gebhart/patrepeval huggingface dataset:
Role of histidine interruption in mitigating the pathological effects of long polyglutamine stretches in SCA1: A molecular approach (2003)

Polyglutamine expansions, leading to aggregation, have been implicated in various neurodegenerative disorders. The range of repeats observed in normal individuals in most of these diseases is 19-36, whereas mutant proteins carry 40-81 repeats. In one such disorder, spinocerebellar ataxia (SCA1), it has been reported that certain individuals with expanded polyglutamine repeats in the disease range (Q(12)HQHQ(12)HQHQ(14/15)) but with histidine interruptions were found to be phenotypically normal. To establish the role of histidine, a comparative study of conformational properties of model peptide sequences with (Q(12)HQHQ(12)HQHQ(12)) and without (Q(42)) interruptions is presented here. Q(12)HQHQ(12)HQHQ(12) displays greater solubility and lesser aggregation propensity compared to uninterrupted Q(42) as well as much shorter Q(22). The solvent and temperature-driven conformational transitions (beta structure <--> random coil --> alpha helix) displayed by these model polyQ stretches is also discussed in the present report. The study strengthens our earlier hypothesis of the importance of histidine interruptions in mitigating the pathogenicity of expanded polyglutamine tract at the SCA1 locus. The relatively lower propensity for aggregation observed in case of histidine interrupted stretches even in the disease range suggests that at a very low concentration, the protein aggregation in normal cells, is possibly not initiated at all or the disease onset is significantly delayed. Our present study also reveals that besides histidine interruption, proline interruption in polyglutamine stretches can lower their aggregation propensity.
A 1H Nuclear‐Magnetic‐Resonance Study of the Solution Conformation of the Isoinhibitor K from Helix pomatia (1978)

The isoinhibitor K from Helix pomatia was investigated by high-resolution 1H nuclear magnetic resonance at 360 MHZ. Detailed studies of the labile protons and the resonances of the aromatic residues indicated extensive homologies between the spatial structures of the snail inhibitor, the basic pancreatic trypsin inhibitor (Kunitz) from bovine tissue and the cos colostrum trypsin inhibitor. Comparison of these three homologous inhibitors indicated that the overall flexibility of the globular protein conformation is reduced and its stability with respect to thermal denaturation raised when the content of amino acids with charged side chains is increased. It is suggested that this relation between amino acid composition and stability of the globular solution structure might be valid also for other classes of homologous proteins.
Scalable Parallel Computing: Technology, Architecture, Programming (1998)

From the Publisher:
This comprehensive new text from author Kai Hwang covers four important aspects of parallel and distributed computing  principles,technology,architecture,and programming  and can be used for several upper-level courses.
Arbitrary Style Transfer in Real-Time with Adaptive Instance Normalization (2017)

Gatys et al. recently introduced a neural algorithm that renders a content image in the style of another image, achieving so-called style transfer. However, their framework requires a slow iterative optimization process, which limits its practical application. Fast approximations with feed-forward neural networks have been proposed to speed up neural style transfer. Unfortunately, the speed improvement comes at a cost: the network is usually tied to a fixed set of styles and cannot adapt to arbitrary new styles. In this paper, we present a simple yet effective approach that for the first time enables arbitrary style transfer in real-time. At the heart of our method is a novel adaptive instance normalization (AdaIN) layer that aligns the mean and variance of the content features with those of the style features. Our method achieves speed comparable to the fastest existing approach, without the restriction to a pre-defined set of styles. In addition, our approach allows flexible user controls such as content-style trade-off, style interpolation, color & spatial controls, all using a single feed-forward neural network.
SGM-Nets: Semi-Global Matching with Neural Networks (2017)

This paper deals with deep neural networks for predicting accurate dense disparity map with Semi-global matching (SGM). SGM is a widely used regularization method for real scenes because of its high accuracy and fast computation speed. Even though SGM can obtain accurate results, tuning of SGMs penalty-parameters, which control a smoothness and discontinuity of a disparity map, is uneasy and empirical methods have been proposed. We propose a learning based penalties estimation method, which we call SGM-Nets that consist of Convolutional Neural Networks. A small image patch and its position are input into SGMNets to predict the penalties for the 3D object structures. In order to train the networks, we introduce a novel loss function which is able to use sparsely annotated disparity maps such as captured by a LiDAR sensor in real environments. Moreover, we propose a novel SGM parameterization, which deploys different penalties depending on either positive or negative disparity changes in order to represent the object structures more discriminatively. Our SGM-Nets outperformed state of the art accuracy on KITTI benchmark datasets.
Molecular recognition at self-assembled monolayers: Optimization of surface functionalization (1993)

Sulfur-based molecules containing biotin and hydroxyl groups have been used to create a wide variety of self-assembled monolayers on gold surfaces. Surface plasmon resonance has been used to study in situ the binding of streptavidin to these monolayers from solution. The self-assembled monolayers allow a high degree of control over the surface properties. The choice of an appropriate biotin-containing molecule, with a spacer segment, and the dilution of this molecule within the monolayer by hydroxythiols, allows optimization of the binding properties of the monolayer—nonspecific interactions between streptavidin and the surface are below detection limits, and specific binding between the streptavidin and biotin groups can be maximized.
Amyloid adhesins are abundant in natural biofilms (2007)

Surface-associated amyloid fibrils have been described by bacteria in the family Enterbacteriaceae, but it is unknown to what extent amyloid adhesins are present in natural biofilms. In this study, amyloid adhesins were specifically stained with Thioflavin T and two conformationally specific antibodies targeting amyloid fibrils. These three independent detection methods were each combined with fluorescence in situ hybridization using fluorescently labelled oligonucleotide probes in order to link phenotype with identity. Escherichia coli mutants with and without amyloid adhesins (curli) served as controls. In biofilms from four different natural habitats, bacteria producing extracellular amyloid adhesins were identified within several phyla: Proteobacteria (Alpha-, Beta-, Gamma- and Deltaproteobacteria), Bacteriodetes, Chloroflexi and Actinobacteria, and most likely also in other phyla. Quantification of the microorganisms producing amyloid adhesins showed that they constituted at least 5-40% of all prokaryotes present in the biofilms, depending on the habitat. Particularly in drinking water biofilms, a high number of amyloid-positive bacteria were identified. Production of amyloids was confirmed by environmental isolates belonging to the Gammaproteobacteria, Bacteriodetes, Firmicutes and Actinobacteria. The new approach is a very useful tool for further culture-independent studies in mixed microbial communities, where the abundance and diversity of bacteria expressing amyloid adhesins seems much greater than hitherto anticipated.
Characterization of Compressibility and Compactibility of Poly(ethylene oxide) Polymers for Modified Release Application by Compaction Simulator (1996)

Poly(ethylene oxide) polymers (PEO) appear to have great potential for controlled release applications. These polymers are hydrophilic with good water solubility, low toxicity, and high swelling capacity. As part of formulation optimization for a large-scale solid dosage form production, physicomechanical characterization of PEO was undertaken using a compaction simulator. Heckel plots for all PEOs were constructed, and yield pressures (Py) at different punch velocities were calculated from the linear portion of the plots. Low Py values, increase of Py with increasing punch speed, upward curvature of the plot, and strain rate sensitivity values indicate that the densification process and consolidation mechanism for PEOs of various molecular weights (0.2 x 10(6) to 7 x 10(6)) are identical and follow plastic deformation. PEOs have a high degree of crystallinity (57-85%) and show significant axial recovery (15-25%) upon decompression and ejection. The low Py values (58-78 MPa) and low mean compaction pressures demonstrate that volume reduction (compressibility) under pressure is excellent. However, due to viscoelastic behavior and large axial expansion, tablets of relatively low tensile strength are produced. These observations suggest the need to blend PEO with highly compactible excipients in order to produce tables on a high-speed production press.
p16 promoter hypermethylation is associated with increased breast cancer risk (2012)

The current study aimed to investigate the effects of p16 hypermethylation on breast cancer quantitatively through a meta-analysis of available case-control studies (including malignant, benign and normal breast cancer tissues). The PubMed, Web of Science and EBSCO databases were searched from their inceptions to February 1, 2012. Crude odds ratios (ORs) with 95% conﬁdence intervals (CIs) were extracted and pooled to assess the strength of the association between p16 hypermethylation and breast cancer risk. A total of eight studies, including 691 breast cancer cases and 525 control cases, were identified for meta-analysis. Statistically significant ORs of p16 hypermethylation were obtained from the breast cancer and control groups (OR, 6.58; 95% CI, 1.15-37.75; P=0.03). However, no significant associations between the methylation and ER and PR status in breast cancer were detected (OR, 1.24; 95% CI, 0.64-2.41; P=0.52; OR, 1.49; 95% CI, 0.81-2.75; P=0.20, respectively). The meta-analysis indicated that p16 hypermethylation significantly increases breast cancer risk. However, no significant associations between the methylation and ER and PR status in breast cancer were detected.
Inactivation of the DNA-Repair GeneMGMTand the Clinical Response of Gliomas to Alkylating Agents (2000)

Methylation of the MGMT promoter in gliomas is a useful predictor of the responsiveness of the tumors to alkylating agents.
Effect of Casting Methods on Castability of Pure Titanium (1993)

Two types of patterns were tested for castability: 1) polyester mesh pattern (20mm x 22mm with 100 open squares) and 2) 20mm x 20mm wax plates 1.0 and 1.5 mm in thickness. These materials were invested using a pre-arranged commercial phosphate-bonded investment for titanium. Three different types of casting machines were selected: 1) a pressure-type casting machine with separate melting and casting chambers, 2) a pressure-type casting machine with one chamber and 3) a centrifugal-type casting machine at 3000 rpm. Pure titanium (> 99.5%) was cast into the molds at a mold temperature of 100 degrees C. The castability of mesh pattern was evaluated in terms of the number of cast segment, and the cast plate was evaluated using X-ray transparent images by a digital imaging technique. The centrifugal casting method showed the best castability among these three casting methods.
Piezoelectric-transducer-based miniature catheter for ultrahigh-speed endoscopic optical coherence tomography (2011)

We developed a piezoelectric-transducer- (PZT) based miniature catheter with an outer diameter of 3.5 mm for ultrahigh-speed endoscopic optical coherence tomography (OCT). A miniaturized PZT bender actuates a fiber and the beam is scanned through a GRIN lens and micro-prism to provide high-speed, side-viewing capability. The probe optics can be pulled back over a long distance to acquire three-dimensional (3D) data sets covering a large area. Imaging is performed with 11 μm axial resolution in air (8 μm in tissue) and 20 μm transverse resolution, at 960 frames per second with a Fourier domain mode-locked laser operating at 480 kHz axial scan rate. Using a high-speed data acquisition system, endoscopic OCT imaging of the rabbit esophagus and colon in vivo and human colon specimens ex vivo is demonstrated.
Dynamics of Brain Resuscitation After Ischemic Anoxia (1981)

The belief that even a few minutes of anoxia result in irreversible brain damage has been put into serious question, so that the possibility of brain resuscitation has taken on a new significance. A major focus for both laboratory and clinical investigation is the development of techniques to protect neurons during the critical reperfusion period after restoration of cerebral blood flow.
CD30+ anaplastic large cell lymphoma: a review of its histopathologic, genetic, and clinical features (2000)

Anaplastic large cell lymphoma (ALCL) represents a generally recognized group of large cell lymphomas. Defining features consist of a proliferation of predominantly large lymphoid cells with strong expression of the cytokine receptor CD30 and a characteristic growth pattern. With the use of molecular and clinical criteria, 3 entities of ALCL have been identified: primary systemic anaplastic lymphoma kinase (ALK)(+) ALCL, primary systemic ALK(-) ALCL, and primary cutaneous ALCL. ALK expression is caused by chromosomal translocations, most commonly t(2;5). ALK(+) ALCL predominantly affects young male patients and, if treated with chemotherapy, has a favorable prognosis. It shows a broad morphologic spectrum, with the "common type," the small cell variant, and the lymphohistiocytic variant being most commonly observed. The knowledge of the existence of these variants is essential in establishing a correct diagnosis. ALK(-) ALCL occurs in older patients, affecting both genders equally and having an unfavorable prognosis. The morphology and the immunophenotype of primary cutaneous ALCL show an overlap with that of lymphomatoid papulosis. Both diseases have an excellent prognosis, and secondary systemic dissemination is only rarely observed. The described ALCL entities usually derive from cytotoxic T cells. In contrast, large B-cell lymphomas with anaplastic morphology are believed to represent not a separate entity but a morphologic variant of diffuse large B-cell lymphoma. Malignant lymphomas with morphologic features of both Hodgkin disease and ALCL have formerly been classified as Hodgkin-like ALCL. Recent immunohistologic studies, however, suggest that ALCLs Hodgkin-like represent either cases of tumor cell-rich classic Hodgkin disease or (less commonly) ALK(+) ALCL or ALK(-) ALCL. (Blood. 2000;96:3681-3695)
Structure and function in rhodopsin: correct folding and misfolding in two point mutants in the intradiscal domain of rhodopsin identified in retinitis pigmentosa. (1996)

The rhodopsin mutants P23H and G188R, identified in autosomal dominant retinitis pigmentosa (ADRP), and the site-specific mutants D190A and DeltaY191-Y192 were expressed in COS cells from synthetic mutant opsin genes containing these mutations. The proteins expressed from P23H and D190A partially regenerated the rhodopsin chromophore with 11-cis-retinal and were mixtures of the correctly folded (retinal-binding) and misfolded (non-retinal-binding) opsins. The mixtures were separated into pure, correctly folded mutant rhodopsins and misfolded opsins. The proteins expressed from the ADRP mutant G188R and the mutant DeltaY191-Y192 were composed of totally misfolded non-retinal-binding opsins. Far-UV CD spectra showed that the correctly folded mutant rhodopsins had helical content similar to that of the wild-type rhodopsin, whereas the misfolded opsins had helical content 50-70% of the wild type. The near-UV CD spectra of the misfolded mutant proteins lack the characteristic band pattern seen in the wild-type opsin, indicative of a different tertiary structure. Further, whereas the folded mutant rhodopsins were essentially resistant to trypsin digestion, the misfolded opsins were degraded to small fragments under the same conditions. Therefore, the misfolded opsins appear to be less compact in their structures than the correctly folded forms. We suggest that most, if not all, of the point mutations in the intradiscal domain identified in ADRP cause partial or complete misfolding of rhodopsin.
Evidence-based management of common chronic lower extremity ulcers (2013)

Chronic lower extremity ulcers are a significant burden on patients and health care systems worldwide. Although relatively common, these wounds can be difficult to treat and present a challenge to physicians. Treatment has often been based on anecdotal accounts; however, there is a growing emphasis on using evidence-based conclusions to guide clinical decisions. In this review article, the standard of care and adjuvant therapies of venous leg ulcers and diabetic foot ulcers are presented from an evidence-based perspective.
Nonmarinediplocraterion luniforme(blanckenhorn 1916) from the hasandong formation (gretaceous) of the Jinju area, Korea (1997)

Abstract Diplocraterion luniforme occurs abundantly in the Cretaceous Hasandong Formation of the Jinju area, Korea. The Hasandong Formation consists of fluvial deposits mainly composed of sandstone, siltstone, mudstone and shale. The formation contains freshwater bivalves such as Trigonioides sp. and Plicatounio sp., fossil tree stumps, carbonized wood, stromatolites, caliche nodules, current ripples and desiccation cracks. The trace fossils Planolites ichnosp., Skolithos ichnosp. and Taenid‐ium ichnosp. are also commonly observed. Diplocraterion luniforme occurs in the gray shale which is considered to have been deposited in floodplain lake environments. This report represents an unusual record of a nonmarine occurrence of Diplocraterion, which has previously been generally regarded as a diagnostic marine trace fossil. Key words: Diplocraterion luniforme nonmarineHasandong FormationKoreaCretaceous Notes Corresponding author.
Modeling principles for QMR medical findings. (1996)

Structured representation of medical information is essential for ensuring the accuracy and reliability of computerized decision support applications. Such systems require input that is error-free and clinically pertinent. This paper reviews existing medical models, particularly those exploited for natural language understanding, and highlights modeling features important to future indexing of medical texts with controlled vocabularies. A hybrid representation derived from existing frame-based and conceptual-graph-based systems is proposed to represent relevant medical terms as used by experts.
Millimeter-scale epileptiform spike patterns and their relationship to seizures (2011)

Advances in neural electrode technology are enabling brain recordings with increasingly fine spatial and temporal resolution. We explore spatio-temporal (ST) patterns of local field potential spikes using a new high-density active electrode array with 500 μm resolution. We record subdural micro-electrocorticographic (μECoG) signals in vivo from a feline model of acute neocortical epileptiform spikes and seizures induced with local administration of the GABA antagonist, picrotoxin. We employ a clustering algorithm to separate 2-dimensional (2-D) spike patterns to isolate distinct classes of spikes unique to the interictal and ictal states. Our findings indicate that the 2-D patterns can be used to distinguish seizures from non-seizure state. We find two statistically significant ST patterns that uniquely characterize ictal epochs. We conclude that millimeter-scale ST spike dynamics contain useful information about ictal state. This finding may be important to understanding mechanisms underlying local circuit activity during seizure generation. Further work will investigate whether patterns we identify can increase our understanding of seizure dynamics and their underlying mechanisms and inform new electrical stimulation protocols for seizure termination.
Distinct regions of c-Mpl cytoplasmic domain are coupled to the JAK-STAT signal transduction pathway and Shc phosphorylation. (1995)

c-Mpl, a member of the hematopoietic cytokine receptor family, is the receptor for thrombopoietin. To investigate signal transduction by c-Mpl, a chimeric receptor, composed of the extracellular domain of human growth hormone receptor and the intracellular domain of c-Mpl, was introduced into the interleukin 3-dependent cell line Ba/F3. In response to growth hormone, this chimeric receptor induced growth in the absence of interleukin 3. Deletion analysis of the 123-amino acid intracellular domain indicated that the elements responsible for this effect are present within the 63 amino acids proximal to the transmembrane domain. Mutation of the recently described box 1 motif abrogated the proliferative response. Tyrosine phosphorylation of the tyrosine kinase JAK-2 and activation of STAT proteins were dependent on box 1 and sequences within 63 amino acids of the plasma membrane. STAT proteins activated by thrombopoietin in a megakaryocytic cell line were purified and shown to be STAT1 and STAT3. A separate region located at the C terminus of the c-Mpl intracellular domain was found to be required for induction of Shc phosphorylation and c-fos mRNA accumulation, suggesting involvement of the Ras signal transduction pathway. Thus, at least two distinct regions are involved in signal transduction by the c-Mpl.
THE TROJAN MONEY SPINNER (2007)

It is obvious that as more and more money moves online, criminals who want to steal that money are moving online as well. Since banks no longer have large sums of money in their vaults and bank robbery has several inherent risks, criminals have found a lucrative and a much lower-risk business in online crime. Email-based phishing has been the first echelon of this change, but the situation is already changing again. Online banks have begun to improve their security and authentication methods. This will very much reduce the effectiveness of phishing that is based on emails and fraudulent sites. There is a clear demand for better solutions in the world of crime. The second echelon of online bank fraud is banking trojans. These trojans infect the computer of an online bank customer. The trojan has visibility to everything the customer does and can use his authenticated banking session to steal his money. Also, a key difference from email-based phishing is that the victim is doing nothing wrong; he is just going to his bank and doing his business, as he should. These attackers are making a lot of money. Relatively few of them are caught, so the problem is only going to get worse. To better understand this problem and its size, we have implemented a new tool for analysing banking trojans. We have run this tool on thousands of recent malware samples to get an idea of how common these banking trojans are, the current trends, the geographical distribution of this problem, and what the targets are. This paper presents our findings.