gebhart/patrepeval huggingface dataset:
Detecting functional modules in the yeast protein–protein interaction network (2006)

Abstract Motivation: Identification of functional modules in protein interaction networks is a first step in understanding the organization and dynamics of cell functions. To ensure that the identified modules are biologically meaningful, network-partitioning algorithms should take into account not only topological features but also functional relationships, and identified modules should be rigorously validated. Results: In this study we first integrate proteomics and microarray datasets and represent the yeast protein–protein interaction network as a weighted graph. We then extend a betweenness-based partition algorithm, and use it to identify 266 functional modules in the yeast proteome network. For validation we show that the functional modules are indeed densely connected subgraphs. In addition, genes in the same functional module confer a similar phenotype. Furthermore, known protein complexes are largely contained in the functional modules in their entirety. We also analyze an example of a functional module and show that functional modules can be useful for gene annotation. Contact: yuan.33@osu.edu Supplementary Information: Supplementary data are available at Bioinformatics online
Assessment of Dual Frequency GNSS Observations from a Xiaomi Mi 8 Android Smartphone and Positioning Performance Analysis (2019)

On May 2018 the world’s first dual-frequency Global Navigation Satellite System (GNSS) smartphone produced by Xiaomi equipped with a Broadcom BCM47755 chip was launched. It is able to receive L1/E1/ and L5/E5 signals from GPS, Galileo, Beidou, and GLONASS (GLObal NAvigation Satellite System) satellites. The main aim of this work is to achieve the phone’s position by using multi-constellation, dual frequency pseudorange and carrier phase raw data collected from the smartphone. Furthermore, the availability of dual frequency raw data allows to assess the multipath performance of the device. The smartphone’s performance is compared with that of a geodetic receiver. The experiments were conducted in two different scenarios to test the smartphone under different multipath conditions. Smartphone measurements showed a lower C/N0 and higher multipath compared with those of the geodetic receiver. This produced negative effects on single-point positioning as showed by high root mean square error (RMS). The best positioning accuracy for single point was obtained with the E5 measurements with a DRMS (horizontal root mean square error) of 4.57 m. For E1/L1 frequency, the 2DRMS was 5.36 m. However, the Xiaomi Mi 8, thanks to the absence of the duty cycle, provided carrier phase measurements used for a static single frequency relative positioning with an achieved 2DRMS of 1.02 and 1.95 m in low and high multipath sites, respectively.
Effect of pregnancy on relaxation of rat aorta to magnesium (1993)

The effect of pregnancy on magnesium induced relaxation of rat aortic smooth muscle was dependent on the agent used to induce contraction in the tissue, probably because pregnancy exerted different actions on receptor and voltage operated calcium channels. This effect of pregnancy was independent of either endothelial function or prostaglandin synthesis. Neither pregnancy nor the presence of magnesium affected the release of intracellular stored calcium.
논문 ; 사료첨가제에 관한 연구 ; 1 . 비타민 . 미네랄제의 첨가수준이 란용종 및 부로일러용 병아리의 성장율 , 사료효율 , 체조성 및 영양소이용율에 미치는 영향 (1972)

To determine the practical level of vitamin-mineral supplement in chicken diets, 280 birds of a commercial broiler and 280 white leghorn cockerels were employed in this experiment. The effects of different levels (0, 0.1, 0.2, 0.4, 0.6%) of vitamin-mineral supplement on the rate of gain, feed efficiency, body composition and nutrient metabolizability of chicks were compared between the two breeds for 9 weeks. The results obtained are summarized as follows: 1. Rate of gain, feed intake and feed efficiency were significantly (p$lt;0.01) depressed, and mortality and incidence of leg-weakness were higher for the chicks received no vitamin-mineral supplement than those received vitamin-mineral supplement. No statistical difference, however, was found for the growing performance among the vitamin-mineral supplemented groups. 2. Growth depression was more severe, and mortality and incidence of leg-weakness were higher in broiler chicks than in leghorn cockerels when fed control diet which was not added vitamin-mineral supplement. 3. Determination of body composition showed that chicks fed the control diet contained more fat than those fed the supplemented diets both on the wet (p$lt;0.05) and dried basis (p$lt;0.01). The ash content of chicken bodies kept on control diet was significantly (p$lt;0.01) lower than those kept on supplemented diets on wet basis. The content of protein of the former, however, was significantly (p$lt;0.01) higher than the latter on dried basis. Although no statistical difference was found, the content of moisture and protein in the bodies of birds received no vitamin-mineral supplement was slightly higher than those fed supplemented diets. Present data revealed that the body composition was not significantly affected by the levels of vitamin-mineral supplement within supplemented groups. 4. Optimum level of the studied vitamin-mineral supplement for maximum profit was found to be 0.2% of the diet with broiler chicks and 0.1% with leghorn cockerels. 5. It was found that chicks received no vitamin-mineral supplement for the first 6 weeks of growing period were not able to recover their body weight when a high level (0.6%) of vitamin-mineral supplement was given for the next 3 weeks of recovering period, although feed efficiency of the group was improved.
Combining Ring-Opening Metathesis Polymerization (ROMP) with Sharpless-Type “Click” Reactions: An Easy Method for the Preparation of Side Chain Functionalized Poly(oxynorbornenes) (2004)

Sharpless 1,3-dipolar cycloadditions (“click reactions”) between azides and acetylenes were used to prepare functional poly(oxynorbornenes) within their side chains. Two different strategies were applied to combine the preparation of ROMP polymers with the 1,3-dipolar cycloaddition approach: (a) the attachment of functional groups (i.e., hydrophobic and hydrogen bonding units) by 1,3-dipolar cycloaddition reactions to 7-oxynorbornenes bearing acetylenes and subsequent ROMP yielding the final polymers; (b) the ROMP polymerization furnishing first poly(oxynorbornenes) bearing acetylenic and azido moieties and subsequently attaching the functional units by use of the “click” reactions onto the modified polymers. Both strategies show efficient functionalization behavior with a high tolerance of functional groups with respect to the functional units attached as demonstrated by 1H and 13C NMR spectroscopy, opening the possibility to prepare a large variety of functionalized poly(oxynorbornenes) by use of only few starting materials.
Composition, flavor extract, protease, and glycosidases of clam bellies collected from clam processing plants (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComposition, flavor extract, protease, and glycosidases of clam bellies collected from clam processing plantsN. Rukma Reddy and George J. FlickCite this: J. Agric. Food Chem. 1989, 37, 2, 341–345Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/jf00086a015https://doi.org/10.1021/jf00086a015research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations4LEARN 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
Characterization of <sup>111</sup>In and <sup>177</sup>Lu‐labeled antibodies binding to CD44v6 using a novel automated radioimmunoassay (2008)

Targeted cancer therapies rely on bifunctional molecules, typically a protein that specifically recognizes tumor cells and a toxic component which is linked to the protein. Therefore, development of such therapies includes detailed characterizations of protein-cell interactions in order to find a good targeting agent. Knowledge of factors such as antibody-antigen specificity, as well as cellular uptake, retention and affinity of the antibody are necessary in order to be successful. In this paper, we have used a novel instrument, LigandTracer Yellow, to characterize the interactions of (111)In and (177)Lu-labeled monoclonal antibodies (MAbs) with CD44v6. Uptake studies with varying specific radioactivity of the chimeric MAb U36 and with an irrelevant antibody for the CD44v6 receptor verified the reliability of the method, as well as the specificity of the antibody-receptor binding. Uptake, retention, and affinity were very similar for the (111)In and (177)Lu-labeled conjugate, and were in line with earlier studies using manual methods. The fact that no adverse effects from labeling were seen, together with the high retention, could make these conjugates promising candidates for imaging and therapy of certain cancer types in the future. The novel LigandTracer technology reduced the workload and reagent spending while providing data with superior time resolution. The obtained results were in agreement with previously reported findings. In addition the real-time detection and higher time resolution made more detailed studies of the interactions possible.
Conductive and Transparent Multilayer Films for Low-Temperature-Sintered Mesoporous TiO<sub>2</sub> Electrodes of Dye-Sensitized Solar Cells (2003)

Conductive transparent thin films made of multilayer coatings consisting of three alternative layers (TiO2/Ag/TiO2, TAT) have been applied to dye-sensitized solar cells (DSCs). We have used sputtering deposition to prepare the transparent layers and measured the optical properties. Mesoporous TiO2 electrodes for DSCs were coated on TAT by a spin-coating and low-temperature sintering method. They were compared to well-known transparent metal oxide glasses (ITO and F-doped SnO2). These DSCs on the TAT coatings yielded a short-circuit photocurrent density of 9 mA/cm2, a photocurrent of 700 mV, and an overall cell efficiency of 3.9% at one sun light intensity.
Multiple nanoemulsion system for an oral combinational delivery of oxaliplatin and 5-fluorouracil: preparation and in vivo evaluation (2016)

Oxaliplatin (OXA) is a third-generation cisplatin analog that has been approved as first-line chemotherapy in combination with 5-fluorouracil (5-FU) for the treatment of resectable and advanced colorectal cancer. However, the therapeutic efficacy of oral OXA and 5-FU is limited by their low bioavailability due to poor membrane permeability. The aim of the present study was to develop an oral delivery system for OXA and 5-FU. We constructed an ion-pairing complex of OXA with a deoxycholic acid derivative (N<sup>α</sup>-deoxycholyl-l-lysyl-methylester, DCK) (OXA/DCK) as a permeation enhancer. Next, we prepared multiple water-in-oil-in-water nanoemulsions incorporating OXA/DCK and 5-FU to enhance their oral absorption. To evaluate their membrane permeability, we assessed in vitro permeabilities of OXA/DCK and 5-FU through an artificial intestinal membrane and Caco-2 cell monolayer. Finally, oral bioavailability in rats and tumor growth inhibition in the colorectal adenocarcinoma cell (CT26)-bearing mouse model were investigated after oral administration of nanoemulsion containing OXA/DCK and 5-FU. The droplet size of the optimized nanoemulsion was 20.3±0.22 nm with a zeta potential of -4.65±1.68 mV. In vitro permeabilities of OXA/DCK and 5-FU from the nanoemulsion through a Caco-2 cell monolayer were 4.80- and 4.30-fold greater than those of OXA and 5-FU, respectively. The oral absorption of OXA/DCK and 5-FU from the nanoemulsion also increased significantly, and the resulting oral bioavailability values of OXA/DCK and 5-FU in the nanoemulsive system were 9.19- and 1.39-fold higher than those of free OXA and 5-FU, respectively. Furthermore, tumor growth in CT26 tumor-bearing mice given the oral OXA/DCK- and 5-FU-loaded nanoemulsion was maximally inhibited by 73.9%, 48.5%, and 38.1%, compared with tumor volumes in the control group and the oral OXA and 5-FU groups, respectively. These findings demonstrate the therapeutic potential of a nanoemulsion incorporating OXA/DCK and 5-FU as an oral combination therapy for colorectal cancer.
Dynamic Bandwidth Allocation Algorithm With Proper Guard Time Management Over Multi-OLT PON-Based Hybrid FTTH and Wireless Sensor Networks (2013)

A passive optical network (PON) is a highly capable access network that effectively converges several service providers, without suffering from any bandwidth deficiency. However, a PON consisting of a single optical line terminal (OLT) for multiple service providers increases the computational complexity for data packet processing in the OLT, resulting in a longer time delay and more packet loss. A multi-OLT PON-based access network is an effective solution for reducing the computational complexity of data packet processing in a hybrid network of multiple service providers. The most important issue concerning the multi-OLT PON is the sharing efficiency of upstream channels among multiple service providers having different packet lengths and data rates. In this paper, we propose a dynamic bandwidth allocation algorithm called adaptive limited dynamic bandwidth allocation for multi-OLT PON (ALDBAM). The proposed scheme is a modified version of adaptive limited dynamic bandwidth allocation (ALDBA) algorithms that we proposed before, where both the ALDBA1 and ALDBA2 schemes are combined with proper guard time management and a modified multipoint control protocol. The simulation results show that the ALDBAM scheme provides lower packet delay with higher bandwidth utilization, higher upstream efficiency, and higher throughput than the conventional ALDBA1 and ALDBA2 schemes.
<title>Accuracy assessment of a clinical biplane fluoroscope for three-dimensional measurements and targeting</title> (1997)

There is considerable interest in using a fluoroscope for accurate three-dimensional measurements for diagnosis and therapy delivery. In this manuscript, we describe the necessary processing used to accurately find three-dimensional points in the field of view of a fluoroscopic imager and experimental results that show the system is capable of submillimetric accuracy. The image produced by a fluoroscope is spatially distorted -- a radial distortion results from the curved geometry of the xray detector and a rotation and translation are caused by an interaction ofthe electrons in the image intensifier tube with the local magnetic fields. Tests indicate that these distortions are significant (on the order of 1 cm) and affect the accuracy with which one can measure objects and distances in the images. By attaching a dense grid of radiopaque beads to the surface of the intensifier, it is possible to measure the amount of distortion present in the final image by comparing the bead positions in the image with the physical position of the beads on the grid. Furthermore, warping parameters can be derived from the bead locations and used to correct the distortion. By tessellating the image into triangular regions and applying a bilinear warping technique, we have been able to dramatically reduce distortion present in the image. Results indicate that after warping, the bead spacing is correct with a median error of 0.03 mm and a maximum error of 0.65 mm; the standard deviation of the distance error is 0.25 mm. Using pairs of images from the fluoroscopes, triangulation techniques are used to find target points in three dimensions assuming a nine-parameter, pinhole camera model. The parameters include the source-to-intensifier distance (SID), the image center (ut, va), the translation of the x-ray source (s, s, si), and the rotation of the fluoroscope about a world coordinate system (O,,y). The world coordinate system is set up using a calibration object that consists of radiopaque beads embedded in a Delrin cylinder. The beads are arranged such that they lie along a helical path; this shape is chosen to help avoid overlap of the beads in each projection image. By placing the calibration object within the field of view, the nine parameters of the model can be determined for each fluoroscope in the biplane system. In vitro experiments were performed using a Philips' Biplane Poly Diagnost I fluoroscope in clinical use at Johns Hopkins Hospital. The system has an SID of approximately 1 m and a 36 cm intensifier diameter. Initial results indicate that the points in space can be found with a high degree of accuracy (within 0.5 mm error) using the fluoroscope. In conclusion, it is possible to use a clinical biplanar fluoroscope for accurately finding three-dimensional points in space which is useful for making anatomical measurements and targeting for therapy delivery. Keywords: Fluoroscope, Computer Vision, Local Optimization, Distortion Correction, Accuracy, Three-dimensional, Measurement.
Transfection of the Giardia lamblia Double-Stranded RNA Virus into Giardia lamblia by Electroporation of a Single-Stranded RNA Copy of the Viral Genome (1990)

The development of a genetic vector for protozoan parasites is a major hurdle yet to be crossed in the study of the molecular and cellular biology of these parasites. We have identified and isolated a double-stranded RNA virus (G. lamblia virus [GLV]) from certain strains of the intestinal parasitic protozoan Giardia lamblia (A. L. Wang and C. C. Wang, Mol. Biochem. Parasitol. 21:269-276, 1986), which is capable of infecting other virus-free strains of G. lamblia (R. L. Miller, A. L. Wang, and C. C. Wang, Exp. Parasitol. 66:118-123, 1988). Here we demonstrate that G. lamblia can be infected with GLV by electroporating uninfected cells with purified single-stranded RNA (E. S. Furfine, T. C. White, A. L. Wang, and C. C. Wang, Nucleic Acids Res. 17:7453-7467, 1989) representing a full-length copy of one strand of the GLV double-stranded RNA genome. To the best of our knowledge, this is the first demonstration in vivo that a single-stranded RNA is a competent replicative intermediate for this class of double-stranded RNA virus. In addition, this result represents the first long-term transfection of a protozoan by a single species of RNA and will hopefully expedite the development of GLV as a genetic transfecting vector.
Thoracic origin of a sympathetic supply to the upper limb: the ‘nerve of Kuntz’ revisited (2001)

An understanding of the origin of the sympathetic innervation of the upper limb is important in surgical sympathectomy procedures. An inconstant intrathoracic ramus which joined the 2nd intercostal nerve to the ventral ramus of the 1st thoracic nerve, proximal to the point where the latter gave a large branch to the brachial plexus, has become known as the 'nerve of Kuntz' (Kuntz, 1927). Subsequently a variety of sympathetic interneuronal connections down to the 5th intercostal space were reported and also described as the nerve of Kuntz. The aim of this study was to determine: (1) the incidence, location and course of the nerve of Kuntz; (2) the relationship of the nerve of Kuntz to the 2nd thoracic ganglion; (3) the variations of the nerve of Kuntz in the absence of a stellate ganglion; (4) to compare the original intrathoracic ramus with sympathetic variations at other intercostal levels; and (5) to devise an appropriate anatomical classification of the nerves of Kuntz. Bilateral microdissection of the sympathetic chain and somatic nerves of the upper 5 intercostal spaces was undertaken in 32 fetuses (gestational age, 18 wk to full term) and 18 adult cadavers. The total sample size comprised 99 sides. Sympathetic contributions to the first thoracic nerve were found in 60 of 99 sides (left 32, right 28). Of these, 46 were confined to the 1st intercostal space only. The nerve of Kuntz (the original intrathoracic ramus) of the 1st intercostal space had a demonstrable sympathetic connection in 34 cases, and an absence of macroscopic sympathetic connections in 12. In the remaining intercostal spaces, intrathoracic rami uniting intercostal nerves were not observed. Additional sympathetic contributions (exclusive of rami communicantes) were noted between ganglia, interganglionic segments and intercostal nerves as additional rami communicantes. The eponym nerve of Kuntz should be restricted to descriptions of the intrathoracic ramus of the 1st intercostal space. Any of these variant sympathetic pathways may be responsible for the recurrence of symptoms after sympathectomy surgery.
Direct Interaction between Quorum-sensing Regulator SmcR and RNA Polymerase Is Mediated by Integration Host Factor to Activate vvpE Encoding Elastase in Vibrio vulnificus (2010)

It has been suggested that quorum sensing is an important signal transduction system regulating the expression of numerous virulence genes in bacterial pathogens. We previously revealed that SmcR, a LuxR homologue of Vibrio vulnificus, activates promoter S, an RpoS-dependent promoter of vvpE encoding a potential virulence factor elastase and binds in vitro to a binding site centered at -196.5. In this study, chromatin immunoprecipitation assays and promoter deletion analyses demonstrated that SmcR binds to the vvpE regulatory region in vivo and directly interacts with RNAP for activation of the vvpE expression. A search for regulatory genes involved in the regulation of elastase production singled out ihfA, which encodes for a subunit of integration host factor (IHF). Levels of both elastase activity and vvpE transcript decreased significantly as a result of inactivation of ihfA, and primer extension analyses demonstrated that IHF regulates the vvpE transcription by activating PS. Direct binding of IHF to the two distinct binding sites centered at -174 and -131, respectively, was determined using an electrophoretic mobility shift assay and a DNase I protection assay. Chromatin immunoprecipitation assays revealed that the interaction of SmcR with RNAP in vivo was mediated by IHF. Collectively, the results proposed a model whereby IHF positions SmcR to contact RNAP by looping the vvpE regulatory DNA, thus allowing precise control of the expression level of VvpE during the pathogenesis of V. vulnificus.