gebhart/patrepeval huggingface dataset:
The structural basis for the negative regulation of thioredoxin by thioredoxin-interacting protein (2014)

The redox-dependent inhibition of thioredoxin (TRX) by thioredoxin-interacting protein (TXNIP) plays a pivotal role in various cancers and metabolic syndromes. However, the molecular mechanism of this regulation is largely unknown. Here, we present the crystal structure of the TRX-TXNIP complex and demonstrate that the inhibition of TRX by TXNIP is mediated by an intermolecular disulphide interaction resulting from a novel disulphide bond-switching mechanism. Upon binding to TRX, TXNIP undergoes a structural rearrangement that involves switching of a head-to-tail interprotomer Cys63-Cys247 disulphide between TXNIP molecules to an interdomain Cys63-Cys190 disulphide, and the formation of a de novo intermolecular TXNIP Cys247-TRX Cys32 disulphide. This disulphide-switching event unexpectedly results in a domain arrangement of TXNIP that is entirely different from those of other arrestin family proteins. We further show that the intermolecular disulphide bond between TRX and TXNIP dissociates in the presence of high concentrations of reactive oxygen species. This study provides insight into TRX and TXNIP-dependent cellular regulation.
Introduction (2007)

By the middle of 2007, Afghans had become increasingly disillusioned with a state-building process that had failed to deliver the peace dividend that they were promised. For many Afghans, the most noticeable change in their lives since the fall of the Taliban has been an acute deterioration in security conditions. Whether it is predatory warlords, the Taliban-led insurgency, the burgeoning narcotics trade or general criminality, the threats to the security and stability of Afghanistan are manifold. The response to those threats, both in terms of the international military intervention and the donor-supported process to rebuild the security architecture of the Afghan state, known as security-sector reform (SSR), has been largely insufficient to address the task at hand. NATO has struggled to find the troops and equipment it requires to complete its Afghan mission and the SSR process, from its outset, has been severely under-resourced and poorly directed. Compounding these problems, rampant corruption and factionalism in the Afghan government, particularly in the security institutions, have served as major impediments to reform and a driver of insecurity. This paper charts the evolution of the security environment in Afghanistan since the fall of the Taliban, assessing both the causes of insecurity and the responses to them. Through this analysis, it offers some suggestions on how to tackle Afghanistan's growing security crisis.
High-Efficiency Separation of Bio-Oil (2013)

Biomass is a CO2-neutral energy source that has considerable reserve. It can replace fossil feedstock in the production of heat, electricity, transportation fuels, chemicals, and various materials. Liquid bio-fuels, which are considered to be substitutes for traditional petrol liquid fuels, can be produced from biomass in different ways, such as high-pressure liquefaction, hydrothermal pyrolysis, and fast pyrolysis.
Cryofocusing inlet with reverse flow sample collection for gas chromatography (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCryofocusing inlet with reverse flow sample collection for gas chromatographyMark A. Klemp, Michael L. Akard, and Richard D. SacksCite this: Anal. Chem. 1993, 65, 18, 2516–2521Publication Date (Print):September 15, 1993Publication History Published online1 May 2002Published inissue 15 September 1993https://pubs.acs.org/doi/10.1021/ac00066a020https://doi.org/10.1021/ac00066a020research-articleACS PublicationsRequest reuse permissionsArticle Views147Altmetric-Citations54LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Vagus Nerve is One Route of Transneural Invasion for Intranasally Inoculated Influenza A Virus in Mice (2004)

Intranasally inoculated neurotropic influenza viruses in mice infect not only the respiratory tract but also the central nervous system (CNS), mainly the brain stem. Previous studies suggested that the route of invasion of virus into the CNS was via the peripheral nervous system, especially the vagus nerve. To evaluate the transvagal transmission of the virus, we intranasally inoculated unilaterally vagectomized mice with a virulent influenza virus (strain 24a5b) and examined the distribution of the viral protein and genome by immunohistochemistry and in situ hybridization over time. An asymmetric distribution of viral antigens was observed between vagal (nodose) ganglia: viral antigen was detected in the vagal ganglion of the vagectomized side 2 days later than in the vagal ganglion of the intact side. The virus was apparently transported from the respiratory mucosa to the CNS directly and decussately via the vagus nerve and centrifugally to the vagal ganglion of the vagectomized side. The results of this study, thus, demonstrate that neurotropic influenza virus travels to the CNS mainly via the vagus nerve.
A novel base-induced cyclisation to produce an aryl ring (1979)

J. A. Murphy and J. Staunton, J. Chem. Soc., Chem. Commun., 1979, 1165 DOI: 10.1039/C39790001165
NATSYN PILOT PLANT (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNATSYN PILOT PLANTC. T. WinchesterCite this: Ind. Eng. Chem. 1959, 51, 1, 19–22Publication Date (Print):January 1, 1959Publication History Published online1 May 2002Published inissue 1 January 1959https://pubs.acs.org/doi/10.1021/ie50589a027https://doi.org/10.1021/ie50589a027research-articleACS PublicationsRequest reuse permissionsArticle Views37Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Responsiveness of 5-HT(1A) and 5-HT2 receptors in the rat orbitofrontal cortex after long-term serotonin reuptake inhibition. (2005)

These results indicate a desensitization of postsynaptic 5-HT(1A) receptors in the OFC but a lack of compensatory adaptation of the 5-HT receptor(s) mediating the main effect of 5-HT in this brain region. These observations imply that the activation of normosensitive postsynaptic 5-HT2-like receptors may mediate the effect of enhanced 5-HT release in the OFC.
Initial Molecular Response at 3 Months May Predict Both Response and Event-Free Survival at 24 Months in Imatinib-Resistant or -Intolerant Patients With Philadelphia Chromosome–Positive Chronic Myeloid Leukemia in Chronic Phase Treated With Nilotinib (2012)

Patients with BCR-ABL1 (IS) of > 10% at 3 months had a lower cumulative incidence of CCyR and MMR and lower rates of EFS versus patients with BCR-ABL1 (IS) of ≤ 10%. Prospective studies may determine whether close monitoring or alternative therapies are warranted for patients with minimal initial molecular response.
An Improved Algorithm for Document Image Enhancing (2016)

Document image from a digital camera or a digital scanner always shows different types of distortions. Therefore, we must perform some corrections to the image object before reading the text information with an OCR engine. To improve the distorted document image's vision quality and the OCR rate, this paper proposed an improved algorithm for document image enhancing by recovering the deformed rectangle object. Firstly, we detect the object to be corrected for skew and perspective distortion. Secondly, we measure the size of the detected object to project the data on the exact real object-size. Third, we divide the entire image to find the position of some specific object points. Finally we deform the pixel grid and map this deformed grid to the destination image to produce the final corrected image. As a result, for the corrected image, the distortions are mostly removed leading the OCR to get much better results. Experimental results show that our approach can efficiently resolve the issue of document image distortion mainly for perspective distortion.
Mechanical properties of poly(ε‐caprolactone) and poly(lactic acid) blends (2008)

Abstract The aim of this work was to better understand the performance of binary blends of biodegradable aliphatic polyesters to overcome some limitations of the pure polymers (e.g., brittleness, low stiffness, and low toughness). Binary blends of poly(ε‐caprolactone) (PCL) and poly(lactic acid) (PLA) were prepared by melt blending (in a twin‐screw extruder) followed by injection molding. The compositions ranged from pure biodegradable polymers to 25 wt % increments. Morphological characterization was performed with scanning electron microscopy and differential scanning calorimetry. The initial modulus, stress and strain at yield, strain at break, and impact toughness of the biodegradable polymer blends were investigated. The properties were described by models assuming different interfacial behaviors (e.g., good adhesion and no adhesion between the dissimilar materials). The results indicated that PCL behaved as a polymeric plasticizer to PLA and improved the flexibility and ductility of the blends, giving the blends higher impact toughness. The strain at break was effectively improved by the addition of PCL to PLA, and this was followed by a decrease in the stress at break. The two biodegradable polymers were proved to be immiscible but nevertheless showed some degree of adhesion between the two phases. This was also quantified by the mechanical property prediction models, which, in conjunction with material property characterization, allowed unambiguous detection of the interfacial behavior of the polymer blends. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genome (2017)

RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the <i>Saccharomyces cerevisiae</i> genome. The scale and precision of these measurements revealed many previously unknown features of this well-studied RBP. Our transcribed genome array (TGA) assayed both rare and abundant transcripts with equivalent proficiency, revealing hundreds of low-abundance targets missed by previous approaches. These targets regulated diverse biological processes including nutrient sensing and the DNA damage response, and implicated Vts1 in de novo gene "birth." TGA provided single-nucleotide resolution for each binding site and delineated a highly specific sequence and structure motif for Vts1 binding. Changes in transcript levels in <i>vts1</i>Δ cells established the regulatory function of these binding sites. The impact of Vts1 on transcript abundance was largely independent of where it bound within an mRNA, challenging prevailing assumptions about how this RBP drives RNA degradation. TGA thus enables a quantitative description of the relationship between variant RNA structures, affinity, and in vivo phenotype on a transcriptome-wide scale. We anticipate that TGA will provide similarly comprehensive and quantitative insights into the function of virtually any RBP.
Evaluation of the photoprotective effect of oral vitamin E supplementation (1994)

<h3>Background and Design:</h3> Solar-induced cutaneous damage is mediated partly via oxidative pathways. Some evidence exists for a photoprotective role of antioxidants. In a double-blind, placebo-controlled study, we examined the effect of a long-term, orally administered antioxidant against UV-induced epidermal damage. Healthy human subjects supplemented their usual diet daily with either 400 IU of oral vitamin E (α-tocopherol acetate) or placebo over a 6-month period. Minimal erythema dose and histologic response to threefold minimal erythema dose exposure were determined at baseline, 1 month, and 6 months. <h3>Results:</h3> The minimal erythema dose did not vary substantially at the three time points within each treatment group or in the vitamin E—supplemented group vs the placebo group. The number of sunburn cells produced by a threefold minimal erythema dose exposure was also not significantly different between the two groups. Of note, however, vitamin E levels in plasma increased only modestly and in skin biopsy specimens were unchanged following 1 month and 6 months of supplementation. <h3>Conclusions:</h3> No clinical or histologic difference in the response to UVB could be detected between the placebo and vitamin E—supplemented groups. In this small study, daily ingestion of 400IU of oral α-tocopherol daily does not provide meaningful photoprotection. (Arch Dermatol. 1994;130:1257-1261)
C/EBP, NF-kappa B, and c-Ets family members and transcriptional regulation of the cell-specific and inducible macrophage inflammatory protein 1 alpha immediate-early gene. (1993)

Macrophage inflammatory protein 1 alpha (MIP-1 alpha) cytokine gene expression is restricted to a limited number of cells of hemopoietic origin and is rapidly and transiently induced by serum and endotoxin in macrophages. A single nuclear DNase I-hypersensitive site, which maps to the proximal promoter of the MIP-1 alpha gene, was identified in macrophage cells but was absent in cells which do not express basal levels of MIP-1 alpha mRNA. The proximal promoter sequences (+36 to -220 bp) are sufficient to confer cell-specific and inducible transcription in transfection assays. In vitro DNA-binding studies revealed five major nuclear protein binding sites in the proximal promoter which bind C/EBP, NF-kappa B, and/or c-Ets family members. Cell-specific differences in DNA binding by members of the NF-kappa B and c-Ets families correlate with the cell-specificity of MIP-1 alpha gene expression and the chromosomal conformation of the promoter. Changes in promoter binding by members of the C/EBP and NF-kappa B families correlate with the transcriptional up-regulation observed in serum- or endotoxin-stimulated macrophages in functional studies.
Diagnosis and treatment of patients with IgA nephropathy in Japan (2016)

Chronic kidney disease (CKD) is a worldwide public health problem that affects millions of people from all racial and ethnic groups. Although CKD is not one specific disease, it is a comprehensive syndrome that includes IgA nephropathy. As reported by the Japanese Society of Nephrology, 13.0 million people have CKD. In Japan, major causes of end-stage kidney disease are type 2 diabetic nephropathy, chronic glomerulonephritis, especially IgA nephropathy, hypertensive nephrosclerosis, and polycystic kidney disease. IgA nephropathy is characterized by polymeric IgA1 with aberrant galactosylation (galactose-deficient IgA1) increased in the blood and deposited in the glomerular mesangial areas, as well as partially in the capillary walls. The tonsils are important as one of the responsible regions in this disease. The clarification of the mechanism of galactose-deficient IgA1 production will pave the way for the development of novel therapies. The results of future research are eagerly awaited. At present, the most important therapeutic goals in patients with IgA nephropathy are the control of hypertension, the decrease of urinary protein excretion, and the inhibition of progression to end-stage kidney disease. Several investigators have reported that renin-angiotensin-aldosterone system inhibitors reduce levels of urinary protein excretion and preserve renal function in patients with IgA nephropathy. In Japan, tonsillectomy and steroid pulse therapy are more effective for patients with IgA nephropathy.
PROBABILISTIC MULTI-PERSON TRACKING USING DYNAMIC BAYES NETWORKS (2015)

Abstract. Tracking-by-detection is a widely used practice in recent tracking systems. These usually rely on independent single frame detections that are handled as observations in a recursive estimation framework. If these observations are imprecise the generated trajectory is prone to be updated towards a wrong position. In contrary to existing methods our novel approach uses a Dynamic Bayes Network in which the state vector of a recursive Bayes filter, as well as the location of the tracked object in the image are modelled as unknowns. These unknowns are estimated in a probabilistic framework taking into account a dynamic model, and a state-of-the-art pedestrian detector and classifier. The classifier is based on the Random Forest-algorithm and is capable of being trained incrementally so that new training samples can be incorporated at runtime. This allows the classifier to adapt to the changing appearance of a target and to unlearn outdated features. The approach is evaluated on a publicly available benchmark. The results confirm that our approach is well suited for tracking pedestrians over long distances while at the same time achieving comparatively good geometric accuracy.
VAPB interacts with and modulates the activity of ATF6 (2008)

A mis-sense point mutation in the human VAPB gene is associated with a familial form of motor neuron disease that has been classified as Amyotrophic Lateral Sclerosis type VIII. Affected individuals suffer from a spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) or an atypical slowly progressing form of ALS. Mammals have two homologous VAP genes, vapA and vapB. VAPA and VAPB share 76% similar or identical amino acid residues; both are COOH-terminally anchored membrane proteins enriched on the endoplasmic reticulum. Several functions have been ascribed to VAP proteins including membrane trafficking, cytoskeleton association and membrane docking interactions for cytoplasmic factors. It is shown here that VAPA and VAPB are expressed in tissues throughout the body but at different levels, and that they are present in overlapping but distinct regions of the endoplasmic reticulum. The disease-associated mutation in VAPB, VAPB(P56S), lies within a highly conserved N-terminal region of the protein that shares extensive structural homology with the major sperm protein (MSP) from nematodes. The MSP domain of VAPA and VAPB is found to interact with the ER-localized transcription factor ATF6. Over expression of VAPB or VAPB(P56S) attenuates the activity of ATF6-regulated transcription and the mutant protein VAPB(P56S) appears to be a more potent inhibitor of ATF6 activity. These data indicate that VAP proteins interact directly with components of ER homeostatic and stress signalling systems and may therefore be parts of a previously unidentified regulatory pathway. The mis-function of such regulatory systems may contribute to the pathological mechanisms of degenerative motor neuron disease.
Improvement of inter‐rater reliability of PANSS items and subscales by a standardized rater training (1998)

The present evaluation focused on the inter-rater reliability of single items and subscales of the Positive and Negative Syndrome Scale (PANSS) before and after a standardized rater training. The results of two independent studies comprising n=23 (study I) and n=12 (study II) psychiatrists and videotaped interviews with schizophrenic patients were analysed. Chance-corrected coefficients of rating agreement with expert standards (weighted kappa) were computed for single items and subscales of the PANSS. The results clearly demonstrate the importance of rater trainings. After three training sessions, 90% of the PANSS items reached an acceptable level of reliability (kappa(w)>0.40) in both evaluated studies, and for 80% of the PANSS items values of kappa(w)>0.60 were achieved.
Break-through for calcium antagonists in the treatment of hypertension based on the Syst-Eur results. (1998)

Break-through for calcium antagonists in the treatment of hypertension based on the Syst-Eur results
Audio-Visual Group Recognition Using Diffusion Maps (2009)

Data fusion is a natural and common approach to recovering the state of physical systems. But the dissimilar appearance of different sensors remains a fundamental obstacle. We propose a unified embedding scheme for multisensory data, based on the spectral diffusion framework, which addresses this issue. Our scheme is purely data-driven and assumes no <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a priori</i> statistical or deterministic models of the data sources. To extract the underlying structure, we first embed separately each input channel; the resultant structures are then combined in diffusion coordinates. In particular, as different sensors sample similar phenomena with different sampling densities, we apply the density invariant Laplace-Beltrami embedding. This is a fundamental issue in multisensor acquisition and processing, overlooked in prior approaches. We extend previous work on <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">group recognition</i> and suggest a novel approach to the selection of diffusion coordinates. To verify our approach, we demonstrate performance improvements in audio/visual speech recognition.
Optimal loop parallelization for maximizing iteration-level parallelism (2009)

This paper solves the open problem of extracting the maximal number of iterations from a loop that can be executed in parallel on chip multiprocessors. Our algorithm solves it optimally by migrating the weights of parallelism-inhibiting dependences on dependence cycles in two phases. First, we model dependence migration with retiming and formulate this classic loop parallelization into a graph optimization problem, i.e., one of finding retiming values for its nodes so that the minimum non-zero edge weight in the graph is maximized. We present our algorithm in three stages with each being built incrementally on the preceding one. Second, the optimal code for a loop is generated from the retimed graph of the loop found in the first phase. We demonstrate the effectiveness of our optimal algorithm by comparing with a number of representative non-optimal algorithms using a set of benchmarks frequently used in prior work.