gebhart/patrepeval huggingface dataset:
A pilot based dynamic channel assignment scheme for wireless access TDMA/FDMA systems (2002)

The authors propose control architecture for implementing a dynamic channel assignment (DCA) algorithm which optimizes two-way channel quality in a TDMA portable radio system. A common control frequency, which is frame-synchronized among base stations, provides (1) beacons for portables to locate base-stations and obtain DCA information, (2) broadcast channels for system and alerting information, and (3) pilot signals to permit portables to evaluate downlink interference. This allows low-complexity radio ports and portables to simultaneously select channels to avoid interference and avoid creating excessive interference. Only local measurements are needed for this autonomous DCA scheme, thus avoiding processing by a centralized controller or communications among distributed controllers. A superframe structure on the control frequency provides redundant information for the beacon and pilot signals to avoid the "blind-slot" problems which cause significant difficulty in other systems for the link transfer (hand off) process. Results from computer simulations demonstrate the good spectrum efficiency of this method. They also show that power control further improves the performance significantly. This work is targeted towards understanding the implications to local exchange networks of wireless system alternatives that could provide access to those networks.
UCNN: Exploiting Computational Reuse in Deep Neural Networks via Weight Repetition (2018)

Convolutional Neural Networks (CNNs) have begun to permeate all corners of electronic society (from voice recognition to scene generation) due to their high accuracy and machine efficiency per operation. At their core, CNN computations are made up of multi-dimensional dot products between weight and input vectors. This paper studies how weight repetition-when the same weight occurs multiple times in or across weight vectors-can be exploited to save energy and improve performance during CNN inference. This generalizes a popular line of work to improve efficiency from CNN weight sparsity, as reducing computation due to repeated zero weights is a special case of reducing computation due to repeated weights. To exploit weight repetition, this paper proposes a new CNN accelerator called the Unique Weight CNN Accelerator (UCNN). UCNN uses weight repetition to reuse CNN sub-computations (e.g., dot products) and to reduce CNN model size when stored in off-chip DRAM-both of which save energy. UCNN further improves performance by exploiting sparsity in weights. We evaluate UCNN with an accelerator-level cycle and energy model and with an RTL implementation of the UCNN PE. On three contemporary CNNs, UCNN improves throughput-normalized energy consumption by 1.2x ~ 4x, relative to a similarly provisioned baseline accelerator that uses Eyeriss-style sparsity optimizations. At the same time, the UCNN processing element adds only 17-24% area overhead relative to the same baseline.
Handbook of Natural Toxins, Volume 8: Bacterial Toxins and Virulence Factors in Disease (1995)

This volume describes the structure and function of bacterial toxins and presents a comprehensive review of virulence factors, providing recent information concerning cell physiology and biochemistry, as well as new toxin tools for experimental studies and clinical therapy. A wide variety of toxic proteins, including the toxins that cause diptheria
Environmentally Friendly Chemical Route to Vanadium Oxide Single-Crystalline Nanobelts as a Cathode Material for Lithium-Ion Batteries (2006)

Orthorhombic V(2)O(5) single-crystalline nanobelts with widths of 100-300 nm, thicknesses of 30-40 nm, and lengths up to tens of micrometers have been synthesized on a large scale in a hydrogen peroxide aqueous solution by an environmentally friendly chemical route. Such nanobelts grow along the direction of [010]. The influence of the reaction time on the crystal structures and morphologies of the resulting products are investigated. A probable dehydration-recrystallization-cleavage mechanism for the formation of V(2)O(5) nanobelts is proposed. The experiments demonstrate that the use of a nanosized belt-like structure can considerably enhance the specific discharge capacity in lithium-ion batteries.
Porphyromonas gingivalis Lipopolysaccharide Contains Multiple Lipid A Species That Functionally Interact with Both Toll-Like Receptors 2 and 4 (2004)

The innate host response to lipopolysaccharide (LPS) obtained from Porphyromonas gingivalis is unusual in that different studies have reported that it can be an agonist for Toll-like receptor 2 (TLR2) as well as an antagonist or agonist for TLR4. In this report it is shown that P. gingivalis LPS is highly heterogeneous, containing more lipid A species than previously described. In addition, purification of LPS can preferentially fractionate these lipid A species. It is shown that an LPS preparation enriched for lipid A species at m/z 1,435 and 1,450 activates human and mouse TLR2, TLR2 plus TLR1, and TLR4 in transiently transfected HEK 293 cells coexpressing membrane-associated CD14. The HEK cell experiments further demonstrated that cofactor MD-2 was required for functional engagement of TLR4 but not of TLR2 nor TLR2 plus TLR1. In addition, serum-soluble CD14 effectively transferred P. gingivalis LPS to TLR2 plus TLR1, but poorly to TLR4. Importantly, bone marrow cells obtained from TLR2(-/-) and TLR4(-/-) mice also responded to P. gingivalis LPS in a manor consistent with the HEK results, demonstrating that P. gingivalis LPS can utilize both TLR2 and TLR4. No response was observed from bone marrow cells obtained from TLR2 and TLR4 double-knockout mice, demonstrating that P. gingivalis LPS activation occurred exclusively through either TLR2 or TLR4. Although the biological significance of the different lipid A species found in P. gingivalis LPS preparations is not currently understood, it is proposed that the presence of multiple lipid A species contributes to cell activation through both TLR2 and TLR4.
A study of allelic imbalance in human breast cancer (1993)

The analysis of loss of heterozygosity (LOH) in tumours can be used to map candidate sites of tumour-suppressor genes in the human genome. A panel of breast cancer patients was assembled as pairs of tumour and lymphocyte DNA samples and LOH studies carried out by Southern hybridization with polymorphic loci mapping to chromosomes 1 and X. Loci on other chromosomes were also studied as controls. Sequences on chromosome 1 were found to be subject to a variety of alterations creating very complex patterns of rearrangements, including LOH. Deletion mapping identified five independent regions of loss, three of which may correspond to regions identified in previous reports, although individually none occurred with high frequency to support the targeting of a specific locus. The short arm of chromosome 1 primarily underwent interstitial deletions whereas the long arm was subject to both whole arm events (gains and losses) and more localized events. Small deletions on chromosome 1 were found exclusively in patients with poorly-differentiated tumours (i.e. tumours of high grade, p&lt;0.05). A similar study of the X chromosome revealed a high frequency of small regionalized deletions, primarily defining three small independent regions, one located in the distal portion of the pseudoautosomal region of Xp, another spanning the pseudoautosomal boundary into the sex-specific sequences of Xp and a possible third on distal Xq. No gains in copy number were identified at any locus on the X chromosome, in distinct contrast to chromosome 1. Small-scale deletions occurring on the X chromosome were found in patients with no spread of cancer to the lymph nodes, thus correlating with a favourable prognosis (p&lt;0.005). Fluorescence in situ hybridization to formalin-fixed paraffin-embedded tumour sections defined the actual copy number of chromosome 1 for nine tumours. The results obtained confirmed the changes established by Southern hybridization.
Polypeptide and Carbohydrate Structure of Recombinant Human Interleukin-6 Produced in Chinese Hamster Ovary Cells (1994)

Journal Article Polypeptide and Carbohydrate Structure of Recombinant Human Interleukin-6 Produced in Chinese Hamster Ovary Cells Get access Tetsuro Orita, Tetsuro Orita Research Lab. I, Fuji-Gotemba Research Laboratories, Chugai Pharmaceutical Co, Ltd1-135 Komakado, Gotemba, Shizuoka 412 Search for other works by this author on: Oxford Academic PubMed Google Scholar Masayoshi Oh-eda, Masayoshi Oh-eda Research Lab. I, Fuji-Gotemba Research Laboratories, Chugai Pharmaceutical Co, Ltd1-135 Komakado, Gotemba, Shizuoka 412 Search for other works by this author on: Oxford Academic PubMed Google Scholar Masakazu Hasegawa, Masakazu Hasegawa Research Lab. I, Fuji-Gotemba Research Laboratories, Chugai Pharmaceutical Co, Ltd1-135 Komakado, Gotemba, Shizuoka 412 Search for other works by this author on: Oxford Academic PubMed Google Scholar Hitoshi Kuboniwa, Hitoshi Kuboniwa Research Lab. I, Fuji-Gotemba Research Laboratories, Chugai Pharmaceutical Co, Ltd1-135 Komakado, Gotemba, Shizuoka 412 Search for other works by this author on: Oxford Academic PubMed Google Scholar Keiko Esaki, Keiko Esaki Research Lab. I, Fuji-Gotemba Research Laboratories, Chugai Pharmaceutical Co, Ltd1-135 Komakado, Gotemba, Shizuoka 412 Search for other works by this author on: Oxford Academic PubMed Google Scholar Norimichi Ochi Norimichi Ochi 1 Research Lab. I, Fuji-Gotemba Research Laboratories, Chugai Pharmaceutical Co, Ltd1-135 Komakado, Gotemba, Shizuoka 412 1To whom correspondence should be addressed. Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 115, Issue 2, February 1994, Pages 345–350, https://doi.org/10.1093/oxfordjournals.jbchem.a124340 Published: 01 February 1994 Article history Received: 15 October 1993 Published: 01 February 1994
Treatment of allergic rhinitis: an evidence-based evaluation of nasal corticosteroids versus nonsedating antihistamines. (1998)

Allergic rhinitis is a high-cost, high-prevalence disease. In the 12 months ending March 31, 1997 $3.1 billion was spent in the United States for medications to manage this illness. Allergic rhinitis affects quality of life and interferes with work productivity. Nonsedating antihistamines are the most common and most expensive therapy for this condition. This study reviewed 13 randomized studies in which blinded investigators compared management of allergic rhinitis by means of intranasal steroids to management by means of nonsedating antihistamine. Evidence tables demonstrated that in all studies in which total nasal symptoms and nasal obstruction were recorded, the nasal steroid was statistically superior to the nonsedating antihistamine. For nasal blockage the nonsedating antihistamines did not perform better than placebo. For all other nasal symptoms the intranasal steroid was statistically superior in most reports and equal or numerically better in the remaining papers. When these data are linked to those from cost analysis and quality-of-life studies, the evidence strongly suggests that nasal steroids should be first-line therapy for allergic rhinitis. In four reports on the combination of a nonsedating antihistamine compared to a nasal steroid alone, there was no significant difference between these two treatments. Like asthma, allergic rhinitis is an inflammatory disease and should be managed with anti-inflammatory medication. Making such a change in the management of allergic rhinitis should increase efficacy and decrease costs.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization (2014)

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. Recent developments in cryo-electron microscopy have enabled structure determination of large protein complexes at almost atomic resolution. Wang et al.combine some of these technologies into an effective workflow, and demonstrate the protocol by solving the atomic structure of an icosahedral RNA virus.
Rac1-MKK3-p38-MAPKAPK2 Pathway Promotes Urokinase Plasminogen Activator mRNA Stability in Invasive Breast Cancer Cells (2002)

We reported previously that down-regulating or functionally blocking alphav integrins inhibits endogenous p38 mitogen-activated protein kinase (MAPK) activity and urokinase plasminogen activator (uPA) expression in invasive MDA-MB-231 breast cancer cells whereas engaging alphav integrins with vitronectin activates p38 MAPK and up-regulates uPA expression (Chen, J., Baskerville, C., Han, Q., Pan, Z., and Huang, S. (2001) J. Biol. Chem. 276, 47901-47905). Currently, it is not clear what upstream and downstream signaling molecules of p38 MAPK mediate alphav integrin-mediated uPA up-regulation. In the present study, we found that alphav integrin ligation activated small GTPase Rac1 preferentially, and dominant negative Rac1 inhibited alphav integrin-mediated p38 MAPK activation. Using constitutively active MAPK kinases, we found that both constitutively active MKK3 and MKK6 mutants were able to activate p38 MAPK and up-regulate uPA expression, but only dominant negative MKK3 blocked alphav integrin-mediated p38 MAPK activation and uPA up-regulation. These results suggest that MKK3, rather than MKK6, mediates alphav integrin-induced p38 MAPK activation. Among the potential downstream effectors of p38 MAPK, we found that only MAPK-activated protein kinase 2 affects alphav integrin-mediated uPA up-regulation significantly. Finally, using beta-globin reporter gene constructs containing uPA mRNA 3'-untranslated region (UTR) and adenosine/uridine-rich elements-deleted 3'-UTR, we demonstrated that p38 MAPK/MAPK-activated protein kinase 2 signaling pathway regulated uPA mRNA stability through a mechanism involving the adenosine/uridine-rich elements sequence in 3'-UTR of uPA mRNA.
Modeling pixel means and covariances using factorized third-order boltzmann machines (2010)

Learning a generative model of natural images is a useful way of extracting features that capture interesting regularities. Previous work on learning such models has focused on methods in which the latent features are used to determine the mean and variance of each pixel independently, or on methods in which the hidden units determine the covariance matrix of a zero-mean Gaussian distribution. In this work, we propose a probabilistic model that combines these two approaches into a single framework. We represent each image using one set of binary latent features that model the image-specific covariance and a separate set that model the mean. We show that this approach provides a probabilistic framework for the widely used simple-cell complex-cell architecture, it produces very realistic samples of natural images and it extracts features that yield state-of-the-art recognition accuracy on the challenging CIFAR 10 dataset.
Usefulness of Megestrol Acetate in Cancer Cachexia and Anorexia (1992)

To assess the effect of megestrol acetate (MA) on the appetite and weight of cancer patients with nonhormone-dependent tumors, a double-blind, placebo-controlled trial was designed. One hundred fifty patients were included: 76 were given MA (240 mg/day orally) for at least 2 months, and 74 were given placebo (P). Body weight, subjective sense of appetite (SSA) evaluated by an analogic linear visual scale scored from 1 to 10, and performance status (PS) were measured before therapy and monthly thereafter. No differences in body weight before and after treatment could be found in any group. However, 32% of the patients in the MA group (95% confidence interval: 20.1-44.6%) gained 2 or more kilograms (P less than 0.001). This group also showed an improvement in SSA (P less than 0.01): an increase greater than or equal to 2 points appeared in 57.5% of patients (95% confidence interval 44.6-69.4%). There was no significant difference in PS for the treatment groups before or after therapy. The percentage of reported adverse events did not differ significantly from one treatment group to the next. We conclude that therapy with MA at a dose of 240 mg/day improved SSA and was associated with moderate weight gain in patients with hormone-insensitive malignancies.
Conservation of promoter sequence but not complex intron splicing pattern in human and hamster genes for 3-hydroxy-3-methylglutaryl coenzyme A reductase. (1987)

Regulation of the expression of 3-hydroxy-3-methyglutaryl coenzyme A (HMG-CoA) reductase is a critical step in controlling cholesterol synthesis. Previous studies in cultured Chinese hamster ovary cells have shown that HMG-CoA reductase is transcribed from a cholesterol-regulated promoter to yield a heterogeneous collection of mRNAs with 5' untranslated regions of 68 to 670 nucleotides in length. Synthesis of these molecules is initiated at multiple sites, and multiple donor sites are used to excise an intron in the 5' untranslated region. In the current paper, I report that human HMG-CoA reductase gene resembles the Chinese hamster gene in having multiple sites of transcription initiation that are subject to suppression by cholesterol. The human gene differs from the hamster gene in that a single donor splice site is used to excise the intron in the 5' untranslated region. All of the resulting RNAs have short 5' untranslated regions of 68 to 100 nucleotides. This difference in the splicing pattern of the first intron is species specific and not a peculiarity of cultured cells in that HMG-CoA reductase mRNAs from Syrian hamster livers resemble those of the cultured Chinese hamster ovary cells. Comparison of the DNA sequences of the HMG-CoA reductase promoters from three different species--humans, Syrian hamsters, and Chinese hamsters--shows a highly conserved region of 179 nucleotides that extends from 220 to 42 nucleotides upstream of the transcription initiation sites. This region is 88% identical between the human and Chinese hamster promoter. When fused to the coding region of the Escherichia coli chloramphenicol acetyltransferase gene, this highly conserved region of the reductase gene directs the cholesterol-regulated expression of chloramphenicol acetyltransferase in transfected hamster cells, further indicating the interspecies conservation of the regulatory elements.
MHCPEP, a database of MHC-binding peptides: update 1997 (1998)

MHCPEP (http://wehih.wehi.edu.au/mhcpep/) is a curated database comprising over 13 000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and where available, experimental method, observed activity, binding affinity, source protein and anchor positions, as well as publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW or FTP.
Glucagon-like peptide-1: A basis for new approaches to themanagement of diabetes (1999)

Type 2 diabetes mellitus is a metabolic disease resulting in raised blood sugar which, if not satisfactorily controlled, can cause severe and often debilitating complications. Unfortunately, for many patients, the existing therapies do not give adequate control. Glucagon-like peptide-1 (GLP-1) is an incretin hormone which has a spectrum of activities which oppose the symptoms of diabetes. Of particular significance is the fact that these actions are glucose-dependent, meaning that the risk of severe hypoglycemia is practically eliminated. The recent elucidation of the key role of dipeptidyl peptidase IV in determining the metabolic stability of GLP-1 has given the rationale for two novel therapeutic strategies, namely, GLP-1 analogs which are resistant to the enzyme and inhibitors of the enzyme which boost levels of endogenous intact GLP-1. These approaches aim to maximize the therapeutic advantages offered by GLP-1 and give the hope of providing effective glycemic control without the risk of overt hypoglycemia.
Reconstitution of rabbit thrombomodulin into phospholipid vesicles. (1987)

The influence of phospholipid on thrombin-thrombomodulin-catalyzed activation of protein C has been studied by incorporating thrombomodulin into vesicles by dialysis from octyl glucoside-phospholipid mixtures. Thrombomodulin was incorporated into vesicles ranging from neutral (100% phosphatidylcholine) to highly charged (30% phosphatidylserine and 70% phosphatidylcholine). Thrombomodulin is randomly oriented in vesicles of different phospholipid composition. Incorporation of thrombomodulin into phosphatidylcholine, with or without phosphatidylserine, alters the Ca2+ concentration dependence of protein C activation. Soluble thrombomodulin showed a half-maximal rate of activation at 580 microM Ca2+, whereas half-maximal rates of activation of liposome-reconstituted thrombomodulin were obtained between 500 microM Ca2+ and 2 mM Ca2+, depending on the composition (protein:phospholipid) of the liposomes. The Ca2+ dependence of protein C activation fits a simple hyperbola for the soluble activator, while the Ca2+ dependence of the membrane-associated complex is distinctly sigmoidal with a Hill coefficient greater than 2.4. In contrast, the Ca2+ dependence of gamma-carboxyglutamic acid (Gla) domainless protein C activation is unchanged by membrane reconstitution (1/2 max = 53 +/- 10 microM) and fits a simple rectangular hyperbola. Incorporation of thrombomodulin into pure phosphatidylcholine vesicles reduces the Km for protein C from 7.6 +/- 2 to 0.7 +/- 0.2 microM. Increasing phosphatidylserine to 20% decreased the Km for protein C further to 0.1 +/- 0.02 microM. Membrane incorporation has no influence on the activation of protein C from which the Gla residues are removed proteolytically (Km = 6.4 +/- 0.5 microM). The Km for protein C observed on endothelial cells is more similar to the Km observed when thrombomodulin (TM) is incorporated into pure phosphatidylcholine vesicles than into negatively charged vesicles, suggesting that the protein C-binding site on endothelial cells does not involve negatively charged phospholipids. In support of this concept, we observed that prothrombin and fragment 1, which bind to negatively charged phospholipids, do not inhibit protein C activation on endothelial cells or TM incorporated into phosphatidylcholine vesicles, but do inhibit when TM is incorporated into phosphatidylcholine:phosphatidylserine vesicles. These studies suggest that neutral phospholipids lead to exposure of a site, probably on thrombomodulin, capable of recognizing the Gla domain of protein C.