gebhart/patrepeval huggingface dataset:
Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions (2023)

Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.
The translocated c-myc oncogene of Raji Burkitt lymphoma cells is not expressed in human lymphoblastoid cells. (1985)

We hybridized Raji Burkitt lymphoma cells, which carry a t(8;14) chromosome translocation, with human lymphoblastoid cells to study the expression of the translocated cellular myc oncogene (c-myc) in the hybrid cells. In Raji cells the c-myc oncogene is translocated to a switch region of the gamma heavy chain locus (S gamma). Because of sequence alterations in the 5' exon of the translocated c-myc oncogene in this cell line, it is possible to distinguish the transcripts of the translocated c-myc gene and of the normal c-myc gene. S1 nuclease protection experiments with a c-myc first exon probe indicate that Raji cells express predominantly the translocated c-myc gene, while the level of expression of the normal c-myc gene is less than 2% of that of the translocated c-myc gene. Somatic cell hybrids between Raji and human lymphoblastoid cells retain the lymphoblastoid phenotype and express only the normal c-myc oncogene. This result indicates that the activation of a c-myc oncogene translocated to a S region depends on the stage of B-cell differentiation of the cells harboring the translocated c-myc gene and not on alterations in the structure of the translocated c-myc oncogene.
Controlled, systematic, and efficient code replacement for running java programs (2008)

In this paper we present PROSE, a system that performs reversible and systematic changes to running Java applications without requiring them to be shut down. PROSE is motivated by scenarios such as hotfixes, online program instrumentation and debugging, and evolution of critical legacy applications. In PROSE, changes to running applications are performed by replacing method bodies. To select which code to replace, PROSE supports matching based on both type information and regular expressions. New code can invoke the method it replaces, facilitating code evolution. Changes are composable, and may be reordered or selectively withdrawn at any time. Furthermore, the dynamic changes are expressed as Java classes rather than through an additional programming language. We describe the architecture of PROSE, the challenges of using aggressive inlining to achieve performance, and use standard benchmarks to demonstrate code performance comparable with, or better than, compile-time systems from the Aspect-Oriented Programming community.
Beam codebook based beamforming protocol for multi-Gbps millimeter-wave WPAN systems (2009)

In order to realize high speed, long range, reliable transmission in millimeter-wave 60 GHz wireless personal area networks (60 GHz WPANs), we propose a beamforming (BF) protocol realized in media access control (MAC) layer on top of multiple physical layer (PHY) designs. The proposed BF protocol targets to minimize the BF set-up time and to mitigate the high path loss of 60 GHz WPAN systems. It consists of 3 stages, namely the device (DEV) to DEV linking, sector-level searching and beam-level searching. The division of the stages facilitates significant reduction in setup time as compared to BF protocols with exhaustive searching mechanisms. The proposed BF protocol employs discrete phase-shifters, which significantly simplifies the structure of DEVs as compared to the conventional BF with phase-and-amplitude adjustment, at the expense of a gain degradation of less than 1 dB. The proposed BF protocol is a complete design and PHY-independent, it is applicable to different antenna configurations. Simulation results show that the setup time of the proposed BF protocol is as small as 2% when compared to the exhaustive searching protocol. Furthermore, based on the codebooks with four phases per element, around 15.1 dB gain is achieved by using eight antenna elements at both transmitter and receiver, thereby enabling 1.6 Gbps-data-streaming over a range of three meters. Due to the flexibility in supporting multiple PHY layer designs, the proposed protocol has been adopted by the IEEE 802.15.3c as an optional functionality to realize Gbps communication systems.
Immunity to Hemophilus influenzae type b. I. The isolation, and some physicochemical, serologic and biologic properties of the capsular polysaccharide of Hemophilus influenzae type b. (1971)

The capsular substance of H. influenzae type b was isolated in a highly purified form. Serologic identity was demonstrated among the polysaccharides of seven different strains of H. influenzae type b. The polysaccharide had a molecular weight greater than 200,000 estimated by gel filtration and 152,000 by analytic ultracentrifugation and was shown to be relatively non-toxic and non-pyrogenic for laboratory animals.
In vitro control of neuronal polarity by glycosaminoglycans (1992)

We have studied the effects of proteoglycans (PGs) and glycosaminoglycans (GAGs) on the growth and morphology of neurons in culture. PGs from glial cells or Engelbreth-Holm-Swarm tumor cells (EHS), pure bovine kidney heparan sulfate (HS), shark cartilage type C chondroïtin sulfate (CSc) and bovine mucosa dermatan sulfate (DS) added to embryonic rat neurons strongly enhanced total neurite growth after 48 h in vitro. No trophic effects were seen when PGs treated with a mixture of glycanases were used. PGs, CSc and HS not only enhanced neurite growth but induced the appearance of a majority of neurons with a single long axon whereas, in contrast, DS increased dendrite growth. GAGs bound to the cell surface and were rapidly internalized, a feature that correlated well with the absence of neurotrophicity of GAGs previously immobilized on the culture substratum. Although the mechanisms involved in GAGs neurotrophic effects and in the separate regulation of neuronal polarity by HS and DS were not elucidated, we found that, as opposed to HS, DS was able to enhance neuronal adhesion and spreading and to maintain a high level of expression of microtubule-associated protein 2 (MAP2), a specific dendritic marker. This finding confirms and extends our previous observations on the role of adhesion in the regulation of dendrite growth.
High Definition Ink-Jet Printing: 10-20&#x3BC;m Dots Eject from an Injection Needle (1998)

The authors developed the novel ink-jet technology using electrostatic force. One of the features of this technology is that the minute ink droplets are ejected from a large aperture. This results in fewer clogging problems than conventional ink-jet technologies. More than 2000 dpi resolution can be achieved with this technology. The dot-size can be modulated by pulse-width modulation. Furthermore, the authors observed the concentration effect of the ink when it is ejected. The essence of this technology is to eject charged ink droplets by electrostatic force. The ink contains positively or negatively charged colorants which disperse in a highly resistive solvent, and are supplied from an ink tank to the tip of an injection needle. The injection needle with an inner diameter of more than 500 &#x3BC;m is the ink-jet electrode. When the signal and bias voltage with the same polarity as that of the colorants is applied to the injection needle, a small meniscus is formed at the tip position. And the charged ink droplets are ejected onto the paper by the electrostatic force between the injection needle and the recording media (paper).In this paper the features of the novel ink-jet technology, experimental setup, observation results, and the printing samples are described.
The bacterial polysaccharide tecogalan blocks growth of breast cancer cells in vivo. (2001)

The growth of supportive tissue during the progression of solid tumors is an absolute requirement for the nourishment of the tumor. The blockade of this proliferative response of normal tissues to the growing tumor should hence inhibit tumor progression. We have shown earlier, that the heparinoid pentosan polysulfate (PPS) can block tumor growth and neoangiogenesis induced by Kaposi's FGF as well as by other heparin-binding growth factors (HBGFs). We now report on the effects of a bacterial polysaccharide, tecogalan, on tumor xenografts of human breast cancer cells. Tecogalan inhibited FGF-dependent SW-13 cells in vitro very similarly to PPS. Growth factor-independent MDA-MB 231 cells were used in animal studies to assess the in vivo potential of tecogalan. Subcutaneous growth of tumors was inhibited by once weekly i.v. administration of tecogalan. PPS single weekly administration showed a similar effect. No gross side effects were observed. Based on our previous studies with these models, we conclude, that tecogalan acts by blocking HBGFs released from tumor cells. Interestingly, single weekly dosing of either PPS or tecogalan appears to be strikingly more efficacious than spreading the dose over several administrations. These findings with a novel compound, tecogalan, and a novel treatment regimen, PPS, suggests a different approach to planning of therapies with these types of drugs.
Severity modeling of propionic acidemia using clinical and laboratory biomarkers (2021)

Support vector machine prioritized biomarkers that helped classify propionic acidemia patients according to severity subtypes, with important ramifications for future clinical trials and management of PA.
CRYPTOSPORIDIUM PARVUM IN CHILDREN WITH DIARRHEA IN MULAGO HOSPITAL, KAMPALA, UGANDA (2003)

A cross-sectional case-control study (ratio = 3:1) was conducted over a 15-month period to determine the prevalence and consequences of cryptosporidiosis in hospitalized diarrheic children (0-5 years old) at Mulago Hospital in Kampala, Uganda. Cryptosporidium parvum was detected and genotyped among 2,446 children of whom 1,779 (72.7%) had diarrhea, and 667 (27.3%) were age- and sex-matched controls. Of the 1,779 children with diarrhea, 532 (29.9%) had persistent (> 14 days) diarrhea and 1,247 (70.1%) had acute diarrhea. Overall, 444 (25.0%) of the 1,779 children with diarrhea had C. parvum, compared with only 57 (8.5%) of the 667 children without diarrhea (chi2 = 80.2, P < or = 0.0001). Within this group of infected children, 72.8% were infected with genotype 1, 18.4% with genotype 2, and 4.1% with a mixture of both genotypes, and 4.1% isolates were either unclassified or C. meleagridis. The prevalence was highest during the rainy months of April to June. Of the 532 children with persistent diarrhea, 166 (31.2%) had C. parvum compared with 278 (22.3%) of the 1,247 children with acute diarrhea (chi2 = 15.8, P < or = 0.0001). There was a significant association between C. parvum and malnutrition including stunting, being underweight, and wasting. Unfavorable outcome (death or failure to resolve within 14 days) occurred in 139 (72.8%) of the 191 children with C. parvum, and in only 65.1% of the 545 without (odds ratio = 1.117, 95% confidence interval = 1.005-1.243, P = 0.05), Of the 191 children with C. parvum, 24 (12.6%) died, compared with 34 (6.2%) of the 545 without C. parvum (P = 0.005). Mortality rates were higher among children with severe dehydration and persistent diarrhea, and in stunted or underweight children infected with C. parvum. Among Ugandan children, cryptosporidiosis, which remains untreatable, is frequently associated with diarrhea and other serious and unfavorable consequences.
Enrollment in low-resource speech recognition systems (2004)

We consider the problem of enrollment for low-resource speech recognition systems designed for noisy environments. Noise robustness concerns, memory and computational constraints, along with the use of compact acoustic models for fast Gaussian computation, make adaptation especially challenging. We derive a maximum a posteriori (MAP) algorithm especially designed for the fast off-line adaptation of these compact acoustic models. It requires less computation and memory than standard feature-space maximum likelihood linear regression (FMLLR) which is another technique well suited for compact acoustic models. In our experiments of speaker enrollment for speech recognition in the car, we present a computationally efficient procedure to simulate noisy conditions with the adaptation data. In these experiments, MAP compares favorably with FMLLR in terms of recognition accuracy. Besides, combining FMLLR and MAP significantly outperforms each technique individually, thus providing an efficient alternative for systems with larger resources.
Incoherent beam combining using stimulated Brillouin scattering in multimode fibers (2001)

A beam combining technique for producing a single, spatially coherent beam from two mutually incoherent (temporally and spatially) lasers is demonstrated and the spatial coherence properties of the resulting beam are characterized. The technique is based on simultaneous excitation of stimulated Brillouin scattering by two independent lasers operating at two different wavelengths in a long multimode optical fiber. Though spectrally independent, the resulting Stokes beams produce essentially identical intensity distributions corresponding to the fundamental fiber mode.
ChemInform Abstract: A Novel Asymmetric Synthesis of α‐ and β‐Amino Aryl Phosphonic Acids. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Intravoxel incoherent motion MR imaging for prostate cancer: An evaluation of perfusion fraction and diffusion coefficient derived from different b‐value combinations (2012)

There has been a resurgent interest in intravoxel incoherent motion (IVIM) MR imaging to obtain perfusion as well as diffusion information on lesions, in which the diffusion was modeled as Gaussian diffusion. However, it was observed that this diffusion deviated from expected monoexponential decay at high b-values and the reported perfusion in prostate is contrary to the findings in dynamic contrast-enhanced (DCE) MRI studies and angiogenesis. Thus, this work is to evaluate the effect of different b-values on IVIM perfusion fractions (f) and diffusion coefficients (D) for prostate cancer detection. The results show that both parameters depended heavily on the b-values, and those derived without the highest b-value correlated best with the results from DCE-MRI studies; specifically, f was significantly elevated (7.2% vs. 3.7%) in tumors when compared with normal tissues, in accordance with the volume transfer constant (K(trans); 0.39 vs. 0.18 min(-1)) and plasma fractional volume (v(p) ; 8.4% vs. 3.4%). In conclusion, it is critical to choose an appropriate range of b-values in studies or include the non-Gaussian diffusion contribution to obtain unbiased IVIM measurements. These measurements could eliminate the need for DCE-MRI, which is especially relevant in patients who cannot receive intravenous gadolinium-based contrast media.
4.4: New Materials for Polymer‐Stabilized Blue Phase (2012)

Abstract Electro‐optical switching of the liquid crystalline Blue Phase exhibits extremely fast response times. However, the unstabilized Blue Phase is characterized by a rather narrow temperature range on the order of a few K. For display applications the operating temperature range needs to be increased. One very promising way is to broaden the stable temperature range by polymer‐stabilization of the Blue Phase. Successful stabilization is achieved by proper material selection/matching of reactive mesogens (RMs) and the chiral host. One prerequisite for application in display manufacturing is excellent UV and heat stability as well as good processability. Improvements in relevant performance parameters will be presented and discussed.
PREDICT - A New Design Tool For Shallow Junction Processes (1985)

A new one-dimensional, process estimator for the design of IC technologies (PREDICT) has been developed which rigorously solves coupled equations describing dopant behavior under modern processing conditions. All of the models in PREDICT have been verified with extensive experimental measurements. Such models include a new ion implantation algorithm with empirical parameters to describe the exponential tail formed through ion channeling, rapid thermal diffusion of B, As and P, accurate oxidation calculations including the effects of pressure, HC1 and doping concentrations, effects of stress and dopant precipitation and clustering, ion pairing, implantation through deposited or grown films (oxide, polysilicon, nitride), concentration effects, etc. PREDICT has been used to do accurate simulations of high dose B and BF2 implants/diffusions in both &lt;100&gt; and &lt;111&gt; Si. Considerations in these calculations include channeling during implantation, the effects of pre-amorphization, damage-induced dislocation networks and the enhanced diffusion of B outside of these networks, and precipitation of B using a 12 atom cluster model.
Delegating a Product of Group Exponentiations with Application to Signature Schemes (Submission to Special NutMiC 2019 Issue of JMC) (2020)

Abstract Many public-key cryptosystems and, more generally, cryptographic protocols, use group exponentiations as important primitive operations. To expand the applicability of these solutions to computationally weaker devices, it has been advocated that a computationally weaker client (i.e., capable of performing a relatively small number of modular multiplications) delegates such primitive operations to a computationally stronger server. Important requirements for such delegation protocols include privacy of the client’s input exponent and security of the client’s output, in the sense of detecting, except for very small probability, any malicious server’s attempt to convince the client of an incorrect exponentiation result. Only recently, efficient protocols for the delegation of a fixed-based exponentiation, over cyclic and RSA-type groups with certain properties, have been presented and proved to satisfy both requirements. In this paper we show that a product of many fixed-base exponentiations, over a cyclic groups with certain properties, can be privately and securely delegated by keeping the client’s online number of modular multiplications only slightly larger than in the delegation of a single exponentiation. We use this result to show the first delegations of entire cryptographic schemes: the well-known digital signature schemes by El-Gamal, Schnorr and Okamoto, over the q -order subgroup in ℤ p , for p , q primes, as well as their variants based on elliptic curves. Previous efficient delegation results were limited to the delegation of single algorithms within cryptographic schemes.
Fermentability of Water-Soluble Portion to Ethanol Obtained by Supercritical Water Treatment of Lignocellulosics (2009)

The water-soluble (WS) portion obtained by supercritical water treatment of lignocellulosics was studied for its fermentability to ethanol. A fermentation test of the WS portion showed it was not fermented to ethanol. Therefore, a wood charcoal treatment was applied to the WS portion to remove furan and phenolic compounds, which are thought to be the inhibitors to sugar fermentability. It was found that treatment with wood charcoal can be effective at removing these inhibitors and improving the fermentability of the WS portion without reducing the levels of fermentable sugars.
Performance analysis of a manipulation task in time-delayed teleoperation (2010)

There is ample research on the stabilization of haptic teleoperation systems under communication time delay. Little attention, however, has so far been paid to the usefulness of delayed haptic feedback on task performance. While the usefulness of haptic feedback in no-delay teleoperation has been previously established, this paper investigates whether haptic feedback helps to improve task performance in the presence of delay. We consider peg-in-the-hole insertion, which is a dexterous manipulation task requiring high force levels at certain points during the task execution. Through a user study involving unilateral and bilateral teleoperation experiments under different delays, it is observed that in both unilateral and bilateral teleoperation, the task completion time increases as delay increases. It is also seen that haptic feedback helps reduce the amount and rate of energy transfer to the environment and the occurrence of larger robot/environment interaction forces. However, with the users mindful of minimizing contact forces, haptic feedback causes the task to take more time compared to no haptic feedback regardless of the time delay. Thus, for tasks where low completion times are crucial given a tolerance for larger forces, unilateral feedback may be sufficient.
Serial Isolates ofCryptococcus neoformansfrom Patients with AIDS Differ in Virulence for Mice (1998)

Serial isolates of Cryptococcus neoformans from patients with chronic infection can exhibit minor karyotype changes as a result of chromosome length polymorphism (CLP). This study investigated whether serial C. neoformans isolates with CLP from 4 patients with AIDS exhibited biologic and phenotypic differences. CLP permits the identification of serial isolates in murine mixed infection. The parameters studied were virulence in mice, capsule size, colony morphology, melanization, protease production, MICs of antifungal drugs, and growth rates in vitro. Two parameters of virulence in mice were studied: persistence in tissue and survival time after lethal infection. Serial C. neoformans isolates were shown to differ in ability to persist in vivo, virulence in a murine infection model, in vitro growth rates at 37 degreesC, and capsule size. Melanin and protease production and MICs of antifungal drugs were comparable for serial isolates. These observations suggest microevolution of C. neoformans during human infection. This process may allow the fungal population to change, escape eradication by the immune system, and thus cause chronic infections.
ChemInform Abstract: Thieno[3,2‐b]benzofuran — Synthesis and Reactions. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.