constraints of rectangular nodes. Its organic shapes maintain a one-to-one aspect ratio, are flexible with their placement, allowing stable zooming and dynamic data values. This poster articulates the tradeoffs that go into generating dynamic treemaps. We then present innovative features that allow Voronoi Treemaps to smoothly represent dynamically-changing data. We demonstrate its use with a deep organizational chart and an animated dataset. User tests confirm that Voronoi Treemaps can be a successful visualization technique.
MSBVH (2011)

When a bounding volume hierarchy is used for accelerating the intersection of rays and scene geometry, one common way to incorporate motion blur is to interpolate node bounding volumes according to the time of the ray. However, such hierarchies typically exhibit large overlap between bounding volumes, which results in an inefficient traversal. This work builds upon the concept of spatially partitioning nodes during tree construction in order to reduce overlap in the presence of moving objects. The resulting hierarchies are often significantly cheaper to traverse than those generated by classic approaches.
A robust ranging scheme for OFDMA-based networks (2009)

Uplink synchronization in orthogonal frequency division multiple-access (OFDMA) systems is a challenging task. In IEEE 802.16-based networks, users that intend to establish a communication link with the base station must go through a synchronization procedure called Initial Ranging (IR). Existing IR schemes aim at estimating the timing offsets and power levels of ranging subscriber stations (RSSs) without considering possible frequency misalignments between the received uplink signals and the base station local reference. In this work, a novel IR scheme is presented for OFDMA systems where carrier frequency offsets, timing errors and power levels are estimated for all RSSs in a decoupled fashion. The proposed frequency estimator is based on a subspace decomposition approach, while timing recovery is accomplished by measuring the phase shift between the usersiquest channel responses over adjacent subcarriers. Computer simulations are employed to assess the effectiveness of the proposed solution and to make comparisons with existing alternatives.
Kernel methods for weakly supervised mean shift clustering (2009)

Mean shift clustering is a powerful unsupervised data analysis technique which does not require prior knowledge of the number of clusters, and does not constrain the shape of the clusters. The data association criteria is based on the underlying probability distribution of the data points which is defined in advance via the employed distance metric. In many problem domains, the initially designed distance metric fails to resolve the ambiguities in the clustering process. We present a novel semi-supervised kernel mean shift algorithm where the inherent structure of the data points is learned with a few user supplied constraints in addition to the original metric. The constraints we consider are the pairs of points that should be clustered together. The data points are implicitly mapped to a higher dimensional space induced by the kernel function where the constraints can be effectively enforced. The mode seeking is then performed on the embedded space and the approach preserves all the advantages of the original mean shift algorithm. Experiments on challenging synthetic and real data clearly demonstrate that significant improvements in clustering accuracy can be achieved by employing only a few constraints.
MK-7622: A First-in-Class M<sub>1</sub> Positive Allosteric Modulator Development Candidate (2018)

Identification of ligands that selectively activate the M<sub>1</sub> muscarinic signaling pathway has been sought for decades to treat a range of neurological and cognitive disorders. Herein, we describe the optimization efforts focused on addressing key physicochemical and safety properties, ultimately leading to the clinical candidate MK-7622, a highly selective positive allosteric modulator of the M<sub>1</sub> muscarinic receptor that has entered Phase II studies in patients with Alzheimer's disease.
Six-axis force–torque sensor with a large range for biomechanical applications (2014)

A silicon six-axis force–torque sensor is designed and realized to be used for measurement of the power transfer between the human body and the environment. Capacitive read-out is used to detect all axial force components and all torque components simultaneously. Small electrode gaps in combination with mechanical amplification by the sensor structure result in a high sensitivity. The miniature sensor has a wide force range of up to 50 N in normal direction, 10 N in shear direction and 25 N mm of maximum torque around each axis.
Fair media access for wireless LANs (2003)

This paper addresses load balancing algorithms for the wireless links to solve the fairness problem, where stations are not able to gain access equally to the shared wireless medium. The fairness problem occurs mostly because of the existence of hidden stations and the presumption of a non-fully connected wireless network topology. In this paper, p/sub ij/-persistent carrier sense multiple access based algorithms are proposed in which a fair wireless access for each user is accomplished using a pre-calculated link access probability. Link access probabilities are calculated at the source station in two ways using connection-based and time-based media access methods. Each active user broadcasts information on either the number of logical connections or the average contention time to the stations within the communication reach. Each station reserves a specific priority for its each link to gain access to the shared medium based on the exchanged information. The proposed algorithms are dynamic and sensitive to the changes in the network topology. They are applicable to all CSMA based media access control protocols to provide a degree of fairness.
Analysis of the role of cysteine residues in isopenicillin N synthetase activity by site-directed mutagenesis. (1987)

The predicted amino acid sequences of isopenicillin N synthetase from both Cephalosporium acremonium and Penicillium chrysogenum have two cysteine residues in analogous positions (Cys-106 and Cys-255 in the C. acremonium numbering). To examine the role of these cysteine residues in the activity of the C. acremonium enzyme, we used site-directed in vitro mutagenesis to change these cysteine residues to serine residues. Mutation of Cys-255 reduces specific activity approximately equal to 50%, whereas mutation of Cys-106 or mutation of both Cys-106 and Cys-255 reduces specific activity about 97%. This suggests that the cysteines are important but not essential for IPNS activity. Alkylation of IPNS also almost completely inactivated the enzyme, but residual activity could have been due to incomplete alkylation. Atomic substitution via genetic manipulation in this case is a more accurate means of assessing the role of sulfhydryl moieties in enzyme activity.
In-Situ Resistance Measurements of RHQT Processed&lt;tex&gt;$rm Nb_3rm Al$&lt;/tex&gt;Superconductors (2005)

The bcc supersaturated solid solution, Nb(Al)/sub ss/ obtained by rapid heating and quenching of a multifilamentary Nb/Al composite wire has shown a change from a disordered to an ordered structure before finally transforming to the A15 Nb/sub 3/Al phase. It is believed that such ordering is responsible for suppressing the critical temperature, T/sub c/, the upper critical magnetic field, B/sub c2/, and the critical current density, J/sub c/. The ordering of the bcc phase can be suppressed by increasing the heating rate, and therefore this should improve the superconducting properties of the resulting Nb/sub 3/Al wires. Enhancement of J/sub c/ can also be achieved if the Nb(Al)/sub ss/ phase is mechanically deformed before transformation. The transformation process was studied in as-quenched and mechanically deformed Nb/Nb(Al)/sub ss/ wires by in-situ resistance measurement under heating at two different rates, 200/spl deg/C/h and 800/spl deg/C/h. The electrical resistivities of the wires decrease abruptly during the transformation from bcc to A15 phases and the process is much faster for mechanically deformed wires. Also, the heating rate affects the onset temperature of the A15 transformation. The results also show that the J/sub c/ of the transformed Nb/sub 3/Al wires increases with increasing reduction in area.
Modulation of Tissue-Specific Immune Response to Cardiac Myosin Can Prolong Survival of Allogeneic Heart Transplants (2002)

The role of immune response to tissue-specific Ags in transplant rejection is poorly defined. We have previously reported that transplantation of cardiac allografts triggers a CD4(+) Th1 cell response to cardiac myosin (CM), a major contractile protein of the heart, and that pretransplant activation of proinflammatory CM-specific T cells accelerates rejection. In this study, we show that administration of CM together with IFA (CM/IFA) can prevent acute rejection of an allogeneic heart transplant. Prolongation of cardiac graft survival is associated with activation of CM- and allo-specific T cells secreting type 2 cytokines (IL-4, IL-5) and reduction of the frequency of proinflammatory IFN-gamma-secreting (type 1) alloreactive T cells. Blocking of IL-4 cytokine with Abs abrogates the prolongation. CM/IFA treatment prevents acute rejection of MHC class I-mismatched, but not fully mismatched grafts. However, if donor heart is devoid of MHC class II expression, CM-IFA administration delays rejection of fully allogeneic cardiac transplants. This finding suggests that the effect of CM modulation depends on the type (direct vs indirect) and strength of recipient's CD4(+) T cell alloresponse. Our results underscore the important role of host immunity to tissue-specific Ags in the rejection of an allograft. This study demonstrates that modulation of the immune response to a tissue-specific Ag can significantly prolong cardiac allograft survival, an observation that may have important implications for the development of novel selective immune therapies in transplantation.
ALPOS: A Machine Learning Approach for Analyzing Microblogging Data (2010)

With the development of Internet, the increasing volume of information posted on micro-blogging sites like Twitter necessitates the need for efficient information filtering. In conventional text classification problems, it is assumed that the feature vectors extracted from the available documents are sufficient to learn good classifiers. However, this conventional approach is not likely to work for Twitter due to the limited number of characters on each tweet. From a higher level, each tweet can be viewed as an abbreviated abstraction of a long document, and we only have a partial observation of this document. To solve the problem caused by the partial observations, we introduce a novel domain adaption/transfer learning approach called Assisted Learning for Partial Observation (ALPOS). The basic idea is to use a large number of multi-labeled examples (source domain) to improve the learning on the partial observations (target domain). In particular, we learn a hidden, higher-level abstraction space, which is meaningful for the multi-labeled examples in the source domain. This is done by simultaneously minimizing the document reconstruction error and the error in a classification model learned in the hidden space by using known labels from the source domain. The partial observations in the target space are then mapped to the same hidden space for recovery and classification. We compare the performance of this method with existing approaches on synthetic data and the well-known Reuters-21578 dataset. We also present experimental results on twitter classification.
Chip-to-chip optical interconnects (2006)

Terabus is based on a silicon-carrier interposer on an organic card containing 48 polymer waveguides. We have demonstrated 4times12 arrays of low power optical transmitters and receivers, operating up to 20 Gb/s and 14 Gb/s per channel respectively
A Recessive Gene Determining Male Sterility in Quinoa (1994)

Plants of the Bolivian quinoa (Chenopodium quinoa Willd.) cultivar Amachuma carry a single nuclear recessive gene which in the homozygous state produces fully formed anthers completely devoid of pollen. Plants heterozygous at this locus are indistinguishable from homozygous male fertiles, and segregation for male sterility follows a normal Mendelian single-gene pattern. This form of male sterility is likely to be of limited use in hybrid quinoa production due to poor stigma exsertion, which results in inefficient pollination.
Pilot contamination problem in multi-cell TDD systems (2009)

This paper considers a multi-cell multiple antenna system with precoding at the base stations for downlink transmission. To enable precoding, channel state information (CSI) is obtained via uplink training. This paper mathematically characterizes the impact that uplink training has on the performance of multi-cell multiple antenna systems. When non-orthogonal training sequences are used for uplink training, it is shown that the precoding matrix used by the base station in one cell becomes corrupted by the channel between that base station and the users in other cells. This problem of pilot contamination is analyzed in this paper. A multi-cell MMSE-based precoding is proposed that, when combined with frequency/time/pilot reuse techniques, mitigate this problem.
Tweet the debates (2009)

We investigate the practice of sharing short messages (microblogging) around live media events. Our focus is on Twitter and its usage during the 2008 Presidential Debates. We find that analysis of Twitter usage patterns around this media event can yield significant insights into the semantic structure and content of the media object. Specifically, we find that the level of Twitter activity serves as a predictor of changes in topics in the media event. Further we find that conversational cues can identify the key players in the media object and that the content of the Twitter posts can somewhat reflect the topics of discussion in the media object, but are mostly evaluative, in that they express the poster's reaction to the media. The key contribution of this work is an analysis of the practice of microblogging live events and the core metrics that can leveraged to evaluate and analyze this activity. Finally, we offer suggestions on how our model of segmentation and node identification could apply towards any live, real-time arbitrary event.
A Soft-Robotic Gripper With Enhanced Object Adaptation and Grasping Reliability (2017)

A novel soft-robotic gripper design is presented, with three soft bending fingers and one passively adaptive palm. Each soft finger comprises two ellipse-profiled pneumatic chambers. Combined with the adaptive palm and the surface patterned feature, the soft gripper could achieve 40-N grasping force in practice, 10 times the self-weight, at a very low actuation pressure below 100 kPa. With novel soft finger design, the gripper could pick up small objects, as well as conform to large convex-shape objects with reliable contact. The fabrication process was presented in detail, involving commercial-grade three-dimensional printing and molding of silicone rubber. The fabricated actuators and gripper were tested on a dedicated platform, showing the gripper could reliably grasp objects of various shapes and sizes, even with external disturbances.
Using hardware performance monitors to understand the behavior of java applications (2004)

Modern Java programs, such as middleware and application servers, include many complex software components. Improving the performance of these Java applications requires a better understanding of the interactions between the application, virtual machine, operating system, and architecture. Hardware performance monitors, which are available on most modern processors, provide facilities to obtain detailed performance measurements of long-running applications in real time. However, interpreting the data collected using hardware performance monitors is difficult because of the low-level nature of the data. We have