gebhart/patrepeval huggingface dataset:
PuDianNao (2015)

Machine Learning (ML) techniques are pervasive tools in various emerging commercial applications, but have to be accommodated by powerful computer systems to process very large data. Although general-purpose CPUs and GPUs have provided straightforward solutions, their energy-efficiencies are limited due to their excessive supports for flexibility. Hardware accelerators may achieve better energy-efficiencies, but each accelerator often accommodates only a single ML technique (family). According to the famous No-Free-Lunch theorem in the ML domain, however, an ML technique performs well on a dataset may perform poorly on another dataset, which implies that such accelerator may sometimes lead to poor learning accuracy. Even if regardless of the learning accuracy, such accelerator can still become inapplicable simply because the concrete ML task is altered, or the user chooses another ML technique. In this study, we present an ML accelerator called PuDianNao, which accommodates seven representative ML techniques, including k-means, k-nearest neighbors, naive bayes, support vector machine, linear regression, classification tree, and deep neural network. Benefited from our thorough analysis on computational primitives and locality properties of different ML techniques, PuDianNao can perform up to 1056 GOP/s (e.g., additions and multiplications) in an area of 3.51 mm^2, and consumes 596 mW only. Compared with the NVIDIA K20M GPU (28nm process), PuDianNao (65nm process) is 1.20x faster, and can reduce the energy by 128.41x.
Traumatic injury induces stress granule formation and enhances motor dysfunctions in ALS/FTD models (2018)

Traumatic brain injury (TBI) has been predicted to be a predisposing factor for amyotrophic lateral sclerosis (ALS) and other neurological disorders. Despite the importance of TBI in ALS progression, the underlying cellular and molecular mechanisms are still an enigma. Here, we examined the contribution of TBI as an extrinsic factor and investigated whether TBI influences the susceptibility of developing neurodegenerative symptoms. To evaluate the effects of TBI in vivo, we applied mild to severe trauma to Drosophila and found that TBI leads to the induction of stress granules (SGs) in the brain. The degree of SGs induction directly correlates with the level of trauma. Furthermore, we observed that the level of mortality is directly proportional to the number of traumatic hits. Interestingly, trauma-induced SGs are ubiquitin, p62 and TDP-43 positive, and persistently remain over time suggesting that SGs might be aggregates and exert toxicity in our fly models. Intriguingly, TBI on animals expressing ALS-linked genes increased mortality and locomotion dysfunction suggesting that mild trauma might aggravate neurodegenerative symptoms associated with ALS. Furthermore, we found elevated levels of high molecular weight ubiquitinated proteins and p62 in animals expressing ALS-causing genes with TBI, suggesting that TBI may lead to the defects in protein degradation pathways. Finally, we observed that genetic and pharmacological induction of autophagy enhanced the clearance of SGs and promoted survival of flies in vivo. Together, our study demonstrates that trauma can induce SG formation in vivo and might enhance neurodegenerative phenotypes in the fly models of ALS.
Current status of meningococcal group B vaccine candidates: capsular or noncapsular? (1994)

Meningococcal meningitis is a severe, life-threatening infection for which no adequate vaccine exists. Current vaccines, based on the group-specific capsular polysaccharides, provide short-term protection in adults against serogroups A and C but are ineffective in infants and do not induce protection against group B strains, the predominant cause of infection in western countries, because the purified serogroup B polysaccharide fails to elicit human bactericidal antibodies. Because of the poor immunogenicity of group B capsular polysaccharide, different noncapsular antigens have been considered for inclusion in a vaccine against this serogroup: outer membrane proteins, lipooligosaccharides, iron-regulated proteins, Lip, pili, CtrA, and the immunoglobulin A proteases. Alternatively, attempts to increase the immunogenicity of the capsular polysaccharide have been made by using noncovalent complexes with outer membrane proteins, chemical modifications, and structural analogs. Here, we review the strategies employed for the development of a vaccine for Neisseria meningitidis serogroup B; the difficulties associated with the different approaches are discussed.
Role of NO mechanism in cardiovascular effects of diaspirin cross-linked hemoglobin in anesthetized rats (1995)

The role of nitric oxide (NO) in the cardiovascular actions of diaspirin cross-linked hemoglobin (DCLHb) was studied in anesthetized rats. The regional circulatory and systemic hemodynamic effects of DCLHb (400 mg/kg iv) were studied using a radioactive microsphere technique in control (untreated) and L-arginine (a NO precursor) pretreated rats. DCLHb produced a significant increase in blood pressure (75%), cardiac output (42%), stroke volume (36%), and total peripheral resistance (45%), without affecting heart rate, when administered to control rats. L-Arginine pretreatment significantly attenuated DCLHb-induced systemic hemodynamic effects. DCLHb-induced increase in blood flow to the skin and spleen was completely blocked, and that to the heart was partially blocked, by L-arginine pretreatment, suggesting that cardiovascular actions induced by DCLHb could be antagonized by the NO precursor L-arginine. The NO synthase (NOS) inhibitor NG-nitro-L-arginine methyl ester (L-NAME) produced significant increases in regional vascular resistance, leading to a decrease in blood flow to all the organs except the heart, where an increase in blood flow and a decrease in vascular resistance was observed. DCLHb, when administered in L-NAME-pretreated rats, accentuated the decrease in blood flow to the gastrointestinal system, spleen, mesentery and pancreas, skin, and musculoskeletal system. These studies provide evidence that the NO precursor L-arginine can attenuate the effects of DCLHb and that DCLHb can potentiate the effect of the NOS inhibitor L-NAME. The role of NO in the mechanism of action of DCLHb was further studied by estimating plasma guanosine 3',5'-cyclic monophosphate (cGMP) in control, DCLHb-treated, L-NAME-treated, and L-NAME followed by DCLHb-treated rats. DCLHb and L-NAME significantly decreased the concentration of circulating cGMP in blood plasma. L-NAME pretreatment potentiated DCLHb-induced decrease in cGMP levels. Because the formation of cGMP is stimulated by NO, these studies provide additional evidence for the involvement of NO in the mechanism of action of DCLHb. It is concluded that NO plays an important role in the cardiovascular effects of DCLHb.
Domain Adaptation for Statistical Classifiers (2006)

The most basic assumption used in statistical learning theory is that training data and test data are drawn from the same underlying distribution. Unfortunately, in many applications, the "in-domain" test data is drawn from a distribution that is related, but not identical, to the "out-of-domain" distribution of the training data. We consider the common case in which labeled out-of-domain data is plentiful, but labeled in-domain data is scarce. We introduce a statistical formulation of this problem in terms of a simple mixture model and present an instantiation of this framework to maximum entropy classifiers and their linear chain counterparts. We present efficient inference algorithms for this special case based on the technique of conditional expectation maximization. Our experimental results show that our approach leads to improved performance on three real world tasks on four different data sets from the natural language processing domain.
Cloning large natural product gene clusters from the environment: Piecing environmental DNA gene clusters back together with TAR (2010)

A single gram of soil can contain thousands of unique bacterial species, of which only a small fraction is regularly cultured in the laboratory. Although the fermentation of cultured microorganisms has provided access to numerous bioactive secondary metabolites, with these same methods it is not possible to characterize the natural products encoded by the uncultured majority. The heterologous expression of biosynthetic gene clusters cloned from DNA extracted directly from environmental samples (eDNA) has the potential to provide access to the chemical diversity encoded in the genomes of uncultured bacteria. One of the challenges facing this approach has been that many natural product biosynthetic gene clusters are too large to be readily captured on a single fragment of cloned eDNA. The reassembly of large eDNA-derived natural product gene clusters from collections of smaller overlapping clones represents one potential solution to this problem. Unfortunately, traditional methods for the assembly of large DNA sequences from multiple overlapping clones can be technically challenging. Here we present a general experimental framework that permits the recovery of large natural product biosynthetic gene clusters on overlapping soil-derived eDNA cosmid clones and the reassembly of these large gene clusters using transformation-associated recombination (TAR) in Saccharomyces cerevisiae. The development of practical methods for the rapid assembly of biosynthetic gene clusters from collections of overlapping eDNA clones is an important step toward being able to functionally study larger natural product gene clusters from uncultured bacteria.
Finite-state modulation codes for data storage (1992)

The authors provide a self-contained exposition of modulation code design methods based upon the state splitting algorithm. They review the necessary background on finite state transition diagrams, constrained systems, and Shannon (1948) capacity. The state splitting algorithm for constructing finite state encoders is presented and summarized in a step-by-step fashion. These encoders automatically have state-dependent decoders. It is shown that for the class of finite-type constrained systems, the encoders constructed can be made to have sliding-block decoders. The authors consider practical techniques for reducing the number of encoder states as well as the size of the sliding-block decoder window. They discuss the class of almost-finite-type systems and state the general results which yield noncatastrophic encoders. The techniques are applied to the design of several codes of interest in digital data recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Impact of Channel Hot Electrons on Current Collapse in AlGaN/GaN HEMTs (2013)

This letter studies the current collapse phenomenon during switching in p-GaN gate AlGaN/GaN high-electron-mobility transistors. It is found that channel hot electrons play a major role in increasing the current collapse and that adding a field plate significantly reduces the effect. By stressing the device with OFF-state pulses of 100 μs× 10 μs with a VGS rise/fall time of 10 ns at Vdc 400 V, compared to the ON-resistance before stress, the ON-resistance was 78 times larger after stress without field plates. With a field plate, it was only 1.8 times larger.
A parallel scan conversion algorithm with anti-aliasing for a general-purpose ultracomputer (1983)

Popular approaches to speeding up scan conversion often employ parallel processing. Recently, several special-purpose parallel architectures have been suggested. We propose an alternative to these systems: the general-purpose ultracomputer, a parallel processor with many autonomous processing elements and a shared memory. The “serial semantics/parallel execution” feature of this architecture is exploited in the formulation of a scan conversion algorithm. Hidden surfaces are removed using a single scanline, z-buffer algorithm. Since exact anti-aliasing is inherently slow, a novel parallel anti-aliasing algorithm is presented in which subpixel coverage by edges is approximated using a look-up table. The ultimate intensity of a pixel is the weighted sum of the intensity contribution of the closest edge, that of the “losing” edges, and that of the background. The algorithm is fast and accurate, it is attractive even in a serial environment, and it avoids several artifacts that commonly occur in animated sequences.
A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae. (1991)

The Escherichia coli su+3 tyrosine tRNA was shown recently to be a leucine-specific tRNA in Saccharomyces cerevisiae. This finding raises the possibility that some determinants for tRNA identity in E. coli may be different in S. cerevisiae. To investigate whether the fungal system is sensitive to the major determinant for alanine acceptance in E. coli, a single G3 . U70 base pair was introduced into the acceptor helix of the su+3 tyrosine tRNA. This substitution converts the identity of the E. coli suppressor in S. cerevisiae from leucine to alanine. Thus, as in E. coli, G3 . U70 is a strong determinant for alanine acceptance that can dominate over other features in a tRNA that might be recognized by alternative charging enzymes.
The identification and purification of a mammalian- like protein kinase C in the yeast Saccharomyces cerevisiae (1991)

We have purified a yeast protein kinase that is phospholipid-dependent and activated by Diacylglycerol (DAG) in the presence of Ca2+ or by the tumour-promoting agent tetradecanoyl-phorbol acetate (TPA). The properties of this enzyme are similar to those of the mammalian protein kinase C (PKC). The enzyme was purified using chromatography on DEAE-cellulose followed by hydroxylapatite. The latter chromatography separated the activity to three distinguishable sub-species, analogous to the mammalian PKC isoenzymes. The fractions enriched in PKC activity contain proteins that specifically bind TPA, are specifically phosphorylated in the presence of DAG and recognized by anti-mammalian PKC antibodies.
Learning Transfer Rules for Machine Translation from Parallel Corpora (2008)

In this paper we present JETCAT, a Japanese-English transfer-based machine translation system. Our main research contribution is that the transfer rules are not handcrafted but are learnt automatically from a parallel corpus. The system has been implemented in Amzi! Prolog, which offers scalability for large rule bases, full Unicode support for Japanese characters, and several APIs for the seamless integration of the translation functionality into common office environments. As a first user interface we have developed a translation environment under Microsoft Word. The dynamic nature of our system allows for an easy customization of the rule base according to the user's personal preferences by simply post-editing the translation results, which leads to an automatic update. The user interface for Microsoft Word also provides the possibility for the user to display token lists, parse trees, and transfer rules, which makes JETCAT also a very useful tool for language students.
Selective growth of rat Schwann cells in neuron- and serum-free primary culture (1987)

A serum-free medium, designated S4 [consisting of Eagle's Minimum Essential Medium supplemented with the following components (mg/liter): endothelial mitogen, 100; vitamin C, 1; insulin, 5; cholera toxin, 0.01; putrescine, 8; sodium selenite, 0.0043; MgCl2 X 6H2O, 40; and albumin, fatty acids, amino acids, vitamins, and trace elements], has been established to select for the growth of Schwann cells from primary cultures of dissociated neonatal rat sciatic nerve in the absence of neurons and without exposure of the cells to serum or antimitotic agents. By immunological criteria, confluent primary cultures, grown on a substrate of extracellular matrix derived from cultured bovine aorta endothelial cells, consist of approximately 90% Schwann cells after maintenance in this serum-free medium. Secondary cultures of at least 99% purity may be established after treatment of primary cultures maintained in S4 with antiserum against a fibroblast surface antigen, Thy 1.1, in conjunction with complement. Such secondary Schwann cells continue to proliferate in S4, with no decrease in purity, through at least 4 passages.
Members of the Arabidopsis HRT/RPP8 Family of Resistance Genes Confer Resistance to Both Viral and Oomycete Pathogens (2000)

Turnip crinkle virus (TCV) inoculation onto TCV-resistant Arabidopsis leads to a hypersensitive response (HR) controlled by the dominant gene HRT. HRT is a member of the class of resistance (R) genes that contain a leucine zipper, a nucleotide binding site, and leucine-rich repeats. The chromosomal position of HRT and its homology to resistance gene RPP8 and two RPP8 homologs indicate that unequal crossing over and gene conversion may have contributed to HRT evolution. RPP8 confers resistance to an oomycete pathogen, Peronospora parasitica. Despite very strong similarities within the HRT/RPP8 family, HRT and RPP8 are specific for the respective pathogens they detect. Hence, the HRT/RPP8 family provides molecular evidence that sequence changes between closely related members of multigene families can generate novel specificities for radically different pathogens. Transgenic plants expressing HRT developed an HR but generally remained susceptible to TCV because of a second gene, RRT, that regulates resistance to TCV. However, several transgenic plants that overexpressed HRT produced micro-HRs or no HR when inoculated with TCV and were resistant to infection. Expression of the TCV coat protein gene in seedlings containing HRT resulted in massive necrosis and death, indicating that the avirulence factor detected by the HRT-encoded protein is the TCV coat protein.
IPF: new insight on pathogenesis and treatment (2010)

Recent years have seen a robust influx of exciting new observations regarding the mechanisms that regulate the initiation and progression of pulmonary fibrosis but the pathogenesis remains poorly understood. The search for an alternative hypothesis to unremitting, chronic inflammation as the primary explanation for the pathophysiology of idiopathic pulmonary fibrosis (IPF) derives, in part, from the lack of therapeutic efficacy of high-dose immunosuppressive therapy in patients with IPF. The inflammatory hypothesis of IPF has since been challenged by the epithelial injury hypothesis, in which fibrosis is believed to result from epithelial injury, activation, and/or apoptosis with abnormal wound healing. This hypothesis suggests that recurrent unknown injury to distal pulmonary parenchyma causes repeated epithelial injury and apoptosis. The resultant loss of alveolar epithelium exposes the underlying basement membrane to oxidative damage and degradation. Emerging concepts suggest that IPF is the result of epithelial-mesenchymal interaction. The initiation of this fibrotic response may depend upon genetic factors and environmental triggers; the role of Th1 or Th2 cell-derived cytokines may also be important. This process appears to be unique to usual interstitial pneumonia/IPF. It is clear that IPF is a heterogeneous disease with variations in pathology, high-resolution computed tomography findings, and patterns of progression. Idiopathic pulmonary fibrosis is a complex disorder, and no unifying hypothesis has been identified at present that explains all the abnormalities.
Metronidazole in a single dose for the treatment of trichomoniasis. Failure of a 1-g single dose. (1982)

To determine the minimum effective dose of metronidazole in the treatment of vaginal trichomoniasis, a randomised clinical trial comparing single 1-g and 2-g doses was carried out on 163 patients attending sexually transmitted diseases and family planning clinics. Seventy-two of 86 (84%) patients receiving a single 2-g dose of metronidazole were cured compared with only 42 of 77 (55%) receiving a 1-g dose. The body weight of the patient was a significant variable affecting treatment outcome only in the latter group; 69% of patients weighing more than 57 kg or less when cured compared with only 43% of those weighing more. Patients who failed after either dose regimen were retreated with a single 2-g dose. Eighteen of 21 (86%) and seven of 10 (70%) failures with the initial 1-g and 2-g doses respectively were cured. A single 1-g dose of metronidazole is not recommended as routine treatment for vaginal trichomoniasis.
Crystal structure of receptor-binding C-terminal repeats from Clostridium difficile toxin A (2005)

Clostridium difficile is a major nosocomial pathogen that produces two large protein toxins [toxin A (TcdA) and toxin B (TcdB)] capable of disrupting intestinal epithelial cells. Both belong to the family of large clostridial cytotoxins, which are characterized by the presence of a repetitive C-terminal repetitive domain (CRD). In TcdA, the CRD is composed of 39 repeats that are responsible for binding to cell surface carbohydrates. To understand the molecular structural basis of cell binding by the toxins from C. difficile, we have determined a 1.85-A resolution crystal structure of a 127-aa fragment from the C terminus of the toxin A CRD. This structure reveals a beta-solenoid fold containing five repeats, with each repeat consisting of a beta-hairpin followed by a loop of 7-10 residues in short repeats (SRs) or 18 residues in long repeats (LRs). Adjacent pairs of beta-hairpins are related to each other by either 90 degree or 120 degree screw-axis rotational relationships, depending on the nature of the amino acids at key positions in adjacent beta-hairpins. Models of the complete CRDs of toxins A and B suggest that each CRD contains straight stretches of beta-solenoid composed of three to five SRs that are punctuated by kinks introduced by the presence of a single LR. These structural features provide a framework for understanding how large clostridial cytotoxins bind to cell surfaces and suggest approaches for developing novel treatments for C. difficile-associated diseases by blocking the binding of toxins to cell surfaces.
In vitro Activity of Diospyrin and Derivatives against Leishmania donovani, Trypanosoma cruzi and Trypanosoma brucei brucei (1996)

Diospyrin and its four synthetic derivatives were tested in vitro against intracellular amastigotes of Leishmania donovani and Trypanosoma cruzi in macrophages and extracellular Trypansoma brucei brucei bloodstream form trypomastigotes. Diospyrin was inactive against L. donovani but had ED50 values of 27 and 50 μm, respectively, against T. cruzi and T.b. brucei. The dimethyl ether derivative was more active than the parent compound against T. cruzi and T.b. brucei, but the hydroquinonoid form was the most active antiparasitic agent with ED50 values of 2.2 and 0.7 μm, respectively, against L. donovani and T.b. brucei.