gebhart/patrepeval huggingface dataset:
Mesoporous materials with zeolite framework: remarkable effect of the hierarchical structure for retardation of catalyst deactivation (2006)

Hierarchical MFI zeolite was synthesized following a synthesis route using organic-inorganic hybrid surfactants; the resultant zeolite with mesoporous/microporous hierarchical structure exhibited remarkably high resistance to deactivation in catalytic activity of various reactions such as isomerization of 1,2,4-trimethylbenzene, cumene cracking, and esterification of benzyl alcohol with hexanoic acid, as compared with conventional MFI and mesoporous aluminosilicate MCM-41.
Complete Sequence of a Novel Highly Divergent Simian T-Cell Lymphotropic Virus from Wild-Caught Red-Capped Mangabeys ( Cercocebus torquatus ) from Cameroon: a New Primate T-Lymphotropic Virus Type 3 Subtype (2002)

Among 65 samples obtained from a primate rescue center located in Cameroon, two female adult red-capped mangabeys (Cercocebus torquatus) (CTO-602 and CTO-604), of wild-caught origin, had a peculiar human T-cell lymphotropic virus type 2 (HTLV-2)-like Western blot seroreactivity (p24, RGD21, +/-K55). Analyses of the simian T-cell lymphotropic virus type 3 (STLV-3)/CTO-604 complete proviral sequence (8,919 bp) indicated that this novel strain was highly divergent from HTLV-1 (60% nucleotide similarity), HTLV-2 (62%), or STLV-2 (62%) prototypes. It was, however, related to STLV-3/PH-969 (87%), a divergent STLV strain previously isolated from an Eritrean baboon. The STLV-3/CTO-604 sequence possesses the major open reading frames corresponding to the structural, enzymatic, and regulatory proteins. However, its long terminal repeat is shorter, with only two 21-bp repeats. Furthermore, as demonstrated by reverse transcriptase PCR, this new STLV exhibits significant differences from STLV-3/PH-969 at the mRNA splice junction position level. In all phylogenetic analyses, STLV-3/CTO-604 and STLV-3/PH-969 clustered in a highly supported single clade, indicating an evolutionary lineage independent from primate T-lymphotropic virus type 1 (PTLV-1) and PTLV-2. Nevertheless, the nucleotide divergence between STLV-3/PH-969 and STLV-3/CTO-604 is equivalent to or higher than the divergence observed between the different HTLV-1 or HTLV-2 subtypes. Thus, the STLV-3/CTO-604 strain can be considered the prototype of a second subtype in the PTLV-3 type. The presence of two related viruses in evolutionarily distantly related African monkeys species, living in two opposite ecosystems (rain forest versus desert), reinforces the possible African origin of PTLV and opens new avenues regarding the search for a possible human counterpart of these viruses in individuals exhibiting such HTLV-2-like seroreactivities.
An updated catalog of prostate cancer predictive tools (2008)

Accurate estimates of risk are essential for physicians if they are to recommend a specific management to patients with prostate cancer. Accurate risk estimates also are required for clinical trial design to ensure that homogeneous, high-risk patient groups are used to investigate new cancer therapeutics. Using the MEDLINE database, a literature search was performed on prostate cancer predictive tools from January 1966 to July 2007. The authors recorded input variables, the prediction form, the number of patients used to develop prediction tools, the outcome being predicted, prediction tool-specific features, predictive accuracy, and whether validation was performed. Each prediction tool was classified into patient clinical disease state and the outcome being predicted. First, the authors described the criteria for evaluation (predictive accuracy, calibration, generalizability, head-to-head comparison, and level of complexity) and the limitations of current predictive tools. The literature search generated 109 published prediction tools, including only 68 that had undergone validation. An increasing number of predictive tools addressed important endpoints, such as disease recurrence, metastasis, and survival. Despite their limitations and the limitations of data, predictive tools are essential for individualized, evidence-based medical decision making. Moreover, the authors recommend wider adoption of risk-prediction models in the design and implementation of clinical trials. Among prediction tools, nomograms provide superior, individualized, disease-related risk estimations that facilitate management-related decisions. Nevertheless, many more predictive tools, comparisons between them, and improvements to existing tools are needed.
Fuzzy and neural network controller (2002)

There are many applications of fuzzy control to practical systems such as electric appliances and factory automation in Japan. On the other hand, applications of neural networks to military and industrial fields attract a lot of researchers in the United States. It is suggested that the two approaches be combined and applied to control problems. The use of both methods is recommended for the construction of intelligent controllers (for example, autonomous or self-organizing controllers). Intelligent controllers are summarized. Fuzzy control is illustrated in a tutorial fashion by a simple example. The design and practical aspects of fuzzy control are examined. Neural networks applied to control problems are discussed. By combining the two methodologies, self-organizing controller can be constructed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Telematics and dangerous goods in the Netherlands (1993)

In 1992, the Telematics and Dangerous Goods project (TGS, Dutch abbreviation) began. In this project, twenty trucks used to transport dangerous goods were equipped with onboard computers, communication facilities and sensors. In the case of a dangerous situation, a structured alarm message is sent to the highway police and the trucking company. The overall aim of the project is to gain practical experience with telematic systems in multi-purpose applications.
Substrate Binding by Human Apurinic/Apyrimidinic Endonuclease Indicates a Briggs-Haldane Mechanism (1997)

Apurinic/apyrimidinic endonuclease (AP endo) makes a single nick 5' to a DNA abasic site. We have characterized this reaction by steady-state and transient-state kinetics with purified human AP endo, which had been expressed in Escherichia coli. The substrate was a 49-base pair oligonucleotide with an abasic site at position 21. This substrate was generated by treating a 49-mer duplex oligonucleotide with a single G/U located at position 21 with uracil-DNA glycosylase. The enzymatic products of the AP endo nicking reaction were a 20-mer with a hydroxyl group at the 3'-terminus and a 28-mer with a phosphodeoxyribose at the 5'-terminus. To obtain maximal enzymatic activity, it was necessary to stabilize the abasic site during treatment with uracil-DNA glycosylase with a reducing agent. Otherwise, a 20-mer with phosphoribose at the 3'-terminus resulted from beta-elimination. In agreement with others, Km and kcat were 100 nM and 10 s(-1), respectively. Heat treatment of the abasic site-containing 49-mer without enzyme also resulted in conversion to the beta-elimination product. The resultant heat degradation product was an efficient inhibitor of AP endo with a Ki of 30 nM. The enzyme required divalent cation (Mg2+) for activity, but bound substrate DNA in the absence of Mg2+. Electrophoretic mobility shift assays indicated that AP endo bound tightly to DNA containing an abasic site and formed a 1:1 complex at low enzyme concentrations. The association and dissociation rate constants for substrate binding to AP endo were determined by using a challenge assay to follow AP endo-substrate complex formation. Heat degradation product together with heparin served as an effective trap for free enzyme. The results are consistent with a Briggs-Haldane mechanism where k(on) and k(off) are 5 x 10(7) M(-1) s(-1) and 0.04 s(-1), respectively (Kd = 0.8 nM), kcat is 10 s(-1), and product release is very rapid (i.e. k(off,product) >> 10 s(-1)). This scheme is in excellent agreement with the measured steady-state kinetic parameters.
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research (2008)

The available HLA-II servers do not match prediction capabilities of HLA-I predictors. Currently available HLA-II prediction servers offer only a limited prediction accuracy and the development of improved predictors is needed for large-scale studies, such as proteome-wide epitope mapping. The requirements for accuracy of HLA-II binding predictions are stringent because of the substantial effect of false positives.
Use of selective extraction and fast chromatographic separation combined with electrophoretic methods for mapping of membrane proteins (2005)

A model system for selective solubilization and fast separation of proteins from the rat liver membrane fraction and purified rat liver plasma membranes for their further proteomic analysis is presented. For selective solubilization, high-pH solutions and a concentrated urea solution, combined with different detergents, are used. After extraction, proteins are separated by anion-exchange chromatography or a combination of anion- and cation-exchange chromatography with convective interaction monolithic supports. This separation method enables fast and effective prefractionation of membrane proteins based on their hydrophobicity and charge prior to one-dimensional (1-D) and 2-D electrophoresis and mass spectrometry. By use of this sample preparation method, the less-abundant proteins can be detected and identified.
Isolation, purification, and radiolabeling of a novel 120-kD surface protein on Blastomyces dermatitidis yeasts to detect antibody in infected patients. (1990)

No well-defined Blastomyces-specific antigens are currently available. We used sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting to identify immunologically active molecules in the cell wall of B. dermatitidis. A major immunoreactive 120-kD protein (WI-1) was present in all five strains studied and comprised 5% of the protein in the cell wall extract obtained after freezing and thawing yeast cells. WI-1 was recognized by serum from all 10 patients with blastomycosis but by none of those from 5 patients with histoplasmosis. It was purified by electroelution, radiolabeled with 125I, and incorporated into a radioimmunoassay (RIA) for serodiagnosis of blastomycosis. Antibody to WI-1 was detected in 58 (85%) of 68 patients with blastomycosis (geometric mean titer, 1:2,981), in two (3%) of 73 patients with histoplasmosis, coccidioidomycosis, sporotrichosis, or candidiasis (titers, 1:86 and 1:91) and in none of 44 healthy persons. WI-1 was shown to be a surface molecule abundant on B. dermatitidis yeasts that were indirectly stained with serum from a rabbit immunized with WI-1. Approximately 0.93 pg of WI-1 or 4.7 x 10(6) WI-1 molecules were found on the surface of an individual yeast using an antigen-inhibition RIA; none was found on Histoplasma capsulatum or Candida albicans yeasts. We conclude that WI-1 is a novel, immunologically active surface molecule on the invasive form of B. dermatitidis and that WI-1 can be used to reliably detect antibody and study the immunopathogenesis of blastomycosis.
Recent Advancements in the Regeneration of Auditory Hair Cells and Hearing Restoration (2017)

Neurosensory responses of hearing and balance are mediated by receptors in specialized neuroepithelial sensory cells. Any disruption of the biochemical and molecular pathways that facilitate these responses can result in severe deficits, including hearing loss and vestibular dysfunction. Hearing is affected by both environmental and genetic factors, with impairment of auditory function being the most common neurosensory disorder affecting 1 in 500 newborns, as well as having an impact on the majority of elderly population. Damage to auditory sensory cells is not reversible, and if sufficient damage and cell death have taken place, the resultant deficit may lead to permanent deafness. Cochlear implants are considered to be one of the most successful and consistent treatments for deaf patients, but only offer limited recovery at the expense of loss of residual hearing. Recently there has been an increased interest in the auditory research community to explore the regeneration of mammalian auditory hair cells and restoration of their function. In this review article, we examine a variety of recent therapies, including genetic, stem cell and molecular therapies as well as discussing progress being made in genome editing strategies as applied to the restoration of hearing function.
Norovirus Gastroenteritis After Fecal Microbiota Transplantation for Treatment of Clostridium difficile Infection Despite Asymptomatic Donors and Lack of Sick Contacts (2013)

1 Virginia Mason Medical Center, Department of Infectious Disease, Seattle, Washington, USA 2 Virginia Mason Medical Center, Digestive Disease Institute, Seattle, Washington, USA 3 Virginia Mason Medical Center, Department of Internal Medicine, Seattle, Washington, USA Correspondence: Margot Schwartz, MD, Virginia Mason Medical Center, Infectious Disease, 1100 Ninth Avenue, Seattle, Washington 98101, USA. E-mail: [email protected]
Inhibition of Smad Antiproliferative Function by CDK Phosphorylation (2004)

Rb family members were the only demonstrated substrates of CDK4 until it was shown recently that Smad3, which plays a key role in mediating TGF-beta antiproliferative responses, is phosphorylated by both CDK4 and CDK2 in vivo and in vitro. CDK phosphorylation of Smad3 inhibits its transcriptional activity and antiproliferative function. The Rb pathway is disrupted in almost all human cancers. Most cancers contain high levels of CDK activity due to frequent inactivation of the p16 tumor suppressor or overexpression of cyclin D1. Therefore, disruption of the Rb pathway not only inactivates Rb, but also likely diminishes Smad activity, which may contribute to tumorigenesis and resistance to the TGF-beta growth-inhibitory effects in cancers. Although genetic mutation of Smad3 has not been reported, CDK phosphorylation of Smad3 may provide an epigenetic mechanism for inhibition of the tumor suppressive function of Smad3 during the early stages of tumorigenesis.
RearType (2010)

RearType is a text input system for mobile devices such as Tablet PCs, using normal keyboard keys but on the reverse side of the device. The standard QWERTY layout is split and rotated so that hands gripping the device from either side have the usual keys under the fingers. This frees up the front of the device, maximizing the use of the display for visual output, eliminating the need for an onscreen keyboard and the resulting hand occlusion, and providing tactile and multi-finger text entry - with potential for knowledge transfer from QWERTY. Using a prototype implementation which includes software visualization of the keys to assist with learning, we conducted a study to explore the initial learning curve for RearType. With one hour's training, RearType typing speed was an average 15 WPM, and was not statistically different to a touchscreen keyboard.
Measuring glomerular number and size in perfused kidneys using MRI (2011)

The goal of this work was to nondestructively measure glomerular (and thereby nephron) number in the whole kidney. Variations in the number and size of glomeruli have been linked to many renal and systemic diseases. Here, we develop a robust magnetic resonance imaging (MRI) technique based on injection of cationic ferritin (CF) to produce an accurate measurement of number and size of individual glomeruli. High-field (19 Tesla) gradient-echo MR images of perfused rat kidneys after in vivo intravenous injection of CF showed specific labeling of individual glomeruli with CF throughout the kidney. We developed a three-dimensional image-processing algorithm to count every labeled glomerulus. MRI-based counts yielded 33,786 ± 3,753 labeled glomeruli (n = 5 kidneys). Acid maceration counting of contralateral kidneys yielded an estimate of 30,585 ± 2,053 glomeruli (n = 6 kidneys). Disector/fractionator stereology counting yielded an estimate of 34,963 glomeruli (n = 2). MRI-based measurement of apparent glomerular volume of labeled glomeruli was 4.89 × 10(-4) mm(3) (n = 5) compared with the average stereological measurement of 4.99 × 10(-4) mm(3) (n = 2). The MRI-based technique also yielded the intrarenal distribution of apparent glomerular volume, a measurement previously unobtainable in histology. This work makes it possible to nondestructively measure whole-kidney glomerular number and apparent glomerular volumes to study susceptibility to renal diseases and opens the door to similar in vivo measurements in animals and humans.
Plasma lipoproteins in the golden Syrian hamster (Mesocricetus auratus): heterogeneity of apoB- and apoA-I-containing particles (1993)

We present the quantitative and qualitative characteristics of the apolipoprotein (apo) B- and apoA-I-containing lipoprotein subspecies in the plasma of male Golden Syrian hamsters. The spectrum of hamster lipoproteins of d < 1.172 g/ml was subfractionated by isopycnic density gradient ultracentrifugation. ApoB-containing subspecies were distributed up to a density of 1.074 g/ml. Hamster very low density lipoproteins (VLDL, d < 1.018 g/ml; approximately 120 mg/dl plasma) were triglyceride (TG)-rich, deficient in cholesteryl ester (CE), and highly heterogeneous in size, containing chylomicron-like particles. ApoVLDL contained proteins analogous to human apoB-100, apoB-48, and apoE. ApoB-containing subspecies with physicochemical properties typical of low density lipoproteins (LDL) were identified as a single, major size species in the density interval from 1.019 to 1.074 g/ml, particle diameter decreasing progressively with increase in density. Hamster LDL-like subspecies were distinguished from their human counterparts by a relative deficiency in core CE (< 30% by wt) and by enrichment in triglyceride. The high M(r) form of apoB was the major apolipoprotein of all LDL-like subfractions, in which apoE was detected as a minor component. Total plasma levels of LDL (d 1.019-1.074 g/ml) amounted to approximately 140 mg/dl (approximately 25% of d < 1.172 g/ml lipoproteins). The distribution of dense apoB-containing subspecies overlapped that of apoA-I-containing, high density lipoprotein-1 (HDL1)-like particles in the density interval approximately 1.039-1.074 g/ml. ApoA-I-containing subspecies with the physical and chemical characteristics of HDL were exclusively present over the density interval 1.074-1.172 g/ml. Quantitatively, these subspecies predominated in hamster plasma (approximately 270 mg/dl). Light, HDL2-like particles of d 1.065-1.103 g/ml (HDLL) were preponderant, (approximately 66% of total HDL). Marked size heterogeneity was evident, and was associated with distinct particle contents of minor apolipoproteins. Both HDLL and heavy HDL (HDLH, d 1.103-1.172 g/ml) were enriched in CE as evidenced by elevated weight ratios of CE:FC (7-9:1) and of CE:TG (up to approximately 50:1). Considered together, the core lipid contents of apoB- and apoA-I-containing lipoproteins are consistent with the hypothesis that the hamster is partially deficient in neutral lipid (CE, TG) transfer activity.
Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I (2008)

Bacterial single-stranded DNA (ssDNA)-binding proteins (SSBs) play essential protective roles in genome biology by shielding ssDNA from damage and preventing spurious DNA annealing. Far from being inert, ssDNA/SSB complexes are dynamic DNA processing centers where many different enzymes gain access to genomic substrates by exploiting direct interactions with SSB. In all cases examined to date, the C terminus of SSB (SSB-Ct) forms the docking site for heterologous proteins. We describe the 2.7-A-resolution crystal structure of a complex formed between a peptide comprising the SSB-Ct element and exonuclease I (ExoI) from Escherichia coli. Two SSB-Ct peptides bind to adjacent sites on ExoI. Mutagenesis studies indicate that one of these sites is important for association with the SSB-Ct peptide in solution and for SSB stimulation of ExoI activity, whereas the second has no discernable function. These studies identify a correlation between the stability of the ExoI/SSB-Ct complex and SSB-stimulation of ExoI activity. Furthermore, mutations within SSB's C terminus produce variants that fail to stimulate ExoI activity, whereas the SSB-Ct peptide alone has no effect. Together, our findings indicate that SSB stimulates ExoI by recruiting the enzyme to its substrate and provide a structural paradigm for understanding SSB's organizational role in genome maintenance.
The Design Space of Data-Parallel Memory Systems (2006)

Data-parallel memory systems must maintain a large number of outstanding memory references to fully use increasing DRAM bandwidth in the presence of rising latencies. Additionally, throughput is increasingly sensitive to the reference patterns due to the rising latency of issuing DRAM commands, switching between reads and writes, and precharging/activating internal DRAM banks. We study the design space of data-parallel memory systems in light of these trends of increasing concurrency, latency, and sensitivity to access patterns. We perform a detailed performance analysis of scientific and multimedia applications and micro-benchmarks, varying DRAM parameters and the memory-system configuration. We identify the interference between concurrent read and write memory-access threads, and bank conflicts, both within a single thread and across multiple threads, as the most critical factors affecting performance. We then develop hardware techniques to minimize throughput degradation. We advocate either relying on multiple concurrent accesses from a single memory-reference thread only, while sacrificing load-balance, or introducing new hardware to maintain both locality of reference and load-balance between multiple DRAM channels with multiple threads. We show that a low-cost configuration with only 16 channel-buffer entries achieves over 80% of peak throughput in most cases
Bootstrapping a Data-Set and Model for Question-Answering in Portuguese (Short Paper) (2019)

Question answering systems are mainly concerned with fulfilling an information query written in natural language, given a collection of documents with relevant information. They are key elements in many popular application systems as personal assistants, chat-bots, or even FAQ-based online support systems. This paper describes an exploratory work carried out to come up with a state-of-the-art model for question-answering tasks, for the Portuguese language, based on deep neural networks. We also describe the automatic construction of a data-set for training and testing the model. The final model is not trained in any specific topic or context, and is able to handle generic documents, achieving 50% accuracy in the testing data-set. While the results are not exceptional, this work can support further development in the area, as both the data-set and model are publicly available.