gebhart/patrepeval huggingface dataset:
Synthetic peptides derived from the steroid binding domain block modulator and molybdate action toward the rat glucocorticoid receptor. (1995)

Modulators are endogenous low-mol-wt inhibitors of glucocorticoid receptor activation, and are mimicked by exogenous sodium molybdate. Activation involves the dissociation of the 90-kDa heat-shock protein from the receptor. The heat-shock protein is thought to bind to a conserved 20-amino-acid region in the steroid-binding domain of the receptor (595-614 of the rat protein). Synthetic peptides corresponding to this amino acid sequence prevented the modulators and sodium molybdate from inhibiting receptor activation. These results imply that the region 595-614 of the rat glucocorticoid receptor is also a modulator/molybdate binding site.
Leveraging Stratification in Twitter Sampling (2016)

With Tweet volumes reaching 500 million a day, sampling is inevitable for any application using Twitter data. Realizing this, data providers such as Twitter, Gnip and Boardreader license sampled data streams priced in accordance with the sample size. Big Data applications working with sampled data would be interested in working with a large enough sample that is representative of the universal dataset. Previous work focusing on the representativeness issue has considered ensuring that global occurrence rates of key terms, be reliably estimated from the sample. Present technology allows sample size estimation in accordance with probabilistic bounds on occurrence rates for the case of uniform random sampling. In this paper, we consider the problem of further improving sample size estimates by leveraging stratification in Twitter data. We analyze our estimates through an extensive study using simulations and real-world data, establishing the superiority of our method over uniform random sampling. Our work provides the technical know-how for data providers to expand their portfolio to include stratified sampled datasets, whereas applications are benefited by being able to monitor more topics/events at the same data and computing cost.
TheSaccharomyces cerevisiaeSpindle Pole Body (SPB) Component Nbp1p Is Required for SPB Membrane Insertion and Interacts with the Integral Membrane Proteins Ndc1p and Mps2p (2006)

The spindle pole body (SPB) in Saccharomyces cerevisiae functions to nucleate and organize spindle microtubules, and it is embedded in the nuclear envelope throughout the yeast life cycle. However, the mechanism of membrane insertion of the SPB has not been elucidated. Ndc1p is an integral membrane protein that localizes to SPBs, and it is required for insertion of the SPB into the nuclear envelope during SPB duplication. To better understand the function of Ndc1p, we performed a dosage suppressor screen using the ndc1-39 temperature-sensitive allele. We identified an essential SPB component, Nbp1p. NBP1 shows genetic interactions with several SPB genes in addition to NDC1, and two-hybrid analysis revealed that Nbp1p binds to Ndc1p. Furthermore, Nbp1p is in the Mps2p-Bbp1p complex in the SPB. Immunoelectron microscopy confirmed that Nbp1p localizes to the SPB, suggesting a function at this location. Consistent with this hypothesis, nbp1-td (a degron allele) cells fail in SPB duplication upon depletion of Nbp1p. Importantly, these cells exhibit a "dead" SPB phenotype, similar to cells mutant in MPS2, NDC1, or BBP1. These results demonstrate that Nbp1p is a SPB component that acts in SPB duplication at the point of SPB insertion into the nuclear envelope.
Evaluation of Very High- and Very Low-Dose Intravitreal Aflibercept in Patients with Neovascular Age-Related Macular Degeneration (2012)

Intravitreal aflibercept 4 mg had a safety profile similar to that of the very low dose 0.15 mg, and was well-tolerated. The 4-mg dose significantly reduced foveal thickening at weeks 4 and 6, significantly improved BCVA at weeks 6, and reduced the need for repeat injection after 8 weeks compared with intravitreal aflibercept 0.15 mg in neovascular AMD patients.
SiC BJT proportional base driver with collector-emitter voltage measurement and a switching regulator (2016)

The biggest concern about SiC BJTs is the power consumed by its driver since a continuous current is needed through the base to maintain the BJT on. This paper focuses on the optimization of SiC BJT base drivers during the conducting state. Previous proportional base drivers used measurements of the collector current to adjust the base current. A different approach is presented in this paper, based on measurements of the collector-emitter voltage. This solution avoids the need for costly high bandwidth current sensors and a DSP/FPGA to process the current measurement. Also, a new method to avoid high voltage decoupling devices is presented to measure the BJT voltage drop, which is later used as a reference for a high speed switching regulator that serves as the voltage supply for the driver. As a result, the base current is instantaneously adjusted to the collector current, minimizing the driver consumption.
Novel Class of Potent and Cellularly Active Inhibitors Devalidates MTH1 as Broad-Spectrum Cancer Target (2017)

MTH1 is a hydrolase responsible for sanitization of oxidized purine nucleoside triphosphates to prevent their incorporation into replicating DNA. Early tool compounds published in the literature inhibited the enzymatic activity of MTH1 and subsequently induced cancer cell death; however recent studies have questioned the reported link between these two events. Therefore, it is important to validate MTH1 as a cancer dependency with high quality chemical probes. Here, we present BAY-707, a substrate-competitive, highly potent and selective inhibitor of MTH1, chemically distinct compared to those previously published. Despite superior cellular target engagement and pharmacokinetic properties, inhibition of MTH1 with BAY-707 resulted in a clear lack of in vitro or in vivo anticancer efficacy either in mono- or in combination therapies. Therefore, we conclude that MTH1 is dispensable for cancer cell survival.
Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion (2007)

Variations in hydrogen-bond strengths are investigated for complexes of nine para-substituted phenols (XPhOH) with a water molecule and chloride ion. Results from ab initio HF/6-311+G(d, p) and MP2/6-311+G(d, p)//HF/6-311+G(d, p) calculations are compared with those from the OPLS-AA and OPLS/CM1A force fields. In the OPLS-AA model, the partial charges on the hydroxyl group of phenol are not affected by the choice of para substituent, while the use of CM1A charges in the OPLS/CM1A approach does provide charge redistribution. The ab initio calculations reveal a 2.0-kcal/mol range in hydrogen-bond strengths for the XPhOH⋯OH(2) complexes in the order X = NO(2) > CN > CF(3) > Cl > F > H >OH >CH(3) > NH(2). The pattern is not well-reproduced with OPLS-AA, which also compresses the variation to 0.7 kcal/mol. However, the OPLS/CM1A results are in good accord with the ab initio findings for both the ordering and range, 2.3 kcal/mol. The hydrogen bonding is, of course, weaker with XPhOH as acceptor, the order for X is largely inverted, and the range is reduced to ca. 1.0 kcal/mol. The substituent effects are found to be much greater for the chloride ion complexes with a range of 11 kcal/mol. For quantitative treatment of such strong ion-molecule interactions the need for fully polarizable force fields is demonstrated.
Research Progress on Main Symptoms of Novel Coronavirus Pneumonia Improved by Traditional Chinese Medicine (2020)

Novel coronavirus (COVID-19) pneumonia has become a major threat to worldwide public health, having rapidly spread to more than 180 countries and infecting over 1.6 billion people. Fever, cough, and fatigue are the most common initial symptoms of COVID-19, while some patients experience diarrhea rather than fever in the early stage. Many herbal medicine and Chinese patent medicine can significantly improve these symptoms, cure the patients experiencing a mild 22form of the illness, reduce the rate of transition from mild to severe disease, and reduce mortality. Therefore, this paper summarizes the physiopathological mechanisms of fever, cough, fatigue and diarrhea, and introduces Chinese herbal medicines (Ephedrae Herba, Gypsum Fibrosum, Glycyrrhizae Radix et Rhizoma, Asteris Radix et Rhizoma, Ginseng Radix et Rhizoma, Codonopsis Radix, Atractylodis Rhizoma, <i>etc.</i>) and Chinese patent medicines (Shuang-huang-lian, Ma-xing-gan-shi-tang, <i>etc.</i>) with their corresponding therapeutic effects. Emphasis was placed on their material basis, mechanism of action, and clinical research. Most of these medicines possess the pharmacological activities of anti-inflammatory, antioxidant, antiviral, and immunity-enhancement, and may be promising medicines for the treatment or adjuvant treatment of COVID-19 patients.
Nanopatterned rGO/ZnO:Al seed layer for vertical growth of single ZnO nanorods (2023)

In this work, we demonstrate a novel low-cost template-assisted route to synthesize vertical ZnO nanorod arrays on Si (100). The nanorods were grown on a patterned double seed layer comprised of reduced graphene oxide (rGO) and Al-doped ZnO nanoparticles. The seed layer was fabricated by spray-coating the substrate with graphene and then dip-coating it into a Al-doped ZnO sol-gel solution. The growth template was fabricated from a double-layer resist, spin-coated on top of the rGO/ZnO:Al seed layer, and patterned by colloidal lithography. The results show a successful chemical bath deposition of vertically aligned ZnO nanorods with controllable diameter and density in the nanoholes in the patterned resist mask. Our novel method can presumably be used to fabricate electronic devices on virtually any smooth substrate with a thermal budget of 1 min at 300 °C with the seed layer acting as a conductive strain-relieving back contact. The top contact can simply be made by depositing a suitable transparent conductive oxide or metal, depending on the specific application.
Multi-Modal Mean-Fields via Cardinality-Based Clamping (2016)

Mean Field inference is central to statistical physics. It has attracted much interest in the Computer Vision community to efficiently solve problems expressible in terms of large Conditional Random Fields. However, since it models the posterior probability distribution as a product of marginal probabilities, it may fail to properly account for important dependencies between variables. We therefore replace the fully factorized distribution of Mean Field by a weighted mixture of such distributions, that similarly minimizes the KL-Divergence to the true posterior. By introducing two new ideas, namely, conditioning on groups of variables instead of single ones and using a parameter of the conditional random field potentials, that we identify to the temperature in the sense of statistical physics to select such groups, we can perform this minimization efficiently. Our extension of the clamping method proposed in previous works allows us to both produce a more descriptive approximation of the true posterior and, inspired by the diverse MAP paradigms, fit a mixture of Mean Field approximations. We demonstrate that this positively impacts real-world algorithms that initially relied on mean fields.
Image Processing (2005)

Image processing-from basics to advanced applications Learn how to master image processing and compression with this outstanding state-of-the-art reference. From fundamentals to sophisticated applications, Image Processing: Principles and Applications covers multiple topics and provides a fresh perspective on future directions and innovations in the field, including: * Image transformation techniques, including wavelet transformation and developments * Image enhancement and restoration, including noise modeling and filtering * Segmentation schemes, and classification and recognition of objects * Texture and shape analysis techniques * Fuzzy set theoretical approaches in image processing, neural networks, etc. * Content-based image retrieval and image mining * Biomedical image analysis and interpretation, including biometric algorithms such as face recognition and signature verification * Remotely sensed images and their applications * Principles and applications of dynamic scene analysis and moving object detection and tracking * Fundamentals of image compression, including the JPEG standard and the new JPEG2000 standard Additional features include problems and solutions with each chapter to help you apply the theory and techniques, as well as bibliographies for researching specialized topics. With its extensive use of examples and illustrative figures, this is a superior title for students and practitioners in computer science, wireless and multimedia communications, and engineering.
Opportunistic Spectrum Access for Cognitive Radio Networks withMultiple Secondary Users (2013)

We develop channel-aware opportunistic spectrum access strategies for cognitive radio networks consisting of multiple secondary users. In addition to balancing between the cost of foregoing weaker transmission opportunities in pursuit of channels that offer better data rates, we consider collisions between primary users (PUs) and secondary users (SUs), and among the SUs themselves. We derive strategies for both cooperative setting where SUs maximize their sum total of throughputs, as well as non-cooperative, game theoretic setting where each SU tries to maximize its own throughput. We show that the optimal schemes for both scenarios are pure threshold policies, where each SU decides to use or skip transmission opportunities by comparing the channel qualities to a fixed threshold. In the non-cooperative case, we establish the existence of Nash equilibrium and develop best response strategies that can converge to equilibria, with SUs relying only on their local observations. We study the tradeoff between maximal throughput in cooperative setting and fairness in the non-cooperative setting, and schemes based on utility functions and pricing that mitigate this tradeoff. Lastly, we analyze the issue of interference of SUs to the PUs. We show numerical results illustrating the schemes and analysis.
Single nucleotide polymorphisms in the CYP2J2 and CYP2C8 genes and the risk of hypertension (2005)

CYP2J2 and CYP2C8 metabolize arachidonic acid (AA) to cis-epoxyeicosatrienoic acids (EETs), which play a central role in regulating renal tubular fluid-electrolyte transport and vascular tone. We hypothesized that functionally relevant polymorphisms in the CYP2J2 or CYP2C8 genes influence hypertension risk. We examined associations between CYP2J2*7 (G-50 T promoter) and CYP2C8*3 (Arg139Lys and Lys399Arg, which are in 100% linkage disequilibrium) polymorphisms and hypertension in a biethnic population from Tennessee. CYP2J2*7 variant allele frequency was significantly higher in African-Americans versus Caucasians (14.1% versus 7.7%, P=0.01), irrespective of hypertension status. When analysed separately by race, the genotype distribution of the CYP2J2*7 variant allele was not significantly different among African-Americans with/without hypertension, but was significantly different among Caucasians with/without hypertension (P=0.03). Indeed, the odds ratio of having hypertension attributable to carrying the CYP2J2*7 variant allele adjusted for age, gender, body mass index and family history was 0.39 (95% confidence interval 0.17-0.89) among Caucasians, suggesting a protective effect. Additional subgroup analyses revealed a significantly lower CYP2J2*7 variant allele frequency in hypertensive versus normotensive Caucasian males (5.6% versus 12.5%, P=0.02) and in hypertensive versus normotensive Caucasians without a family history of hypertension (1.5% versus 11.0%, P=0.03). With respect to the CYP2C8*3 variant, genotype distribution and allele frequencies were similar between normotensive and hypertensive subjects. This study provides evidence for an association between CYP2J2*7 genotype and hypertension in Caucasian males and Caucasians without a family history of hypertension, but suggests no association between CYP2C8*3 genotype and hypertension. Confirmation of these findings in additional populations is warranted.
DeepVideoMVS: Multi-View Stereo on Video with Recurrent Spatio-Temporal Fusion (2021)

We propose an online multi-view depth prediction approach on posed video streams, where the scene geometry information computed in the previous time steps is propagated to the current time step in an efficient and geometrically plausible way. The backbone of our approach is a real-time capable, lightweight encoder-decoder that relies on cost volumes computed from pairs of images. We extend it by placing a ConvLSTM cell at the bottleneck layer, which compresses an arbitrary amount of past information in its states. The novelty lies in propagating the hidden state of the cell by accounting for the viewpoint changes between time steps. At a given time step, we warp the previous hidden state into the current camera plane using the previous depth prediction. Our extension brings only a small overhead of computation time and memory consumption, while improving the depth predictions significantly. As a result, we outperform the existing state-of-the-art multi-view stereo methods on most of the evaluated metrics in hundreds of indoor scenes while maintaining a real-time performance. Code available: https://github.com/ardaduz/deep-video-mvs
Scientific Opinion on the public health hazards to be covered by inspection of meat (swine) (2011)

Abstract A qualitative risk assessment identified Salmonella spp., Yersinia enterocolitica, Toxoplasma gondii and Trichinella spp. as the most relevant biological hazards in the context of meat inspection of swine. A comprehensive pork carcass safety assurance is the only way to ensure their effective control. This requires setting targets to be achieved in/on chilled carcasses, which also informs what has to be achieved earlier in the food chain. Improved Food Chain Information (FCI) enables risk‐differentiation of pig batches (hazard‐related) and abattoirs (process hygiene‐related). Risk reduction measures at abattoir level are focused on prevention of microbial contamination through technology‐ and process hygiene‐based measures (GMP/GHP‐ and HACCP‐based), including omitting palpation/incision during post‐mortem inspection in routine slaughter, as well as hazard reduction/inactivation meat treatments if necessary. At farm level, risk reduction measures are based on herd health programmes, closed breeding pyramids and GHP/GFP. Chemical substances listed in Council Directive 96/23/EC were ranked into four categories. Dioxins, dioxin‐like polychlorinated biphenyls and chloramphenicol were ranked as being of high potential concern. However, chemical substances in pork are unlikely to pose an immediate or short term health risk for consumers. Opportunities for risk‐based inspection strategies by means of differentiated sampling plans taking into account FCI were identified. Regular update of sampling programmes and inclusion of inspection criteria for the identification of illicit use of substances were also recommended. Meat inspection is a key component of the overall surveillance system for pig health and welfare but information is currently under‐utilised. The changes proposed to the pig meat inspection system will lead to some reduction in the detection probability of diseases and welfare conditions. The difference is likely to be minimal for diseases/conditions that affect several organs. To mitigate the reduced detection probability, palpation and/or incision should be conducted as a follow‐up to visual inspection whenever abnormalities are seen.
Noise dosimetry for tactical environments (2016)

Noise exposure and the subsequent hearing loss are well documented aspects of military life. Numerous studies have indicated high rates of noise-induced hearing injury (NIHI) in active-duty service men and women, and recent statistics from the U.S. Department of Veterans Affairs indicate a population of veterans with hearing loss that is growing at an increasing rate. In an effort to minimize hearing loss, the U.S. Department of Defense (DoD) updated its Hearing Conservation Program in 2010, and also has recently revised the DoD Design Criteria Standard Noise Limits (MIL-STD-1474E) which defines allowable noise levels in the design of all military acquisitions including weapons and vehicles. Even with such mandates, it remains a challenge to accurately quantify the noise exposure experienced by a Warfighter over the course of a mission or training exercise, or even in a standard work day. Noise dosimeters are intended for exactly this purpose, but variations in device placement (e.g., free-field, on-body, in/near-ear), hardware (e.g., microphone, analog-to-digital converter), measurement time (e.g., work day, 24-h), and dose metric calculations (e.g., time-weighted energy, peak levels, Auditory Risk Units), as well as noise types (e.g., continuous, intermittent, impulsive) can cause exposure measurements to be incomplete, inaccurate, or inappropriate for a given situation. This paper describes the design of a noise dosimeter capable of acquiring exposure data across tactical environments. Two generations of prototypes have been built at MIT Lincoln Laboratory with funding from the U.S. Army, Navy, and Marine Corps. Details related to hardware, signal processing, and testing efforts are provided, along with example tactical military noise data and lessons learned from early fieldings. Finally, we discuss the continued need to prioritize personalized dosimetry in order to improve models that predict or characterize the risk of auditory damage, to integrate dosimeters with hearing-protection devices, and to inform strategies and metrics for reducing NIHI.
P105 Treatment of the lower gastrointestinal tract Klebsiella infections by recombinant bacteriocin KvarIa (2022)

Abstract Background Hospital-acquired infections (HAI) are one of the leading worldwide health care issues. The most prevalent HAI are the Klebsiella species. K. quasipneumoniae strains tend to colonize the gastrointestinal tract (GI) and show high rates of resistance against antibiotics. Orally delivered recombinant bacteriocins, like klebicins, could be employed as oral antimicrobials to eradicate multidrug-resistant Klebsiella from the intestinal tract prior to/during hospitalization. Methods This study aimed to investigate the antimicrobial efficacy of orally delivered Eudragit - coated klebicin (KvarIa) in a murine lower gastrointestinal tract model of K. quasipneumoniae infection. Four study groups were used (3 animals/group) to test the antimicrobial efficacy of orally delivered klebicin KvarIa: vehicle-only group (control, phosphate-buffered saline), and other three groups with bacteria, antibiotic therapy, and 100 µg of uncoated Kvarla, 100 µg coated KvarIa, 1000 µg coated KvarIa. Faecal and tissue samples were used for Klebsiella haemolysin gene (khe) analysis using RT-PCR. Results The gastrointestinal K. quasipneumoniae colonization was achieved only in the antibiotic-treated mice groups ((i) penicillin, streptomycin or (ii) penicillin, streptomycin, and metronidazole) followed by the introduction of K. quasipneumoniae. Analysis of the antimicrobial efficacy of Kvarla showed that coated-KvarIa significantly reduced colonization of K. quasipneumoniae in both mice groups compared to the control group. The amounts of K. quasipneumoniae changed from 6.3 x 107 CFU/50mg on the 18th day to 3.9 x 105 CFU/50mg on the 22nd day (p = 0.01) in the Eudragit S100-coated KvarIa 100 µg group and from 4.0 x 107 CFU/50mg on the 18th day to 1.6 x 105 CFU/50mg on 22nd day (p = 0.009) in the Eudragit S100-coated KvarIa 1000 µg group. Conclusion Our study demonstrates that colonization of mice intestinal tract by K. quasipneumoniae can be achieved after eradication of resident gut microbiota with antibiotics. Furthermore, using this murine model, we showed that orally delivered encapsulated klebicins substantially reduce K. quasipneumoniae colonization in the lower gastrointestinal tract.