gebhart/patrepeval huggingface dataset:
ProVal: A protein‐scoring function for the selection of native and near‐native folds (2003)

A low-resolution scoring function for the selection of native and near-native structures from a set of predicted structures for a given protein sequence has been developed. The scoring function, ProVal (Protein Validate), used several variables that describe an aspect of protein structure for which the proximity to the native structure can be assessed quantitatively. Among the parameters included are a packing estimate, surface areas, and the contact order. A partial least squares for latent variables (PLS) model was built for each candidate set of the 28 decoy sets of structures generated for 22 different proteins using the described parameters as independent variables. The C(alpha) RMS of the candidate structures versus the experimental structure was used as the dependent variable. The final generalized scoring function was an average of all models derived, ensuring that the function was not optimized for specific fold classes or method of structure generation of the candidate folds. The results show that the crystal structure was scored best in 64% of the 28 test sets and was clearly separated from the decoys in many examples. In all the other cases in which the crystal structure did not rank first, it ranked within the top 10%. Thus, although ProVal could not distinguish between predicted structures that were similar overall in fold quality due to its inherently low resolution, it can clearly be used as a primary filter to eliminate approximately 90% of fold candidates generated by current prediction methods from all-atom modeling and further evaluation. The correlation between the predicted and actual C(alpha) RMS values varies considerably between the candidate fold sets.
Reovirus-Like Sequences Isolated from Adult Asian Citrus Psyllid, (Hemiptera: Psyllidae:Diaphorina citri) (2009)

The Asian citrus psyllid, Diaphorina citri Kuwayama, (Insecta: Hemiptera: Psyllidae), has been identified as a damaging pest and an efficient vector of the plant infecting bacterium (Candidatus Liberibacter asiaticus) which is strongly associated with the disease Huanglongbing (HLB), known as 'Citrus greening disease'. Huanglongbing has caused extensive economic losses in the citrus industries worldwide. Traditional control measures of the psyllid have proven to be ineffective and costly. Biological control measures have been shown to provide environmentally friendly management tools for insect pests. In this study, an expression library was prepared from adult psyllids in search of new pathogens that can be use as biological control agents. We identified 2 viral sequences: one 616 base pairs and a second, 792 base pairs. Both had significant similarity to viruses within the insect Reovirus group. Phylogenetic and homology comparisons indicated that the viral sequences were most closely related to the viruses in the Family Reoviridae, Genus Fijivirus, specifically Nilaparvata lugens reovirus, NLRV.
The End-of-Treatment Ribavirin Concentration Predicts Hepatitis C Virus Relapse (2013)

Our study results highlight the relevance of measuring plasma RBV concentrations during and at the end of HCV treatment, with a view to avoiding virologic relapse.
Female Reproductive Factors and Major Eye Diseases in Asian Women –The Singapore Malay Eye Study (2014)

Women who had menopause at a younger age were more likely to have glaucoma. This association needs to be confirmed in other studies.
Nanostructured and Photoelectrochemical Systems for Solar Photon Conversion (2009)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTNanostructured and Photoelectrochemical Systems for Solar Photon ConversionStacey F. BentView Author Information Stanford UniversityCite this: J. Am. Chem. Soc. 2009, 131, 9, 3405–3406Publication Date (Web):February 11, 2009Publication History Published online11 February 2009Published inissue 11 March 2009https://pubs.acs.org/doi/10.1021/ja900723mhttps://doi.org/10.1021/ja900723mbook-reviewACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views2080Altmetric-Citations1LEARN 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 SUBJECTS:Chemical structure,Photoelectrochemistry,Solar cells,Solar energy,Solar energy conversion Get e-Alerts
A 2000&#x00B0;/s dynamic range bulk mode dodecagon gyro for a commercial SOI technology (2011)

This paper reports on the design and suggested fabrication steps of a bulk mode dodecagon disk gyroscope. A major contribution of this work, compared to prior art, is that it enables the fabrication of this important class of gyroscopes in commercially available and low-cost SOI technologies - e.g. MEMSCAP's SOIMUMPs. The structure was simulated using COMSOL, operates at 8.14 MHz, and exhibits a competitive rate sensitivity of ~2.3 pA/°/s, a high dynamic range of 2000°/s, and a mechanical noise of 1°/√hr, for a quality factor of 10,000.
Combination of Quantitative MRI Fat Fraction and Texture Analysis to Evaluate Spastic Muscles of Children With Cerebral Palsy (2021)

<b>Background:</b> Cerebral palsy (CP) is the most common cause of physical disability in childhood. Muscle pathologies occur due to spasticity and contractures; therefore, diagnostic imaging to detect pathologies is often required. Imaging has been used to assess torsion or estimate muscle volume, but additional methods for characterizing muscle composition have not thoroughly been investigated. MRI fat fraction (FF) measurement can quantify muscle fat and is often a part of standard imaging in neuromuscular dystrophies. To date, FF has been used to quantify muscle fat and assess function in CP. In this study, we aimed to utilize a radiomics and FF analysis along with the combination of both methods to differentiate affected muscles from healthy ones. <b>Materials and Methods:</b> A total of 9 patients (age range 8-15 years) with CP and 12 healthy controls (age range 9-16 years) were prospectively enrolled (2018-2020) after ethics committee approval. Multi-echo Dixon acquisition of the calf muscles was used for FF calculation. The images of the second echo (TE = 2.87 ms) were used for feature extraction from the soleus, gastrocnemius medialis, and gastrocnemius lateralis muscles. The least absolute shrinkage and selection operator (LASSO) regression was employed for feature selection. RM, FF model (FFM), and combined model (CM) were built for each calf muscle. The receiver operating characteristic (ROC) curve and their respective area under the curve (AUC) values were used to evaluate model performance. <b>Results:</b> In total, the affected legs of 9 CP patients and the dominant legs of 12 healthy controls were analyzed. The performance of RM for soleus, gastrocnemius medialis, and gastrocnemius lateralis (AUC 0.92, 0.92, 0.82, respectively) was better than the FFM (AUC 0.88, 0.85, 0.69, respectively). The combination of both models always had a better performance than RM or FFM (AUC 0.95, 0.93, 0.83). FF was higher in the patient group (FF<sub>S</sub> 9.1%, FF<sub>GM</sub> 8.5%, and FF<sub>GL</sub> 10.2%) than control group (FF<sub>S</sub> 3.3%, FF<sub>GM</sub> 4.1%, FF<sub>GL</sub> 6.6%). <b>Conclusion:</b> The combination of MRI quantitative fat fraction analysis and texture analysis of muscles is a promising tool to evaluate muscle pathologies due to CP in a non-invasive manner.
Nontoxic antimicrobials that evade drug resistance (2015)

Drugs that act more promiscuously provide fewer routes for the emergence of resistant mutants. But this benefit often comes at the cost of serious off-target and dose-limiting toxicities. The classic example is the antifungal amphotericin B (AmB), which has evaded resistance for more than half a century. We report dramatically less toxic amphotericins that nevertheless evade resistance. They are scalably accessed in just three steps from the natural product, and bind their target (the fungal sterol, ergosterol) with far greater selectivity than AmB. Hence, they are less toxic and far more effective in a mouse model of systemic candidiasis. Surprisingly, exhaustive efforts to select for mutants resistant to these more selective compounds revealed that they are just as impervious to resistance as AmB. Thus, highly selective cytocidal action and the evasion of resistance are not mutually exclusive, suggesting practical routes to the discovery of less toxic, resistance-evasive therapies. Less selective pharmacological action is generally associated with decreased vulnerability to resistance, but also with increased toxicity1,2. The classic example is amphotericin B Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research,
ZGridBC: Zero-Knowledge Proof Based Scalable and Privacy-Enhanced Blockchain Platform for Electricity Tracking (2023)

The total number of solar power-producing facilities whose Feed-in Tariff (FIT) Program-based ten-year contracts will expire by 2023 is expected to reach approximately 1.65 million in Japan. If the facilities that produce or consume renewable energy would increase to reach a large number, e.g., two million, blockchain would not be capable of processing all the transactions. In this work, we propose a blockchain-based electricity-tracking platform for renewable energy, called ‘ZGridBC,’ which consists of mutually cooperative two novel decentralized schemes to solve scalability, storage cost, and privacy issues at the same time. One is the electricity production resource management, which is an efficient data management scheme that manages electricity production resources (EPRs) on the blockchain by using UTXO tokens extended to two-dimension (period and electricity amount) to prevent double-spending. The other is the electricity-tracking proof, which is a massive data aggregation scheme that significantly reduces the amount of data managed on the blockchain by using zero-knowledge proof (ZKP). Thereafter, we illustrate the architecture of ZGridBC, consider its scalability, security, and privacy, and illustrate the implementation of ZGridBC. Finally, we evaluate the scalability of ZGridBC, which handles two million electricity facilities with far less cost per environmental value compared with the price of the environmental value proposed by METI (=0.3 yen/kWh).
Intelligent Luminescence for Communication Display and Identification (2007)

Text-reading proficiency may depend on not only the integrity of both processing routes but also their capacity for interaction, with critical roles for the left inferior parietal lobule and posterior arcuate fasciculus. These findings have fundamental as well as clinical implications.
Synergistic Anticancer Therapy by Ovalbumin Encapsulation‐Enabled Tandem Reactive Oxygen Species Generation (2020)

The anticancer efficacy of photodynamic therapy (PDT) is limited due to the hypoxic features of solid tumors. We report synergistic PDT/chemotherapy with integrated tandem Fenton reactions mediated by ovalbumin encapsulation for improved in vivo anticancer therapy via an enhanced reactive oxygen species (ROS) generation mechanism. O<sub>2</sub><sup>.-</sup> produced by the PDT is converted to H<sub>2</sub> O<sub>2</sub> by superoxide dismutase, followed by the transformation of H<sub>2</sub> O<sub>2</sub> to the highly toxic <sup>.</sup> OH via Fenton reactions by Fe<sup>2+</sup> originating from the dissolution of co-loaded Fe<sub>3</sub> O<sub>4</sub> nanoparticles. The PDT process further facilitates the endosomal/lysosomal escape of the active agents and enhances their intracellular delivery to the nucleus-even for drug-resistant cells. Cisplatin generates O<sub>2</sub><sup>.-</sup> in the presence of nicotinamide adenine dinucleotide phosphate oxidase and thereby improves the treatment efficiency by serving as an additional O<sub>2</sub><sup>.-</sup> source for production of <sup>.</sup> OH radicals. Improved anticancer efficiency is achieved under both hypoxic and normoxic conditions.
The Central Role of Macrophages in Trypanosomiasis-Associated Anemia:Rationale for Therapeutical Approaches (2010)

Bovine African trypanosomiasis causes severe economical problems on the African continent and one of the most prominent immunopathological parameters associated with this parasitic infection is anemia. In this report we review the current knowledge of the mechanisms underlying trypanosomiasis-associated anemia. In first instance, the central role of macrophages and particularly their activation state in determining the outcome of the disease (i.e. trypanosusceptibility versus trypanotolerance) will be discussed. In essence, while persistence of classically activated macrophages (M1) contributes to anemia development, switching towards alternatively activated macrophages (M2) alleviates pathology including anemia. Secondly, while parasite-derived glycolipids such as the glycosylphosphatidylinositol (GPI) induce M1, host-derived IL-10 blocks M1-mediated inflammation, promotes M2 development and prevents anemia development. In this context, strategies aimed at inducing the M1 to M2 switch, such as GPI-based treatment, adenoviral delivery of IL-10 and induction of IL-10 producing regulatory T cells will be discussed. Finally, the crucial role of iron-homeostasis in trypanosomiasis-associated anemia development will be documented to stress the analogy with anemia of chronic disease (ACD), hereby providing new insight that might contribute to the treatment of ACD.
Cytotoxicity screening of 23 engineered nanomaterials using a test matrix of ten cell lines and three different assays (2011)

In vitro toxicity of the analyzed engineered nanomaterials cannot be attributed to a defined physicochemical property. Therefore, the accurate identification of nanomaterial cytotoxicity requires a matrix based on a set of sensitive cell lines and in vitro assays measuring different cytotoxicity endpoints.
A coordinated approach for throttle and wastegate control in turbocharged spark ignition engines (2012)

This paper presents a control approach for turbocharged spark ignition engines that coordinates the throttle and wastegate air path actuators in order to improve driveability without significant compromise in efficiency. The coordinated controller is based on a two-input single-output (TISO) architecture which can be tuned through classical frequency response techniques using linearizations of a nonlinear mean value engine model. A systematic tuning method for the TISO architecture based on prior work is recommended and explained. The controller is evaluated in simulation with a one-dimensional GT-Power model and its performance is compared to that of a controller that does not coordinate the throttle and wastegate.
A novel radiolabeled vasopressin antagonist: [3H-Phe]-desGlyd(CH2)5D-Tyr(Et)VAVP, [3H]-SK&F 101926. (1987)

We report the vasopressin receptor-binding properties of [3H-Phe]-desGlyd(CH2)5D-Tyr(Et)VAVP, [3H]-SK&F 101926, the first radiolabeled vasopressin receptor antagonist. We chose to radiolabel SK&F 101926 because this vasopressin analog is a potent antagonist of vascular V1 and renal V2 vasopressin receptors in all species studied. [3H]-SK&F 101926 bound with a single high affinity to intact vascular smooth muscle cells (A-10; KD = 0.5 nM), and plasma membranes A-10 cells (KD = 0.4 nM) and rat liver (KD = 0.2 nM). In competition experiments with [3H]-SK&F 101926 and [3H]arginine vasopressin ([3H]AVP) using cell and liver membranes, the affinity rank orders of vasopressin analogs were the same and were typical for the V1 receptor subtype. In competition binding experiments with [3H]-SK&F 101926 using cell and liver membranes, guanosine 5'-(beta,gamma-imido)triphosphate did not significantly alter the affinity of the V1 antagonist d(CH2)5Tyr(Me)AVP, but the affinity of AVP was decreased. These data indicate that the V1 receptor can exist in at least two affinity states that are modulated by guanine nucleotides. [3H]-SK&F 101926 also bound specifically and with high affinity to V2 receptors of MDCK cells. We conclude that [3H]-SK&F 101926 binds with high affinity to V1 and V2 vasopressin receptors and is a powerful new tool for the identification of vasopressin receptors and the study of molecular mechanisms involved in the interaction of vasopressin with its receptors.
Dopamine receptor subtype 2 and somatostatin receptor subtype 5 expression influences somatostatin analogs effects on human somatotroph pituitary adenomas in vitro (2005)

Dopamine (DA) and somatostatin (SRIF) receptor agonists inhibit growth hormone (GH) secretion by pituitary adenomas. We investigated DA subtype 2 receptor (DR2) and SRIF receptor (sst) subtypes 2 and 5 expression in 25 GH-secreting pituitary adenomas and tested in primary culture the effects on GH and prolactin (PRL) secretion of sst agonists selectively interacting with sst2 (BIM-23120), sst5 (BIM-23206), and sst2 and sst5 (BIM-23244). All adenomas expressed sst2; eight adenomas expressed both sst5 and DR2, eight sst5 but not DR2, and eight DR2 but not sst5. One tissue lacked expression of DR2 and sst5. GH secretion was inhibited by BIM-23120 in all samples, while it was reduced by BIM-23206 only in adenomas not expressing DR2. BIM-23120's inhibitory effects correlated with sst2 and DR2 expression, whereas DR2 expression correlated inversely with BIM-23206 inhibitory effects on GH secretion. In seven mixed GH-/PRL-secreting pituitary adenomas, PRL secretion was inhibited in sst5-expressing tumors by BIM-23206, but not by BIM-23120. BIM-23244 reduced PRL secretion only in adenomas expressing sst2, sst5 and DR2. sst5 and DR2 expression correlated directly with BIM23206 inhibitory effects on PRL secretion. Our results suggest that adenomas expressing DR2 are less likely to respond to clinically available SRIF analogs in terms of GH secretion inhibition. Therefore, drugs interacting also with DR2 might better control secretion of pituitary adenomas.
ChemInform Abstract: Synthesis of β‐Nitroamines via Classical Mannich and Aza‐Henry Reactions (2013)

Abstract Review: 130 refs.
Cognitive slowing in multiple sclerosis is strongly associated with brain volume reduction (2006)

This study shows that, in MS patients, accuracy of processing is not compromised unless high working memory demands are involved. Problems in neurocognitive functioning in MS are mainly modulated by speed and stability of speed processing, in particular when attention-demanding controlled information processing is required. Abnormalities in these domains are most strongly associated with brain volume loss, confirming that pathology beyond focal lesions is important in MS.
Tetrathiafulvalene-annulated [28]hexaphyrin(1.1.1.1.1.1): a multi-electron donor system subject to conformational control (2013)

Tetrathiafulvalenes (TTF)-annulated [28]hexaphyrin affords an electron rich flexible π-conjugated system whose limiting conformations can be controlled through choice of solvents. The conformation-dependent intramolecular charge transfer character, as well as electron reserve capability of the hexakis-TTF annulated hexaphyrin, was analyzed.
Machine Vision Navigation in Spine Surgery (2021)

The advancements in computing and digital localizer technologies has led to the evolving clinical application of image-guided technology for the surgical management of spinal disorders. Image-guided spinal navigation addresses the limitations of fluoroscopy and improves the accurate placement of fixation screws. Several navigation platforms are currently available, each having its own unique advantages and disadvantages. The most recent spinal navigation system developed utilizes machine vision structured light imaging which creates a precise and detailed three-dimensional image of the exposed surface anatomy and co-registers it to a pre-operatively or intra-operatively acquired image. This system improves upon the intraoperative workflow and efficiency of the navigation process. With the continued advancements in machine vision, there is a potential for clinical applications that extend beyond surgical navigation. These applications include reducing the potential for wrong level spine surgery and providing for real-time tracking of spinal deformity correction. As the adoption and clinical experience with navigation continues to expand and evolve, the technology that enables navigation also continues to evolve.
E2A Deficiency Leads to Abnormalities in αβ T-Cell Development and to Rapid Development of T-Cell Lymphomas (1997)

The E2A gene products, E12 and E47, are critical for proper early B-cell development and commitment to the B-cell lineage. Here we reveal a new role for E2A in T-lymphocyte development. Loss of E2A activity results in a partial block at the earliest stage of T-lineage development. This early T-cell phenotype precedes the development of a T-cell lymphoma which occurs between 3 and 9 months of age. The thymomas are monoclonal and highly malignant and display a cell surface phenotype similar to that of immature thymocytes. In addition, the thymomas generally express high levels of c-myc. As assayed by comparative genomic hybridization, each of the tumor populations analyzed showed a nonrandom gain of chromosome 15, which contains the c-myc gene. Taken together, the data suggest that the E2A gene products play a role early in thymocyte development that is similar to their function in B-lineage determination. Furthermore, the lack of E2A results in development of T-cell malignancies, and we propose that E2A inactivation is a common feature of a wide variety of human T-cell proliferative disorders, including those involving the E2A heterodimeric partners tal-1 and lyl-1.