gebhart/patrepeval huggingface dataset:
An efficient group communication architecture over ATM networks (2002)

NYNET (ATM wide-area network testbed in New York state) Communication System (NCS) is a multithreaded message-passing tool developed at Syracuse University that provides low-latency and high-throughput communication services over Asynchronous Transfer Mode (ATM)-based high-performance distributed computing (HPDC) environments. NCS provides flexible and scalable group communication services based on dynamic grouping and tree-based multicasting. The NCS architecture, which separates the data and control functions, allows group operations to be implemented efficiently by utilizing the control connections when transferring status information (e.g. topology information, routing information). Furthermore, NCS provides several different algorithms for group communication and allows programmers to select an appropriate algorithm at runtime. The authors overview the general architecture of NCS and present the multicasting services provided by NCS. They analyze and compare the performance of NCS with that of other message-passing tools such as p4, PVM, and MPI in terms of primitive performance and performance.
Human multilineage progenitor cell sensitivity to 4-hydroperoxycyclophosphamide. (1985)

This institution has documented consistent reconstitution of hematopoiesis in patients treated with marrow lethal chemoradiotherapy who are "rescued" by reinfusion of autologous cryopreserved marrow cells incubated with 4-hydroperoxycyclophosphamide (4-HC) for in vitro purging of occult tumor cells. After 4-HC incubation, the reinfusion marrow cells showed marked reduction in committed progenitor cell (BFU-E, CFU-GM) frequency, and often total absence of detectable progenitors, without significant loss of marrow reconstituting ability. Since BFU-E and CFU-GM assays did not predict marrow reconstituting ability after 4-HC incubation, we sought to determine whether multilineage progenitor cells (CFU-GEMM) might be more resistant to 4-HC incubation and therefore a more reliable predictive assay in this setting. We found that BFU-E, CFU-GM, and CFU-GEMM all show similar dose-related sensitivity to in vitro incubation with 4-HC and do not appear representative of the cell(s) responsible for marrow reconstitution.
Infectious Titer Assay for Adeno-Associated Virus Vectors with Sensitivity Sufficient to Detect Single Infectious Events (2004)

A highly sensitive assay for determination of infectious titers of recombinant adeno-associated virus (AAV) by limiting dilution analysis is described. This assay is capable of detecting single infectious events and can therefore provide an absolute rather than relative measure of infectivity. The assay utilizes a HeLa-derived AAV2 Rep/Cap-expressing cell line, D7-4, grown in 96-well plates and infected with replicate 10-fold serial dilutions of AAV2 vectors in the presence of adenovirus type 5. Forty-eight hours after infection, vector genome replication is determined by quantitative PCR (Q-PCR). A linear relationship between vector genome input and replicated copy number (slope = 2670 copies per vector genome) was determined, enabling detection of one infectious event per well by Q-PCR. The observed binomial distribution of the end-point data confirmed that single infectious events could be detected, and allowed calculation of infectious titers by the Kärber method. Analysis of an AAV2 reference vector, AAV-hFIX16, in 21 independent determinations gave an average ratio of AAV vector genomes (VG) to infectious units (IU) of 8.3 +/- 4.2 VG/IU, a value close to the theoretical limit. No significant differences in vector particle-to-infectious unit ratios were observed between vectors purified by column chromatography (9.3 +/- 5.0 VG/IU, n = 7) and cesium chloride gradient ultracentrifugation (6.4 +/- 3.2 VG/IU, n = 7).
Pneumonia, Myocarditis and Reactive Arthritis due to Chlamydia Pneumoniae (1993)

A 37 year old HLA B27 negative man developed erythema nodosum, pneumonia, myocarditis and oligoarthritis due to Chlamydia pneumoniae. He recovered completely over a four month period. This is the first clinical description of reactive arthritis caused by C. pneumoniae.
Multiplexed readout of transmon qubits with Josephson bifurcation amplifiers (2014)

Achieving individual qubit readout is a major challenge in the development of scalable superconducting quantum processors. We have implemented the multiplexed readout of a four transmon qubit circuit using nonlinear resonators operated as Josephson bifurcation amplifiers. We demonstrate the simultaneous measurement of Rabi oscillations of the four transmons. We find that multiplexed Josephson bifurcation is a high-fidelity readout method, the scalability of which is not limited by the need of a large-bandwidth, nearly quantum-limited amplifier as is the case with linear readout resonators.
A Reliable (k, n) Image Secret Sharing Scheme (2006)

This paper presents a reliable image secret sharing method which incorporates two k-out-of-n secret sharing schemes: i) Shamir's secret sharing scheme and ii) matrix projection secret sharing scheme. The technique allows a colored secret image to be divided as n image shares so that: i) any k image shares (k les n) are sufficient to reconstruct the secret image in the lossless manner and ii) any (k - 1) or fewer image shares cannot get enough information to reveal the secret image. It is an effective, reliable and secure method to prevent the secret image from being lost, stolen or corrupted. In comparison with other image secret sharing methods, this approach's advantages are its large compression rate on the size of the image shares, its strong protection of the secret image and its ability for the realtime processing
A comparison of megestrol acetate, nandrolone decanoate and dietary counselling for HIV associated weight loss (2001)

This randomized, prospective study compared three treatments, nandrolone decanoate (ND), megestrol acetate (MA) or dietary counselling, for managing human immunodeficiency syndrome (HIV) associated weight loss. It was centred on a Tertiary referral hospital, Sydney, Australia. Fifteen patients were randomized to receive ND (100 mg/fortnight), or MA (400 mg/day) or dietary counselling for 12 weeks. Those patients randomized to dietary counselling were further randomized to receive nandrolone or megestrol after completing the dietary counselling arm. Weight, fat free mass (FFM), percentage body fat mass (FM), dietary intake and appetite were assessed before commencing and at the completion of each treatment arm. Weight increased significantly in all treatment arms (dietary counselling 1.13 kg +/- 0.36, nandrolone 4.01 kg +/- 1.68, megestrol 10.20 kg +/- 4.51, p < 0.05 paired t-test). FFM increased significantly in patients receiving ND (3.54 +/- 1.98 kg, p=0.001) and those receiving MA (2.76 +/- 0.55 kg, p=0.002), whereas the change in those receiving dietary counselling alone was not significant. Percentage body fat mass increased significantly only in those receiving MA (7.77 +/- 4.85%, p=0.049). The change in weight and percentage body fat mass was significantly greater in those receiving MA than the other two treatment arms. The increase in FFM was significantly greater in both the nandrolone and megestrol arms than the dietary counselling arm. It was concluded that ND and MA both resulted in an increase in FFM greater than dietary counselling alone. Megestrol produced a significantly greater increase in weight, percentage fat mass, intake and appetite than did the other two treatment arms, suggesting it may be the preferred agent, particularly in a palliative care setting in which weight, appetite and intake increase are desirable without regard to the composition of the body. The long-term use of these agents in people with HIV should be reviewed in the context of improved survival on highly active antiretroviral therapy regimens.
A replication-competent promoter-trap retrovirus (1996)

A promoter-trap retrovirus has been constructed in which a promoterless polyomavirus middle T antigen gene was inserted in the U3 region of the long terminal repeat of a replication-competent Moloney murine leukemia virus. The resulting virus, designated PyT, was used to infect mouse mammary glands in situ. As expected, mammary tumors appeared in some infected animals. These tumors were found to contain PyT proviruses of the predicted structure. From one such tumor, the PyT provirus and surrounding sequences from the integration site were cloned. The provirus was found to have integrated adjacent to the promoter of a novel mouse gene (TRAP1) that was expressed at low levels in various mouse tissues. These data show that the PyT retrovirus provides a sensitive means of detecting active promoters in vivo.
Time-Reversal Detection Using Antenna Arrays (2008)

The paper studies detection of a target buried in a rich scattering medium by time reversal. We use a multi-static configuration with receive and transmit arrays of antennas. In time reversal, the backscattered field is recorded, time reversed, and retransmitted (mathematically or physically) into the same scattering medium. We derive two array detectors: the time-reversal channel matched filter when the target channel response is known; and the time-reversal generalized-likelihood ratio test (TR-GLRT) when the target channel response is unknown. The noise added in the initial probing step to the time-reversal signal makes the analysis of the TR-GLRT detector non trivial. The paper derives closed form expressions for the signal-to-noise ratio gain provided by this detector over the corresponding conventional clutter subtraction energy detector in the two extreme conditions of weak and strong (electronic additive) noise and shows that time reversal provides, under weak noise, the optimal waveform shape to probe the environment. We analyze the impact of the array configuration on the detection performance. Finally, experiments with electromagnetic data collected in a multipath scattering laboratory environment confirm our analytical results. Under the realistic conditions tested, time reversal provides detection gains over conventional detection that range from 2 to 4.7 dB.
β‐Lactamase of Bacillus licheniformis 749/C at 2 Å resolution (1990)

Two crystal forms (A and B) of the 29,500 Da Class A beta-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 A resolution, the starting model for which was a 3.5 A structure obtained from A-form crystals. The beta-lactamase has an alpha + beta structure with 11 helices and 5 beta-strands seen also in a penicillin target DD-peptidase of Streptomyces R61. Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 A resolution. The R factor is 0.208 for the 27,330 data greater than 3 sigma (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conserved Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of beta-lactam substrates is facilitated by interactions with Lys-234, Thr-235, and Ala-237 in a conserved beta-strand peptide, which is antiparallel to the beta-lactam's acylamido linkage; an exposed cavity near Asn-170 exists for acylamido substituents. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth beta-strand. A very similar binding site architecture is seen in the DD-peptidase.
Chimeric papillomavirus-like particles expressing a foreign epitope on capsid surface loops (2001)

Neutralization capsid epitopes are important determinants for antibody-mediated immune protection against papillomavirus (PV) infection and induced disease. Chimeric L1 major capsid proteins of the human PV type 16 (HPV-16) and the bovine PV type 1 (BPV-1) with a foreign peptide incorporated into several capsid surface loops self-assembled into pentamers or virus-like particles (VLP). Binding patterns of neutralizing monoclonal antibodies (MAb) and immunization of mice confirmed (i) that regions around aa 282-286 and 351-355 contribute to neutralization epitopes and identified the latter region as an immunodominant site and (ii) that placing a foreign peptide in the context of an assembled structure markedly enhanced its immunogenicity. Pentamers disassembled from wild-type HPV-16 and BPV-1 VLPs displayed some of the neutralization epitopes that were detected on fully assembled VLPs, but were deficient for binding a subset of neutralizing MAb that inhibit cell attachment.
Precursors to Nonoxide Macromolecules and Ceramics (1988)

There is great interest in developing molecular precursors for boron-nitrogen polymers and boron nitride solid state materials, and one general procedure is described in this report. Combinations of B-trichloroborazene and hexamethyldisilazane lead to formation of a gel which, upon thermolysis, gives hexagonal boron nitride. The BN has been characterized by infrared spectroscopy, x-ray powder diffraction and transmission electron microscopy.
Delivery of MicroRNA-126 by Apoptotic Bodies Induces CXCL12-Dependent Vascular Protection (2009)

Apoptosis is a pivotal process in embryogenesis and postnatal cell homeostasis and involves the shedding of membranous microvesicles termed apoptotic bodies. In response to tissue damage, the CXC chemokine CXCL12 and its receptor CXCR4 counteract apoptosis and recruit progenitor cells. Here, we show that endothelial cell-derived apoptotic bodies are generated during atherosclerosis and convey paracrine alarm signals to recipient vascular cells that trigger the production of CXCL12. CXCL12 production was mediated by microRNA-126 (miR-126), which was enriched in apoptotic bodies and repressed the function of regulator of G protein (heterotrimeric guanosine triphosphate-binding protein) signaling 16, an inhibitor of G protein-coupled receptor (GPCR) signaling. This enabled CXCR4, a GPCR, to trigger an autoregulatory feedback loop that increased the production of CXCL12. Administration of apoptotic bodies or miR-126 limited atherosclerosis, promoted the incorporation of Sca-1+ progenitor cells, and conferred features of plaque stability on different mouse models of atherosclerosis. This study highlights functions of microRNAs in health and disease that may extend to the recruitment of progenitor cells during other forms of tissue repair or homeostasis.
Antitumor Efficacy of the Novel RAF Inhibitor GDC-0879 Is Predicted by BRAFV600E Mutational Status and Sustained Extracellular Signal-Regulated Kinase/Mitogen-Activated Protein Kinase Pathway Suppression (2009)

Oncogenic activation of the BRAF serine/threonine kinase has been associated with initiation and maintenance of melanoma tumors. As such, development of pharmacologic agents to target RAF proteins or their effector kinases is an area of intense investigation. Here we report the biological properties of GDC-0879, a highly selective, potent, and orally bioavailable RAF small-molecule inhibitor. We used extracellular signal-regulated kinase (ERK)-1/2 and mitogen-activated protein kinase/ERK kinase (MEK)-1/2 phosphorylation as biomarkers to explore the relationship between tumor outcome and pharmacodynamic inhibition of the RAF-MEK-ERK pathway. In GDC-0879-treated mice, both cell line- and patient-derived BRAF(V600E) tumors exhibited stronger and more sustained pharmacodynamic inhibition (>90% for 8 hours) and improved survival compared with mutant KRAS-expressing tumors. Despite the involvement of activated RAF signaling in RAS-induced tumorigenesis, decreased time to progression was observed for some KRAS-mutant tumors following GDC-0879 administration. Moreover, striking differences were noted for RAF and MEK inhibition across a panel of 130 tumor cell lines. Whereas GDC-0879-mediated efficacy was associated strictly with BRAF(V600E) status, MEK inhibition also attenuated proliferation and tumor growth of cell lines expressing wild-type BRAF (81% KRAS mutant, 38% KRAS wild type). The responsiveness of BRAF(V600E) melanoma cells to GDC-0879 could be dramatically altered by pharmacologic and genetic modulation of phosphatidylinositol 3-kinase pathway activity. These data suggest that GDC-0879-induced signaling changes are dependent on the point of oncogenic activation within the RAS network. Taken together, these studies increase our understanding of the molecular determinants for antitumor efficacy resulting from RAF pathway inhibition and have implications for therapeutic intervention in the clinic.
Bioluminescence in a strain of the human pathogenic bacterium Vibrio vulnificus (1986)

We report the existence of a bioluminescent strain of the human pathogen Vibrio vulnificus. The isolate was obtained from blood following a fatal wound infection and thus represents the first description of an infection caused by a luminescent bacterium.
Place Cells and Place Recognition Maintained by Direct Entorhinal-Hippocampal Circuitry (2002)

Place cells in hippocampal area CA1 may receive positional information from the intrahippocampal associative network in area CA3 or directly from the entorhinal cortex. To determine whether direct entorhinal connections support spatial firing and spatial memory, we removed all input from areas CA3 to CA1, thus isolating the CA1 area. Pyramidal cells in the isolated CA1 area developed sharp and stable place fields. Rats with an isolated CA1 area showed normal acquisition of an associative hippocampal-dependent spatial recognition task. Spatial recall was impaired. These results suggest that the hippocampus contains two functionally separable memory circuits: The direct entorhinal-CA1 system is sufficient for recollection-based recognition memory, but recall depends on intact CA3-CA1 connectivity.
Randomized, Double-Blind, Placebo-Controlled Study Evaluating the Efficacy and Safety of AS-013, a Prostaglandin E 1 Prodrug, in Patients With Intermittent Claudication (1997)

These promising clinical data indicate that AS-013, a new prodrug of prostaglandin E1, could provide an effective and acceptable treatment for patients with intermittent claudication. Studies to investigate the optimal dosing regimen, duration of clinical benefit, and effects in more severe forms of peripheral arterial disease are warranted.
Downregulated MTAP expression in myxofibrosarcoma: A characterization of inactivating mechanisms, tumor suppressive function, and therapeutic relevance (2014)

Myxofibrosarcomas are genetically complex and involve recurrently deleted chromosome 9p, for which we characterized the pathogenically relevant target(s) using genomic profiling. In 12 of the 15 samples, we detected complete or partial losses of 9p. The only aggressiveness-associated, differentially lost region was 9p21.3, spanning the potential inactivated methylthioadenosine phosphorylase (MTAP) that exhibited homozygous (4/15) or hemizygous (3/15) deletions. In independent samples, MTAP gene status was assessed using quantitative- and methylation-specific PCR assays, and immunoexpression was evaluated. We applied MTAP reexpression or knockdown to elucidate the functional roles of MTAP and the therapeutic potential of L-alanosine in MTAP-preserved and MTAP-deficient myxofibrosarcoma cell lines and xenografts. MTAP protein deficiency (37%) was associated with MTAP gene inactivation (P < 0.001) by homozygous deletion or promoter methylation, and independently portended unfavorable metastasis-free survival (P = 0.0318) and disease-specific survival (P = 0.014). Among the MTAP-deficient cases, the homozygous deletion of MTAP predicted adverse outcome. In MTAP-deficient cells, MTAP reexpression inhibited cell migration and invasion, proliferation, and anchorage-independent colony formation and downregulated cyclin D1. This approach also attenuated the tube-forming abilities of human umbilical venous endothelial cells, attributable to the transcriptional repression of MMP-9, and abrogated the susceptibility to L-alanosine. The inhibiting effects of MTAP expression on tumor growth, angiogenesis, and the induction of apoptosis by L-alanosine were validated using MTAP-reexpressing xenografts and reverted using RNA interference in MTAP-preserved cells. In conclusion, homozygous deletion primarily accounts for the adverse prognostic impact of MTAP deficiency and confers the biological aggressiveness and susceptibility to L-alanosine in myxofibrosarcomas.
Data prefetching by dependence graph precomputation (2001)

Data cache misses reduce the performance of wide-issue processors by stalling the data supply to the processor. Prefetching data by predicting the miss address is one way to tolerate the cache miss latencies. But current applications with irregular access patterns make it difficult to accurately predict the address sufficiently early to mask large cache miss latencies. This paper explores an alternative to predicting prefetch addresses, namely precomputing them. The Dependence Graph Precomputation scheme (DGP) introduced in this paper is a novel approach for dynamically identifying and precomputing the instructions that determine the addresses accessed by those load/store instructions marked as being responsible for most data cache misses. DGP's dependence graph generator efficiently generates the required dependence graphs at run time. A separate precomputation engine executes these graphs to generate the data addresses of the marked load/store instructions early enough for accurate prefetching. Our results show that 94% of the prefetches issued by DGP are useful, reducing the D-cache miss stall time by 47%. Thus DGP takes us about half way from an already highly tuned baseline system toward perfect D-cache performance. DGP improves the overall performance of a wide range of applications by 7% over tagged next line prefetching, by 13% over a baseline processor with no prefetching, and is within 15% of the perfect D-cache performance.
MATH GO! PROTOTYPE OF A CONTENT BASED MATHEMATICAL FORMULA SEARCH ENGINE (2008)

In recent years, mathematical content has started appearing on the web. As with other types of information, search capabilities must be provided to users to retrieve their required information. Conventional text-based search engines fall short of providing math-aware fine grain search. Several efforts have been made in the recent past to develop web-accessible mathematical and scientific search systems. We identify major issues in developing math search systems and present techniques for addressing them. The issues involved in developing such a system include query format, representation of mathematical content, as well as their comparison for matching purposes. The results generated by the formula search system must strive to maximize the standard measures of precision, recall. It should also sort the query hits according to some domain specific measure and provide the hits to the user as a ranked list. This paper presents our efforts in developing a mathematical search engine for mathematical content retrieval. We present the Math GO! System to search and present the mathematical information encoded in mathematical expressions. Our approach uses the concept of template based math block identification, vector representation, searching from mathematical topic based clusters and relevance ranking. The search system interacts with the user through a simple query mechanism and provides ranked listing of results. The system is comprised of a modular architecture to organize, query, compare and presentation of math results to the user. We compare our approach with existing approaches and present the results. We have achieved encouraging results with the system.