gebhart/patrepeval huggingface dataset:
Mechanical Mapping of Single Membrane Proteins at Submolecular Resolution (2011)

The capacity of proteins to carry out different functions is related to their ability to undergo conformation changes, which depends on the flexibility of protein structures. In this work, we applied a novel imaging mode based on indentation force spectroscopy to map quantitatively the flexibility of individual membrane proteins in their native, folded state at unprecedented submolecular resolution. Our results enabled us to correlate protein flexibility with crystal structure and showed that α-helices are stiff structures that may contribute importantly to the mechanical stability of membrane proteins, while interhelical loops appeared more flexible, allowing conformational changes related to function.
A Microservice Decomposition Method Through Using Distributed Representation of Source Code (2021)

This research proposed a novel decomposition method for refactoring monolithic applications into microservices applications using a neural network model (code2vec) for creating code embeddings from the monolithic application source code. As a Result, semantically similar code embeddings are clustered through a hierarchical clustering algorithm to produce microservices candidates to resemble the domain model more efficiently. The quality characteristics of the results were measured using two metrics for measuring cohesion. These metrics were Cohesion at Message Level (CHM) and Cohesion at Domain Level (CHD). Also, four applications were used as test cases with different sizes ranging from small to big applications. The proposed method showed promising results in terms of cohesion when compared to other decomposition methods. The proposed method scored better scores in 5 out of 8 tests compared to other methods. Also, averaged CHD and CHM results were 0.52 and 0.76, respectively, for the proposed method, better results when compared to the other methods.
Applying Eptc and Seeding Alfalfa (Medicago sativa) Simultaneously (1987)

Alfalfa ( Medicago sativa L. ‘Vernal′) was seeded broadcast or in drill rows spaced 18 cm apart in the same operation that EPTC ( S -ethyl dipropylcarbamothioate) was applied. For broadcast seeding, EPTC was applied as herbicide-treated crop seed, as granules mixed with crop seed, or as granules applied with the crop seed, but with the seed and granules carried in separate boxes on the seeder. For drill-row seeding, EPTC was applied between the rows in subsurface lines as a liquid or granular formulation; and within the rows as herbicide-treated seed, as granules mixed with the seed, or as granules carried in a box separate from the seed. Weed control and crop tolerance with the more effective simultaneous applications of EPTC were similar to those with conventional preplant-incorporated applications. To seed alfalfa (either broadcast or in drill rows) and apply EPTC in one operation, the methods wherein untreated seed and a granular formulation of EPTC were applied together but from separate boxes on the seeder were the most practical, because the mechanical components, the seed, and the formulated herbicide are all commercially available.
Inositol 1,4,5-trisphosphate receptors are autoantibody target antigens in patients with Sjögren's syndrome and other systemic rheumatic diseases (2007)

IP3R2 and IP3R3 double knock-out mice present with exocrine dysfunctions such as secretion deficits of saliva and pancreatic juice. Therefore, we investigated whether the presence of antibodies to IP3Rs could be found in patients with Sjögren's syndrome, and the location of the epitopes. Subjects included 35 primary Sjögren's syndrome, 39 secondary Sjögren's syndrome, 144 rheumatoid arthritis, and 96 other connective tissue disease patients. As controls, 33 healthy subjects were included. Immunoblot was conducted using recombinant proteins IP3R1, IP3R2, and IP3R3 made from full-length cDNA, and core, T604, and EL for epitope mapping. Antibodies to IP3R1 in sera from patients with primary Sjögren's syndrome, secondary Sjögren's syndrome, and rheumatoid arthritis were found to be positive in 17 of 35 (48.6%), 13 of 39 (33%), and 34 of 124 (27.4%) cases, respectively. These frequencies were significantly higher than the 1 of 33 (3.0%) found in normal healthy subjects. The frequency of anti-IP3R2 antibodies in rheumatoid arthritis was found to be higher than those found in Sjögren's syndrome, systemic lupus erythematosus, and systemic sclerosis. Anti-IP3R2 antibodies found in rheumatoid arthritis primarily recognized residues 578–2171 of the internal coupling and regulatory domain. On the other hand, anti-IP3R1 found in Sjögren's syndrome recognized residues 224–604 of the core protein IP3R1. Anti-IP3R1 antibodies were present in 48.6% of primary Sjögren's syndrome and in 3.0% of normal healthy subjects. Anti-IP3R2 antibodies were detected most frequently in rheumatoid arthritis. Locations of the antigenic epitopes were found to differ among the disease conditions.
Data from Serum Biomarker Panels for the Detection of Pancreatic Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Serum–biomarker based screening for pancreatic cancer could greatly improve survival in appropriately targeted high-risk populations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Eighty-three circulating proteins were analyzed in sera of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC, &lt;i&gt;n&lt;/i&gt; = 333), benign pancreatic conditions (&lt;i&gt;n&lt;/i&gt; = 144), and healthy control individuals (&lt;i&gt;n&lt;/i&gt; = 227). Samples from each group were split randomly into training and blinded validation sets prior to analysis. A Metropolis algorithm with Monte Carlo simulation (MMC) was used to identify discriminatory biomarker panels in the training set. Identified panels were evaluated in the validation set and in patients diagnosed with colon (&lt;i&gt;n&lt;/i&gt; = 33), lung (&lt;i&gt;n&lt;/i&gt; = 62), and breast (&lt;i&gt;n&lt;/i&gt; = 108) cancers.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Several robust profiles of protein alterations were present in sera of PDAC patients compared to the Healthy and Benign groups. In the training set (&lt;i&gt;n&lt;/i&gt; = 160 PDAC, 74 Benign, 107 Healthy), the panel of CA 19–9, ICAM-1, and OPG discriminated PDAC patients from Healthy controls with a sensitivity/specificity (SN/SP) of 88/90%, while the panel of CA 19–9, CEA, and TIMP-1 discriminated PDAC patients from Benign subjects with an SN/SP of 76/90%. In an independent validation set (&lt;i&gt;n&lt;/i&gt; = 173 PDAC, 70 Benign, 120 Healthy), the panel of CA 19–9, ICAM-1 and OPG demonstrated an SN/SP of 78/94% while the panel of CA19–9, CEA, and TIMP-1 demonstrated an SN/SP of 71/89%. The CA19–9, ICAM-1, OPG panel is selective for PDAC and does not recognize breast (SP = 100%), lung (SP = 97%), or colon (SP = 97%) cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The PDAC-specific biomarker panels identified in this investigation warrant additional clinical validation to determine their role in screening targeted high-risk populations. &lt;i&gt;Clin Cancer Res; 17(4); 805–16. ©2010 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Proximal Extrahepatic Bile Duct Tumors (1989)

Fifty-two consecutive patients with proximal extrahepatic bile duct tumors were treated by one of us (J.G.F.) between 1974 and 1987 at Memorial Sloan-Kettering Cancer Center, New York, NY. Thirty-eight patients (73%) underwent palliative procedures aimed at relieving the biliary obstruction (group A) and 14 patients (27%) were operated on with curative intent (group B). The choice of the surgical procedure employed to relieve the biliary obstruction did not significantly influence the length of survival of patients in group A in whom the median survival was 13.5 months and the in-hospital mortality was 15.7%. Fifty percent of the patients in group B underwent major liver resections to macroscopically encompass the tumor. In this group, although 35% of the patients experienced major complications, no in-hospital mortalities were encountered and the median actuarial survival was 38 months. The projected and crude 5-year survival rates were 28% and 21%, respectively. Age, gender, extent of resection, microscopic status of margins of resection, and grade of the lesion did not affect the length of survival in patients in group B. Locoregional failure, either isolated or as a component of peritoneal failure, was detected in the 6 patients in whom the disease has recurred. Eighty-three percent of the patients in whom the disease has recurred were dead within 12 months of the diagnosis of recurrence. Two long-term survivors (14%) developed second primary tumors in the follow-up period.
The Ever‐Challenging Quassinoids (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Oversampled filter banks as error correcting codes: theory and impulse noise correction (2005)

Oversampled filter banks (OFBs) provide an overcomplete representation of their input signal. This paper describes how OFBs can be considered as error-correcting codes acting on real or complex sequences, very much like classical binary convolutional codes act on binary sequences. The structured redundancy introduced by OFBs in subband signals can be used to increase robustness to noise. In this paper, we define the notions of code subspace, syndrome, and parity-check polynomial matrix for OFBs. Furthermore, we derive generic expressions for projection-based decoding, suitable for the case when a simple second-order model completely characterizes the noise incurred by subband signals. We also develop a nonlinear hypotheses-test based decoding algorithm for the case when the noise in subbands is constituted by a Gaussian background noise and impulsive errors (a model that adequately describes the action of both quantization noise and transmission errors). Simulation results show that the algorithm effectively removes the effect of impulsive errors occurring with a probability of 10/sup -3/.
ChemInform Abstract: Stereocontrolled Approaches to (+)‐ and (‐)‐γ‐Trifluoromethyl‐GABOB, a New Hydroxymethylene (Statine) Dipeptide Isostere. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Dental Amalgam Phasedown in New Zealand: A 20-year Trend (2020)

Despite having no official policy on reducing the use of dental amalgam, the Faculty of Dentistry is following the global trend in reducing its use, with composite resin now well established as the predominant restorative material used. If the current rate of decline persists unchecked, the Faculty of Dentistry could transition to being amalgam free by 2020, although it seems likely that the characteristics and principles of use of the material (and its removal) will be taught for some time to come. This knowledge is important to planning curriculum changes needed to prepare graduates for clinical practice.
Electrochemical-surface enhanced Raman spectroscopy (E-SERS) of uric acid: a potential rapid diagnostic method for early preeclampsia detection (2012)

An increased level of uric acid in urine and plasma is indicative of the development of preeclampsia, a hypertensive disorder that can occur during pregnancy. The preliminary steps towards developing a rapid tool for early diagnosis of preeclampsia using electrochemical SERS (E-SERS) for the detection of uric acid in urine are presented herein. Characterization of the uric acid species was completed using cyclic voltammetry, UV spectroscopy, Raman spectroscopy and electrochemical surface-enhanced Raman spectroscopy (E-SERS). E-SERS was capable of easily detecting uric acid directly at concentrations <1 mM in urine simulant, without the need for costly enzymes and bulky equipment, and thus demonstrates promise as a rapid point-of-care diagnostic tool for detection of early onset preeclampsia in developing nation settings.
Susceptibility weighted imaging of stroke brain in response to normobaric oxygen (NBO) therapy (2015)

The neuroprotective effect of oxygen leads to recent interest in normobaric oxygen (NBO) therapy after acute ischemic stroke. However, the mechanism remains unclear and inconsistent outcomes were reported in human studies. Because NBO aims to improve brain tissue oxygenation by enhancing oxygen delivery to ischemic tissue, monitoring the oxygenation level changes in response to NBO becomes necessary to elucidate the mechanism and to assess the efficacy. Susceptibility weighted imaging (SWI) which provides a new MRI contrast by combining the magnitude and phase images is fit for purpose. SWI is sensitive to deoxyhemoglobin level changes and thus can be used to evaluate the cerebral metabolic rate of oxygen. In this study, SWI was used for in vivo monitoring of oxygenation changes in a rat model of permanent middle cerebral artery occlusion (MCAO) before, during and after 30 min of NBO treatment. Regions of interest in ischemic core, penumbra and contralateral normal area were generated based on diffusionweighted imaging and perfusion imaging. Significant differences in SWI indicating different oxygenation levels were generally found: contralateral normal &gt; penumbra &gt; ischemic core. Ischemic core showed insignificant increase in oxygenation during NBO and returned to pre-treatment level after termination of NBO. Meanwhile, the oxygenation levels slightly increased in contralateral normal and penumbra regions during NBO and significantly decreased to a level lower than pre-treatment after termination of NBO, indicating secondary metabolic disruption upon the termination of transient metabolic support from oxygen. Further investigation of NBO effect combined with reperfusion is necessary while SWI can be used to detect hemorrhagic transformation after reperfusion.
Endodontic therapy for fused mandibular molar (1997)

Variations in tooth morphology present a clinical challenge when endodontic treatment is required. A case of conservative endodontic therapy for a fused mandibular second and third molar is presented.
Iron metabolism gene expression and prognostic features of hepatocellular carcinoma (2018)

Iron metabolism is crucial to hepatocellular carcinoma progression and is a key determinant of prognosis. Protein-protein interactions within the iron metabolism gene network were analyzed using the European Molecular Biology Laboratory's Search Tool for Recurring Instances of Neighbouring Genes/Proteins database. We obtained 423 liver hepatocellular carcinoma gene expression profiles from the Cancer Genome Atlas database. The expression and pathway enrichment of representative iron intake genes (TFRC and DMT1), utilization genes (FTH1, FTL, HIF1A, HMOX1, SLC25A37, and SLC25A38), and efflux genes (FLVCR1 and SLC40A1) was investigated in tumor and adjacent tissues. We determined the relationship between iron metabolism and the prognostic features of liver hepatocellular carcinoma. The liver metabolism genes TFRC and FLVCR1 were related to survival, disease status, and prognosis in patients with hepatocellular carcinoma. Our results provide novel insight into liver cancer therapy.
Fake News Detection Using Deep Learning Techniques (2019)

News is crucial part of our life. In day to day life current news are helpful to enhance knowledge what happen around the world. So most of peoples prefer watching news most of the peoples generally prefer reading newspaper early in the morning enjoying with cup of tea. If news is fake that will mislead peoples sometimes fake news utilized to spread rumors about things or it will affect some political leader positions just because of fake news. So it's crucial to find the fake news. So we proposed system to detect fake news but now a day's data on web or social media is increasing vastly and it is so hectic to detect news is fake or not by looking all data and it is time consuming so we utilize classification techniques to classify huge data. Here we proposed fake news detection system based on classification such as Logistic regression (LR), Naïve bayes (NB), Support vector machine (SVM), Random forest (RF) and deep neural network (DNN). We compare all machine learning techniques for detecting fake news.
Spontaneous transmitter release is critical for the induction of long-term and intermediate-term facilitation inAplysia (2012)

Long-term plasticity can differ from short-term in recruiting the growth of new synaptic connections, a process that requires the participation of both the presynaptic and postsynaptic components of the synapse. How does information about synaptic plasticity spread from its site of origin to recruit the other component? The answer to this question is not known in most systems. We have investigated the possible role of spontaneous transmitter release as such a transsynaptic signal. Until recently, relatively little has been known about the functions of spontaneous release. In this paper, we report that spontaneous release is critical for the induction of a learning-related form of synaptic plasticity, long-term facilitation in Aplysia. In addition, we have found that this signaling is engaged quite early, during an intermediate-term stage that is the first stage to involve postsynaptic as well as presynaptic molecular mechanisms. In a companion paper, we show that spontaneous release from the presynaptic neuron acts as an orthograde signal to recruit the postsynaptic mechanisms of intermediate-term facilitation and initiates a cascade that can culminate in synaptic growth with additional stimulation during long-term facilitation. Spontaneous release could make a similar contribution to learning-related synaptic plasticity in mammals.
Development of an Antigen Detection ELISA for Bancroftian Filariasis Using BmSXP-Specific Recombinant Monoclonal Antibody (2019)

Lymphatic filariasis is a mosquito-borne parasitic disease responsible for morbidity and disability that affects 1.2 billion people worldwide, mainly the poor communities. Currently, filarial antigen testing is the method of choice for the detection of bancroftian filariasis, and to date, there are two commonly used tests. In the present study, a recently reported recombinant monoclonal antibody (5B) specific to <i>Bm</i>SXP filarial antigen was used in developing an ELISA for the detection of circulating filarial antigen in sera of patients with bancroftian filariasis. The performance of the ELISA was evaluated using 124 serum samples. The ELISA was positive with all sera from microfilaremic bancroftian filariasis patients (<i>n</i> = 34). It also showed 100% diagnostic specificity when tested with sera from 50 healthy individuals and 40 patients with other parasitic diseases. The developed assay using the novel 5B recombinant monoclonal antibody could potentially be a promising alternative antigen detection test for bancroftian filariasis.
Ion beam effects on the composition and structure of glass surfaces (1989)

Changes in the surface composition and structure of a number of alkali silicate glasses, bombarded by 1–5 keV argon ions, have been characterized by x-ray photoelectron spectroscopy. Quantitative analyses of peak area changes indicate that the glass surfaces are dealkalized by the ion beam, and decomposition of the respective O 1s spectra reveal that the surfaces simultaneously repolymerize.
Superadditive effects of multiple lesions in a connectionist architecture: Implications for the neuropsychology of optic aphasia. (2000)

Neuropsychological disorders have traditionally been understood in terms of a focal lesion to a single component of a cognitive architecture. Optic aphasia (OA) defies explanation in this way. In OA, naming of visual stimuli is impaired in the absence of general visual agnosia or anomia. OA has been explained by positing multiple semantic systems or multiple functional pathways to visual naming. M. J. Farah (1990) instead sketched a parsimonious account based on multiple lesions--to pathways mapping visual input to semantic and semantics to naming responses--and the assumption that the effects of the lesions are superadditive. The authors demonstrate superadditive effects of damage in a connectionist architecture and model other phenomena associated with OA. Multiple lesions with superadditivity provide a novel class of explanations for neuropsychological deficits that previously seemed to imply the existence of highly specialized processing components.
Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group (2020)

The selectivity of histone deacetylase inhibitors (HDACis) is greatly impacted by the zinc binding groups. In an effort to search for novel zinc binding groups, we applied a parallel medicinal chemistry (PMC) strategy to quickly synthesize substituted benzamide libraries. We discovered a series containing 2-substituted benzamides as the zinc binding group which afforded highly selective and potent HDAC3 inhibitors, exemplified by compound <b>16</b> with a 2-methylthiobenzamide. Compound <b>16</b> inhibited HDAC3 with an IC<sub>50</sub> of 30 nM and with unprecedented selectivity of >300-fold over all other HDAC isoforms. Interestingly, a subtle change of the 2-methylthio to a 2-hydroxy benzamide in <b>20</b> retains HDAC3 potency but loses all selectivity over HDAC 1 and 2. This significant difference in selectivity was rationalized by X-ray crystal structures of HDACis <b>16</b> and <b>20</b> bound to HDAC2, revealing different binding modes to the catalytic zinc ion. This series of HDAC3 selective inhibitors served as tool compounds for investigating the minimal set of HDAC isoforms that must be inhibited for the HIV latency activation in a Jurkat 2C4 cell model and potentially as leads for selective HDAC3 inhibitors for other indications.
ChemInform Abstract: Two New Hydrides: RbCaH3 and Rb2CaH4 (1988)

Abstract , are observed during a study of the RbH‐CaH2 system.
Nitric Oxide Donor-Based Cancer Therapy: Advances and Prospects (2017)

The increasing understanding of the role of nitric oxide (NO) in cancer biology has generated significant progress in the use of NO donor-based therapy to fight cancer. These advances strongly suggest the potential adoption of NO donor-based therapy in clinical practice, and this has been supported by several clinical studies in the past decade. In this review, we first highlight several types of important NO donors, including recently developed NO donors bearing a dinitroazetidine skeleton, represented by RRx-001, with potential utility in cancer therapy. Special emphasis is then given to the combination of NO donor(s) with other therapies to achieve synergy and to the hybridization of NO donor(s) with an anticancer drug/agent/fragment to enhance the activity or specificity or to reduce toxicity. In addition, we briefly describe inducible NO synthase gene therapy and nanotechnology, which have recently entered the field of NO donor therapy.